Add news<\/a><\/p>\n Read Rami Eitan’s paper on reconstructing cancer karyotypes from short read data on BioRxiv <\/a><\/p>\n Congratulations to Roye Rozov for being awarded the Deutsch Excellence Scholarship for PhD students in the School of Computer Science, TAU. Read Kobi Perl’s paper <\/a>on the connection between the transcriptome and proteome in non-proliferating tissues.<\/p>\n Read Adi’s paper<\/a> with colleagues from Talma Hendler’s group showing that sleep deprivation leads to deterioration in the modularity of the brain.<\/p>\n Didi Amar has left the group for a postdoc in Stanford. Roye Rozov’s new paper “Faucet: streaming de novo assembly graph construction” was accepted to RECOMB-seq 2017 and will be presented in Hong Kong in May.<\/p>\n David Pellow’s paper <\/a>on improving the performance of minimizers, with Y. Oresntein and C. Kingsford’s team, has been accepted to ISMB 2017 and will be presented in Prague in July.<\/p>\n Read our new paper<\/a> in Molecular Systems Biology in collaboration with Rohs and Taipale groups analyzing shape readout for over 400 transcription factors using HT-Selex data.<\/p>\n We welcome Nimrod who is joining the group as an MSc student, after a BSc in Computer Science from TAU.<\/p>\n Read our new report<\/a> with colleagues from MIT and CMU on the properties of minimizers using lexicographic, random k-mer ordering and small universal hitting sets. Read Didi Amar’s and Shai Izraeli’s paper<\/a> on classifying 20 different cancer subtypes based on mutations only, with applications to cancer of unknown primary, genetic interactions and more.<\/p>\n Our paper<\/a> on classification cancers via mutations is one of six papers accepted for oral presentations in the Highlight Track of RECOMB in May 2017<\/a> in Hong Kong.<\/p>\n The full version of Roye Rozov’s paper<\/a> on Recycler, our algorithm for plasmid discovery, has been published in Bioinformatics.<\/p>\n Read Ron Zeira’s paper<\/a> on sorting by cuts, joins and duplications in JCB. This is the full version of the CPM 2015 extended abstract.<\/p>\n Read our new study<\/a>, with Irit Gat-Viks, Fuad Iraqi and others, performing eQTL analysis of Collaborative Cross (CC) mice livers.<\/p>\n Congrats to Rami, whose thesis and degree are now official.<\/p>\n Rami’s thesis, Reconstructing cancer karyotypes from paired-end reads and copy number data, is available here.<\/a><\/p>\n Read Yaron Orenstein’s paper <\/a>with Doron Gerber’s group on analysis of binding site affinity using microfluidics, SELEX – and bioinformatics.<\/p>\n Congratulations to Didi, whose doctoral degree has been confirmed by TAU.<\/p>\n Didi’s thesis, Novel methods for integrative analysis of heterogeneous large scale biomedical data, is available here.<\/a><\/p>\n 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.<\/p>\n Read our papers (with colleagues) on compact universal k-mer hitting sets <\/a>and copy number evolution problems, <\/a>which will be presented in WABI 2016.<\/p>\n Yaron Orenstein’s new paper <\/a>reviews models based on protein binding microarrays and high-throughput SELEX, and compares them to in vivo binding.<\/p>\n Read Ron Shamir’s viewpoint in Cell Systems <\/a>on collaborations between “wet” and computational scientists.<\/p>\n Richmind is a new method for analysis of large-scale fMRI results, proposing several statistical approaches for enrichment testing.<\/p>\n See our new paper <\/a>and website<\/a>.<\/p>\n Richmind was developed by Adi Maron-Katz and Didi Amar together with Talma Hendler’s brain research group.<\/p>\n In analyzing methylation and gene expression patterns of hundreds of breast cancer samples, we identified subtypes of luminal-A cancer with distinct prognostic signatures.<\/p>\n Read Dvir Netanely’s paper <\/a>for this study, a collaboration with Ella Evron, Ayelet Avraham and Idit Ben-Baruch.<\/p>\n The question of efficiently transforming one copy number profile to another is motivated by cancer evolution.<\/p>\n Our paper <\/a>on the topic, by Ron Zeira and Meirav Zehavi, was presented in CPM 2016 and published.<\/p>\n Congratulations to Adi who was awarded the PhD in Medicine, co-supervised by Talma Hendler and Ron Shamir.<\/p>\n A workshop <\/a>“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.<\/a><\/p>\n Our <\/a>Recycler algorithm <\/a>for identifying plasmid sequences from short read data was presented by Roye Rozov in RECOMB-seq 2016 in Santa Monica, CA.<\/p>\n Read our Genome Research paper <\/a>with Rachel Bell, Carmit Levy and others on the impact of enhancer methylation across 25 cancer types.<\/p>\n Read Adi’s new paper <\/a>on using functional enrichment for analysis of resting state brain fMRI of subjects before and after stress.<\/p>\n 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. Congrats to Dvir for passing the PhD proposal exam. Didi has submitted his PhD thesis and Meirav has completed her brief postdoc in TAU. Farewell to both!<\/p>\n 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. Read our new paper <\/a>(with Doron Gerber and others) on a new microfulidic application that accurately measures protein-DNA affinities.<\/p>\n David Pellow has joined the group as a PhD student after a master with Carl Kingsford at CMU. Our paper <\/a>describing an algorithm for detecting plasmids from de novo assembly graphs is now available.<\/p>\n Adi Maron Katz has completed her PhD studies and is moving temporarily to California. 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 (!) Read our NAR paper <\/a>analyzing together 15000 expression profiles spanning 50 diseases. Read Ron Zeira’s paper <\/a>on sorting genomes in linear time using the operations of single cut, single join and whole chromosome duplication, published in the CPM proceedings.<\/p>\n Congrats to Ron for passing the PhD proposal exam. Ron’s topic is “Models for Structural and Numerical Alterations in Cancer”.<\/p>\n Read here <\/a>our paper on discovering flexible modules in 3-way time series data, with applications to gene expression and fMRI. 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. <\/a> Congratulations to Dvir who won the best poster prize of the 2015 Israeli Bioinformatics Symposium. <\/a> Highlights of the new version: ChIP-Seq analysis, handling of multiple data sets, network visualization via Cytoscape. 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 <\/a>. Congratulations to Roye Rozov for winning the IBM PhD fellowship in an international competition.<\/p>\n Read the paper <\/a>on our new server <\/a>and software for assigning new genes to pathways.<\/p>\n Congratulations to Didi Amar <\/a>, who won the annual Safra Student Excellence Prize.<\/p>\n Read our new paper <\/a>on integrating annotation pipelines of newly sequenced organisms.<\/p>\n The files of reference motifs in Amadeus and Allegro <\/a>were updated. 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”.<\/p>\n Yaron has completed his PhD and has just moved to MIT to do a postdoc in Bonnie Berger’s group.<\/p>\n TRF2 is a preferential core promoter regulator in Drosophila. Read the study <\/a>reporting on our collaboration with Tamar Juven-Gershon et al.<\/p>\n Read here <\/a>Roye Rozov’s fast lossless compression algorithm for NGS data.<\/p>\n Our new study in Frontiers in Genetics <\/a>examines exhaustive cloning attempts in C. elegans and reveals that piRNAs, transposons, and repeat sequences are efficiently cloned in yeast, but not in bacteria.<\/p>\n Genes that share a common function tend to co-localize in the human genome. 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.<\/p>\n The paper <\/a>summarizes the TRIREME project <\/a>, 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.<\/p>\n For passing the PhD candidacy exam. Didi’s thesis topic is “Novel methods for integrative analysis of heterogeneous large scale biomedical data”.<\/p>\n For being awarded the Deutsch Excellence Scholarship for PhD students.<\/p>\n The workshop <\/a>will take place on Tuesday, April 8th 2014, 10:15-14:00, PC Classroom, 09 Sherman Building, Tel Aviv University.<\/p>\n Roye Rozov presented the BARCODE algorithm for compression of deep sequencing data in RECOMB-Seq <\/a>.<\/p>\n For passing the PhD candidacy exam. Roye’s thesis topic is “On reducing complexity of deep sequencing data analysis”.<\/p>\n A workshop <\/a>“Basic tools for computational genomics – first steps with EXPANDER” will be given by Adi Maron-Katz on Tuesday 18 March 2014.<\/p>\n Read our new NAR paper <\/a>on comparison of High-Throughput SELEX, protein binding microarrays and ChiP-seq.<\/p>\n A paper <\/a>presenting the new module map construction algorithm was published by NAR.<\/p>\n ModMap, a new tool for producing a map of related functional modules by joint analysis of two networks is now available here.<\/a><\/p>\n Ron’s past and present students, teachers and colleauges celebrated his 60th birthday in a workshop.<\/a><\/p>\n 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<\/a>, in Toronto.<\/p>\n Among the new features: Gene sets enrichment analysis (GSEA) and integration of AMADEUS software for de novo motif discovery. Our PLoS Genetics paper <\/a>shows that different stresses can have very different effects on yeast telomeres, and identifies a central pathway in the telomeric response to environmental stress. Read our recent paper <\/a>(a collaboration with Carmit Levy), which identifies two microRNAs that regulate the invasive and proliferative programs in melanoma.<\/p>\n Read our paper <\/a>(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. A hands-on workshop on Expander, Amadeus and Spike tools will take place on May 19. Congratulations to Dr. Guy Karlebach, who was awarded his PhD for the thesis “Modeling and Analysis of Perturbations in Gene Regulatory Networks”<\/a>.<\/p>\n Congratulations to Ron Zeira, who was awarded his MSc for the thesis “Post-silicon test optimization using methods from bioinformatics”<\/a>. Read our paper in PLoS Computational Biology<\/a> describing a new method for identifying pairs of modules manifesting differential co-expression. The Dicer software is available here<\/a>.<\/p>\n Read the new Nature Biotechnology paper <\/a>where several groups of transcription factor binding modelers compare their methods and improve inference.<\/p>\n A faster and more accurate algorithm for highways of horizontal gene transfer was published in Bioinformatics.<\/a><\/p>\n DICER is a new tool for finding interacting gene groups using differential co-expression analysis. The software <\/a>is now available.<\/p>\n A new algorithm for pinpointing new candidate genes in arabidopsis and tomato pathways has been published. <\/a>The Morph software <\/a>can be used online or downloaded.<\/p>\n RAP <\/a>is a new algorithm for de novo motif finding using protein binding microarray data, presented in RECOMB Regulatory Genomics Meeting.<\/p>\n Read our recent study <\/a>of four state of the art algorithms for motif discovery using protein binding microarray profiles, including our new Amadeus-PBM algorithm.<\/a><\/p>\n Read the new Nature Methods paper <\/a>where the crowd of DREAM network modelers join forces to improve inference.<\/p>\n Read our paper in JCB <\/a>on a new kernel-based method for utilizing protein interaction networks to improve cancer classification.<\/p>\n Read our RECOMB-seq paper <\/a>on population-based improvement of multiread assignment in NGS data.<\/p>\n Read the paper <\/a>on analysis of a protease deficient mutant of A. Fumigatus.<\/p>\n 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.<\/a><\/p>\n Read the news item in the AFTAU newsletter<\/a> on patterns of chromosomal abnormality in cancer.<\/p>\n Read our report in Genome Research<\/a>, on a striking new motif pair in C. elegans promoters.<\/p>\n 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!<\/a><\/p>\n A new Bioinformatics textbook for Biology students<\/a>, edited by Pevzner and Shamir was published by Cambridge University Press.<\/p>\n See the new JDA paper by Ozery-Flato and Shamir An O(n3\/2<\/sup>\u221alog(n)) algorithm for sorting by reciprocal translocations<\/a>.<\/p>\n Our paper on highways of horizontal gene transfer was published in J. Computational Biology<\/a>.<\/p>\n Test out HiDe<\/a>, a new software package for inferring highways of horizontal gene transfer.<\/p>\n The group’s website has been completely overhauled by Annelyse Thevenin<\/a>. You can see the new items here<\/a>.<\/p>\n\n June 2017: Reconstructing cancer karyotypes<\/a>
\n <\/h3>\n\n May 2017: Roye Rozov wins the Deutsch Excellence Scholarship<\/a>
\n <\/h3>\n
\nThe awarding ceremony will take place on Thursday May 18, at 15:15, in the Open Space Lab in the School of Computer Science.<\/p>\n\n April 2017: Gene expression buffered on the protein level<\/a>
\n <\/h3>\n\n April 2017: Sleep and brain modularity<\/a>
\n <\/h3>\n\n March 2017: Farewell to Didi!<\/a>
\n <\/h3>\n
\nDidi has been a leader in the group for a long time – as a master, doctoral and postdoctoral student.
\nWe wish him great success in the next steps.<\/p>\n\n March 2017: Faucet accepted to RECOMB-seq<\/a>
\n <\/h3>\n\n March 2017: Minimizers paper accepted to ISMB<\/a>
\n <\/h3>\n\n February 2017: The interplay of DNA sequence and shape in regulatory motifs<\/a>
\n <\/h3>\n\n February 2017: Welcome to Nimrod Rapoport<\/a>
\n <\/h3>\n\n January 2017: New analysis of minimizers and universal hitting sets<\/a>
\n <\/h3>\n
\nOur analysis shows how to significantly improve the performance of minimizers.<\/p>\n\n January 2017: Mutation-based cancer classification paper in Oncogene.<\/a>
\n <\/h3>\n\n January 2017: Oncogene paper accepted for RECOMB Highlight track<\/a>
\n <\/h3>\n\n December 2016: Recycler published in Bioinformatics.<\/a>
\n <\/h3>\n\n Nov 2016: SCJD paper published.<\/a>
\n <\/h3>\n\n October 2016: Crosstalk between drug and lipid metabolism via CC mice<\/a>
\n <\/h3>\nSeptember 2016: Congratulations to Rami Eitan for his MSc!<\/h4>\n
September 2016: SELMAP paper published<\/h4>\n
September 2016: Congratulations to Dr. Didi Amar!<\/h4>\n
September 2016: Welcome to Gal Dinstag<\/h4>\n
August 2016: Two group papers in WABI 2016<\/h4>\n
August 2016: Modeling protein-DNA binding in vitro<\/h4>\n
July 2016: Opinion in Cell Systems<\/h4>\n
July 2016: Richmind tool and paper are on<\/h4>\n
July 2016: New breast cancer subtypes discovered<\/h4>\n
June 2016: Paper on copy number transformation problem published<\/h4>\n
June 2016: Congratulations to Adi Maron Katz<\/h4>\n
23 May 2016: Expander workshop<\/h4>\n
April 2016: Recycler presented in RECOMB-seq<\/h4>\n
March 2016: Enhancer methylation in cancer<\/h4>\n
February 2016: Analysis of stress using brain fMRI<\/h4>\n
February 2016: TAF-1 dysfunction in XDP<\/h4>\n
\nRead more.<\/a><\/p>\nDecember 2015: Congratulations to Dvir Netanely<\/h4>\n
\nDvir’s topic is “Multi-omics analysis of high-throughput genomic data for the identification of breast cancer subtypes”.<\/p>\nDecember 2015: Farewell to Didi and Meirav<\/h4>\n
\nBoth are going to Berkeley for the Simons Institute program on Algorithmic Challenges in Genomics <\/a>.
\nDidi’s postdoc is joint to the Simons and the Safra Center <\/a>and after the program he will be back to the group for the rest of the year.<\/p>\nDecember 17, 2015: A hands-on workshop on using some of our favorite tools<\/h4>\n
\nSee here<\/a> for details and registration.<\/p>\nDecember 2015: QPID quantifies protein-DNA binding affinities<\/h4>\n
October 2015: Welcome to David Pellow<\/h4>\n
\nWelcome David!<\/p>\nOctober 2015: Recycler paper posted<\/h4>\n
August 2015: Farewell to Adi and Gil<\/h4>\n
\nAdi has been THE person behind Expander for over a decade and it would not have existed without her.
\nBest of luck to Adi! We hope you will find the right meditative state between Stanford and the Silicone Valley.<\/p>\n
\nWe enjoyed having you around and hope to continue our collaboration.<\/p>\nAugust 2015: Very large scale integrated analysis of disease expression profiles<\/h4>\n
\nThe Adeptus database and project data are available here <\/a>.<\/p>\nJune 2015: SCJD extended abstract published<\/h4>\n
June 2015: Congratulations to Ron Zeira<\/h4>\n
June 2015: TWIGS paper published<\/h4>\n
\nThe paper appeared in the ISMB\/ECCB 2015 proceedings issue of Bioinformatics.<\/p>\nMay 2015: Dvir Netanely wins the Safra Center Retreat best poster prize<\/h4>\n
\n37 posters were presented during the Retreat that took place on 31\/5-1\/6\/2015 in Maagan, Sea of Galilee.<\/p>\nMay 2015: Dvir Netanely wins the IBS best poster prize<\/h4>\n
\nDvir’s poster dealt with his breast cancer analysis work.<\/p>\nMay 2015: Expander 7 is released<\/h4>\n
\nCheck it out!<\/a><\/p>\nApril 2015: Twigs website is announced<\/h4>\n
\nThe work will be presented in ISMB 2015 and will appear in Bioinformatics.<\/p>\nMarch 2015: Roye Rozov wins IBM fellowship<\/h4>\n
February 2015: the Morph-R paper is published<\/h4>\n
December 2014: Didi Amar wins the Safra Prize<\/h4>\n
December 2014: An ensemble approach to genome annotation<\/h4>\n
November 2014: Motif update in Amadeus and Allegro<\/h4>\n
\nThese are used to test if motifs discovered de novo by the software are actually known transcription factor or microRNA binding sites.<\/p>\nSeptember 2014: Congratulations to Kobi Perl !<\/h4>\n
September 2014: Farewell to Yaron Orenstein.<\/h4>\n
September 2014: Dissecting core promoter regulation The Transcription factor.<\/h4>\n
September 2014: Fast compression algorithm published.<\/h4>\n
July 2014: using clonability to study the barriers of information transfer between prokaryotes and eukaryotes.<\/h4>\n
July 2014: co-localization of co-functioning genes in the human genome<\/h4>\n
\nWe showed this in our recent NAR paper <\/a>using 3D information from HI-C experiments and in other ways.<\/p>\nJuly 2014: Our group talks in ISMB 14 SIGs<\/h4>\n
May 2014: Integrated omics analysis of DNA damage response published in Science Signaling<\/h4>\n
April 2014: Congratulations to David Amar!<\/h4>\n
April 2014: Congratulations to Yaron Orenstein!<\/h4>\n
April 2014: Workshop on advanced computational genomics tools: network analysis and gene regulation<\/h4>\n
March 2014: BARCODE presented<\/h4>\n
March 2014: congratuations to Roye Rozov!<\/h4>\n
March 2014: Expander workshop<\/h4>\n
February 2014: Comparing high-throughput technologies for TFBS detection<\/h4>\n
February 2014: Module map paper published<\/h4>\n
January 2014: ModMap inaugurated<\/h4>\n
December 2013: Ron Shamir’s 60th<\/h4>\n
November 2013: Comparing high throughput methods for studying TF binding<\/h4>\n
November 2013: Expander version 6.2 is released<\/h4>\n
\nSee details.<\/a><\/p>\nSeptember 2013: Telomere length and stress<\/h4>\n
\nThis work was done in collaboration with Martin Kupiec and other colleagues.
\nSee also news item <\/a>on this study.<\/p>\nAugust 2013: microRNAs in melanoma<\/h4>\n
June 2013: Optimal design of double-stranded DNA de Bruijn sequence<\/h4>\n
\nThe software is available here <\/a>.<\/p>\nMay 2013: A hands-on workshop on using some of our tools<\/h4>\n
\nSee here<\/a> for registration.<\/p>\nApril 2013: Congratulations to Dr. Guy Karlebach<\/h4>\n
March 2013: Congratulations to Ron Zeira<\/h4>\n
\nRon is starting his PhD in the group.<\/p>\nMarch 2013: DICER: a new algorithm for differential co-expression<\/h4>\n
January 2013: Modeling transcription factor binding<\/h4>\n
January 2013: Improved HGT highway paper published<\/h4>\n
January 2013: DICER tool announced<\/h4>\n
December 2012: Morph algorithm published in Plant Cell<\/h4>\n
October 2012: Ultra-fast and accurate motif finder from PBM data<\/h4>\n
September 2012: a comparative study of motif discovery methods for PBMs<\/h4>\n
July 2012: Modeling networks the community way<\/h4>\n
July 2012: On using networks in classification<\/h4>\n
April 2012: More accurate expression evaluation from multireads<\/h4>\n
April 2012: Aspergillus mutant analysis<\/h4>\n
February 2012: Morph poster wins a prize<\/h4>\n
January 2012: Aneuploidy and cancer<\/h4>\n
January 2012: A new regulatory motif in the nematode<\/h4>\n
December 2011: A new version of Expander<\/h4>\n
November 2011: Bioinformatics for Biologists textbook<\/h4>\n
October 2011: A new paper on reciprocal translocation<\/h4>\n
September 2011: HGT highways paper<\/h4>\n
September 2011: HiDe software for HGT highways<\/h4>\n
September 2011: A new website<\/h4>\n
August 2011: A new article<\/h4>\n