Read Hagai's paper on BioRxiv about the pitfalls in network-based module detection algorithms, how to overcome them, and about DOMINO, a novel algorithm that performs very well on gene expression and GWAS data.
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
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.
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
April 2016: Recycler presented in RECOMB-seq
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.
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.
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
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
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.
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
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
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
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(n3/2√log(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
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