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Publications and Software

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

​Selected Publications

  1. Preuss, I., Yakhini, Z., & Anavy, L. (2021). Data Storage Based on Combinatorial Synthesis of DNA Shortmers. bioRxiv.‏

  2. A Levy-Jurgenson, X Tekpli, VN Kristensen, Z Yakhini.

    Spatial Transcriptomics Inferred from Pathology Whole-Slide Images Using Deep Learning Links Tumor Heterogeneity to Survival in Breast and Lung Cancer.

    bioRxiv, 2020

  3. A Akavia, H Shaul, M Weiss, Z Yakhini

    Linear-Regression on Packed Encrypted Data in the Two-Server Model

    WAHC’19: Proceedings of the 7th ACM Workshop on Encrypted Computing & Applied Homomorphic Cryptography November 2019 Pages 21–32

    doi: 10.1145/3338469.3358942

  4. S Ben-Elazar, B Chor, Z Yakhini

    The Functional 3D Organization of Unicellular Genomes

    Scientific reports 9 (1), 1-13

    doi: 10.1038/s41598-019-48798-7

  5. Golberg A, Sheviryov J, Solomon O, Anavy L, Yakhini Z.

    Molecular harvesting with electroporation for tissue profiling.

    Scientific Reports. 2019

    doi: 10.1038/s41598-019-51634-7

  6. Anavy L, Vaknin I, Atar O, Amit R, Yakhini Z.

    Data storage in DNA with fewer synthesis cycles using composite DNA letters.

    Nature Biotechnology. 2019

    doi: 10.1038/s41587-019-0240-x

  7. Levy-Jurgenson A., Tekpli X., Kristensen V.N., Yakhini Z.

    Predicting Methylation from Sequence and Gene Expression Using Deep Learning with Attention.  Algorithms for Computational Biology. AlCoB 2019.

  8. Peleg, Yonatan & Shefer, Shai & Anavy, Leon & Chudnovsky, Alexandra & Israel, Alvaro & Golberg, Alexander & Yakhini, Zohar.

    Sparse NIR Optimization method (SNIRO) to quantify analyte composition with visible (VIS)/near infrared (NIR) spectroscopy (350nm-2500nm).

    doi: 10.1016/j.aca.2018.11.038.

    Analytica Chimica Acta. 2018

  9. Maya Polishchuk, Inbal Paz, Zohar Yakhini, Yael Mandel-Gutfreun

    SMARTIV: combined sequence and structure de-novo motif discovery for in-vivo RNA binding data

    doi: 10.1093/nar/gky453

    Nucleic Acids Research, 2018

  10. Alexander Chemodanov, Gabriel Jinjikhashvily, Oz Habiby, Alexander Liberzon, Alvaro Israel, Zohar Yakhini, Alexander Golberg.
    Net primary productivity, biofuel production and CO2 emissions reduction potential of Ulva sp. (Chlorophyta) biomass in a coastal area of the Eastern Mediterranean,
    doi: 10.1016/j.enconman.2017.06.066
    Energy Conversion and Management, 2017

  11. Levy, Lior, Leon Anavy, Oz Solomon, Roni Cohen, Michal Brunwasser-Meirom, Shilo Ohayon, Orna Atar, Sarah Goldberg, Zohar Yakhini, and Roee Amit.

    A synthetic oligo library and sequencing approach reveals an insulation mechanism encoded within bacterial σ54 promoters.

    doi: 10.1016/j.celrep.2017.09.063

    Cell reports 2017

  12. 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

  13. 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 proteomicsdoi: 10.1109/TCBB.2015.2452901
    IEEE Transactions on Comp Bio and Bioinformatics 2017

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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

  19. 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

  20. 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

  21. 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

  22. 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

  23. 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

  24. 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

  25. 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

  26. 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

  27. 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

  28. 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

  29. 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

  30. 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.

  31. 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

  32. 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.

  33. 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

  34. 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

  35. 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

  36. 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

  37. 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

  38. 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

  39. 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


Software  developed by the group, with some explanations, can be found in the group GitHub and/or in the following links

  • CARBP – a tool for the design of RNA cassettes containing multiple binding sites for RNA-binding proteins (RBPs).

  • MULSEA – a tool for identifying mutual enrichment in aggregated ranked lists with applications to gene expression regulation. Developed by Dalia Cohn-Alperovich.

  • 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.

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