News

February 2017: The interplay of DNA sequence and shape in regulatory motifs

Read our new paper in Molecular Systems Biology in collaboration with Rohs and Taipale groups analyzing shape readout for over 400 transcription factors using HT-Selex data.

January 2017: New analysis of minimizers and universal hitting sets

Read our new report with colleagues from MIT and CMU on the properties of minimizers using lexicographic, random k-mer ordering and small universal hitting sets.
Our analysis shows how to significantly improve the performance of minimizers.

January 2017: Oncogene paper accepted for RECOMB Highlight track

Our paper on classification cancers via mutations is one of six papers accepted for oral presentations in the Highlight Track of RECOMB in May 2017 in Hong Kong.

January 2017: Mutation-based cancer classification paper in Oncogene.

Read Didi Amar's and Shai Izraeli's paper on classifying 20 different cancer subtypes based on mutations only, with applications to cancer of unknown primary, genetic interactions and more.

December 2016: Recycler published in Bioinformatics.

The full version of Roye Rozov's paper on Recycler, our algorithm for plasmid discovery, has been published in Bioinformatics.

Nov 2016: SCJD paper published.

Read Ron Zeira's paper on sorting by cuts, joins and duplications in JCB.
This is the full version of the CPM 2015 extended abstract.

October 2016: Crosstalk between drug and lipid metabolism via CC mice

Read our new study , with Irit Gat-Viks, Fuad Iraqi and others, performing eQTL analysis of Collaborative Cross (CC) mice livers.

September 2016: Congratulations to Rami Eitan for his MSc!

Congrats to Rami, whose thesis and degree are now official.

Rami's thesis, Reconstructing cancer karyotypes from paired-end reads and copy number data, is available here.

September 2016: SELMAP paper published

Read Yaron Orenstein's paper with Doron Gerber's group on analysis of binding site affinity using microfluidics, SELEX - and bioinformatics.

September 2016: Congratulations to Dr. Didi Amar!

Congratulations to Didi, whose doctoral degree has been confirmed by TAU.

Didi's thesis, Novel methods for integrative analysis of heterogeneous large scale biomedical data, is available here.

September 2016: Welcome to Gal Dinstag

We welcome Gal, who is joining the group as a master student after having completed a BSc in CS/Bioinformatics at BGU with Michal Ziv-Ukelson.

August 2016: Two group papers in WABI 2016

Read our papers (with colleagues) on compact universal k-mer hitting sets and copy number evolution problems, which will be presented in WABI 2016.

August 2016: Modeling protein-DNA binding in vitro

Yaron Orenstein's new paper reviews models based on protein binding microarrays and high-throughput SELEX, and compares them to in vivo binding.

July 2016: Opinion in Cell Systems

Read Ron Shamir's viewpoint in Cell Systems on collaborations between "wet" and computational scientists.

July 2016: Richmind tool and paper are on

Richmind is a new method for analysis of large-scale fMRI results, proposing several statistical approaches for enrichment testing.

See our new paper and website.

Richmind was developed by Adi Maron-Katz and Didi Amar together with Talma Hendler's brain research group.

July 2016: New breast cancer subtypes discovered

In analyzing methylation and gene expression patterns of hundreds of breast cancer samples, we identified subtypes of luminal-A cancer with distinct prognostic signatures.

Read Dvir Netanely's paper for this study, a collaboration with Ella Evron, Ayelet Avraham and Idit Ben-Baruch.

June 2016: Paper on copy number transformation problem published

The question of efficiently transforming one copy number profile to another is motivated by cancer evolution.

Our paper on the topic, by Ron Zeira and Meirav Zehavi, was presented in CPM 2016 and published.

June 2016: Congratulations to Adi Maron Katz

Congratulations to Adi who was awarded the PhD in Medicine, co-supervised by Talma Hendler and Ron Shamir.

23 May 2016: Expander workshop

A workshop "Basic tools for computational genomics - first steps with EXPANDER" will be given by Tom Hait on Monday 23 May 2016, between 10:00-14:00, in PC classroom Sherman 009, TAU.

April 2016: Recycler presented in RECOMB-seq

Our
Recycler algorithm for identifying plasmid sequences from short read data was presented by Roye Rozov in RECOMB-seq 2016 in Santa Monica, CA.

March 2016: Enhancer methylation in cancer

Read our Genome Research paper with Rachel Bell, Carmit Levy and others on the impact of enhancer methylation across 25 cancer types.

February 2016: Analysis of stress using brain fMRI

Read Adi's new paper on using functional enrichment for analysis of resting state brain fMRI of subjects before and after stress.

February 2016: TAF-1 dysfunction in XDP

We participated in a study on XDP, a variant of Parkinson's disease, which concluded that the TAF-1 gene dysfunctions in patients, and identified a large group of altered genes based on blood microarrays.
Read more.

December 2015: Congratulations to Dvir Netanely

Congrats to Dvir for passing the PhD proposal exam.
Dvir's topic is "Multi-omics analysis of high-throughput genomic data for the identification of breast cancer subtypes".

December 2015: Farewell to Didi and Meirav

Didi has submitted his PhD thesis and Meirav has completed her brief postdoc in TAU.
Both are going to Berkeley for the Simons Institute program on Algorithmic Challenges in Genomics .
Didi's postdoc is joint to the Simons and the Safra Center and after the program he will be back to the group for the rest of the year.

Farewell to both!

December 17, 2015: A hands-on workshop on using some of our favorite tools

A hands-on workshop on Cytoscape, Modmap and Dicer tools will take place on December 17, between 10:00 - 12:00, in PC Classroom 09, Sherman Building.
See here for details and registration.

December 2015: QPID quantifies protein-DNA binding affinities

Read our new paper (with Doron Gerber and others) on a new microfulidic application that accurately measures protein-DNA affinities.

October 2015: Welcome to David Pellow

David Pellow has joined the group as a PhD student after a master with Carl Kingsford at CMU.
Welcome David!

October 2015: Recycler paper posted

Our paper describing an algorithm for detecting plasmids from de novo assembly graphs is now available.

August 2015: Farewell to Adi and Gil

Adi Maron Katz has completed her PhD studies and is moving temporarily to California.
Adi has been THE person behind Expander for over a decade and it would not have existed without her.
Best of luck to Adi! We hope you will find the right meditative state between Stanford and the Silicone Valley.

Gil is returning to MIT after a very fruitful summer, including both deep sequencing algorithmics (together with Roye) and a stint in Israel's official Frisbee team (!)
We enjoyed having you around and hope to continue our collaboration.

August 2015: Very large scale integrated analysis of disease expression profiles

Read our NAR paper analyzing together 15000 expression profiles spanning 50 diseases.
The Adeptus database and project data are available here .

June 2015: SCJD extended abstract published

Read Ron Zeira's paper on sorting genomes in linear time using the operations of single cut, single join and whole chromosome duplication, published in the CPM proceedings.

June 2015: Congratulations to Ron Zeira

Congrats to Ron for passing the PhD proposal exam. Ron's topic is "Models for Structural and Numerical Alterations in Cancer".

June 2015: TWIGS paper published

Read here our paper on discovering flexible modules in 3-way time series data, with applications to gene expression and fMRI.
The paper appeared in the ISMB/ECCB 2015 proceedings issue of Bioinformatics.

May 2015: Dvir Netanely wins the Safra Center Retreat best poster prize

Congratulations again to Dvir who won also the best poster prize of the 10th annual Retreat of the Edmond J. Safra Center for Bioinformatics at Tel Aviv University.
37 posters were presented during the Retreat that took place on 31/5-1/6/2015 in Maagan, Sea of Galilee.

May 2015: Dvir Netanely wins the IBS best poster prize

Congratulations to Dvir who won the best poster prize of the 2015 Israeli Bioinformatics Symposium.
Dvir's poster dealt with his breast cancer analysis work.

May 2015: Expander 7 is released

Highlights of the new version: ChIP-Seq analysis, handling of multiple data sets, network visualization via Cytoscape.
Check it out!

April 2015: Twigs website is announced

Twigs, an algorithm based on Gibbs sampling that identifies flexible subgroups in 3-way data (gene x patient x time for gene expression, brain voxel x subject x TR for fMRI), is now available here .
The work will be presented in ISMB 2015 and will appear in Bioinformatics.

March 2015: Roye Rozov wins IBM fellowship

Congratulations to Roye Rozov for winning the IBM PhD fellowship in an international competition.

February 2015: the Morph-R paper is published

Read the paper on our new server and software for assigning new genes to pathways.

December 2014: Didi Amar wins the Safra Prize

Congratulations to Didi Amar , who won the annual Safra Student Excellence Prize.

December 2014: An ensemble approach to genome annotation

Read our new paper on integrating annotation pipelines of newly sequenced organisms.

November 2014: Motif update in Amadeus and Allegro

The files of reference motifs in Amadeus and Allegro were updated.
These are used to test if motifs discovered de novo by the software are actually known transcription factor or microRNA binding sites.

September 2014: Congratulations to Kobi Perl !

Congrats to Kobi for passing the PhD candidacy exam. Kobi's topic is "Understanding of developmental and physiological conditions of the inner ear using transcriptome and proteome analysis".

September 2014: Farewell to Yaron Orenstein.

Yaron has completed his PhD and has just moved to MIT to do a postdoc in Bonnie Berger's group.

September 2014: Dissecting core promoter regulation The Transcription factor.

TRF2 is a preferential core promoter regulator in Drosophila. Read the study reporting on our collaboration with Tamar Juven-Gershon et al.

September 2014: Fast compression algorithm published.

Read here Roye Rozov's fast lossless compression algorithm for NGS data.

July 2014: using clonability to study the barriers of information transfer between prokaryotes and eukaryotes.

Our new study in Frontiers in Genetics examines exhaustive cloning attempts in C. elegans and reveals that piRNAs, transposons, and repeat sequences are efficiently cloned in yeast, but not in bacteria.

July 2014: co-localization of co-functioning genes in the human genome

Genes that share a common function tend to co-localize in the human genome.
We showed this in our recent NAR paper using 3D information from HI-C experiments and in other ways.

July 2014: Our group talks in ISMB 14 SIGs

Hear our group members in Boston: Yaron Orenstein will talk on HT-SELEX motif finding in the RegGen SIG, and Didi Amar will talk on pathway biomarkers in the Network Biology SIG.

May 2014: Integrated omics analysis of DNA damage response published in Science Signaling

The paper summarizes the TRIREME project , in which integrated deep sequencing methods were used to examine the cellular response to ionizing radiation. It reveals transcriptional regulation, epigenetic changes, and lincRNAs that are central to the DNA damage response.

April 2014: Congratulations to David Amar!

For passing the PhD candidacy exam. Didi's thesis topic is "Novel methods for integrative analysis of heterogeneous large scale biomedical data".

April 2014: Congratulations to Yaron Orenstein!

For being awarded the Deutsch Excellence Scholarship for PhD students.

April 2014: Workshop on advanced computational genomics tools: network analysis and gene regulation

The workshop will take place on Tuesday, April 8th 2014, 10:15-14:00, PC Classroom, 09 Sherman Building, Tel Aviv University.

March 2014: BARCODE presented

Roye Rozov presented the BARCODE algorithm for compression of deep sequencing data in RECOMB-Seq .

March 2014: congratuations to Roye Rozov!

For passing the PhD candidacy exam. Roye's thesis topic is "On reducing complexity of deep sequencing data analysis".

March 2014: Expander workshop

A workshop "Basic tools for computational genomics - first steps with EXPANDER" will be given by Adi Maron-Katz on Tuesday 18 March 2014.

February 2014: Comparing high-throughput technologies for TFBS detection

Read our new NAR paper on comparison of High-Throughput SELEX, protein binding microarrays and ChiP-seq.

February 2014: Module map paper published

A paper presenting the new module map construction algorithm was published by NAR.

January 2014: ModMap inaugurated

ModMap, a new tool for producing a map of related functional modules by joint analysis of two networks is now available here.

December 2013: Ron Shamir's 60th

Ron's past and present students, teachers and colleauges celebrated his 60th birthday in a workshop.

November 2013: Comparing high throughput methods for studying TF binding

Yaron Orenstein presented new insights on comparing transcription factor binding models learned from PBM, HT-SELEX and ChIP data, in the RECOMB/ISCB Conference on Regulatory and System Genomics, in Toronto.

November 2013: Expander version 6.2 is released

Among the new features: Gene sets enrichment analysis (GSEA) and integration of AMADEUS software for de novo motif discovery.
See details.

September 2013: Telomere length and stress

Our PLoS Genetics paper shows that different stresses can have very different effects on yeast telomeres, and identifies a central pathway in the telomeric response to environmental stress.
This work was done in collaboration with Martin Kupiec and other colleagues.
See also news item on this study.

August 2013: microRNAs in melanoma

Read our recent paper (a collaboration with Carmit Levy), which identifies two microRNAs that regulate the invasive and proliferative programs in melanoma.

June 2013: Optimal design of double-stranded DNA de Bruijn sequence

Read our paper (forthcoming in ISMB 2013) on design of shortest possible double stranded DNA sequences covering all k-mers, with applications to protein-binding microarrays and synthetic enhancers.
The software is available here .

May 2013: A hands-on workshop on using some of our tools

A hands-on workshop on Expander, Amadeus and Spike tools will take place on May 19.
See here for registration.

April 2013: Congratulations to Dr. Guy Karlebach

Congratulations to Dr. Guy Karlebach, who was awarded his PhD for the thesis "Modeling and Analysis of Perturbations in Gene Regulatory Networks".

March 2013: Congratulations to Ron Zeira

Congratulations to Ron Zeira, who was awarded his MSc for the thesis "Post-silicon test optimization using methods from bioinformatics".
Ron is starting his PhD in the group.

March 2013: DICER: a new algorithm for differential co-expression

Read our paper in PLoS Computational Biology describing a new method for identifying pairs of modules manifesting differential co-expression. The Dicer software is available here.

January 2013: Modeling transcription factor binding

Read the new Nature Biotechnology paper where several groups of transcription factor binding modelers compare their methods and improve inference.

January 2013: Improved HGT highway paper published

A faster and more accurate algorithm for highways of horizontal gene transfer was published in Bioinformatics.

January 2013: DICER tool announced

DICER is a new tool for finding interacting gene groups using differential co-expression analysis. The software is now available.

December 2012: Morph algorithm published in Plant Cell

A new algorithm for pinpointing new candidate genes in arabidopsis and tomato pathways has been published. The Morph software can be used online or downloaded.

October 2012: Ultra-fast and accurate motif finder from PBM data

RAP is a new algorithm for de novo motif finding using protein binding microarray data, presented in RECOMB Regulatory Genomics Meeting.

September 2012: a comparative study of motif discovery methods for PBMs

Read our recent study of four state of the art algorithms for motif discovery using protein binding microarray profiles, including our new Amadeus-PBM algorithm.

July 2012: Modeling networks the community way

Read the new Nature Methods paper where the crowd of DREAM network modelers join forces to improve inference.

July 2012: On using networks in classification

Read our paper in JCB on a new kernel-based method for utilizing protein interaction networks to improve cancer classification.

April 2012: More accurate expression evaluation from multireads

Read our RECOMB-seq paper on population-based improvement of multiread assignment in NGS data.

April 2012: Aspergillus mutant analysis

Read the paper on analysis of a protease deficient mutant of A. Fumigatus.

February 2012: Morph poster wins a prize

The poster on Morph algorithm by Didi Amar and Oren Tzfadia has won a prize at the annual meeting of the Genetics Society of Israel.

January 2012: Aneuploidy and cancer

Read the news item in the AFTAU newsletter on patterns of chromosomal abnormality in cancer.

January 2012: A new regulatory motif in the nematode

Read our report in Genome Research, on a striking new motif pair in C. elegans promoters.

December 2011: A new version of Expander

Among the new features in Version 6: Degas algorithm for disease-dysregulated subnetworks, ISA bi-clustering implementation, Hierarchical clustering tree partition, and support for similarity dataA new Check it out!

November 2011: Bioinformatics for Biologists textbook

A new Bioinformatics textbook for Biology students, edited by Pevzner and Shamir was published by Cambridge University Press.

October 2011: A new paper on reciprocal translocation

See the new JDA paper by Ozery-Flato and Shamir An O(n3/2log(n)) algorithm for sorting by reciprocal translocations.

September 2011: HGT highways paper

Our paper on highways of horizontal gene transfer was published in J. Computational Biology.

September 2011: HiDe software for HGT highways

Test out HiDe, a new software package for inferring highways of horizontal gene transfer.

September 2011: A new website

The group's website has been completely overhauled by Annelyse Thevenin. You can see the new items here.

August 2011: A new article

Read the new article in Molecular Oncology by Sharon Rashi Elkeles et al on P53's role in transcriptional modulation induced by ionizing radiation