Publications and Software

A complete publication list can be found here(pdf) or here(Google Scholar)

Selected publications

  • Hedenfalk I., Duggan D., Chen Y., Radmacher M., Bittner M., Simon R., Meltzer P., Gusterson B., Esteller M., Raffeld M., Yakhini Z., Ben-Dor A., Dougherty E., Kononen J., Bubendorf L., Fehrle W., Pittaluga S., Gruvberger S., Loman N., Johannsson O., Olsson H., Wilfond B., Sauter G., Kallioniemi O.-P., Borg A., Trent J.,
    Gene-Expression Profiles in Hereditary Breast Cancer,
    doi: 10.1056/NEJM200102223440801
    N Engl J Med 2001
  • Bittner, P Meltzer, Y. Chen, Y. Jiang, E. Seftor, M. Hendrix, M. Radmacher, R. Simon,
    Z. Yakhini, A. Ben-Dor, N. Sampas, E. Dougherty, E. Wang, F. Marincola, C. Gooden, J. Lueders, A. Glatfelter, P. Pollock, J. Carpten, E. Gillanders, D. Leja, K. Dietrich, C. Beaudry, M. Berens, D. Alberts, V. Sondak, N. Hayward, J. Trent,
    Molecular classification of cutaneous malignant melanoma by gene expression profiling,
    doi: 10.1038/35020115
    Nature 2000
  • Ben-Dor, L. Bruhn, N. Friedman, I. Nachman and Z. Yakhini,
    Tissue Classification with Gene Expression Profiles,
    doi: 10.1089/106652700750050943
    RECOMB 2000 (conference version) and Journal of Computational Biology, 2000.
    RECOMB Test of Time Award 2012
  • Amir Ben-Dor, Ron Shamir and Zohar Yakhini,
    Clustering gene expression patterns,
    doi: 10.1089/106652799318274
    RECOMB 1999 (conference version) and Journal of Computational Biology
    RECOMB Test of Time Award 2011
  • Amir Ben-Dor, Benny Chor, Richard M. Karp, Zohar Yakhini,
    Discovering Local Structure in Gene Expression Data: The Order-Preserving Submatrix Problem,
    doi: 10.1089/10665270360688075
    RECOMB 2002 (conference version) and Journal of Computational Biology
    RECOMB Test of Time Award 2014
  • Chen MM, Ashley EA, Deng DX, Tsalenko A, Deng A, Tabibiazar R, Ben-Dor A, Fenster B, Yang E, King JY, Fowler M, Robbins R, Johnson FL, Bruhn L, McDonagh T, Dargie H, Yakhini Z, Tsao PS, Quertermous T,
    Novel role for the potent endogenous inotrope apelin in human cardiac dysfunction.
    doi: 10.1161/01.CIR.0000091235.94914.75
    Circulation 2003
  • Barrett MT, Scheffer A, Ben-Dor A, Sampas N, Lipson D, Kincaid R, Tsang P, Curry B, Baird K, Meltzer PS, Yakhini Z, Bruhn L, Laderman S.
    Comparative genomic hybridization using oligonucleotide microarrays and total genomic DNA,
    doi: 1073/pnas.0407979101
    PNAS 2004
  • Doron Lipson, Yonatan Aumann, Amir Ben-Dor, Nathan Linial, Zohar Yakhini,
    Efficient Calculation of Interval Scores for DNA Copy Number Data Analysis,
    doi: 10.1089/cmb.2006.13.215
    RECOMB 2005 (conference version) and Journal of Computational Biology
  • Doron Lipson , Zohar Yakhini , Yonatan Aumann,
    Optimization of probe coverage for high-resolution oligonucleotide aCGH,
    doi: 1093/bioinformatics/btl316
    ECCB 2006 (conference version) and Bioinformatics 2007.
  • Eran Eden, Doron Lipson, Sivan Yogev, and Zohar Yakhini,
    A Novel Approach to Motif Discovery with Applications in Transcription Factor Binding and Methylation Data Analysis.
    doi: 10.1371/journal.pcbi.0030039
    PLoS Computational Biology
  • Dehan, Ben-Dor, Liao, Lipson, Frimer, Reinstein, Simansky, Krupsky, Yaron, Friedman, Rechavi, Perlman, Aviram-Goldring, Izraeli, Bittner, Yakhini, Kaminski,
    Chromosomal aberrations and gene expression profiles in non-small cell lung cancer,
    doi: 10.1016/j.lungcan.2006.12.010
    Lung Cancer 2007.
  • Shlomit Farkash-Amar, Doron Lipson, Andreas Polten, Alon Goren, Charles Helmstetter,
    Zohar Yakhini, Itamar Simon,
    Global organization of replication time zones of the mouse genome,
    doi: 1101/gr.079566.108
    Genome Research 2008
  • Eran Eden, Roy Navon, Israel Steinfeld, Doron Lipson, Zohar Yakhini,
    GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists,
    doi: 1186/1471-2105-10-48
    BMC Bioinformatics 2009
  • Espen Enerly, Israel Steinfeld, Kristine Kleivi, Suvi-Katri Leivonen, Miriam R Aure, Hege G Russnes,
    Jo Anders Rønneberg, Hilde Johnsen, Roy Navon, Einar Rødland, Rami Mäkelä, Bjørn Naume, Merja Perälä, Olli Kallioniemi, Vessela N Kristensen, Zohar Yakhini, Anne-Lise Børresen-Dale,
    miRNA-mRNA integrated analysis reveals roles for miRNAs in primary breast tumors,
    doi: 10.1371/journal.pone.0016915
    PLoS One 2011
  • Limor Leibovich, Zohar Yakhini,
    Efficient motif search in ranked lists and applications to variable gap motifs,
    doi: 10.1093/nar/gks206
    Nucleic Acids Research 2012
  • Israel Steinfeld, Roy Navon, Robert Ach, Zohar Yakhini,
    miRNA target enrichment analysis reveals directly active miRNAs in health and disease,
    doi: 10.1093/nar/gks1142
    Nucleic Acids Research 2013
  • Ragle-Aure M, Steinfeld I, Baumbusch L, Liestøl K, Lipson D, Nyberg S, Naume B, Kleivi-Sahlberg K, Kristensen VN, Børresen-Dale AL, Lingjaerde OC, Yakhini Z
    Identifying in-trans process associated genes in breast cancer by integrated analysis of copy number and expression data
    doi: 10.1371/journal.pone.0053014
    PLoS One 2013
  • D Nejman, R Straussman, I Steinfeld, M Ruvolo, D Roberts, Z Yakhini, H Cedar,
    Molecular rules governing de novo methylation in cancer,
    doi: 1158/0008-5472.CAN-13-3042
    Cancer Research 2014
  • L Leibovich, Z Yakhini,
    Mutual enrichment in ranked lists and the statistical assessment of position weight matrix motifs,
    doi: 10.1186/1748-7188-9-11
    Algorithms in Molecular Biology 2014
    Conference version: WABI 2013
  • Sharon, D van Dijk, Y Kalma, L Keren, O Manor, Z Yakhini, E Segal,
    Probing the effect of promoters on noise in gene expression using thousands of designed sequences,
    Genome Research 2014
  • Shalem, Sharon, Lubliner, Regev, Lotan-Pompan, Yakhini, Segal,
    Systematic Dissection of the Sequence Determinants of Gene 3’End Mediated Expression Control,
    doi: 10.1371/journal.pgen.1005147
    PLoS Genetics 2015
  • Vitkin E, Golberg A, Yakhini Z,
    BioLEGO—a web-based application for biorefinery design and evaluation of serial biomass fermentation,
    doi: 10.1142/S2339547815400038
    Technology 2015
  • Drory-Retwitzer, Polishchuk, Churkin, Kifer, Yakhini, Barash,
    RNAPattMatch: a web server for RNA sequence/structure motif detection based on pattern matching with flexible gaps,
    doi: 10.1093/nar/gkv435,
    Nucleic Acids Research 2015
  • Haakensen Vilde D, Steinfeld Israel, Saldova Radka, Shehni Akram Asadi, Kifer Ilona, Naume Bjørn, Rudd Pauline M, Børresen-Dale Anne-Lise, Yakhini Zohar,
    Serum N-glycan analysis in breast cancer patients–Relation to tumour biology and clinical outcome,
    doi: 10.1016/j.molonc.2015.08.002
    Molecular Oncology 2015
  • Dalia Cohn-Alperovich, Alona Rabner, Ilona Kifer, Yael Mandel-Gutfreund, Zohar Yakhini,
    Mutual enrichment in aggregated ranked lists with applications to gene expression regulation
    doi: 10.1093/bioinformatics/btw435
    Bioinformatics 2016
  • Shay Ben-Elazar, Benny Chor, Zohar Yakhini,
    Extending partial haplotypes to full genome haplotypes using chromosome conformation capture data
    doi: 10.1093/bioinformatics/btw453
    Bioinformatics 2016
  • Weingarten-Gabbay, Elias-Kirma, Nir, Gritsenko, Stern-Ginossar, Yakhini, Weinberger, Segal,
    Systematic discovery of cap-independent translation sequences in human and viral genomes,
    doi: 10.1126/science.aad4939
    Science 2016
  • I Kifer, RM Branca, A Ben-Dor, L Zhai, P Xu, J Lehtio, Z Yakhini,
    Optimizing analytical depth and cost efficiency of IEF-LC/MS proteomics
    doi: 10.1109/TCBB.2015.2452901
    IEEE Transactions on Comp Bio and Bioinformatics 2017
  • M Levo, T Avnit-Sagi, M Lotan-Pompan, Y Kalma, A Weinberger, Z Yakhini, E Segal,
    Systematic Investigation of Transcription Factor Activity in the Context of Chromatin Using Massively Parallel Binding and Expression Assays
    doi: 10.1016/j.molcel.2017.01.007
    Molecular Cell 2017


  • GOrilla – a tool for identifying and visualizing enriched GO terms in ranked lists of genes. Developed by Roy Navon, Eran Eden, Israel Steinfeld and Doron Lipson.
  • BioLego – a system for high-scale simulations of biomass fermentation in serial two organism processes. Includes the source code with installation instructions and all biological and validation results. Developed by Edward Vitkin in collaboration with Dr. Alex Golberg lab, TAU
  • MonoClad– find meaningful partitions using semi-supervised class discovery. Developed by Israel Steinfeld and Roy Navon.
  • DRIM – a tool for discovering motifs in a list of ranked DNA sequences. Developed by Eran Eden.
  • HaarSeg– a segmentation algorithm for tiling microarrays. Developed by Erez Ben-Yaacov.
  • UnMeRFi– Under-Methylated Region Finder. Developed by Israel Steinfeld.
  • Stepgram – application for aberration calling in aCGH data Developed by Doron Lipson.
  • ATRHunter– find approximate tandem repeats in a genomic sequence. Developed by Ydo Wexler.
  • GeneSelector – find a small subset of genes for classification of expression data. Developed by Ari Frank.
  • ProbeSpec – for mapping the specificity of all candidate probes for a given sequence. Developed by Doron Lipson.
  • SimTree – online tool for computing the similarity between RNA secondary structures. Developed by Eran Eden and Izhar Wallach.