News and events

August 2018: Ben-Tal awarded the Kazan Chair

Prof. Nir Ben-Tal, E. J. Safra Center member (Life Sciences), was awarded the Kazan Chair of Structural Biology.
Prof. Ben-Tal is a faculty member of the School of Neurobiology, Biochemistry & Biophysics. His research focuses on computational structural biology, covering both method development and applications to selected problems.
 

July 2018: Rice wins Teaching Award

Anna Rice, EJSCB PhD fellow (Mayrose lab, Life Sciences) won the 2018 Outstanding Teaching Award for teaching the course "Tools in Bioinformatics for biologists" in the Faculty of Life Sciences.

This is the second time that Anna wins this prize. It was awarded to Anna also in 2016.
 

July 2018: Eight EJSCB researchers awarded ISF grants

E. J. Safra members and affiliates Profs. Gil Ast, Judith Berman, Daniel Chamovitz, Ron Shamir, Roded Sharan, David Sprinzak and Drs. David Burstein and Omri Wurtzel - were all awarded research grants from the Israel Science Foundation (ISF) in the 2018-2019 grants cycle.

The ISF is the main body supporting breakthrough basic science in Israel, based on scientific excellence within the different fields of knowledge, in a wide variety of funding opportunities.
 

July 2018: "E. J. Safra Young" forum meets "Trendlines" senior management

Trendlines is an investment and incubator company for start-ups in the field of medicine and agritech. Yuval Almougy, Trendline's VP for new investments, was a guest speaker of the E. J. Safra Young Researchers' forum on July 9.

Yuval presented the incubator model, in which large companies invest in start-ups infrastructure financially and administratively. He also talked about the criteria that investors use when considering financing a new company and gave specific tips for the bioinformatics area.
 

July 2018: Gelbart wins ISM best poster prize

Maoz Gelbart, EJSCB PhD fellow (Stern lab, Life Sciences) won the best poster prize in the annual meeting of the Israel Society for Microbiology (ISM) which took place on July 3-4, 2018 in Ben Gurion University.

The ISM strives to encourage and promote scientific progress, alongside awakening the public at large to the contribution and importance of the Microbiology community to society and to the country.

Maoz presented his work titled "Exposing the extreme evolution of HIV in acute infection".
 

July 2018: New EJSCB member, Dr. David (Dudu) Burstein

Dr. David (Dudu) Burstein has joined the School of Molecular Cell Biology & Biotechnology at the Life Sciences Faculty in July 2018. Dr. Burstein completed BSc and MSc in Bioinformatics and a PhD in Life Sciences, all from TAU. Since 2013 he held a postdoctoral position at the University of California, Berkeley. In his research at Berkeley, Dr. Burstein used a computational and experimental approach for prediction and validation of protein function, building upon the genomic and community context provided by metagenomics. His research focused on discovery and investigation of novel families of CRISPR-Cas systems.

Dr. Burstein is an alumnus of the Edmond J. Safra Center: He was an EJSCB MSc and PhD fellow during his studies at TAU, under the supervision of Prof. Tal Pupko, EJSCB member (Life Sciences). Dr. Burstein is the sixteenth EJSCB student fellow who receives tenure track position in the academia.

In his lab at TAU, Dr. Burstein investigates key interaction mechanisms within microbial communities including novel CRISPR-Cas systems, antibiotic resistance genes, and bacterial secretion systems. He combines cutting-edge metagenomic techniques to study microorganisms in their natural environments, along with tailored machine-learning and molecular biology methods to predict and experimentally examine the functions of the studied systems. His goal is to improve the understanding of mechanisms shaping the microbial world and to promote their application in biotechnology and medicine.

Dr. Burstein won the prestigious Alon Fallowship in a national competition for young faculty members.
 

June 2018: E. J. Safra Young meets Dr. Burstein

On June 25 the EJSCB Young Researchers' Forum (nicknamed "E.J. Safra Young") hosted Dr. David Burstein.

Dr. Burstein talked about the CRISPR/Cas system, a new tool in molecular biology. He gave an overview of existing approaches and introduced relevant applications to this system.

Starting July 1st 2018 Dr. Burstein will be joining the School of Molecular Cell Biology & Biotechnology (Life Sciences) as a senior lecturer. He is a former EJSCB PhD student.
 

June 2018: Catav and Segal win CS excellence awards

Amnon Catav and Shahar Segal, EJSCB 3rd year undergraduate fellows, were among the 2018 outstanding undergraduates of the School of Computer Science.

Certificates were awarded to them in a ceremony that took place on June 14 at TAU.
 

June 2018: EJSCB undergraduate fellows won a prize for a project in Computer Science

A project competition took place on May 31, 2018 at the School of Computer Science.

EJSCB undergraduate fellows Reut Yedidim and Gal Yankovitz won the second prize in the annual projects competition of the CS school. They won the prize for the project "Predicting genetic interactions", supervised by EJSCB Prof. Roded Sharan. A third participant in the project and the prize was Tal Yankovitz, Gal's twin brother and CS student.

The prize was awarded during a ceremony that took place on June 14 at TAU.
 

June 2018: Nussinov wins ISCB highest award

EJSCB member Prof. Emerita Ruth Nussinov (School of Medicine), Senior Principal Scientist and Principal Investigator at the National Cancer Institute, NIH, is being honored as the 2018 winner of the ISCB Accomplishment by a Senior Scientist Award.

Each year, the International Society for Computational Biology (ISCB) recognizes a leader in the fields of computational biology and bioinformatics with the Accomplishments by a Senior Scientist Award. This is the highest award bestowed by ISCB in recognition of a scientist's significant research, education, and service contributions. Prof. Nussinov will receive her award and present a keynote address at ISCB's premiere annual meeting, the 2018 Intelligent Systems for Molecular Biology (ISMB) conference in Chicago, Illinois, being held on July 6-10, 2018.

See the article on Nussinov's achievements.
 

May 2018: Gophna elected to the European Academy of Microbiology

Congratulations to Prof. Uri Gophna, EJSCB member (Life Sciences), who was elected to the European Academy of Microbiology(EAM).

The EAM is a leadership group of eminent microbiology experts who strive to promote excellence in microbiology across Europe and beyond.
Members are elected by the Federation of European Microbiological Societies.
 

May 2018: Inauguration of the Koret initiative

A new collaboration initiative was forged between the Center for Computational Biology at UC Berkeley (CCB) and the E.J. Safra Center for Bioinformatics at TAU. The initiative is supported by a $5 million grant from the Koret Foundation.

On May 2, the initiative was inaugurated in a ceremony at TAU. Prof. Josef Klafter, TAU president, Dr. Anita Friedman, president of the Koret Foundation, and Prof. Ron Shamir greeted the audience. Prof. Klafter awarded a certificate to Dr. Friedman.

Maoz Gelbart, E. J. Safra PhD fellow (Life Sciences), gave a short talk titled "Evolution of HIV" describing his research, conducted in collaboration with CCB researchers.

A capacity audience of researchers and students in bioinformatics filled the Jaglom Auditorium. The representatives of the Edmond J. Safra Philanthropic Foundation in Israel, Mr. Juir Torenheim and Mr. Ariel Greenberg, were guests of honor.

The Koret Initiative also supports a Stanford-TAU program on smart cities, led by Prof. Irad Ben Gal. It was also inaugurated in the ceremony.

For pictures from the event, click here.
 
Prof. Joseph Klafter, TAU President, Dr. Anita Friedman, Koret President and Prof. Ron Shamir, EJSCB Head
Prof. Joseph Klafter awarding a certificate to Dr. Anita Friedman
Maoz Gelbart, EJSCB PhD fellow (Stern's lab, Life Sciences) gives a short talk

May 2018: Dan David Prize laureates in Personalized Medicine

On May 6, three international leaders in cancer research were awarded the prestigious Dan David Prize in the field of Personalized Medicine: Prof. Carlo Croce (Ohio State U), Prof. Mary-Claire King (U of Washington), and Prof. Bert Vogelstein (Johns Hopkins School of Medicine).

On May 7, each laureate held a discussion group with TAU students and researchers. The participants had the opportunity to talk to the laureates and raise questions in an intimate atmosphere.

The discussion groups were organized by the Dan David Prize and the Edmond J. Safra Center for Bioinformatics.
 
Prof. Carlo Croce, Ohio State U
Read more
Prof. Mary-Claire King, U of Washington
Read more
Prof. Bert Vogelstein, Johns Hopkins School of Medicine
Read more


April 2018: Three EJ Safra fellows receive RECOMB travel awards

Three past and present EJ Safra PhD fellows, Dana Silverbush (CS, Sharan), Elior Rahmani (LS, E. Halperin) and Alon Diament (Engineering, Tuller) were among the recipients of the RECOMB travel awards. The awards were given to students whose work was accepted for presentation in the conference.

RECOMB (Research in Computational Molecular Biology), the leading conference series on the theory of computational biology, is an international scientific conferences series bridging the areas of computational, mathematical, statistical and biological sciences.

In the picture: Alon Diament (second from left), Dana Silverbush (sixth from left), Elior Rahmani (seventh from left).
 

March 2018: New TAU-Berkeley Bioinformatics program

TAU and University of California, Berkeley, announced a $5 million joint initiative in bioinformatics. The initiative is funded by the Koret Foundation, and will support a joint program of TAU and UC Berkeley in Bioinformatics and Computational Biology.

TAU president, Prof. Joseph Klafter, UC Berkeley Chancellor, Prof. Carol T. Christ and the Koret Foundation head, Dr. Anita Friedman, announced the initiative and signed the memorandum of understanding in the Bay Area last week.

The five-year funding of the partnership will enable a variety of activities for the TAU and Berkeley bioinformatics communities. Among them are joint research grants, joint annual workshops, visitors and seminar series, and more.

The program will be run jointly by the Edmond J. Safra Center for Bioinformatics at TAU and the Center of Computational Biology at UC Berkeley.

Based in San Francisco, the Koret Foundation is committed to strengthening the Bay Area community and to supporting the US-Israel relationship and the Jewish community worldwide.

Read more on the announcement in TAU newsroom and in Jerusalem Post , The Jewish News of Northern California and Ynet.
 

February 2018: Goz wins ISMBE student award

Eli Goz, EJSCB former PhD fellow, (Tuller lab, Engineering) won a PhD student prize in ISMBE meeting, a biomedical engineering conference, that took place on February 22, 2018 in Haifa.

The prize was awarded to Eli for his research titled: Development of computational models for engineering viral genomes.

The conference is organized, annually, by the Israel Society of Medical and Biological Engineering (ISMBE). It brings hundreds of participants from academia, industry and medical institutions and serves as a platform for cooperation and presentation of groundbreaking research and development in the field.
 

February 2018: Shomron and Yoffe: Early detection of preeclempsia in pregnant women

Preeclampsia is a pregnancy complication characterized by high blood pressure and damage to other organs. It begins after 20 weeks of pregnancy and is dangerous to the mother and the fetus.

EJSCB member Dr. Noam Shomron and his PhD student, former EJSCB fellow, Liron Yoffe (Medicine) and colleagues developed a breakthrough method for early detection of preeclampsia. They identified 25 RNA markers that predict with high accuracy if a woman is likely to develop preeclampsia. The findings lay the basis for developing a simple blood test for predicting preeclampsia.

The results were published in Scientific Reports, in JewishPress and in Ynet.
 

January 2018: Promise in treating pancreatic cancer

Israeli scientists have shed light on the inverse correlation between an oncogene and the expression of an oncosuppressor microRNA as the reason for extended pancreatic cancer survival. The study can lead to the development of a drug cocktail for this deadly disease and other cancers.

The study was led by Prof. Ronit Sachi-Fainaru (TAU) in cooperation with Prof. Eytan Ruppin of the University of Maryland, an Emeritus of the EJSCB, Prof. Galia Blum and Prof. Iris Barshack (Hebrew University), and Dr. Talia Golan (Sheba Medical Center).

The research revealed for the first time significant genetic link between markers and pancreatic cancer patient survival. Moreover, drugs based on the discovery significantly extended the lives of mice in the pancreatic cancer model.

The study was published in Nature Communications. It was also featured in the newspaper Israel Hayom and in the online news Gen.
 

January 2018: Masrati wins excellent teaching award

EJSCB PhD fellow Gal Masrati (Ben-Tal lab, Life Sciences) won a special recognition certification of the TAU Rector for his teaching achievements in the academic year 2016-2017.

The Rector will award a certificate to Gal in a ceremony that will take place in March 12 2018.

It is the second year in a row that Gal wins this award.
 

January 2018: The Young Researchers' Forum: The first SafraThon

The Young Researchers' Forum initiated a new series of meetings called "SafraThon". The first SafraThon took place in January 15 2018. In the meeting participants exchanged knowledge on variety of scientific and academic topics.

The Forum also formed a database that contains useful information. The Forum invites the young researchers to use it and to update it with relevant pieces of information, data and skills.
 

The Young Researchers' Forum monthly meeting

On December 25 2017 the EJSCB young researchers' forum hosted Moshe Einhorn, a former MSc student of Prof. Itay Mayrose, EJSCB member (Life Sciences). Moshe Einhorn is the Co-founder and CTO of Genoox, a company that is developing a tool for identify mutations in genes in DNA sequencing data. The tool is provided to hospitals' laboratories.
 

January 2018: Ben-Tal: Understanding how proteins evolve

A new study by Dr. Rachel Kolodny (Computer Science, University of Haifa), Dr. Sergey Nepomnyachiy and EJSCB member Prof. Nir Ben-Tal (Life Sciences) sheds light on how proteins emerged and evolved during human history.

The study, published in a PNAS paper, included a development of efficient algorithmic tools and a computational pipeline that were applied to a representative set of over 20,000 proteins.

The research, which has raised considerable interest, was also featured in highlighted news in TAU's website.
 

February 2018: EJSCB sponsored meeting

The annual meeting of the Genetic Society of Israel, FRONTIERS IN GENETICS XI, will take place on February 7 at Tel Aviv University. The goal of the society is to promote genetics research and education about recent developments in genetics. EJSCB is among the sponsors of the meeting.

The president of the society is EJSCB member Prof. Martin Kupiec (Life Sciences). EJSCB member Prof. Karen Avraham (Medicine) is among its elected board of directors.

For registration click here.
For abstract submission click here.
 

October 2017: Shamir: A blood-based Parkinson's disease signature

A large-scale study of blood expression profiles revealed a 87-gene signature that distinguishes between idiopathic (non-genetic) Parkinson's disease patients and healthy controls. The study, published recently in Neurology was based on expression profiles of more than 500 individuals. Research groups from Germany, France, USA, Slovenia and Israel took part in the EU-funded GenePark study. The bioinformatic analysis was led by the group of EJSCB member Ron Shamir (Computer Science).

See also the news and views in Nature Reviews Neurology.
 

December 2017: Kupiec: A new mechanism for breaking down protein blocks

Protein blocks characterize neurodegenerative diseases such as Alzheimer's disease. These blocks have so far been considered irreversible. A new study by EJSCB member Prof. Martin Kupiec (Life Sciences) identified a protein (Std1) that undergoes a reversible aggregation: blocks of the protein disappear when conditions change.

The discovery may open a new way to treat diseases caused by accumulation of proteins in our cells such as diabetes, Alzheimer's and Parkinson's.

The results were published in the journal Molecular Cell and highlighted in ScienceDaily .
Read more.
 

February 2018: Rechavi wins the Blavatnik Prize for young scientists

Dr. Oded Rechavi (Life Sciences), EJSCB Affiliate, won the Blavatnik Prize for young scientists.
The Blavatnik awards program acknowledges excellent scientists and engineers at the beginning of their academic careers. It is program of the Blavatnik Family Foundation, operated by the New York Academy of Sciences. This year, prizes were awarded for the first time in Israel, in cooperation with the Israel Academy of Sciences. Dr. Oded Rechavi is one of three winners.

Dr. Rechavi won the award for his pioneering work in revealing new mechanisms and processes of inheritance that do not depend on changes in the DNA sequence. His research offers a first step towards treating diseases in which genetic factors have not been identified.

The prize will be awarded at a ceremony in Jerusalem on February 4, 2018.
 

December 2017: Avram, Masrati and Netanely win outstanding lecturer award

EJSCB PhD fellows Oren Avram (Pupko lab, Life Sciences) and Gal Masrati (Ben-Tal lab, Life Sciences) and former EJSCB PhD fellow Dvir Netanely (Shamir lab, Computer Science) won outstanding lecturer awards for the academic year 2016-2017.

They are included among one hundred most excellent lecturers at TAU for that year.
 

March 2017: Sabi wins ISMBE 2017 award

Renana Sabi, EJSCB PhD fellow, (Tuller lab, Engineering) was awarded a prize at the conference of Biomedical Engineering that took place in March 7, 2017 in Haifa.

The conference is organized annually by the Israel Society of Medical and Biological Engineering (ISMBE). The conference brings hundreds of participants from academia, industry and medical institutions and it serves as a platform for cooperation and presentation of groundbreaking research and development in the field.

Renana won the prize in the area of "Synthetic and Systems Biology" for her talk titled "The Unique Role of Translation Elongation in the Regulation of mRNA Translation".
 

October 2017: Orenstein joins BGU

Dr. Yaron Orenstein, Former EJSCB PhD fellow (Shamir lab, Computer Science) joined Ben-Gurion University as a senior lecturer in the Department of Electrical and Computer Engineering.
He was previously a postdoc at Prof. Bonnie Berger's group at MIT.

Dr. Orenstein is the fifteenth EJSCB fellow who receives a tenure track position in academia.
 

December 2017: Kupiec wins the Michael Landau Prize

Prof. Martin Kupiec, Edmond J. Safra Center member of the Life Sciences Faculty, won the Michael Landau Prize for Science in the field of Genetics for 2017.

The Landau Foundation was established in 1970 and named after Dr. Michael Landau, who headed the National Lottery in its early years. The prize is awarded to researchers who have achieved a breakthrough in their research and have won international recognition.

The award ceremony will take place in December 25, 2017.
 

November 2017: Mayrose promoted to Associate Professor

Edmond J. Safra Center member Itay Mayrose was promoted to Associate Professor with tenure. Prof. Mayrose joined the Department of Molecular Biology and Ecology of Plants at the Faculty of Life Sciences in 2012.

Mayrose studies plant evolution and phylogenetics. His group uses comparative bioinformatics approaches to understand the evolutionary dynamics of plant genomes, and develops computational tools to gain novel biological insights from various kinds of data.

Prof. Mayrose is an alumnus of the EJSCB: in the academic year 2008-2009, he was Edmond J. Safra postdoc fellow. He is the third EJSCB fellow to reach professorship at TAU.
 

September 2017: Gelbart wins "Best Lightning Talk" prize

Edmond J. Safra PhD fellow Maoz Gelbart (Stern lab, Life Sciences) won the Best Lightning Talk Prize at the 6th graduate student conference in Genetics, Genomics and Evolution, which took place on September 18, 2017 at Bar Ilan University.

The prize was given for his talk titled "Crossing the species barrier: evolutionary rate shifts unveil different adaptation strategies in HIV-1 and SIV".
The prize was awarded by the Israeli Center of Research Excellence (I-CORE) Gene Regulation in Complex Human Disease.
 

July 2017: Ella Petter wins Final 2017 award

Edmond J. Safra undergraduate fellow, Ella Petter, won the FINAL excellence award for 2017 .

The award is granted annually to a few outstanding students in computer science in Israeli universities. The prize is aiming to encourage excellent achievements in the software engineering area.

Ella is a third year student in the bioinformatics BSc program, and has also won this year an excellence fellowship from the Edmond J. Safra Center.

 

July 2017: Wilentzik wins Life Sciences award

Edmond J. Safra PhD fellow, Roni Wilentzik (Gat-Viks's lab, Life Sciences) won the 2017 Life Sciences Faculty award for excellence in research. The award is presented once a year to several graduate students who have excelled in their research.

Roni has presented her research in a meeting of the Dean of Life Sciences Faculty with the awardees.

 

July 2017: Weiner wins Life Sciences award

Edmond J. Safra PhD fellow, Iddo Weiner (Tuller's lab, Engineering and Yacoby's lab Life Sciences) won the 2017 Life Sciences Faculty award for excellence in research. The award is presented once a year to several graduate students who have excelled in their research.

Iddo was also invited to speak at the annual Life Sciences Faculty student graduation ceremony.

 

June 2017: Amar wins the Final prize

Former EJSCB postdoc fellow Dr. David Amar (Shamir lab, Computer Science) won the Final Prize for Research, for his work titled "Digesting high dimensional biomedical data collected over time across different subjects".

To encourage excellence in the field of machine learning and data mining Final company awarded five prizes to students and postdocs who performed an outstanding research project in those areas.

Dr. Amar won the prize based on the following publications, which were published while being an EJSCB PhD and postdoc fellow:
"A hierarchical Bayesian model for flexible module discovery in three-way time-series data"

"Integrated analysis of numerous heterogeneous gene expression profiles for detecting robust disease-specific biomarkers and proposing drug targets"

"Utilizing somatic mutation data from numerous studies for cancer research: proof of concept and applications".

Dr. Amar is now a postdoc at Stanford University.

 

June 2017: Levy Karin wins Ernst Mayr Award

Eli Levy Karin, EJSCB PhD fellow (Pupko & Mayrose labs, Life Sciences) won the Ernst Mayr award for an outstanding student talk at the Evolution 2017 conference in Portland, Oregon.

Eli won for her lecture "TraitRateProp: an integrated model of phenotypic trait changes and site-specific sequence evolution".

The Ernst Mayr Award is given to the presenter of an outstanding student talk in the field of systematics at the annual meetings of the Society of Systematic Biologists (SSB). This is SSB's premier award, and is judged by the quality and creativity of the research completed over the course of the student's Ph.D.

Notably, former EJSCB PhD fellow Dr. Haim Ashkenazy (Pupko lab, Life Sciences) was also among the finalists for the award, for his talk "Multiple sequence alignment averaging improves phylogeny reconstruction".
 

March 2017: Diament wins ISMBE 2017 student award

Alon Diament, Edmond J. Safra PhD fellow (Tuller's lab, Engineering) won the outstanding PhD students award of the Israel Society for Medical and Biological Engineering (ISMBE) for 2017.

The ISMBE conference , which took place in March 2017 in Haifa, brings together academic researchers from Israel and abroad, medical doctors, and representatives of companies from the industry. It serves as a forum for collaborations and for presenting pioneering research and developments in Biomedical Engineering. About 600 participants took part in the 2017 conference.

Alon was one of six PhD students winning the award for his research titled "Development of models for simulation and gene expression engineering based on large scale measurements".
 

July 2017: Steuerman wins Women in Science PhD Fellowship

Yael Steuerman, Edmond J. Safra PhD fellow (Gat-Viks' lab, Life Sciences) won the Shulamit Aloni Scholarship for Advancing Women in Exact Sciences and Engineering, awarded by the Israel Ministry of Science and Technology.

Ms. Shulamit Aloni was a social activist and Israel Prize laureate for a special contribution to the country and the society, and served as Minister of Science in 1993-1996. In her various roles and public activities, Ms. Aloni dealt with issues relating to the status of women and the advancement of women and their inclusion in the public agenda. The goal of the scholarship program is to increase the number of women engaged in science and technology, in the exact sciences and in engineering.
 

June 2017: Clinical Genomics Analysis workshop

The 8th Clinical Genomics Analysis workshop was held on June 8, 2017 at the IBM research lab in Haifa. It was jointly organized by IBM research and EJSCB.

The workshop hosted more than 100 participants, including students, clinicians, researchers, and developers from both academia and industry, and included nine talks and a vibrant poster and demo session. The focus of the workshop was on the analysis of disease-related data, where multiple data types were presented, including genomic data, behavioral data, mobile data, and more.

The keynote speaker was Prof. André Brown from Imperial College London. Other speakers were from the University of Exeter, the University of Manchester, IBM research, Teva Pharmaceuticals, Tel Aviv University, Bar-Ilan University, the Technion, and the Hebrew University.
 

May 2017: A symposium with the 2017 Dan David Prize laureates

On May 21, Prof. Svante Pääbo, Max Planck Institute for Evolutionary Anthropology and Prof. David Reich, Harvard Medical School, were awarded the prestigious 2017 Dan David Prize for their leading role in developing analytical and computational tools to study DNA from ancient humans.

On May 24 a symposium with the Laureates, titled "Ancient DNA tells a tale of yore", was organized at TAU by the Dan David Prize, Prof. Israel Hershkovitz (Medicine) and the EJSCB. Prof. Svante Pääbo talked about "Archaic genomic" and Prof. David Reich talked about "Ancient DNA and the new science of the Human past".

The talks were followed by an open discussion that was moderated by Prof. Israel Hershkovitz and EJSCB member Prof. Saharon Rosset (Statistics).
 

May 2017: Geiger elected into the Israel Young Academy

Congratulations to Dr. Tamar Geiger, Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine and EJSCB Affiliate, for being elected into the Israel Young Academy .

Joining the global trend, in 2012 the Israel Academy established the Israel Young Academy (IYA) with the intention of creating a framework comprising the country's leading young scholars in the humanities, social sciences, and natural sciences.

In elections held at its annual assembly on May 18, 2017, the Israel Young Academy chose nine new members. The new members are outstanding scholars who have demonstrated excellence in their research fields and have contributed to society in the public arena.
 

May 2017: IBS 2017

The 19th Israel Bioinformatics Symposium (IBS) took place on May 15, 2017 at the Weizmann Institute. IBS is the main annual conference of the Israeli Bioinformatics community. This year's event brought together 480 participants. The program included keynote talks by Prof. Eytan Domany (Weizman) and Gad Getz (Broad Institute), regular talks by bioinformatics faculty members, and a lively poster session.

The IBS was organized by Dr. Igor Ulitsky, former EJSCB PhD fellow, now on the faculty of Weizmann. Another member of the program committee was Prof. Irit Gat-Viks, EJSCB Faculty Fellow (Life Sciences).

The EJSCB supported the conference and also provided two prizes to students in the best poster competition. EJSCB member Prof. Ron Shamir presented the prizes to the winners; Kerem Weiner Caster and Guy Kelman, both from the Hebrew University.

Another poster prize, in honor of the late HUJI bioinformatics student Eran Cohen, was awarded to EJSCB former PhD fellow, Dvir Netanely, for his work titled "PROMO: An interactive tool for analyzing large high-throughput genomic datasets".
 

May 2017: Roded Sharan wins RECOMB "Test of Time Award"

EJSCB member Prof. Roded Sharan (Computer Science) received the RECOMB "Test of Time Award" for the year 2017. The award was given to Sharan and coauthors Richard M. Karp (Berkeley) Jacob Scott and Trey Ideker (UCSD) for their 2005 RECOMB paper
"Efficient Algorithms for Detecting Signaling Pathways in Protein Interaction Networks"
.

The award is given for the paper published in the RECOMB conference 12 years earlier that had the largest impact on subsequent research.

This is the second year in a row that Sharan wins the Test of Time award.
 

April 2017: Teaching workshop at Weizmann

A workshop titled "Teaching (Computational) Genomics in 2017" was held at the Weizmann Institute on April 6, 2017.

The workshop was co-organized by Prof. Tzachi Pilpel of Weizmann and Prof. Ron Shamir, EJSCB member (Computer Science). It was co-sponsored by the Feinberg School and Weizmann and the EJSCB. The goal of the workshop was to exchange ideas and curricula and to demonstrate teaching methods in graduate and undergraduate classes covering modern computational and non-computational genomics.

Eight speakers from various universities gave talks, describing their teaching approach and also giving a demo class-like lecture. The keynote speaker was Prof. Lior Pachter of Berkeley and Caltech. Some 40 faculty members and graduate students attended the workshop, which contained many lively discussions. The workshop was viewed as highly successful by all participants.
 

April 2017: Eisenberg: RNA editing in the octopus

A team of scientists led by EJSCB member Prof. Eli Eisenberg (Physics) and Prof. Joshua Rosenthal (Marine Biological Laboratory, University of Chicago) has shown that octopuses practice a rare type of genetic alteration called RNA editing.

It is used to fine-tune the information encoded by the genes without altering the genes themselves. The editing is extensive, far greater than in any other animal group. The editing can be linked to the high intelligence of the octopus, as it re-codes genes that are important for the nervous systems. Interestingly, only the intelligent coleoid cephalopods; octopuses, squid, and cuttlefish do so.

The study was published in the journal Cell and was also featured in 3 Quarks Daily .
 

March 2017: Shamir wins the Kadar Family award

Prof. Ron Shamir, EJSCB member from the School of Computer Science, won the prestigious Kadar Family Award for Outstanding Research.

The Kadar Family Award for Outstanding Research at TAU, inaugurated in 2015, celebrates pioneering scientists and scholars who have reached the highest levels of excellence in both research and teaching.
The Award is granted annually to four TAU researchers, two senior and two junior faculty members, from across the entire spectrum of faculties and disciplines on the TAU campus.
 

January 2017: Three EJSCB members receive ICA "Outstanding Research" grants

Three members of the EJSCB, Prof. Gil Ast and Dr. Ran Elkon (Medicine) and Prof. Ron Shamir (Computer Science), were awarded special grants from the Israel Cancer Association.

Recognized as "Outstanding Research", the three researchers were awarded enlarged grants for their grant proposals, and certificates were presented to them in an annual ceremony of the Israel Cancer Association (ICA) on March 16, 2017.
 

Abadi wins the Ariane de Rothschild Fellowship

Shiran Abadi, PhD EJSCB fellow (Mayrose's lab, Life Sciences Faculty) won the prestigious fellowship of the Ariane de Rothschild Women Doctoral Program.

By providing the opportunity for talented female scholars to pursue their research, the Ariane de Rothschild Women Doctoral Program promotes gender equality within the academic world. The program awards four outstanding female doctoral students scholarships to study at Tel Aviv University. Addressing the continuing under-representation of women in Israeli higher education, the scholarships are designed to enhance the academic standing of talented women scholars in a variety of fields.
 

Gat-Viks first Center woman fellow to become TAU Professor

Edmond J. Safra Center Faculty Fellow, Irit Gat-Viks, was promoted to Associate Professor with tenure. Prof. Gat-Viks joined the Department of Cell Research & Immunology in the Faculty of Life Sciences in 2010. Her group studies how variations in the genomes of individuals shape phenotypic diversity. The research is focused on the immune response as a key intermediate in how genotypes manifest as disease phenotypes.

Prof. Gat-Viks is an alumnus of the EJSCB: in the academic year 2005-2006, the first year of the Center, she was Edmond J. Safra PhD fellow in the School of Computer Science. She is the first EJSCB woman fellow to reach professorship at TAU.
 

January 2017: TAU-UT Big Data and Health workshop

A two-day workshop of TAU & University of Toronto (UT) on "Big-data and Health" took place in TAU on 23-24 January 2017 at TAU. The workshop, sponsored by EJSCB, enabled clinical, biological and computational researchers from TAU and UT to share their work and initiate collaborations.

The workshop hosted nine speakers from UT and a similar number from TAU. The program included four main sessions: (1) Integrating and utilizing new big-data modalities in health research (2) Big-Data omics in biomedical research (3) Personalizing healthcare and (4) Statistical modeling of medical data.

The talks addressed cutting-edge research topics and challenges in the area of big-data in health care systems and biomedical research, and their utilization for advancing personalized medicine. The fascinating talks planned highly diverse topics, from electronic medical records, health management and disease biomarkers to wearable devices and diagnosis via speech analysis.

The workshop was organized by EJSCB faculty fellow Dr. Ran Elkon (Medicine) and EJSCB member Prof. Saharon Rosset (Statistics). Three talks were given by EJSCB researchers (Computer Science, Statistics and Life Sciences).

Following the workshop, TAU and UT announced a joint call for collaborative projects on the topic of Big-Data and Health.
 

January 2017: Shomron on intuition in Globes

Read the article on intuition in Globes magazin where Dr. Noam Shomron (Medicine) and others discuss intuition in science, medicine and management.
 

January 2017: Diament and Steuerman win EJSCB excellence award

EJSCB PhD Alon Diament (Tuller's group, Engineering) and Yael Steuerman (Gat-Viks' group, Life Sciences) are the winners of the Edmond J. Safra Center Excellent Research Student Prize for the academic year 2016-2017.

The prize, initiated two years ago, is given annually to 1-2 students based on academic excellence. The winners are selected by the Center's Fellowship Committee. It was awarded to Alon and Yael in the Center's annual fellowship ceremony on January 3, 2017 at TAU.

Alon develops computational models of gene expression based on analysis of high-throughput next generation sequencing (NGS) data. He seeks to answer fundamental biological questions related to the 3D organization of genes in genomes and to mechanisms of gene translation, and develops algorithms for gene expression engineering.

Yael develops novel computational methods to investigate the immuno-genetics basis of the response to influenza infection. In her research Yael combines prior knowledge on the immune system with genetic information and gene expression profiles both from bulk samples and at the single cell level to explore the contribution of the immune system to the susceptibility of the host to influenza infection.

Congratulations to Alon and Yael !
 

December 2016: Ast and Perlson: Food supplement may be a key to treatment of rare disease

A new study finds that a food supplement may help reversing the detrimental effects of Familial Dysautonomia (FD), a rare debilitating neurodegenerative disorder. Approximately 1 in 30 Jewish persons of Eastern European ancestry are carriers of the mutation for the disease.

The research, led jointly by EJSCB member Prof. Gil Ast and Prof. Eran Perlson of TAU's Medicine Faculty, generated a mouse model of FD to examine the neuron degeneration caused by FD and to observe the positive effects of the novel therapy. The researchers identified the molecular pathway that leads to neurodegeneration in FD and demonstrated that the food supplement phosphatidylserine can slow progression of neurodegeneration.

The study was published in PLOS Genetics.
Read a report and an interview with Prof. Ast in the on-line newspaper Hayadan.
 

December 2016: ERC grant to Eldar

Dr. Avigdor Eldar, EJSCB affiliate researcher in the Faculty of Life Sciences, was awarded the prestigious research grant of the European Research Council (ERC) for her project "Multilevel selection for specificity and divergence in bacteria".

Evolution over multiple levels of selection - from selfish genes to organisms and populations - is crucial for our understanding of many key events in evolution, such as the evolution of multi-cellularity, social order and the dynamics of host-parasite interactions. Multilevel selection, however, poses considerable theoretical and empirical challenges in its analysis, which can be overcome by studying bacteria. Many bacterial signaling pathways operate at multiple levels of selection and concurrently show rapid divergence. The goal of Dr. Eldar's research is to understand how molecular constrains and multi-level selection combine to diversify such signaling pathways. Specifically, Dr. Eldar will study how cell-to-cell communication between bacterial cells and their genomic parasites give rise to the diversification of bacterial 'languages'. It will be done by combining experimental approaches, structural and genomic bioinformatics analysis and mathematical modeling.
 

December 2016: ERC grant to Levy

Dr. Carmit Levy, EJSCB affiliate researcher of the School of Medicine, was awarded the prestigious research grant of the European Research Council (ERC) for her project "Aligning pigmentation and repair: a holistic approach for UV protection dynamics".

The human body takes different measures in order to protect itself against the results of ultra violet (UV) exposure and its accompanied hazards, such as skin cancer. Despite extensive studies regarding the molecular regulation of the two main UV protection mechanisms, namely, the DNA repair system and the pigmentation system, a comprehensive theory that simultaneously accounts for the two systems is still missing. Hence, the ground-breaking goal of Carmit's proposal is to elucidate, for the first time, the dynamic control used to schedule and synchronize the UV protection subsystems.
 

December 2016: ERC grant to Shkolnisky

Prof. Yoel Shkolnisky, EJSCB member, of the Department of Applied Mathematics at the School of Mathematical Sciences, was awarded the prestigious research grant of the European Research Council (ERC) for his project "Cryo-electron microscopy: mathematical foundations and algorithms". The project will address the mathematical challenges of cryo-EM and develop reliable and robust algorithms for processing cryo-EM data.

In cryo-electron microscopy (cryo-EM) molecular images are taken by an electron microscope, and then the structure of a molecule is recovered from the images using sophisticated algorithms. Due to hardware breakthroughs in the past three years, cryo-EM has made a giant leap forward, introducing unprecedented capabilities that may revolutionize our biological understanding. As extracting information from cryo-EM experiments completely relies on mathematical algorithms, deep novel mathematical challenges must be solved. These challenges focus on integrating information from huge sets of extremely noisy images reliably and efficiently.
 

November 2016: EJ Safra Center Mixer

A mixer of the EJ Safra Center took place on November 23 2016.
Some 90 members of the bioinformatics community at TAU, including undergraduate and graduate students and faculty members have gathered on the lawn for informal encounters and a lunch.

For the first time, the new Safra Center Affiliates and their groups took part in the event.

Students and researchers from various faculties discussed in groups their bioinformatics research and studies and had the chance to get to know new colleagues of the bioinformatics discipline at TAU.
 


Sharan Joins the RECOMB steering committee

Prof. Roded Saharan, Edmond J. Safra Center Member from the School of Computer Science, has joined the RECOMB steering committee.
RECOMB (Research in Computational Molecular Biology) is an international scientific conferences series bridging the areas of computational, mathematical, statistical and biological sciences. It is considered the leading conference series on the theory of computational biology.
The 21th annual RECOMB will take place in Hong Kong in May 3-7, 2017.
 

Waldman and Halperin: The genetic history of Indian Jews

Bene Israel and Cochin Jews are two distinct and unique Jewish communities in India whose origin and history is largely unknown. Some oral traditions on the arrival of Jewish ancestors of these communities to India go back thousands of years, but historical records are available for only the last ~1000 years for Cochin Jews and for ~300 years for Bene Israel.

To explore the genetic history of these two communities, Dr. Yedael Waldman, a former EJSCB PhD fellow and a postdoctoral fellow in the lab of Prof. Alon Keinan (Cornell University) and the lab of Prof. Eran Halperin, EJSCB member (School of Computer Science and Life Sciences Faculty) and their colleagues, applied advanced population genetics tools on DNA samples collected from members of these communities, as well as from other Jewish, Indian and worldwide populations. They concluded that while showing genetic similarity to other Indian populations, both communities have considerable Jewish ancestry not present in other Indian populations. Thus, both communities are admixed populations with Jewish and Indian ancestry.

These studies show the power of genetic analysis to advance our knowledge of human history also in cases where other disciplines lack the relevant data to do so.

Read the study on Bene Israel in PLoS ONE and its coverage in Haaretz newspaper (Hebrew and English) and Science Daily .
Read the study on Cochin Jews in Human Genetics and its coverage in Haaretz newspaper.


Shomron and colleagues: potential breakthrough in halting breast cancer metastasis

Dr. Noam Shomron, Edmond J. Safra Center member from the School of Medicine, and colleagues have developed a method that may halt breast cancer metastasis.

The researchers sought a way to disrupt the migration of cancer cells in the body by down-regulating a particular gene. To do that, they chose to manipulate the micro-RNAs that control that gene's expression. They produced two different micro-RNA molecules, which when used on female mice stopped breast cancer metastasis. The researchers are hopeful that the results might be applicable to human patients, since the effect of micro-RNAs on mouse and human cells is often similar.

Read the paper published in Nature Communication and interviews with Dr. Shomron in: Haaretz newspaper, Walla news portal and TV Channel 10 .
 

Eight new Affiliates join the Center

Eight new researchers have joined the EJSCB as E.J. Safra Center Affiliates. The affiliates are leaders of groups in TAU whose research is close to bioinformatics or are sophisticated users of bioinformatics methods. The affiliates and their students will be invited to participate in the activities of the Center.

By adding this new tier of researches to the Center, we hope to bring together developers, implementers and advanced bioinformatics users, in order to foster cooperation and enhance bioinformatic collaborations.

For the list of the E.J. Safra Center Affiliates click here.
 

Karen Avraham's research among Israeli discoveries that influenced the world

The research of Prof. Karen Avraham, EJSCB member from the Faculty of Medicine, on the genetics of hearing, is highlighted in an exhibition of the Ministry of Science and Technology.

The exhibition, titled ISRAELI DISCOVERIES AND DEVELOPMENTS THAT INFLUENCED THE WORLD, is presented in the departure hall of Ben Gurion International Airport and is also available online here.
 

July 2016: Honorable Mention to Eli Goz on Ebola analysis

The work titled "Computational large scale exploration of functional regions in Ebola for therapy and vaccination", by Eli Goz, EJSCB PhD fellow of the Department of Biomedical Engineering at the Faculty of Engineering (Tuller's lab) received an Honorable Mention as part of the Fight Against Ebola Award competition that was presented at ISMB 2016.

ISMB is the leading conference of the International Society of Computational Biology and Bioinformatics. It was held in Orlando, Florida on July 2016.
 

July 2016: Tuller wins Juludan Prize

Prof. Tamir Tuller, EJSCB member, of the Dept. of Biomedical Engineering at the Faculty of Engineering, won the 2016 Juludan Research Prize.
The prize is awarded annually by the Technion for outstanding research projects in the exact sciences and advanced technologies whose application is directly geared to medicine.

Prof. Tuller won the prize for his research on "Deciphering, modeling and engineering the way 'synonymous/silent' codes of the transcript affect its expression".
 

July 2016: Eight EJSCB members awarded grants from the ISF

EJSCB members Profs. Gil Ast, Karen Avraham, Uri Gophna, Tal Pupko, and Drs. Irit Gat-Viks, Iftach Nachman, Noam Shomron, Adi Stern - were all awarded grants from the Israel Science Foundation (ISF) in the 2016-2017 grants cycle.

ISF is Israel's predominant source of grants funding basic research, and the grant funding is excellence-based and highly competitive.
 

May 2016: Joint IBM - EJSCB workshop

The seventh Clinical Genomic Analysis Workshop (CGA) was held on May 25, 2016 at the IBM Research lab in Haifa. It was organized by IBM Research - Haifa and the EJSCB.

The workshop provides a forum for clinical, biological and computational researchers and developers from academia and industry, to share their work, exchange ideas, and discuss work in progress.

The 2016 CGA workshop hosted about 100 participants and included diverse clinical genomics topics, spanning electronic health records, genomics and exogenous data. The forum addressed future research directions and trends in the area of personalized healthcare and the use of Big Data technologies for optimizing the individual care.

The keynote speaker was Prof. Mads Melbye, Executive Vice President of the Statens Serum Institut & The Danish National Biobank, Denmark. Other leading speakers were from IBM Research, Israeli academia, Israel Ministry of Health and Hadassah Medical Center.
 


May 2016: IBS 2016 - EJSCB sponsored conference

The 18th Israel Bioinformatics Symposium (IBS) took place on May 18, 2016 at Haifa University. The symposium was supported by the EJSCB.

IBS is the main annual get-together of the Israeli Bioinformatics community. This year's conference brought together nearly 400 participants. The program included talks by senior and young researchers, a lively poster session and online video keynote lecture by Prof. Gene Myers, director of Max Planck Institute, Dresden, who is among the pioneers of bioinformatics.

The IBS was organized by Prof. Sagi Snir and by Dr. Eyal Privman, former EJSCB PhD fellow, now on the faculty of Haifa University. The EJSCB supported the conference and also provided two prizes to students in the best poster competition. The winners were Yuval Sedan of the Hebrew University and Yishai Pinto of Bar Ilan University. EJSCB member Prof. Tal Pupko gave the prizes to the winners.
 




April 2016: CAPRI 2016 at TAU

The 6th CAPRI evaluation meeting took place on April 17-19 at TAU. It was organized by EJSCB member Prof. Haim Wolfson, and supported by the EJSCB.

CAPRI (Critical Assessment of Predicted Interactions) is a community wide experiment designed to test methods for predicting the structure of macromolecular complexes based on the known structure of their components.

The meeting program included two special keynote lectures by the Nobel laureate in Chemistry from 2004, Aaron Ciechanover from the Technioin, and the Nobel laureate in Chemistry from 2013, Michael Levitt from Stanford.

The program also included an overview of the performance of protein docking and scoring procedures obtained for targets evaluated since the spring of 2013. There was also a hands-on workshop on integrative modeling of protein-protein interactions and larger multi-molecular assemblies, which introduced participants to state-of-the-art computational methods and web-servers.
 

April 2016: Shamir and Sharan win RECOMB 2016 "Test of Time award"

EJSCB members Ron Shamir and Roded Sharan received the RECOMB 2016 "Test of Time Award", for their 2004 paper "Identification of protein complexes by comparative analysis of yeast and bacterial protein interaction data" (with T. Ideker, B. Kelley, and R. M. Karp).

The award is given for the paper published in the RECOMB conference 12 years earlier that had the largest impact on subsequent research.


April 2016: Rahmani and Rubinstein win Maus and Deutsch prizes

Edmond J. Safra MSc fellow Elior Rahmani (E. Halperin's group) and former EJSCB PhD fellow Amir Rubinstein (B. Chor's group), both from the School of Computer Science, won the Maus and Deutsch Prizes, respectively, for the academic year 2015-2016.

The prize is awarded annually to a few research students at the School of Computer Science acknowledging excellent achievements in studies and research.

Congratulations to Elior and Amir !


March 2016: Pola Abram wins WIX award

Edmond J. Safra undergraduate fellow, Pola Abram, won the WIX excellence award. The award is part of a new scholarship program awarded together by WIX Engineering Company and TAU School of Computer Science rewarding software engineering excellence.

Pola is a third year student in the bioinformatics undergraduate program, and has won excellence fellowships from the EJSCB throughout her studies.
She will be given the award by the company representative during a ceremony for outstanding students of the School of Computer Science on June 9th.

February 2016: Wolfson is ISCB Fellow

Prof. Haim Wolfson, EJSCB member of the School of Computer Science, has been elected as a Fellow of the International Society of Computational Biology (ISCB) in the Fellows Class of 2016.

Wolfson was elected for pioneering the introduction of Computer Vision motivated 3D pattern discovery algorithms into computational structural biology, co-developing the geometric hashing methodology, and developing highly efficient algorithms for protein structural alignment, protein-protein docking, binding site comparison, and integrative modeling of large multi-molecular assemblies.

Fellow status is given to ISCB members that have distinguished themselves through exceptional contributions to the fields of computational biology and bioinformatics.
The 2016 Fellows will be introduced at ISMB 2016 in Orlando, Florida in July.

February 2016: Shomron and Hendler target mind-body connection in stress

Our ability to cope with stress depends on how efficiently our body and mind regulate their response to it. Poor recovery from extremely stressful encounters can trigger post-traumatic stress disorder (PTSD). Insight into the multilevel sequence of events - from cellular changes to brain function, emotional responses, and observed behavior - will help medical professionals make more informed decisions concerning interventions.

A new study by Prof. Talma Hendler (TAU School of Medicine and Sourasky Medical Center) and Dr. Noam Shomron, EJSCB member (School of Medicine) provides such insight. Using genetic and brain imaging technologies, the researchers determined that the brain function responsible for regulating stress response intertwines with molecular regulatory elements to produce a personal profile of resilience to stress. Their findings may lead to a future blood test that would facilitate preventive or early intervention in professions prone to high stress or trauma (combat soldiers and policemen, for example).

Read the PLoS One paper and article and an interview with Prof. Hendler and Dr. Shomron on Haaretz. The reserach was featured also in the online newspaper "The Times of Israel" .

Baran and Kaufman win EJSCB excellence prize

EJSCB PhD Yael Baran (E. Halperin's group, Computer Science) and Shachar Kaufman (Rosset's group, Statistics) are the winners of the Edmond J. Safra Center Excellent Research Student Prize for the academic year 2015-2016.

The prize, initiated last year, is given to 1-2 students annually based on academic excellence. The winners are selected by the Center's Fellowship Committee. It was awarded to Yael and Shachar in the Center's annual fellowship ceremony on 23 December 2015 in TAU .

Yael develops methods for the analysis of population-scale genomic data in order to identify the genetic basis of common diseases. Specifically, she constructs statistical models for describing patterns of genetic variation in human populations, and uses these models to find disease-related genes. One aspect Yael focuses on is the description of human genetic variation as a function of geographic origin.

Shachar is developing novel statistical analysis methods for genetic association studies. Such studies are often characterized by complex pedigree and ancestry structures, and involve nontrivial sampling schemes. Existing methods are prone to make too many false discoveries in these settings, and Shachar's work guarantees proper control of such errors. Moreover, his new methodology offers superior detection of true associations, which helps shed light on the genetic factors affecting, for example, complex diseases like breast cancer and multiple sclerosis.

Congratulations to Yael and Shachar!
 

December 2015: Halperin's study on assortative mating featured in Science Daily

A study published in PNAS and featured on Science Daliy showed that genetic ancestry, as well as facial characteristics, may play an important part in who we select as mates .

The study was co-authored by EJSCB Faculty Fellow Prof. Eran Halperin, used population genomics and quantitative social sciences to gauge the relatedness of parents in a study of asthma in Mexican and Puerto Rican children.

Read more.

December 2015: Tuller first Center Fellow to become TAU professor

Edmond J. Safra Center member Tamir Tuller was promoted to Associate Professor with tenure. Prof. Tuller joined the Department of Biomedical Engineering in the Faculty of Engineering in 2011.

He heads a Laboratory of Computational Systems and Synthetic Biology.

Prof. Tuller is an alumnus of the EJSCB: In 2007 he was an Edmond J. Safra postdoc fellow in the School of Computer Science. He is thus the first EJSCB Fellow to reach professorship at TAU.

December 2015: Schwartz joins WIS

Dr. Schraga Schwartz received a tenure-track faculty position in the Weizmann Institute of Science. Schwartz was Edmond J. Safra fellow while doing his PhD in the lab of Prof. Gil Ast, Sackler Faculty of Medicine.

Dr. Schwartz is a faculty member at the Department of Molecular Genetics in WIS. His lab aims to understand the code of RNA modifications.

Schwartz is the thirteenth alumnus of the Edmond J. Safra Center who receives a tenure-track position.

December 2015: Benjamini joins the Israel Academy of Sciences and Humanities

Prof. Yoav Benjamini is among nine outstanding academic scholars who were inducted into the Israel Academy of Sciences and Humanities.

Prof. Benjamini, Edmond J. Safra Center member, from the Department of Statistics and Operations Research, is co-developer of the widely used and cited False Discovery Rate concept and methodology.
He served as president of the Israel Statistical Association and received the Israel Prize for research in statistics and economics in 2012.

The Israel Academy of Sciences and Humanities is responsible for promoting scientific excellence, providing advice to the government on scientific issues of national importance and maintaining scientific relations with similar bodies in other countries.

Read more.

Young Researchers' Forum meets Prof. Uzi de-Haan

On November 19 the EJSCB young researchers' forum hosted Professor Uzi de-Haan from the Technion, a member of the Technion patent committee and the founder of the Technion Entrepreneurship center.

Prof. de-Haan gave a talk titled: "The role of graduate students in technology transfer and academic spin offs: evidence from 8 leading US research universities and the postdoc startup program Runway at the Jacobs Technion-Cornell Institute in NYC".

In his talk, Prof. de-Haan shared his experience and knowledge about the interface between academia and industry, and introduced the Startup Postdoctoral Program, a Technion-Cornell joint program.
 

October 2015: Eisenberg on RNA editing, the new hope in cancer

Cancer is driven by alterations of the genetic information, most commonly through mutations in DNA that deregulate normal cellular functions and push cell growth into overdrive. However, DNA mutations are not the only way to alter genetic sequence information. During the past decade, it was shown that RNA editing, a process through which changes are made to the nucleotide sequences of RNAs, is a widespread phenomenon, with more than a million sites of editing detected so far in humans.

Now, three independent groups of investigators, one of them led by Erez Levanon, (Bar-Ilan U) and Eli Eisenberg, EJSCB member (TAU) , have revealed that RNA editing levels are significantly altered across cancer types, introducing RNA mutations that alter the genomic information in a tumor-specific way. A small fraction of these mutations may affect RNA or protein function in a clinically significant way, promoting cancer progression. In some cancers higher levels of editing in patients corresponded with less favorable clinical outcomes.

These findings highlight the importance of RNA mutations in understanding cancer biology, and open new directions for diagnostics and prognostic purposes. In addition, identifying the proteins or pathways that are consistently mutated at the RNA level could offer new targets for therapeutics, including the possibility of guiding the endogenous RNA editing mechanism to 'correct' these mutations.

Read an interview with Prof. Eli Eisenberg in Haaretz.
 

Spatial organization and function in the genome

The 3-D organization of genes in the genome is far from random. Many studies suggest that constraints on gene expression and function have shaped this organization. For example, studies in yeast have revealed that highly expressed genes tend to co-localize, as do gene targets of the same transcription factors, possibly resulting in more efficient transcription.

Alon Diament, EJSCB PhD fellow of Dr. Tamir Tuller, from the Faculty of Engineering, together with Prof. Ron Pinter of the Technion, developed a novel, unbiased measure of gene function and expression similarity and used it to reveal a strong link between 3-D localization and function in eukaryotes. The study, published in Nature Communications, provides the first global analysis at single-gene resolution of the spatial organization in multiple eukaryotes.

Read the descriptions of the work in Galileo and BioTechniques.
 

September 2015: New EJSCB member: Prof. Yoel Shkolnisky

Professor Yoel Shkolnisky of the Department of Applied Mathematics, School of Mathematical Sciences is a new member in the Edmond J. Safra Center for Bioinformatics. Professor Shkolnisky received his PhD in Computer Science from TAU in 2005, under the supervision of Prof. Amir Averbuch. He held a Gibbs Assistant Professor position at the Applied Mathematics Program at Yale University between 2005 and 2008, and joined TAU on 2009. Professor Shkolnisky won the prestigious Alon Fellowship and the Krill Prize for Excellence in Scientific Research.

The main research focus of Prof. Shkolnisky is developing algorithms for structure determination in cryo-electron microscopy (cryo-EM). With recent technological breakthroughs, cryo-EM now allows to determine high-resolution structures of proteins and macromolecular complexes without the need for crystals. This is done using a series of algorithms that integrate the massive amount of data produced by the microscope into a three dimensional model of the molecule. Professor Shkolnisky's group is developing fast, robust, and reliable algorithms for structure determination that would allow to fully realize the tremendous potential of the new microscopy technologies.
 

EJSCB sponsored workshop

A workshop on "Computational modeling of gene expression and its evolution" will take place on 13-15/10/2015 at Tel Aviv University.

Dozens of researchers from Israel, Europe, and the USA will participate in this workshop. Among the topics that will be discussed: new approaches for computationally modeling various biophysical aspects of gene expression; computational modeling and understanding the relation between gene expression and transcript evolution; and computational modeling and understanding gene expression in diseases.

One of the organizers of the conference is Dr. Tamir Tuller, EJSCB member. The conference is a flagship CECAM conference and is supported by the EJSCB.

Registration to the conference is free of charge, but to attend the conference advance registration is required.
If you are interested to register and possibly submit an abstract please send an e-mail here.
 

August 2015: Rosset: What is a muse in the lab?

Prof. Saharon Rosset, EJSCB member from the Department of Statistics and Operations Research, participated in a TV children program "What is a muse in the lab?". The program presents scientific subjects to children in a comprehensible, interesting and nontrivial way.

During the program, aired on August 10, 2015 in TV channels 22 and 23, Prof. Rosset engaged a group of curious children and their host in a discussion on the meaning of statistics and its uses, including demonstration of fun examples and games.

Watch the program here.
 

New EJSCB Faculty Fellow: Dr. Ran Elkon

Dr. Ran Elkon joined Tel Aviv University at the School of Medicine, the department of Human Molecular Genetics and Biochemistry. He completed his PhD in Tel Aviv university under the supervision of Prof. Yosef Shiloh (School of Medicine) and Prof. Ron Shamir (School of Computer Science), and did his postdoctoral training in the lab of Prof. Reuven Agami at the Netherlands Cancer Institute (Amsterdam).

Dr. Elkon's research focuses on mechanisms of gene regulation and aims at elucidating, using bioinofrmatic methods, how interruptions in cellular regulatory mechanisms contribute to the development of human pathological conditions, primarily cancer. Gene regulation is a multi-layered process and Dr. Elkon mainly studies three key tiers of it (1) Regulation of gene transcription; (2) Regulation of transcript stability and (3) Regulation of protein translation. His study of these tiers of gene regulation utilizes various cutting-edge deep-sequencing techniques that allow genomic-scale delineation of regulatory modes that were so far largely unexplored.
 

July 2015: Jerby wins first student prize for cancer research

Livnat Jerby-Arnon, former EJSCB PhD fellow, from the Ruppin's lab in the School of Computer Science, won the first prize for students' cancer research by the DJERASSI-ELIAS Institute of Oncology , at the Sackler School of Medicine, Tel Aviv University.

The research titled "Identifying Cancer-Specific Vulnerabilities Based on Data- Driven Detection of Synthetic Lethality" was published in the journal Cell in August 2014.
 

July 2015: Jerby wins Women in Science postdoc award

Livnat Jerby-Arnon, former EJSCB PhD fellow, from the Ruppin's lab in the School of Computer Science, won the 2015 National Postdoctoral Award for Advancing Women in Science.

The Weizmann Institute of Science runs a nationwide fellowship program offering financial support to outstanding female PhD graduates. The purpose is to enable female scientists postdoctoral training at leading international institutions for two years, with the objective that they return to Israel for an academic career.

Livnat was one of ten female PhD graduates who won the fellowship in recognition of their outstanding achievements in science.
 

June 2015: Clinical Genomic Analysis Workshop 2015 of IBM Research-Haifa and EJSCB

The sixth Clinical Genomic Analysis Workshop , organized by IBM Research - Haifa and the Tel Aviv University's Edmond J. Safra Center for Bioinformatics, was held on June 7, 2015 at the IBM Research lab in Haifa.
It brought together an audience of about 100 participants from academia, hospitals and industry, for talks, posters and panels.

A special focus of this year's workshop was clinical metagenomics and, specifically, the interplay between microbial communities and the human host and its effect on our health and behavior.
The keynote speakers were J. Madernas (McGill University) and G. Getz (Massachusette General Hospital).
 

May 2015: EJSCB fellows win best poster prizes at IBS 2015

The 2015 Israeli Bioinformatics Symposium (IBS), that took place on May 26th at TAU, is the main annual get-together of the Israeli bioinformatics community and it drew some 300 participants.
The conference included talks of senior and young researchers, a keynote lecture and a lively poster session.
It was organized by EJSCB members Prof. Tal Pupko (Chair), Dr. Itay Mayrose and Dr. Noam Shomron, and Oren Avram, EJSCB MSc fellow in Pupko's lab.
The EJSCB supported the conference and provided poster prizes.

The winners of two of the three best poster prizes were EJSCB fellows. Dr. Naama Hurwitz, former EJSCB postdoctoral fellow, of Wolfson's lab, got the prize for "An Integrated Suite for Membrane Protein Docking" and Dvir Netanely, EJSCB PhD fellow, of Shamir's lab, got the prize for "Identification of Breast Cancer Subtypes Using High-Throughput Genomic Data".
 

May 2015: Dan David Prize laureates in Bioinformatics at TAU

On May 17, three international leaders in bioinformatics and computational biology were awarded the prestigious Dan David Prize for their contributions to bioinformatics: Dr. Cyrus Chothia, (MRC Laboratory of Molecular Biology, Cambridge), Prof. David Haussler (University of California, Santa Cruz), and Prof. Michael Waterman (University of Southern California).

On May 18, an international symposium with the laureates, titled "Using bioinformatics to understand the complexity of human biology", was organized at TAU by the EJSCB and Dan David Prize. Prof. Waterman talked about "Big Data from DNA Sequencing," and Prof. Haussler gave a talk titled "Odyssey into the Human Genome". The talks were followed by a round table discussion with the three laureates. In addition, the guests held small discussion groups with TAU students and faculty.
 
Dr. Cyrus Chothia, (MRC Laboratory of Molecular Biology, Cambridge)
Read more
Prof. David Haussler, University of California, Santa Cruz
Read more
Prof. Michael Waterman, University of Southern California
Read more

May 2015: Shamir interviewed in Israel National Radio

On May 12, 2015 Prof. Shamir, Head of the EJSCB, was interviewed in the Israel National Radio, on the occasion of awarding the 2015 Dan David Prize in the future dimension for bioinformatics research.

Prof. Shamir talked about the birth of bioinformatics discipline in the 1990, how it contributed to the Human Genome Project, and how it has evolved since to address complex computational problems and to organize and analyze enormous amounts of biomedical data collected today.

He also predicted that the public will greatly benefit from these advancements soon, when synthesis between genetic information, medical health records and bioinformatics tools will be achieved.

Read/hear the interview
 

May 2015: Young researchers' forum meets Nir Friedman of Weizmann

Dr. Nir Friedman, of the Department of Immunology at Weizmann Institute, was invited by the Young EJ Safra Researchers' forum. He met the students on May 7, 2015.

Dr. Friedman described his career path and the transition he made from Physics to Biology, emphasizing the process of decision making, difficulties along the way and the significance of such a change.
 

May 2015: A special seminar on Prize4Life

On May 5, 2015 the EJSCB hosted a special seminar by Dr. Neta Zach, Chief Scientific Officer of the Prize4Life organization.

Prize4Life's mission is to accelerate the discovery of treatments and cure for Amyotrophic Lateral Sclerosis (ALS) by using powerful incentives to attract new researchers and drive innovation.

Dr. Zach gave a talk titled "Using the Power of Big Data and Crowdsourcing for Catalyzing Breakthroughs in ALS".
 

May 2015: Sharan wins the Kadar Family Award

Prof. Roded Sharan, EJSCB member from the School of Computer Science, won the Kadar Family award.

The Kadar Award, a generous contribution of the Naomi Prawer Kadar Foundation, is given annually to four TAU faculty members in recognition for having reached the highest levels of academic achievement and peer recognition for their research at TAU. Prof. Sharan won the award in the category of Junior Faculty members.

A certificate of recognition will be awarded to hime during the week of the TAU Board of Governors.
 

April 2015: EJSCB mixer

A mixer of the EJ Safra Center took place on April 30, 2015.

Some 80 members of the bioinformatics community of TAU, grad students, undergrads and faculty, gathered on the lawn for introductions, a chat, and lunch together.

Students and researchers from the different faculties had the chance to meet and to discuss, in an informal atmosphere, their bioinformatics research and studies.
 

April 2015: Top representation of TAU bioinformatics in RECOMB

RECOMB, the leading international meeting in theoretical foundations of bioinformatics, took place on April 12-15 2015 in Warsaw, Poland.
43 contributed and highlight papers were selected for presentation in the conference, with acceptance rate of ~20% for the contributed papers.

TAU students and faculty presented five contributed papers, achieving the highest number of accepted contributed papers among all presenting institutes.
 

March 2015: Alon Fishel on the Rector's list

Alon Fishel, a second year student in the bioinformatics undergraduate track, is on the Rectors outstanding students list for 2014-15.

Out of all some fifteen thousand undergraduates in TAU, 36 students were selected for the prestigious honor based on excellence in their studies. Alon was awarded a certificate of recognition in a ceremony that took place on March 2015.
 

February 2015: Oren and Pupko's paper wins PNAS Cozzareli Prize

A paper by former PhD Edmond J. Safra fellow, Yaara Oren, and her advisor, Prof. Tal Pupko, Edmond J. Safra Center member from the Faculty of Life Sciences, won the 2014 PNAS Cozzarelli Prize award.

The paper "Transfer of noncoding DNA drives regulatory rewiring in bacteria" by Yaara Oren, Mark B. Smith, Nathan I. Johns, Millie Kaplan Zeevi, Dvora Biran, Eliora Z. Ron, Jukka Corander, Harris H. Wang, Eric J. Alm, and Tal Pupko, is one of six papers published in PNAS 2014 to earn this distinction.

The Cozzarelli Prize recognizes recently published PNAS papers of outstanding scientific excellence and originality. The certificate will be awarded during the PNAS Editorial Board Meeting on April 26, 2015, held in Washington, DC.
 

February 2015: Dan David Prize announces 2015 laureates in bioinformatics

The Dan David Prize honors outstanding individuals with scientific, technological, cultural, and social achievements having an impact on our world. Each year fields are chosen within the three Time Dimensions: Past, Present and Future. The prize for each dimension is US$ 1 million. The Dan David Prize is a joint international enterprise, endowed by the Dan David Foundation and headquartered at Tel Aviv University.

The field of Bioinformatics was chosen as the future dimension for the year 2015.
The Dan David Prize laureates were just announced:

Dr. Cyrus Chothia, MRC Laboratory of Molecular Biology in Cambridge and University College London
Prof. David Haussler, University of California, Santa Cruz
Prof. Michael Waterman, University of Southern California
See additional details on the laureates in the Dan David Prize website .

The prizes will be awarded in a ceremony that will be held at TAU on Sunday, May 17, 2015.

February 2015: Young researchers' forum meets Compugen's Benita

Dr. Yair Benita, Head Computational Research & Discovery at Compugen Ltd. was a guest of the Edmond J. Safra young researchers' forum on February 5 at TAU.
Dr. Benita described the bioinformatics work conducted in his firm. The rest of the meeting was dedicated to an open discussion about the bioinformatics industry.
 

January 2015: TAU-CRG-EJSCB meeting

TAU welcomed a delegation of nine scientists from the Centre of Genomic Regulation (CRG) Barcelona, for a joint symposium at TAU entitled "Gene Regulation, Genomics and Stem Cells in Disease," partly sponsored by the EJSCB. The delegation was led by Prof. Juan Valcarcel, the coordinator of the Gene Regulation, Stem Cells and Cancer Program at CRG. The TAU coordinators were EJSCB members Profs. Gil Ast and Karen Avraham.

Eighteen speakers, a mixture of highly renowned senior scientists and young PIs, presented their research in front of 120 participants from TAU and neighbouring institutions and hospitals. A mixture of state of the art talks and a vibrant forum for discussions made the symposium highly successful, opening numerous dialogs on potential collaborations. On an institutional level the CRG and TAU will support the collaborations by coordinating technology, know-how, and student exchanges.
 

January 2015: Eisenberg and Alon: Squid edit their RNA extensively

Squid edit a lot of gene transcripts, preferentially those with nervous system function. Shahar Alon, former EJSCB PhD fellow and his advisor, Eli Eisenberg, EJSCB member of the School of Physics and their colleagues investigated RNA editing in squids. While RNA editing is rare in mammals and fruit flies, squid seem to use RNA editing much more frequently. In terms of the types of RNA transcripts that are edited, changes to the genetic code were more common in RNA transcripts associated with brain physiology, which is consistent with other organisms that have been looked at including humans.

Why so much editing in squid? The answer is not clear, but researchers suggest that RNA editing could be related to the sophistication of their complex nervous system and behaviors compared with their "cousins", clams and oysters. Read the eLife journal paper , and an interview with Prof. Eisenberg in Haaretz.
 

January 2015: Jerby wins the Rothschild Postdoctoral Fellowship

Livnat Jerby, Edmond J. Safra former PhD fellow, in the laboratory of Prof. Eytan Ruppin, at the School of Computer Science, won the Rothschild Postdoctoral Fellowship for 2015.

The Rothschild Fellowship program was established in 1979 to help young scholars of outstanding academic merit and potential to advance in their respective fields. Up to twelve Rothschild Fellowships are awarded each year in the Natural, Exact or Life Sciences and Engineering. Livnat will start her postdoctorate in a few months.
 

January 2015: Shiloh is the first winner of Olav Thon Prize

Prof. Yosef Shiloh, Edmond J. Safra Center member, was awarded the Olav Thon Prize for natural sciences and medicine.
The prize will be awarded to Prof. Shiloh, a researcher investigating the genetics of cancer, at a ceremony in Norway on March 5th, 2015.
The prize was established by the Norwegian billionaire Olav Thon, who decided to donate all of his money to philanthropic projects focusing on education and the sciences. Prof. Shiloh is the first recipient of the prize.
 

December 2014: David Amar and Eli Levy Karin win EJSCB Excellence Prize

EJSCB PhD fellows Eli Levy Karin (Pupko's lab, Life Sciences) and David (Didi) Amar from (Shamir's lab, Computer Science), are the winners of the Edmond J. Safra Center Excellent Research Student Prize for the academic year 2014-2015.

The prize, presented for the first time, was determined by the Center's Fellowship Committee. It was awarded to Eli and Didi in the Center's annual fellowship ceremony that was held on 31 December 2014 in TAU. This new prize will be awarded annually to acknowledge research achievements and to promote research excellence of the Center's student fellows.

Eli's research uses information in biological molecules to better understand how evolution shapes species. Eli analyzes DNA and protein sequences using advanced statistical and computational tools. Currently, she focuses on discovering phenotypic traits that affect the rate of species evolution.

Didi develops algorithms for integrated analysis of large-scale heterogeneous biological data from many biomedical studies. The goal is to create a simple summary of highly complex analysis, which can lead researchers to novel insights, and help physicians in tailoring individual treatments to patients.
 




December 2014: Keren Yizhak featured in eLife

Keren Yizhak, who was until recently EJSCB PhD fellow in Ruppin's lab (Computer Science), was interviewed by the journal eLife.

In a series of interviews with young researchers, eLife explores how they became interested in science, what they are working on at present, and what they hope to achieve in the future.

Keren Yizhak uses computational techniques to study biological phenomena, focusing on the metabolic changes that occur in cells during cancer and ageing.
She will soon start a postdoc in the Broad Institute at Harvard.

Read the interview.
 

December 2014: ERC grant to EJSCB faculty fellow Dr. Irit Gat-Viks

Dr. Irit Gat-Viks, Edmond J.Safra Center faculty fellow in the Faculty of Life Sciences, was awarded the prestigious European Research Council (ERC) research grant.

Her project, titled "A genetic view of Influenza infection", is aiming to understand how genetic variation in immune responses leads to inherited variation in complex physiological traits, in health and disease.

The ERC Starting grants for young investigators support promising researchers who have the proven potential of becoming independent research leaders and encourage the creation of excellent new research teams or strengthen others that have been recently created.
 

September 2014: Prof. Karen Avraham elected president of FISEB

Prof. Karen Avraham, Edmond J. Safra Center member, was elected congress president of the Federation of the Israel Societies for Experimental Biology (FISEB).

FISEB is a federation of all the Israeli Societies for Experimental Biology that was established in 1995.
Since 1996, it organizes ILANIT, the national tri-annual conference of FISEB in Eilat.
The Israeli Society for Bioinformatics and Computational Biology (ISBCB) is a society member of FISEB.
 

August 2014: Ben-Tal's study offers a global view of the protein universe

How are proteins related to each other?
Which physicochemical considerations affect protein evolution, and how?
EJSCB member, Prof. Nir Ben-Tal, and his colleagues, Sergey Nepomnyachiy (New York University) and Rachel Kolodny (Haifa University), published a study in the journal PNAS which addresses these questions by computing a network of protein similarity.
The network contains a large connected component, as well as isolated 'islands', revealing the complex nature of protein space, which includes continuous and discrete regions.

Read the PNAS paper and editorial article .
Read an article published on Israeli newspaper, Haaretz.
 

August 2014: New Edmond J. Safra member, Dr. Adi Stern

Dr. Adi Stern, who will be joining the department of Molecular Microbiology and Biotechnology at the Faculty of Life Sciences in October 2014, is the newest member of the Edmond J. Safra Center . Dr. Stern received her B.Sc. in the multidisciplinary program in Biology and Psychology from TAU, and holds an additional degree in Mathematics. She completed her M.Sc. and Ph.D. at the Faculty of Life Sciences at TAU. She was a post-doctoral fellow at the Weizmann Institute of Sciences, and recently returned from a second post-doctoral fellowship in UC Berkeley and UCSF. Dr. Stern is also an alumnus of the EJSCB: She was a EJS PhD Fellow in 2005.

Dr. Stern studies the evolution of viruses and their hosts. She uses a highly multidisciplinary approach spanning computational biology, theory of evolution, and "wet" molecular biology to answer basic questions on how viruses change and adapt in the face of constantly changing environments. By understanding the rules that govern viral evolution, Dr. Stern believes we will one day be able to "trap" viruses in a cage of their own constraints. Ultimately, her work may enable forecasting viral evolution and preventing viral epidemics.
 

August 2014: Prof. Sharan a "Highly Cited Researcher"

Thomson Reuters announced its list of 2014 Highly Cited Researchers. Researchers earned the distinction by writing the greatest numbers of reports officially designated as Highly Cited Papers - ranking among the top 1% most cited in the period 2002-2012, in their subject field.

This year, EJSCB member, Prof. Roded Sharan, was one of 117 Highly Cited Researchers recognized in computer science. Prof. Sharan is a faculty member in the School of Computer Science.

More info can be found here .
 

July 2014: Halperin wins Juludan Prize

Prof. Eran Halperin, EJSCB Faculty Fellow, of the School of Computer Science and the Department of Molecular Microbiology and Biotechnology, won the 2014 Juludan Research Prize.
The prize is awarded annually for outstanding research projects in the exact sciences and advanced technologies whose application is directly geared to medicine.

Prof. Halperin won the prize for the work summarized in his papers:
"Estimating local ancestry in admixed populations" . American Journal of Human Genetics, 2008 and

"A model-based approach for analysis of spatial structure in genetic data" . Nature Genetics, 2012.
 

July 2014: EJSCB young researchers' forum meets the bioinformatics industry

The EJSCB young researchers' forum has initiated a meeting with representatives from the Israeli bioinformatics industry.
A workshop, held in July 10 in TAU, hosted Guy Kol, NRGENE's VP of R&D, and Ben Gardus of EVOGENE.
The guests presented their companies and described the bioinformatics work that is being conducted at each firm. Most of the meeting was dedicated to open discussion on the bioinformatics industry world.

See a photo taken during the meeting:
 


June 2014: Co-sponsored meeting by EJSCB and the I-CORE Gene Regulation

Co-sponsored by the Edmond J. Safra Center for Bioinformatics, the I-CORE Gene Regulation in Complex Human Disease spring meeting took place on June 1, 2014 at Tel Aviv University, featuring genomics researcher Prof. Evan Eichler from the Department of Genome Sciences at the University of Washington, Seattle, US.

Prof. Eichler described the latest data about the genetics of autism spectrum disorder and the functional studies in zebrafish addressing the mechanisms leading to this devastating disease (recently published in the journal Cell, July 2014).

 

June 2014: The annual Israeli Bioinformatics Symposium

The 16th Israeli Bioinformatics Symposium (IBS 2014) took place in Bar-Ilan University on June 24.

IBS is the main annual get-together of the Israeli Bioinformatics community. It included a special lecture by Michael Levitt, the Nobel Prize laureate in Chemistry for 2013.
EJSCB sponsored the conference and provided two prizes to students in the best poster competition.

One of the prizes was awarded to Hadas Zur, EJSCB PhD fellow in the laboratory of Dr. Tamir Tuller, EJSCB member, of the Department of Biomedical Engineering, Faculty of Engineering (see picture below. Hadas Zur is the first from the right).

Prof. Ron Shamir, Head of EJSCB, presented the prizes to the winners (see picture below).
 




June 2014: Edmond J. Safra Center PhD fellow wins the Anita Borg fellowship

Yael Steuerman, EJSCB PhD fellow in the laboratory of Dr. Irit Gat-Viks of the Cell Research and Immunology Department, Life Sciences Faculty, has won the Anita Borg scholarship.

Dr. Anita Borg devoted her adult life to revolutionizing the way we think about technology and dismantling barriers that keep women and minorities from entering computing and technology fields.
Google is honoring Anita's memory and support women in technology with the Google Anita Borg Memorial Scholarship . The scholarship encourages women to excel in computing and technology and become active role models and leaders in the field.
 

June 2014: Clinical Genomic Analysis Workshop 2014 of IBM Research-Haifa and the Edmond J. Safra Center for Bioinformatics

The Analytics department at IBM Research - Haifa (HRL) and the Edmond J. Safra Center for Bioinformatics organized the Fifth Clinical Genomic Analysis Workshop. The workshop was held at the IBM Research site on the Haifa University campus.

The seminar provided a forum for research and development communities from both academia and industry to share their work, exchange ideas, and discuss issues, problems, and works-in-progress. The forum also addressed some future research directions and trends in the area of personalized healthcare and the use of "omics" technology for optimizing the individual care.

The program attracted nearly 100 attendees, and included the keynote speaker, Isaac Kohane, Co-Director of the Center for Biomedical Informatics at Harvard Medical School.
Speakers and panelists include leaders from IBM research, Israel Ministry of Health, Teva Pharmaceuticals, John Hopkins University and Sheba Medical Center.

For the program click here.


May 2014: Distinguished E. J. Safra Center visitor: David Sankoff

Prof. David Sankoff, one of the pioneers and the trailblazers in bioinformatics, was awarded an honorary doctorate from TAU on a ceremony held on 15 May 2014.

Prof. Sankoff was a guest of the Edmond J. Safra Center during his visit. He gave a talk on "Analyzing the remarkable evolution of genome structure in the flowering plants" in the Center's Distinguished Speaker series, and met for discussions with students and senior researchers in bioinformatics.
 

ERC grant to Edmond J. Safra Center member

Prof. Judith Berman, EJSCB member, of the Faculty of Life Sciences, was awarded the prestigious research grant of the European Research Council (ERC) for her research project titled: "Ploidy change as a rapid mechanism of adaptation".

Prof. Berman's project investigates how new traits such as drug resistance arise rapidly using Candida albicans, the most prevalent fungal pathogen of humans. Microbial pathogens are a major cause of mortality world-wide and the development of resistance to anti-microbial drugs is a perpetual challenge. Fungi are particularly challenging pathogens; because they and their human hosts are eukaryotes, the arsenal of antifungal agents is limited and the appearance of drug resistance is a serious concern. Antifungal drugs can appear much more rapidly than expected by conventional theories based on frequencies of single mutations.

The ERC's mission is to encourage the highest quality research in Europe through competitive funding and to support investigator-driven frontier research across all fields, on the basis of scientific excellence.
 



May 2014: The journal Genetics chose a paper of PhD EJSCB fellow, and his advisor, EJSCB member, as its media release for the May 2014 issue

The journal Genetics chose a paper of Shachar Kaufman, PhD EJSCB fellow, and his advisor Prof. Saharon Rosset, EJSCB member, as its media release for the May 2014 issue.

The new study gives a statistical framework that can substantially increase the power of genome-wide association studies (GWAS) to detect genetic influences on human disease, by taking advantage of additional available data sources (such as other samples from the same population as the GWAS) and standard assumptions about the distribution in the population (such as Hardy-Weinberg equilibrium).

See the media release here.
See the blog post of the Genetics Society of America here.
 

March 2014: Team Science Award to Edmond J. Safra Center member

Two TAU research teams received the prestigious Team Science Awards from US Melanoma Research Alliance (MRA).
The Team Science Awards are the centerpiece of the MRA research fund, which seeks to promote transformational melanoma research for swift clinical implementation.

One of the awards was granted to researchers in TAU Sackler Faculty of Medicine, Dr. Gal Markel, together with Dr. Tamar Geiger and EJSCB member Dr. Noam Shomron, who heads the TAU Functional Genomics Laboratory.

The goal of their study is to discover the mechanisms that allow tumors to evade the immune system, in order to disarm those mechanisms, making the tumor susceptible to the patient's own immune response.
Read more .

February 2014: Edmond J. Safra Center young researchers' forum

PhD student fellows in the Edmond J. Safra Center initiated a new forum for students conducting bioinformatics research at TAU.
Bioinformatics research at TAU spans dozens of research students from 26 groups across four faculties. The new forum will give these students an opportunity to meet in an informal and relaxed atmosphere, to get to know each other better, and to discuss issues of interest.
The EJSCB welcomes this idea and will support this activity.

35 students attended the first meeting that took place on 20 February 2014, and was devoted to setting the foundations of the new forum. See a photo taken during the meeting.


February 2014: Edmond J. Safra Faculty fellow wins the 2014 Krill Prize for excellence in scientific research

Edmond J. Safra Faculty Fellow, Dr. Irit Gat-Viks, will be awarded the Krill Prize for Excellence in Scientific Research for 2014.
Dr. Gat-Viks is a senior lecturer in the Department of Cell research and Immunology, the George S Wise Faculty of Life Sciences. The Krill prize, funded by the Krill family, is awarded annually to six excellent young untenured researchers in Exact Sciences, Life Sciences, Medicine, Agriculture and Engineering at Israeli universities.
Recipients are selected by the Wolf Foundation, out of outstanding candidates nominated by all Israeli universities. The selection is based on the candidate´s excellence and the importance of his or her field of research.
The prize will be awarded to Dr. Gat-Viks on 24 April, 2014.

January 2014: Alon and Golan win the Rothschild Postdoctoral Fellowship

Shahar Alon, Edmond J. Safra former PhD fellow, in the laboratory of Prof. Eli Eisenberg,at the School of Physics, and David Golan, Edmond J. Safra PhD fellow, in the laboratory of Prof. Saharon Rosset, at the Department of Statistics and Operations Research, have won the prestigious Rothschild Postdoctoral Fellowship for 2014.

The Rothschild Fellowship program was established in 1979 to help young scholars of outstanding academic merit and potential to advance in their respective fields. Up to twelve Rothschild Fellowships are awarded each year in the Natural, Exact or Life Sciences and Engineering. Shahar Alon is now a postdoctoral fellow in MIT and David Golan is a postdoctoral fellow in Stanford University.

December 2013: An "anti-aging algorithm" developed by EJSCB member and fellow

Studies have shown calorie restriction can be effective in slowing aging and extending the lifespan.
Keren Yizhak, EJSCB PhD fellow, together with EJSCB member Prof. Eytan Ruppin and colleagues from Bar-Ilan University, have developed a computer algorithm that predicts which genes can be "turned off" to create the same anti-aging effect as calorie restriction.
The findings, reported in Nature Communications, could lead to the development of new drugs to treat aging.

Keren Yizhak was quoted on this study in numerous scientific newspapers. See the following articles:

Science Daily
Nature World News Huffington Post
Communications of the ACM
Financial Express
Cosmetics
 

December 2013: A special workshop celebrating 60th birthday of EJSCB Head

A special workshop: "Bioinformatics, Optimization and Graphs" celebrating the sixtieth birthday of EJSCB member and head Prof. Ron Shamir, took place on December 12, 2013 in Tel Aviv University.

The program, organized by Prof. Shamir's past students, included plenary talks by several world-class leaders and founding fathers of bioinformatics. It attracted over 100 attendees, including many EJSCB students and researchers.
TAU president Prof. Yoseph Klafter opened the event, followed by greetings by Prof. Yishay Mansour, Head of I-CORE Center of Excellence in Algorithms. The international speakers were Profs. Ilan Adler, UC Berkeley, Dorit Hochbaum, UC Berkeley, Richard Karp, UC Berkeley, Hans Lehrach, MPI Berlin, Itsik Pe'er, Columbia University, Pavel Pevzner, UC San Diego, Martin Vingron, MPI Berlin and Michael Waterman, University of Southern California.
Additional talks were given by Prof. Martin Golumbic, University of Haifa, Drs. Amos Tanay and Rotem Sorek, Weizmann Institute. EJSCB member Prof. Martin Kupiec and EJSCB PhD fellow, Yaron Orenstein. .

For more pictures from the event, click here.


December 2013: A new research, by Edmond J. Safra member and colleagues, pinpoints right antidepressant for each patient

A new discovery by Dr. Noam Shomron, EJSCB member and his colleague Dr. David Gurwitz, may make it possible to prescribe the most effective antidepressant based on a simple blood test.
The scientists were able to identify genes in blood cells that are linked to the creation of receptors in brain cells and that respond differently to antidepressants in different people.
The study, which was published in the Journal Translational Psychiatry, could change perceptions on the origins of depression and the mechanisms that trigger it.

Hear an interview of Dr. Shomron on the Israeli Radio 103 FM.

Read an article published on Israeli newspaper, Haaretz.
 

November 2013: EJSCB student interviewed in a science blog on predicting the effect of gene over-expression

Allon Wagner, EJSCB PhD fellow, together with EJSCB members Profs. Eytan Ruppin and Uri Gophna and their colleagues, published a new paper in the journal PNAS. They built software models of cells that simulate the complex interplay of genes inside them, and developed an algorithm called EDGE to predict a cell's fate if it activates or expresses one of its genes at unnaturally high levels.

EDGE relies on a genome-scale metabolic model, an emerging computational paradigm for studying metabolism. The study shows EDGE's applicability to human disease by demonstrating its ability to detect toxic genes whose expression tends to be suppressed in cancer cells.

Allon was interviewed about this study in "First Look", the PNAS science blog.
 

November 2013: Mixer of the Edmond J. Safra Center for Bioinformatics

On November 14, 2013, the first EJSCB Mixer for the year took place. The mixers, bringing together bioinformatics graduate students, undergrads and faculty members, aim to increase cohesion and foster informal interactions within the bioinformatics community on campus.
More than 80 EJSCB faculty members, EJSCB fellows and other members of the TAU bioinformatics community were gathered together outdoors on the lawn during the lunch hour.
In the first part of the event, students divided into groups and groups split into pairs. The members of each pair gave each other an "elevator talk" (a 2-minute introduction to who they are and what they do and aspire). Afterwards the groups reassembled and each one introduced his pair partner to the group. Later, students and researchers from the different faculties had the chance to meet and to talk to each other over pizza.

For more pictures from the event, click here.


October 2013: New research by Edmond J. Safra member and fellow: Coffee and Beer May Affect the Stability of your Genome

Caffeine and alcohol affect cellular aging, genome stability, and the risk for different diseases, according to new research led by Prof. Martin Kupiec, Edmond J. Safra member. In a paper published in the scientific journal Public Library of Science, Prof. Kupiec and his team: Dr. Gal Hagit Romano, EJSCB former postdoctoral fellow, Yaniv Harary, and other researchers tested how different environmental stressors affect elements of the genome.

Their results show that caffeine and alcohol alter the length of telomeres, nucleoprotein structures located at the ends of chromosomes which are implicated in cellular aging, cancer, and different diseases.

This study was completed in collaboration with scientists from the Blavatnik School of Computer Sciences at Tel Aviv University: Prof. Roded Sharan, Prof. Eytan Ruppin, Prof. Ron Shamir, all EJSCB members, Dr. Assaf Gottlieb, former EJSCB postdoctoral fellow, as well as Prof. Dana Pe'er from Columbia University.
Read more.
 



September 2013: Globes cover story highlights work by Edmond J. Safra Center member and fellows

The cover story of the October Globes magazine highlights a new genetic software developed by Dr. Noam Shomron, Edmond J. Safra Center member, and his students Gershon Celniker, Ofer Isakov and Liron Yoffe, all Edmond J. Safra PhD fellows.
The researchers developed a computational tool to analyze personal genome sequences and present their medical potential consequences for doctors and patients. The application, available on smart phones, can have broad potential use for personal use of genetic information.
Read more.
 

September 2013: Edmond J. Safra former fellow appointed to faculty position

Dr. Mukul Bansal, former Edmond J. Safra Postdoctoral fellow in the lab of Prof. Ron Shamir, School of Computer Science, Tel Aviv University, received a tenure-track faculty position at the University of Connecticut.
Dr. Bansal is an Assistant Professor in the Department of Computer Science & Engineering, University of Connecticut.
 

September 2013: The 2nd Graduate Students Conference in Genetics, Genomics and Evolution

The Edmond J. Safra Center for Bioinformatics sponsored the "2nd Graduate Students Conference in Genetics, Genomics and Evolution," which took place on Sept. 2, 2013 at the Weizmann Institute of Science.
The goal of this conference was to create a forum in which PhD students present their current research to an audience that specializes in the different fields of genetics.
In addition, both MSc and PhD students were encouraged to present their work in posters, with the aim of sparking an exchange of ideas and feedback in a more informal setting.
The conference featured 19 lectures and 35 posters. More than 110 faculty and students attended the conference.

David Gokhman, from Liron Carmel's group at the Hebrew University, was awarded the Best Lecture Prize on "Paleoepigenetics: Reconstructing the DNA methylation maps of archaic hominins" and will use the award to present his research at the symposium, "Evolution of Modern Humans: From Bones to Genomes," in March 2014 in Sitges, Spain.
Binyamin Knisbacher, from Erez Levanon's group at Bar-Ilan University, was awarded the Best Poster Prize on "Identification of DNA editing in retrotransposons of diverse genomes " and will use his award to present his research at the "American Society of Human Genetics Annual Conference" in Boston in October 2013.
The Conference was co-sponsored by I-CORE Gene Regulation in Complex Human Disease and the Genetic Society of Israel.



 

August 2013: Edmond J. Safra member heads the program committee of RECOMB 2014

Prof. Roded Sharan, Edmond J. Safra Center member, is the Program Committee Chair of RECOMB 2014: the 18th International Conference on Research in Computational Molecular Biology that will take place in April 2-5, 2014, Pittsburgh, USA.
RECOMB is the leading theoretical conference in computational molecular biology. The conference features highly selective peer-reviewed papers and keynote talks by eminent scientists .
 

July 2013: Seven EJSCB members awarded grants from the ISF

EJSCB members Profs. Gil Ast and Judith Berman, Dr. Irit Gat-Viks, Profs Eran Halperin, Tal Pupko, Eytan Ruppin and Ron Shamir were all awarded grants from the Israel Science Foundation (ISF) in the 2013 grants cycle.
ISF is Israel's predominant source of grants funding basic research, and the grant funding is excellence-based and highly competitive.
 

July 2013: Edmond J. Safra former fellow appointed to faculty position

Dr. Igor Ulitsky, former Edmond J. Safra PhD fellow at the lab of Prof. Ron Shamir, of the School of Computer Science, received a tenure-track faculty position in Weizmann Institute.
Dr. Ulitsky is a Senior Scientist at the Department of Biological Regulation.
 

July 2013: Edmond J. Safra former fellow appointed to faculty position

Dr. Eyal Privman, former Edmond J. Safra PhD fellow at the lab of Prof. Tal Pupko, of Life Sciences Faculty, received a tenure-track faculty position in Haifa University.
Dr. Privman is a faculty member in the Department of Evolutionary and Environmental Biology.
 

July 2013: Dr. Noam Shomron publishes a new book

A new book edited by Edmond J. Safra Center member, Dr. Noam Shomron, titled: "Deep Sequencing Data Analysis" was recently published in the Methods in Molecular Biology series of Springer Protocols, Humana Press.
The new genetic revolution is fuelled by Deep Sequencing (or Next Generation Sequencing) devices, which can read billions of nucleotides per reaction. When carefully planned, any experimental question which can be translated into reading nucleic acids can be applied. In Deep Sequencing Data Analysis, experts in the field detail methods that are now commonly used to study the multi-facet deep sequencing data field.

Authoritative and practical, Deep Sequencing Data Analysis seeks to aid scientists in the further understanding of key data analysis procedures for deep sequencing data interpretation.
 

June 2013: Annual Israeli Bioinformatics Symposium

The 2013 Israel Bioinformatics Symposium (IBS) took place on June 27th at the Ben Gurion University, celebrating the 15th annual meeting of the Israeli society of Bioinformatics and Computational Biology.
IBS is the main annual get-together of the Israeli bioinformatics community and it drew some 400 participants. The conference included outstanding talks of senior and young researchers, two intriguing keynote lectures and a record number of 106 posters.
The EJSCB supported the conference and provided prizes to students in the best poster competition. Mor Lurie-Weinberger, PhD Safra fellow, of the lab of Prof. Uri Gophna, of Life Sciences Faculty was awarded one of the best poster prizes.
 

June 2013: Prof. Leroy Hood: Special Seminar at TAU

The Edmond J. Safra Center for Bioinformatics hosted Prof. Lee Hood at Tel Aviv University.
Prof. Hood is the founder and president of the Institute for Systems Biology, a leading institute with the mission to "revolutionize science, transform human health, and ensure environmental sustainability".
Prof. Hood spoke to a packed audience at the Sackler School of Medicine at Tel Aviv University about "A Systems Approach to Disease: Systems Medicine is Transforming Healthcare.
A pioneer in the systems approach to biology and medicine, Prof. Hood received the National Medal of Science from President Obama at a White House ceremony in 2013. He has received many awards, including the Lasker Award for Studies of Immune Diversity, the Kyoto Prize in advanced technology, the Heinz Award for pioneering work in Systems Biology, and the NAE 2011 Fritz J. and Delores H. Russ Prize for automating DNA sequencing that revolutionized biomedicine and forensic science.
His research has encompassed molecular immunology, biotechnology and genomics and he has played a major role in founding more than fourteen biotechnology companies.
I-CORE for Gene Regulation in Complex Human Disease co-sponsored the event.



May 2013: "Meet the New TAU Faculty" event

Please join us in a meeting introducing new faculty members who joined the Sackler School of Medicine and the Life Sciences Faculty this year.
Among the new faculty is Edmond J. Safra Center member, Dr. Itay Mayrose, of the Dept. of Molecular Biology & Ecology of Plants, Life Sciences Faculty.

When: Wednesday, May 22, 14-16 (refreshments at 14).

Where: Lola Hall, Sackler School of Medicine.

For more info click here .


May 2013: A special talk by editor at EMBO reports

A special talk will be held by
Dr. Barbara Pauly,
Editor at EMBO reports on:
"EMBO and its publications - a short introduction"
More details .


April 2013: Edmond J. Safra Center member develops novel diagnosis of Schizophrenia

A team led by Dr. Noam Shomron, Edmond J. Safra Center member, developed a new technique to diagnose schizophrenia at an early stage.
The technique uses neurons of the sense of smell taken from the nose. Previously, the diagnosis could only be done post mortem by examining the nerve cells in the brain.
The result was reported recently in the medical journal Neurobiology of Disease .
Read more .
Hear an interview of Dr. Shomron on the Israeli National Radio.
Read an article that was published on the Wall Street Journal.
The work was also featured in 'Reuters'.


April 2013: Edmond J. Safra fellow is awarded Adams fellowship

Livnat Jerby, EJSCB PhD Fellow in the laboratory of Prof. Eytan Ruppin in the School of Computer Science, was awarded the prestigious Adams fellowship for the academic year 2013-2014.


April 2013: I-CORE for Gene Regulation in Complex Human Disease and the Edmond J. Safra Center for Bioinformatics host a Korean NIH delegation

A team from the Korean National Institutes of Health visited Tel Aviv University and participated in a conference, the TAU-KNIH Symposium: Population Biobanking in the Post-Genomic Era, on April 23, 2013.

Opening remarks were made by Dr. Myeong-Chan Cho, the Director-General of the KNIH and Prof. Raanan Rein, Vice President of Tel Aviv University.
The day continued with lectures on the Korean Biobank Project, one of the foremost and comprehensive biobank projects in the world. Participants heard about how chromatin organization and epigenetic "talk" with alternative splicing and how a human cell collection is being used for drug-response ?biomarkers discovery. Issues surrounding human identification and DNA privacy in the genomic era were reported.

Prof. Karen Avraham, a member of the Edmond J. Safra Center for Bioinformatics and I-CORE member described research on gene and mutation discovery in the new era, using high-throughput techniques. The day was concluded with a panel discussion on population biobanking for promoting international biomedical research.



April 2013: TEDMED event in Washington broadcast at TAU

TEDMED 2013, an international event featuring TED talks of leading innovators in health and medicine, was streamed via internet to TAU on April 18, 2013.
Faculty and students from the TAU community gathered together to watch lectures by prominent speakers taking part in TEDMED Live at the Kennedy Center, Washington DC from April 16-20, 2013.
Lectures in Medicine, Technology, and Healthcare took place, including a lecture by NIH Director Francis Collins. Other lectures included: "What's the new way to ask big questions in science?", "Why do we use mice to study human diseases?" and "Can you coordinate the dance of your bodies' 100 trillion microorganisms?".
The TAU event was organized by EJSCB and the I-CORE for Gene Regulation.

March 2013: Edmond J. Safra Center member among elected members to the HUGO Council

Prof. Karen Avraham, Edmond J. Safra Center member, is one of the newly elected members to the HUGO Council .
HUGO is The Human Genome Organization that was initiated in 1988, as the genome initiatives got under way in individual nations, the need for an international coordinating scientific body had been under discussion. Its main objectives are to investigate the nature, structure, function and interaction of the genes, genomic elements and genomes of humans and relevant pathogenic and model organisms. to foster the interaction, coordination, and dissemination of information and technology between investigators and the global society in genomics, proteomics, bioinformatics, systems biology, and the clinical sciences by promoting quality education, comprehensive communication, and accurate, comprehensive, and accessible knowledge resources for genes, genomes and disease.

February 2013: Edmond J. Safra Center member heads a research team discovers a new mode of reproduction in the most prevalent human fungal pathogen

Candida albicans is a fungus that causes disease and lethal infection, killing hundreds of thousands around the world each year. Until now researchers knew that Candida reproduces only by simple cell division, in which each cell is almost identical to its predecessor, and each cell is a diploid, i.e., it contains two copies of the genome.
In a new study headed by Edmond J. Safra Center member, Prof. Judith Berman, of the Department of Molecular Microbiology and Biotechnology, the researchers have found that under certain conditions the fungus cells contain only a single copy of the genetic material. Each of these cells has only one copy of the chromosomes. Mating between two of these cells creates new diploid cells with two copies of each chromosome.

"We did not know about the existence of those cells in the fungus, and the discovery allows us to better understand how the various changes occur in the cells, especially when the fungus develops drug resistance" says Prof. Judith Berman. She added that the discovery of cells with only one copy of the genetic material allows researchers to work with cells more easily and more efficiently in order to develop antifungal drugs. The findings were published in the scientific journal Nature.
Berman and colleagues may pave the way to better understanding the modes of reproduction of other fungi that cause diseases. Hear an interview of Prof. Judith Berman on Israel National radio.

February 2013: Edmond J. Safra Center member is Editor in Chief of Genetics Research

Edmond J. Safra Center member, Dr. Noam Shomron, of the Department of Cell & Developmental Biology, the Sackler Faculty of Medicine, is the Editor in Chief of the Cambridge University Press Journal Genetics Research. The journal focuses on the use of new technologies, such as massive parallel sequencing together with bioinformatics analysis, to produce increasingly detailed views of how genes function in tissues and how these genes perform, individually or collectively, in disease etiology.

February 2013: Edmond J. Safra Center member leads Israeli effort to assist children with rare genetic disease

Edmond J. Safra Center member, Dr. Noam Shomron, of the Department of Cell & Developmental Biology, the Sackler Faculty of Medicine, heads the first international branch of the Rare Genomics Institutes. The US-based institute is a non-profit organization to assist children with rare genetic disease based on a model of crowd-source funding. Dr. Noam Shomron is the director of the organization in Israel. Read more .

February 2013: Five Edmond J. Safra Center members are partners in new national Centers of Excellence

The Israel Minister of Education announced the results of a competition for the establishment of centers of excellence (I-COREs) initiated by the Israel Higher Education Council. Tel Aviv University is a major partner in two of the announced I-COREs.

Edmond J. Safra Center members Prof. Danny Chamovitz, Prof. Roded Sharan and Prof. Eytan Ruppin, are partners in a new I-CORE. The center will be focusing on comprehensive understanding and modeling of plant responses to multiple abrupt a biotic stresses and to prolonged climatic changes. The center contains groups from TAU, Ben-Gurion University, Weizmann Institute and the Hebrew University, and is led by Prof. Hillel Fromm of TAU.

Edmond J. Safra Center members Prof. Haim Wolfson and Prof. Nir Ben-Tal are on the winning team of another I-CORE, which is focused on Structural Cell Biology. This center is lead by Prof. Gideon Schreiber from the Weizmann Institute. It includes scientists from the Weizmann Institute of Science, TAU and the Technion. The Center's Bioinformatics activities will be based at TAU.




February 2013: Edmond J. Safra Center member is president of the Genetics Society of Israel

Prof. Martin Kupiec, of the Dept of Molecular Microbiology & Biotechnology, was elected President of the Genetics Society of Israel.
Prof. Kupiec replaced Edmond J. Safra Center member Prof. Karen Avraham, who was the former president.

The Genetics Society of Israel promotes genetics research and education about recent developments in genetics. The society provides a forum for communication among scientists who are involved in genetics research in model organisms, in medicine, in agriculture and education.

January 2013: Edmond J. Safra faculty members participate in a Swiss-Israel Bioinformatics Symposium

A "Swiss-Israel bioinformatics symposium" took place in Biel-Bienne, Switzerland on Wednesday 30/1/2013.
It was hosted by the Swiss Institute of Bioinformatics (SIB), in conjunction with its annual gathering. In this one-day symposium, representatives from different SIB groups, as well as from Weizmann Institute, the Hebrew University and Tel Aviv University presented short research talks on various areas of bioinformatics. Prof. Haim Wolfson, Edmond J. Safra Center member and Dr. Iftach Nachman, Edmond J. Safra Center Faculty Fellow, represented TAU in this event.

January 2013: Thomas Jefferson University Delegation Visits Edmond J. Safra Center and I-CORE

The Edmond J. Safra Center for Bioinformatics and I-CORE/Gene Regulation in Complex Human Disease sponsored a delegation on Jan. 21, 2013 from Thomas Jefferson University, Philadelphia, Pennsylvania, USA (TJU), and spent the day at a joint meeting at the Sackler Faculty of Medicine entitled "Computation and Medicine". Speakers included investigators from Tel Aviv and Bar-Ilan Universities. Edmond J. Safra Center members Iftach Nachman, Karen Avraham, Noam Shomron and Eytan Ruppin described their latest research findings and their use of computational biology to study human disease. These were complemented by talks by TJU faculty, including Isidore Rigoutsos on microRNA targeting, Jan Hoek on the microRNA regulatory network in liver regeneration, Gyorgy Hajnoczky on the ER:mitochondrial synapse, Raj Vadigepalli and Jim Schwaber on regulatory networks, Karen Knudsen on molecular approaches to targeting prostate cancer and Laurence Eisenlohr on MHC class II processing of viral antigens. Questions and discussions are leading to collaborative interactions between scientists and students from TJU, Tel Aviv and Bar-Ilan Universities. The meeting was organized by Edmond J. Safra Center member Noam Shomron and Mark Tykocinski, Dean of Jefferson Medical College.



December 2012: Edmond J. Safra Center Faculty fellow and PhD student fellow reveal genome data privacy loophole in a paper in Science

Prof. Eran Halperin, Edmond J. Safra Center Faculty fellow, and David Golan, Edmond J. Safra PhD fellow, participated in a study that revealed the vulnerability of public databases to privacy issues. In their study, which was published in Science, they show that based on a small number of biomarkers in the Y chromosome, one can find the surname of some individuals, using web searches in public databases. Moreover, they show specific examples, where the combination of demographic information such as age and state of residence, together with the Y chromosome, can reveal the identity of an individual. For example, they located the famous geneticist Craig Venter based on his publicly available genome, his state of residence (California), and his age. Moreover, they identified the full names of a few people from the Coriell database, which is presumed to be anonymous. These findings resulted in a wide coverage of the international media, and a few precaution steps have already been taken by the National Institute of Health in the US, particularly removing the information about the age of subjects from public databases. Read more in an interview with Prof. Halperin from the Israeli radio Galley Zahal.

December 2012: Edmond J. Safra Center member received the Hestrin Prize for excellent biochemical research

Prof. Tal Pupko, Edmond J. Safra Center member, has been awarded with the Hestrin Prize of the Israeli Society of Biochemistry and Molecular Biology. The prize is given to a young Israeli biochemist at the beginning of his/her independent career, in acknowledgement of scientific work performed mainly in Israel.

December 2012: Edmond J. Safra Center member is 2012 ACM fellow

Prof. Ron Shamir, Edmond J. Safra Center for Bioinformatics member, has been elected as 2012 ACM Fellow for contributions to bioinformatics ACM has recognized 52 of its members for their contributions to computing that are fundamentally advancing technology in healthcare, cyber security, science, communications, entertainment, business, and education. The 2012 ACM Fellows personify the highest achievements in computing research and development from the world's leading universities, corporations, and research labs, with innovations that are driving economic growth in the digital environment. "These men and women are advancing the art and science of computing with enormous impacts for how we live and work," said ACM President Vinton G. Cerf. "The impact of their contributions highlights the role of computing in creating advances that range from commonplace applications to extraordinary breakthroughs, and from the theoretical to the practical."

December 2012: Edmond J. Safra Center member heads a committee at ISMB 2013

Edmond J. Safra Center member, Prof. Nir Ben-Tal, of the Department of Biochemistry, at the Faculty of Life Sciences, heads the ISMB 2013 Proceedings Committee. ISCB, the International Society for Computational Biology, conducts an annual flagship conference ,ISMB, which has become the largest conference on computational biology worldwide. It is taking place in July 2013 in Berlin, Germany. The Proceedings track in the conference will present peer-reviewed papers selected from a large number of submissions of new research by the community. The head of the Proceedings Committee leads the reviewing work of over a hundred scientists, organized into a dozen subocmmittees.

Edmond J. Safra Center member is a keynote speaker at the largest international conference in Computational Biology

Edmond J. Safra Center member, Prof. Gil Ast, Chair of Department of Human Molecular Genetics & Biochemsitry, at Sackler School of Medicine at TAU, is a keynote speaker at ISMB/ECCB 2013: The joint event combining the 21st Annual International Conference on Intelligent Systems for Molecular Biology and the 12th European Conference on Computational Biology, which will take place in July 2013 in Berlin, Germany. ISCB, the International Society for Computational Biology, conducts an annual flagship conference ,ISMB, which has become the largest conference on computational biology worldwide. The ISMB conference series aims at attracting the top research contributions in all areas of computational molecular biology. ECCB is the main European Conference in Bioinformatics. ISMB and ECCB are held together in Europe every third year.


October 2012: EJ Safra Center member is the new chief editor of a leading bioinformatics journal.

Edmond J. Safra Center member, Prof. Ruth Nussinov, was selected as Editor-in-Chief of PLOS Computational Biology, one of the leading Bioinformatics journals. Prof. Nussinov, from the Dept. of Human Molecular Genetics and Biochemistry, Sackler School of Medicine at TAU, draws her future vision for PLOS Computational Biology: " The Society, its meetings, and the journal all have a common goal: enhancing and promoting excellence in computational biology. Outstanding research with clear biological relevance, which leads to fundamental new insights into important biological problems, is the hallmark of future contributions by our community to biology". To read more click here.


October 2012: New Edmond J. Safra member: Prof. Judith Berman

Professor Judith Berman has joined the Department of Molecular Microbiology and Biotechnology in the Faculty of Life Sciences and is a new member in the Edmond J. Safra Center. Professor Berman received her B.Sc. from the Department of Plant Pathology at Cornell University in the US, performed her Ph.D. in the Department of Biochemistry at the Weizmann Institute of Science and did post-doctoral research at Cornell University, where she initiated work on telomere, the chromosome ends, using yeast as a model system. For over 25 years she was a faculty member at the University of Minnesota, where she rose through the ranks and was awarded the Distinguished McKnight University Professorship.

Dr. Berman’s research focuses on genome and chromosome structure and function, with special interest in questions concerning chromosome stability, centromere function, telomere evolution and replication initiation mechanisms. She generally uses yeast for her studies, with a major focus on Candida albicans, a resident of the human gastrointestinal tract and the most prevalent fungal pathogen of humans. Her work includes studies of ploidy (genome copy number) and aneuploidy (imbalance in the number of chromosomes) and her group has pioneered studies of centromere flexibility at the level of DNA sequence and protein copy number. She uses computational and bioinformatics approaches to gain insights into the dynamics of chromosome structures. Using a combination of molecular, genetic and genomic tools, together with computational analysis of large scale genomics data, Prof. Berman strives to understand the dynamic mechanisms that maintain genome integrity in the face of stress conditions that increase genome changes. The work has implications for how a normally organism can become a serious pathogen. The work also provides a useful framework for studying the more complex genome dynamics that occur during cancer cell proliferation.


August 2012: Edmond J. Safra Center member appointed to the Young Israel Academy for Sciences.

Prof. Roded Sharan, Edmond J. Safra Center member, was appointed as a member of The Young Israeli Academy for Sciences.
The Israel Academy of Sciences is joining the general trend in the world and establishing 'The Young Israel Academy of Sciences'. The Young Academy members are scientists of the humanities and exact sciences aged up to 45, and who have demonstrated excellence in research, original thinking, and have won prestigious awards or grants.
Prof. Sharan is one of twenty scientists who were appointed to the Academy on its inauguration year. The appointment is for four years.


July 2012 : A former Edmond J. Safra PhD fellow wins the outstanding poster award at International Society for Computational Biology conference

A former Edmond J. Safra PhD fellow, David Burstein, was awarded the outstanding poster award at ISMB12: The 20th conference of International Society for Computational Biology held in California, July, 2012.
David Burstein presented the poster: "Fishing for Virulent Factors: Machine Learning Predictions and Experimental Validations of Bacterial Effectors" (coauthored with Tal Zusman, Ziv Lifshitz, Michael Peeri, Gil Segal and Tal Pupko).


July 2012: Edmond J. Safra PhD fellow wins the UNESCO-L'OREAL Prize for 2012

Edmond J. Safra PhD fellow, Osnat Zomer-Penn, is among three young women scientists in Israel who won the UNESCO-L'OREAL Prize for 2012 to promote women in science. During her PhD studies, at the laboratory of Prof. Tal Pupko, Osnat developed computerized tools to study the evolution of the HIV virus which causes AIDS, and to compare the genomes of different strains of viruses that are common in different geographical areas.

The UNESCO-L'OREAL Prize will allow Osnat to conduct work on the genetics of autism. In her research, which will commence shortly at the University of Washington in Seattle, Osnat will analyze genomes sequences that were collected from hundreds of families that have children with autism. By comparing the genomes of autistic children to those of their parents who are not autistic, Osnat will try to understand what causes the difference between the child and the parents. To read more click here.

Edmond J. Safra Faculty Fellow among '40 promising young people in Israel' chosen by a newspaper

Prof. Eran Halperin, Edmond J. Safra Faculty Fellow, was chosen by the Israeli newspaper 'De Marker' as one of '40 promising young people' in Israel in various domains of activity.
In its July 2012 issue De Marker published an article where Prof. Halperin was chosen as a young scientist who is standing in the forefront of genetics research in Israel.
The article notes that despite his young age, Prof. Halperin has already published about 80 articles and received awards for his academic accomplishments. Moreover he has already developed algorithms that are used by many laboratories worldwide. For the full article click here.

June 2012: Edmond J. Safra Center member is a Fellow of the International Society of Computational Biology

Prof. Ron Shamir, Edmond J. Safra Center for Bioinformatics member, has been selected as a Fellow of the International Society of Computational Biology (ISCB) in the Fellows Class of 2012. The ISCB Fellows program was created to honor members who have distinguished themselves through outstanding contributions to the fields of computational biology and bioinformatics.

June 2012: Prof. Danny Chamovitz publishes a new book.

Prof. Danny Chamovitz, Edmond J. Safra Bioinformatics Center member, published a new book called "What A Plant Knows."
The book provides a detailed and accessible glimpse into the study of flora, and particularly how plants see the world and react to it.
In the book, Chamovitz describes relatively new insights on plants. He claims that a plant can see things and is able to process the information and act, often in the most efficient way possible. A plant, explains Chamovitz, is not only a living, breathing creature, but is also intelligent and adaptive, responsive to its environment and able to react to it in real time, but slowly.
"Externally we are very different from plants, and it seems to us that we live and they are something midway between still and a living creature," says Chamovitz, "but inside we have a lot in common. True, they have no brain or nervous system, but they have an equivalent to almost every sense that we have. Plants are seeing, smelling, touching and interact with each other, and have an effective mechanism for making decisions based on the information they get. They do things that we did not imagine they could do".

Read more in an interview with Prof. Chamovitz from the Israeli newspaper Calcalist.

June 2012: Edmond J. Safra Center Faculty Fellow and colleagues develop a method to pinpoint geographic origins

The researchers Prof. Eran Halperin, an Edmond J. Safra Center Faculty Fellow, and Dr. Eleazar Eskin from UCLA have created a remarkably accurate method to pinpoint a person’s geographic origins. The method is based on genetic analysis and represents a leap forward in geneticists' ability to trace the origins of people with ancestors from multiple parts of the world. Beyond the fascinating glimpse into history that comparative genetic mapping can provide, a more immediately useful function could be to predict a person’s propensity for certain diseases based on genetic lineage. By combining the probabilities of certain mutations appearing across hundreds of thousands of genomic sites, Prof. Halperin and his colleagues were able to identify the geographic origins of the study's participants to within a few hundred kilometers, on average.
"We were able to map individuals from all over the world on a three-dimensional globe,” says Eran Halperin. “So it's fair to say that the approach is applicable to many populations".
Read an interview with Prof. Halperin from the Israeli newspaper Haaretz.

May 2012: A joint seminar of the IBM Research department, Haifa and the Edmond J. Safra Center

The Analytics department at IBM Research - Haifa (HRL) and the Edmond J. Safra Center for Bioinformatics organized a one-day leadership seminar on clinical genomic analysis. The seminar was held at the IBM Research site on the Haifa University campus.
The workshop provided a forum for research and development communities from both academia and industry to share their work, exchange ideas, and discuss issues, problems, and works-in-progress. The forum also addressed some future research directions and trends in the area of personalized healthcare and the use of "omics" techonology for optimizing the individual care. The program attracted nearly 100 attendees, and included plenary talks, a panel of clinicians on Real World Evidence, and a poster session. For the full program click here

See also a blog on the meeting

May 12: A paper by an Edmond J. Safra member and a PhD fellow is the cover story of the May 2012 issue of the CACM journal

The cover story of the May 2012 issue of the Communications of the ACM is "Comparative Analysis of Protein Networks: Hard Problems, Practical Solutions" by Edmond J. Safra Center for Bioinformatics PhD fellow, Nir Atias, and Edmond J. Safra Center for Bioinformatics member, Prof. Roded Sharan. The paper explores the explosion of molecular data in biological research and at the comparative network analysis used to tackle the resulting computational problems. A combination of heuristic, parameterized, and integer linear programming-based approaches have led to new insights about biological problems and solved some key problems in comparative network analysis as well.

April 2012: Prof. Karen Avraham awarded Teva's Founders Award for 2011

Prof. Karen Avraham, an Edmond J. Safra Center for Bioinformatics member, and Prof. Eli Sprecher, both of the Sackler Faculty of Medicine at Tel Aviv University, were awarded the Teva Pharmaceutical Industries Ltd. Founders Prize for 2011. They received the prize at a memorial ceremony for Eli Hurvitz, the former chairman and CEO of Teva. This is the 19th year that the prize has been awarded to outstanding researchers in the life sciences and biomedical professions. The recipients are selected by Teva in conjunction with The Israeli Academy of Sciences and Humanities.

Prof. Avraham serves as vice dean and is a member of the Department of Biochemistry and Human Molecular Genetics at Tel Aviv University. The prize citation stated that "Prof. Avraham is one of the leading researchers in the world in inherited hearing loss. Her work is an impressive example of lifetime achievement in the medical sciences, and it demonstrates excellence in research. Professor Avraham is a central figure in the human genetic research in Israel. In addition to research excellence, she is a model of citizenship in the scientific community and has made extraordinary contributions to the global community of human genetics researchers".

March 2012: New Edmond J. Safra member: Dr. Itay Mayrose

Dr. Itay Mayrose has joined the Department of Molecular Biology and Ecology of Plants at the Faculty of Life Sciences and is a new member in the Edmond J. Safra Center. Dr. Mayrose received his B.Sc. from the multidisciplinary program of biology and computer science at Tel-Aviv University, has an M.Sc. in Zoology and performed his Ph.D. at Cell Research and Immunology. Before joining Tel-Aviv University he was a fellow in the Beaty Biodiversity research Centre at the University of British Columbia, Canada.

The main research interests of Dr. Mayrose are concerned with the broad field of plant evolution and phylogenetics. He uses comparative, bioinformatics approaches to gain insights into the fascinating evolutionary dynamics of plant genomes and in particular, those that are concerned with plant domestication. Using a combination of computational tools with large scale genomics data Dr. Mayrose aims to gain novel insights into the evolutionary consequences of plant domestication and the evolutionary selection forces that shaped their genomes. By identifying unique patterns of selection acting on certain genes, he aims to reveal common genomics characteristics of plant crops that are important for human consumption.

March 2012: New Edmond J. Safra member: Dr. Tamir Tuller

In the Fall of 2011, Dr. Tamir Tuller has joined the Faculty of Engineering at Tel Aviv University and is a new member in the Edmond J. Safra Center for Bioinformatics. In 2007 Dr. Tuller was an Edmond J. Safra Postdoc Fellow at the School of Computer Science. Dr. Tuller has a multidisciplinary academic background spanning computer science, electrical engineering, life sciences, and medical sciences. Before joining Tel-Aviv University he was a fellow in the faculty of mathematics and computer science and the department of molecular genetics at the Weizmann institute of Science.

Dr. Tuller performs multi-disciplinary research focusing on various aspects of gene expression and specifically gene translation. His research includes developing, integrating, and employing scientific approaches from disciplines such as: biophysics, statistics, synthetic, molecular, and evolutionary biology, computer science and engineering, in an exhaustive synergistic manner. His research goals include: understanding the evolution of gene translation, computational modeling of this process, and developing novel approaches for engineering it.

March 12: Edmond J. Safra Center for Bioinformatics member Prof. Ron Shamir interviewed by Medical Daily

Edmond J. Safra Center for Bioinformatics member Prof. Ron Shamir was interviewed for an article in the Medical Daily newsletter about the connections between chromosome abnormality and cancer.

March 2012: The first Edmond J. Safra Center for Bioinformatics Mixer

On March 14, 2012, the first Edmond J. Safra Center for Bioinformatics Mixer took place. More than 60 Edmond J. Safra faculty members, Edmond J. Safra fellows and other members of the TAU bioinformatics community were gathered together outdoors on the lawn for a one hour event. During the first half, students were randomly divided into groups and gave brief summaries of their work to participants from other labs. The rest of the time, people from the different faculties had the chance to meet and to talk to each other over pizza.

For more pictures from the event, click here.

February 2012: Edmond J. Safra PhD fellow wins best poster award at ISM 12 Annual Meeting.

Mor Lurie-Weinberger, Edmond J. Safra PhD fellow, won the best poster award, for one of the five best presented posters out of 112 posters at Israeli Society of Microbiology conference that was held at Bar Ilan University, February 13-14, 2012.

Mor presented the poster titled: Inter-domain lateral gene transfer - the case of methanogenic archaea.

February 2012: EJSCB and eight of its members highlighted in TAU newsletter on Personalized Medicine

The 2012 issue of the Tel Aviv University Review, the university's annual publication about a leading area of research, included seven Edmond J. Safra Faculty members (Prof. Karen Avraham, Prof. Yosef Shiloh, Dr. Eran Halperin, Dr. Noam Shomron, Prof. Roded Sharan, Prof. Eytan Ruppin, and Prof. Ron Shamir) and a Ph.D. Student Fellow (Ms. Maya Schushan). The issue focused on personalized medicine, and these eight researchers were among the researchers who were interviewed and whose projects and achievements were described. In particular, the Edmond J. Safra Center for Bioinformatics was highlighted in a sidebar about the important contributions of bioinformatics in enabling cutting-edge research in medicine. See the accompanying article.
Maya Schushan, EJS Center for Bioinformatics PhD fellow

February 2012: Edmond J. Safra program members uncover the “Neighboring Gene Effect”

In the post-genomic era, it is possible to inactivate a gene by just removing it from the genome (this procedure is called gene knock-out or deletion), In fact, in model organisms such as yeast, this has been done for each and every one of the 6,000 genes, creating a collection of gene deletions. These collections are extremely useful; for example, one can discover drug targets by screening for mutants resistant to a certain drug. Edmond J. Safra Program members, Prof. Martin Kupiec, from the Department of Molecular Microbiology and Biotechnology, Prof. Eytan Ruppin and Prof. Roded Sharan from the School of Computer Science, have found a curious phenomenon: in many cases, the effect observed after deleting a certain gene (e.g., drug resistance) is caused not by the deleted gene, but by its neighbor, the gene located next-door on the chromosome. This phenomenon has serious consequences on our ability to identify the function of genes. Graduate students Taly Ben Shitrit and Nir Yossef developed an algorithm to predict cases of “neighboring gene effect”.The results were recently published in the journal Nature Methods. See the article for further details. Hear an interview of Prof. Kupiec on the Israeli National Radio.

February 2012: Prof. Yoav Benjamini wins The Israel Prize for 2012

The Israel Prize is the highest award conferred by the state of Israel in a wide range of areas. The award ceremony is held every year on the night of Independence Day in Jerusalem attended by the heads of the state. The prize committee wrote that Prof. Benjamini is an example of integration between applications statistician, whose contributions are in many branches of science, worldwide and in Israel, and the theoretical statistician, who develops new statistical tools. The main contribution of Professor Benjamini is an innovative and groundbreaking approach, "false discovery rate", proposed by him in collaboration with Prof. Yosef Hochberg, to handle multiple testing. This approach has been adopted and is very broadly used in many scientific areas, including bioinformatics

February 2012: A paper of Edmond J. Safra student and faculty member is one of the Top 10 popular articles published in a Molecular Systems Biology Journal in 2011

The paper "Predicting selective drug targets in cancer through metabolic networks" by Ori Folger, Livnat Jerby, Christian Frezza, Eyal Gottlieb, Edmond J. Safra program member Prof. Eytan Ruppin and Tomer Shlomi was one of the Top 10 most popular research articles published in the Journal of Molecular Systems Biology in 2011.
The paper appeared in Molecular Systems Biology, 7:501, June 2011. Livnat, who was MSc student while collaborating in this work, is now an Edmond J. Safra PhD fellow.

December 2011: Edmond J. Safra Program member heads the Program Committee of RECOMB 2012

Prof. Benny Chor, Edmond J. Safra Program member, is the Program Committee Chair of RECOMB 2012: the 16th annual international conference on Research on Computational Molecular Biology.
RECOMB is the leading theoretical conference in computational molecular biology. The conference features highly selective peer-reviewed papers and keynote talks by eminent scientists. The 2012 meeting is the 16th RECOMB meeting and it will take place in Barcelona in April 2012.

November 2011: The Open Collaborative Research agreement between IBM Research – Haifa and E.J. Safra researchers is extended

The collaboration research agreement (OCR) that was signed last year between IBM Research – Haifa and three Edmond J. Safra Program members, Dr. Eran Halperin, Dr. Saharon Rosset and Prof. Ron Shamir, has been extended, and a second award from IBM was granted to the EJ Safra program members.
A joint IBM-Safra seminar took place on November the 3rd at TAU, in which several talks on research progress were presented by Safra members and students and by IBM researchers. Dr. Shai Fine, senior manager of analytics at IBM Research – Haifa, opened the event. He expressed his delight with the progress of the research and with the tightening of collaborations between the two communities. Dr. Fine presented the award to Prof. Shamir.
Left to right: Ron Shamir (EJS researcher), Shai Fine (senior manager, IBM), Saharon Rosset (EJS researcher), Michal Rosen-Zvi (machine learning group, head, IBM), not shown in the picture:Eran Halperin (EJS researcher)

September 2011: Prof. Ron Shamir publishes a new book

A new book edited by Edmond J. Safra Program member, Prof. Ron Shamir, and by Prof. Pavel Pevzner of University of California, San Diego, titled: 'Bioinformatics for Biologists', was recently published by Cambridge University Press, UK.
This textbook is aimed at introducing biology undergraduate majors to the key computational ideas in bioinformatics, on a (relatively) non-technical yet rigorous level. In this concise textbook, the authors' fresh pedagogical approaches lead biology students from first principles towards computational thinking. A team of renowned bioinformaticians take innovative routes to introduce computational ideas in the context of real biological problems.

August 2011: EJ Safra program member and student develop model to fight cancer

Scientists are constantly on the hunt for treatments that can selectively target cancer cells, leaving other cells in our bodies unharmed. Prof. Eytan Ruppin, (picture inlaid), Edmond J. Safra Program member from the School of Computer Science and Sackler Faculty of Medicine at TAU, together with Prof. Eyal Gottlieb of the Beatson Institute for Cancer Research in Glasgow, UK, and Dr. Tomer Shlomi of the Technion, have taken a big step forward: They have successfully created the first computerized genome-scale model of cancer cell metabolism. The model can be used to predict which drugs are lethal to the function of a cancer cell and harmless to normal cells.
The computer model was developed by Prof. Ruppin's graduate students Uri Folger and EJ Safra Msc fellow Livnat Jerby (picture inlaid).
The results were recently published in the journal Nature. See the article for further details. Hear an interview of Prof. Ruppin on the Israeli National Radio.

July 2011: Dr. Irit Gat-Viks wins the Allon Fellowship

Edmond J.Safra Faculty Fellow Dr. Irit Gat-Viks was awarded the highly prestigious Allon Fellowship for the year 2011-2012. The Allon Fellowships are prizes for excellence awarded in a nationwide competition among the best candidates for recruitment in Israeli universities. Dr. Gat-Viks joined TAU Life Sciences Faculty and became an Edmond J. Safra Fellow in spring 2011. She is also an alumnus of the Program as she was a Postdoc Fellow of the Edmond J. Safra Program in the year 2007.
Dr. Gat-Viks is studying how variations in the genomes of individuals shape their complex disease phenotypes. She is focusing on the immune system, and uses genomic knowledge to understand whether and how inflammatory gene expression variability translates genetic and environmental variation into phenotypic diversity in health and disease. Dr. Gat-Viks develops computational methods in statistics, probabilistic modeling, machine learning and high throughput data analysis to understand the 'black box' that lies between genotype and phenotype, and eventually, to devise biomarkers for diagnosis and therapeutics.

June 2011: EJ Safra program member leads a winning team in a national competition for a new Center of Excellence

The Israel Minister of Education announced the results of a competition for the establishment of centers of excellence initiated by the Israel Higher Education Council. Tel Aviv University is a major partner in all three Centers of Excellence (I-CORE) announced. One of the Centers is focused on the Systems-Level Analysis of the Molecular Basis for Human Diseases: From Genomics to Personalized Therapy. The Center is composed of 34 scientists and physicians from TAU, the Hebrew University, Bar Ilan University and Sheba and Hadassa Medical Centers. The center’s bioinformatics activity will be based at TAU and rely on the expertise of the EJ Safra Program members. The TAU team is led by Prof. Karen Avraham, Edmond J. Safra Program Steering Committee member from the Sackler Faculty of Medicine. Other EJ Safra members include Dr. Noam Shomron, Dr. Irit Gat-Viks, Prof. Eytan Ruppin, Prof. Yossi Shiloh, and Prof. Ron Shamir.

June 2011: Two EJ Safra program members win TAU Research Prizes

TAU Research Authority Council has announced the TAU Research prizes for the academic year 2010-2011. Selecting the winners from among all university researchers was based on the number of submitted research proposals, the financial scope of awarded grants and overall research activity.
Prof. Ron Shamir, School of Computer Science and head of the Edmond J. Safra Bioinformatics Program, was awarded the prize in the category of Outstanding Researcher in Exact Sciences, Life Sciences and Medicine.
Prof. Roded Sharan, School of Computer Science and Edmond J. Safra Program member, was awarded the prize in the category of Outstanding Young Researcher in Exact Sciences, Life Sciences and Medicine.

May 2011: E.J. Safra Retreat, Hagoshrim, Upper Galilee

May 2011: E.J. Safra Retreat, Hagoshrim, Upper Galilee More

May 2011: Distinguished EJ Safra visitor: Michael S. Waterman

On May 2011, Prof. Michael S. Waterman of University of Southern California was a visitor of Tel Aviv University and the EJ Safra Program. He was conferred an honorary doctorate from Tel Aviv University and gave a lecture to a packed lecture hall on "Sequence Comparison Without Alignment".

April 2011 - Prof. Ron Shamir wins RECOMB 2011 Test of Time Award

Prof. Ron Shamir has won the RECOMB 2011 "Test of Time Award". The award is given to the most cited paper in the RECOMB conference since its publication 12 years earlier. RECOMB is the leading international conference in bioinformatics.

The award was given for the 1999 paper "Clustering Gene Expression Patterns" coauthored Amir Ben-Dor and Zohar Yakhini. According to Google Scholar, the journal version of the paper, published in the Journal of Computational Biology, was cited 790 times to date.
 

March 2011 - Prof. Roded Sharan interviewed in Nature Biotechnology.

Prof. Roded Sharan was recently interviewed in the journal Nature Biotechnology bout the project called model organism encyclopedia of DNA elements (modENCODE). Here is an excerpt from the journal:

“A major challenge will be data Integration […]. Roded Sharan, a computational biologist at Tel Aviv University, agrees, adding that integrative analysis is required to identify an organism’s signaling and regulatory pathways and to elucidate how they vary over time and across cell types. He notes that current algorithmic work is focused on analyzing at most a few networks at a time and will have to be significantly scaled up to understand the complex developmental programs of fly or worm.”
 

March 2011 – A paper of Prof. Eytan Ruppin and Moran Cabili is among the most cited Nature Biotechnology papers in the last five years.

The paper “Network-based prediction of human tissue-specific metabolism”, by Tomer Shlomi, Moran N Cabili (then an Edmond J. Safra student fellow), Markus J Herrgard, Bernhard Ø Palsson and Edmond J. Safra Program member Prof. Eytan Ruppin (Nat. Biotechnol. 26, 1003–1010, 2008) has been declared one of the past five years’ most highly cited research articles in the journal Nature Biotechnology.

Both Dr. Shlomi (who completed a PhD in bioinformatics from TAU and is now a faculty member at the Technion) and Prof. Ruppin were interviewed about their work and their perspective on the area. See the article for further details.
 
From the interview :

March 2011: Prof. Ron Shamir wins the Michael Landau Prize in Bioinformatics for 2011

Prof. Ron Shamir, the head of the Edmond J. Safra Bioinformatics Program at TAU, has won the prestigious 2011 Michael Landau Award for Science and Research in the field of Bioinformatics.

The Landau Foundation was established in 1970 and named after Dr. Michael Landau, who headed the National Lottery in its early years. Since 2001, the Foundation has allocated annual achievement awards to researchers in science and research, and to artists from the performing arts. The prize is awarded to researchers who have achieved a breakthrough in their research and have won international recognition. This is the first time a prize is awarded in the area of bioinformatics. The award ceremony will take place in April 2011.
 

March 2011: Prof. Yosef Shiloh wins The Israel Prize for 2011

Prof. Yosef Shiloh, a professor of Human Molecular Genetics at the Sackler School of Medicine, and Edmond J. Safra Program member, has won the Israel Prize in the area of life sciences for 2011.

The Israel Prize is the highest award conferred by the state of Israel in a wide range of areas. The award ceremony is held every year on the night of Independence Day in Jerusalem attended by the heads of the state. The prize committee wrote that Prof. Shiloh was "groundbreaking researcher in human genetics".
 

February 2011: E.J. Safra Program member wins the AACR G.H.A. Clowes Memorial Award

Prof. Yosef Shiloh, a Professor of Human Molecular Genetics and Biochemistry at the Sackler School of Medicine, and E.J. Safra Program member, has won the Clowes Memorial Award for 2011. The award, given by the American Association for Cancer Research, recognizes an individual with outstanding recent accomplishments in basic cancer research. This is the first time this prestigious award is given to an Israeli scientist.

Prof. Shiloh will deliver his award lecture entitled "Mining rare genetic disorders for new insights into human biology: lessons from ataxia-telangiectasia", at the AACR 102nd Annual Meeting 2011 in Orlando, to be held on April 4, 2011.
 

February 2011: Prof. Nir Ben-Tal publishes a new book

Edmond J. Safra Program member Prof. Nir Ben-Tal and his former student Dr. Amit Kessel, co-authored the book “Introduction to Proteins: Structure, Function and Motion ”. With so many known structures of proteins alone and in complexes with ligands, nucleic acids and other proteins it is time to look for general principles. The book aims exactly at that. It provides energetic guidelines for understanding protein folding and stability; it describes models of molecular recognition and allostery as a basis for understanding protein-ligand interactions; it compares globular (water-soluble) proteins to membrane proteins and intrinsically unstructured proteins; and it explains biological functionality based on structural and energetic guidelines. The principles are demonstrated using several protein structures. Prof. Ben-Tal uses the book in the course “Introduction to structural biology” which is given at TAU.
 

August 2010: E.J. Safra fellow wins the best RECOMB paper award

Nir Atias, E.J. Safra PhD fellow, was awarded the best paper award in RECOMB: The 14th annual international conference on Research on Computational Molecular Biology, Lisbon, August 12-15, 2010.

Nir presented his paper " An Algorithmic Framework for Predicting Side-Effects of Drugs " (coauthored with Roded Sharan).

 

 
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E.J. Safra fellow appointed to faculty position

Dr. Svetlana Bunimovich, E.J. Safra postdoctoral fellow, received a tenure-track faculty position in Israeli University.
Dr. Svetlana Bunimovich is now a faculty member at Ariel University Center.
 

July 2010: E.J. Safra fellow wins the best student presentation award at ISMB

Keren Yizhak, E.J. Safra MSc fellow, was awarded the best student paper presentation at ISMB: The 18th annual international conference on
Intelligent Systems for Molecular Biology, Boston, July 10.
Keren presented her paper "Integrating quantitative proteomics and metabolomics with a genome-scale metabolic network model" (coauthored with Tomer Bnyamini, Wolfram Liebermeister, Eytan Ruppin and Tomer Shlomi)

 

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June 2010: IBM Haifa Research Lab collaborates with E.J. Safra researchers

An agreement for open collaborative research (OCR) was signed between the IBM Haifa Research Laboratory (HRL) and the Edmond J. Safra Program: Three Edmond J. Safra Program members, Dr. Eran Halperin, Dr. Saharon Rosset and Prof. Ron Shamir, won the OCR award, and will conduct research jointly with researchers from the Machine Learning Group at IBM-HRL, headed by Dr. Michal Rosen-Zvi. The joint research will focus on Clinical Genomic Analysis.
The collaboration was launched in a kickoff meeting at TAU on June 10th 2010 in which some 25 researchers from IBM and TAU listened to 8 lectures by the Safra members and IBM researchers. Dr. Shai Fine, Senior Manager, Analytics department, greeted the attendees, described his expectations from the collaboration, and presented the award to Prof. Shamir.
The OCR (Open Collaboration Research) awards program of IBM supports collaborative research projects between IBM and researchers at universities within the areas of Computer Science, Engineering, Mathematics and other disciplines.
Ron
Ron Ron
 

May 2010: E.J. Safra Retreat, Neve Ilan, Judea mountains 

May 2010: E.J. Safra Retreat, Neve Ilan, Judea mountains More
 

A meeting with new faculty members

contents: A meeting with the new faculty members in Life Sciences and Sackler Faculty of Medicine, including a Safra member Dr. Iftach Nachman, will take place on 23 Dec, 2009. For details see here

September 2009: Safra visitor: Prof. Peter Gogarten

Professor J. Peter Gogarten from the University of Connecticut is a visitor of the Edmond J. Safra Program during the academic year 2009-10.

Professor Gogarten studies evolution using a variety of computational methods. He is best known for rooting of the tree of life, and for his early recognition of horizontal gene transfer as an important force in microbial evolution.  Currently the main focus of his research is comparative genomics and horizontal gene transfer; he is also interested in the early evolution of life, the evolution of gene families, and in the evolution of inteins, self slicing introns and homing endonucleases.

 

New Safra Faculty member: Dr. Iftach Nachman

Dr. Iftach Nachman has joined the Faculty of Life Sciences. Dr. Nachman's recruitment was facilitated in part by the Edmond J. Safra Bioinformatics Program. Dr. Nachmancompleted a PhD in computational biology at the Hebrew University, and combined experimental and computational work during his postdoc at Harvard University and the Broad Institute.

Dr. Nachman is studying how cells within populations decide to change their state. He is looking at such change processes in both yeast (meiosis) and mammalian cells (reprogramming and differentiation), trying to understand why similar cells respond differently to the same conditions. His work combines live cell fluorescent imaging, microfluidics and image analysis to follow thousands of cells for long periods of time, as they make decisions based on their environment. He uses modeling, statistical and computational methods to analyze these experiments.
 

In addition to his Safra Faculty Fellowship, Dr. Nachman has won the prestigious Alon Fellowship in a nation-wide competition for young faculty members.
 

May 2009:  E.J. Safra Retreat, Ohalo, Sea of Galilee

May 2009:  E.J. Safra Retreat, Ohalo, Sea of Galilee. More

Computer cluster upgraded

April 2009: The computer cluster was roughly doubled in strength, by adding seven new nodes to the cluster. Each node has a two quad core processors 1u rack mounted; each processor is AMD Opteron™ CPU 2382 @2.6GHz.. IN addition, another 4TB of Netapp storage was added.

2008: Prof. Karen Avraham won the Michael Bruno Memorial Prize

Prof. Karen Avraham, a professor of Human Molecular Genetics at the Sackler School of Medicine, and Edmond J. Safra Program member, won the Michael Bruno Memorial Prize in 2008.

The Michael Bruno Memorial Awards are awarded each year to Israeli scholars and scientists of truly exceptional promise, whose achievements to date suggest future breakthroughs in their respective fields. Candidates must not yet have passed the age of fifty. Prof. Michael Bruno served as Governor of the Bank of Israel between 1986 and 1991, as well as Chair of the Board of the Rothschild Prizes Organization. After his untimely death in 1996, it was decided to dedicate the awards to his memory.

New Safra Faculty member: Dr. Eran Halperin

Dr. Eran Halperin joined Tel Aviv University in a joint position at the School of Computer Science and the department of Molecular Microbiology and Biotechnology. Dr. Halperin's recruitment was facilitated in part by the Edmond J. Safra Bioinformatics Program. He completed a PhD in Computer Science at Tel Aviv University, conducted a postdoctoral research at Princeton and Berkeley and was until recently a member of the International Computer Science Institute, Berkeley.

Dr. Halerpin's research focuses on computational genetics. He develops computational and statistical tools to improve the interpretation of high-throughput genotype and sequencing data and to facilitate association studies of complex disease such as cancer, asthma, or diabetes. His methods are also applied in the context of population genetics, where evolutionary and historic events such as recombination rates, admixture events, migration patterns, etc., are revealed through the analysis of the structure of genetic variation. Dr. Halperin's research is highly interdisciplinary, spanning fields such as statistics, machine learning, algorithms, population genetics, and human genetics.

New Safra Member: Dr. Noam Shormon

Dr. Noam Shomron has joined the Faculty of Medicine and is a new member in the Safra program. Dr. Shomron is studying MicroRNAs, short non-coding cellular RNAs that are thought to regulate many of our genes. His research focuses on better understanding the mechanism governing these molecules and how they exert their activity. He explores the number of miRNAs, their genomic positions, conservation and biogenesis process, their maturation, their specific targeting and their mode of affecting cell decision in health and disease. Dr. Shomron combines extensive bench work, bioinformatics, and expertise with high-throughput techniques. Through this combination, he strives to reach a global, systems view of the mechanistic role of microRNAs.

September 2008: Safra Visitor: Elad Ziv

Professor Elad Ziv from the Institute for Human Genetics and the Comprehensive Cancer Center in UCSF is a visitor of the Edmond J. Safra Program during the academic year 2008-9.
Professor (MD) Ziv is studying complex traits and diseases through whole-genome association studies in admixed populations. His main focus is on studying breast cancer, however he has been actively working on revealing genetic markers for other conditions such as aging, asthma, cardiovascular diseases, etc. Professor Ziv also has a considerable interest in population genetics and in particular in population substructure and its effects on association studies.

June 2008: Honorary Doctor of Philosophy to Mrs. Lily Safra

On June 12, 2008 Mrs. Lily Safra was awarded an honorary doctor of philosophy from Tel Aviv University. learn more

June 2008 Safra retreat, Achziv more

June 2008 Safra retreat, Achziv more

January 2008: Three Safra Fellows awarded Wolf Prize for students

Three Fellows of the Safra Bioinformatics Program - Igor Ulitsky and Adi Stern, PhD students, and David Burstein, an M.Sc. student, were awarded the prestigious Wolf Prize for students for the year 2008.

Igor Ulitsky was also elected to give a talk in the Wolf Prizes awards ceremony. His talk was titled "DNA chips as a diagnostic tool - achievements and challenges".

September 2007: Two Safra fellows appointed to faculty positions

Two Safra postdoctoral fellows received tenure-track faculty positions in Israeli universities. Dr. Yanai Ofran is now a faculty member at Bar Ilan University, and Dr. Michal Ziv-Ukelson is now a faculty member at the Department of Computer Science, Ben Gurion University.

 

May 2007: Distinguished Safra visitor: Richard M. Karp

On May 2007, Prof. Richard M. Karp of University of California Berkeley was a visitor of Tel Aviv University and the Safra Program. He was conferred an honorary doctorate from Tel Aviv University and gave a lecture to a packed lecture hall on "Computational Discovery of Genetic Regulatory Networks".

May 2007: Safra retreat, Ohalo more

May 2007: Safra retreat, Ohalo more

April 2007: New bioinformatics cluster is activated

A new computer cluster for use by TAU bioinformatics groups has been installed. The cluster has 14 dual CPU, dual core computers, Intel Xeon 5150. Each computer has 4GB of memory. The cluster is accompanied by 4TB of fast NAS storage.

September 2006

A new bioinformatics track opened in the MSc programs of Computer Science, Life Sciences and Medicine
learn more

June 2006: Safra retreat, Nahsholim more

June 2006: Safra retreat, Nahsholim more