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Agilent Literature Search version 3.1.1 is released on August 1, 2014. This version works with Cytoscape 3.1 and is available in Cytoscape app store

ENViz version 3.1.1 is released on July 24, 2014. This version works with Cytoscape 3.1 and is available in Cytoscape app store .

In press:

Vitkin E; Ben-Dor A; Shmoish M; Hartmann MF; Yakhini Z; Wudy SA; Hochberg Z. “ Peer group normalization and urine to blood context in steroid metabolomics: The case of CAH and obesity.” Steroids,  Jul 17, 2014;88C:83-89. DOI: 10.1016/j.steroids.2014.07.003.

Sharon E, van Dijk D, Kalma Y, Keren L, Manor O, Yakhini Z, Segal E. “Probing the effect of promoters on noise in gene expression using thousands of designed sequences.” Genome Research, Jul 16, 2014. PII: gr.168773.113.


logo ENViz: A Cytoscape app for integrated statistical analysis and visualization of sample-matched data with multiple datatypes
Anya Tsalenko, Roy Navon, Israel Steinfeld, Michael Creech, Zohar Yakhini and Allan Kuchinsky

ENViz (Enrichment Analysis and Visualization) is a Cytoscape plugin that performs joint enrichment analysis of two types of sample matched datasets in the context of systematic annota-tions. Such datasets may be gene expression or any other high-throughput data collected in the same set of samples. The enrichment analysis is done in the context of pathway information, gene ontology (GO) or any custom annotation of the data. The results of the analysis consist of significant associations between profiled elements of one of the datasets to the annotation terms. The results of the enrichment analysis are visualized as an interactive Cytoscape network, and can be visually overlaid on biological pathways or GO hierarchy. Available in Cytoscape App store

miTEA miTEA: miRNA Target Enrichment Analysis miRNA
Israel Steinfeld, Roy Navon and Zohar Yakhini

miTEA is a tool for identifying and visualizing enriched miRNA targets in ranked lists of genes. It searches for enriched miRNA targets that appear densely at the top of a ranked list of genes. Available at


GO GOrilla GOtree
Gene Ontology enRIchment anaLysis and visuaLizAtion tool.
GOrilla is a tool for identifying and visualizing enriched GO terms in ranked lists of genes. Available at


ALS Agilent Literature Search
Mines scientific literature to find publications related to search terms and to create interaction networks based on the search result.
Available in Cytoscape App store



Provides effective visualization and analysis platform to analyse expression data on a given network.
Available in Cytoscape App store


Selected Publications

Sharon, E; Kalma, Y; Sharp, A; Raveh-Sadka, T; Levo, M; Zeevi, D; Keren, L; Yakhini, Z; Weinberger, A; and Segal, E. “Inferring Gene Regulatory Logic From High-Throughput Measurements of Thousands of Systematically Designed Promoters.” Nature Biotechnology 30 (6), June 2012: 521-530. DOI: 10.1038/nbt.2205.

Johansson, HJ; Sanchez, BC; Mundt, F; Forshed, J; Kovacs, A; Panizza, E; Hultin-Rosenberg, L; Lundgren, B; Martens, U; Mathe, G; Yakhini, Z; Helou, K; Krawiec, K; Kanter, L; Hjerpe, A; Stal, O; Linderholm, BK; and Lehtio, J. “Retinoic Acid Receptor Alpha is Associated with Tamoxifen Resistance in Breast Cancer.” Nat Commun 4 (2175), July 19, 2013. DOI:10.1038/ncomms3175.

Ben-Elazar, S; Yakhini, Z; and Yanai, I. “Spatial Localization of Co-regulated Genes Exceeds Genomic Gene Clustering in the Saccharomyces Cerevisiae Genome.” Nucleic Acids Research 41 (4), Feb. 1, 2013: 2191-2201. DOI 10.1093/nar/gks1360.

Steinfeld, I; Navon, R; Ach, R; and Yakhini, Z. “miRNA Target Enrichment Analysis Reveals Directly Active miRNAs in Health and Disease.” Nucleic Acids Res. 41(3) Feb 1, 2013. DOI: 10.1093/nar/gks1142.

Leibovich, L; and Yakhini, Z. "Efficient Motif Search in Ranked Lists and Applications to Variable Gap Motifs." Nucleic Acids Res. (40) 13, March 13, 2012: 5832-47. DOI: 10.1093/nar/gks206.

Zehavi, L; Avraham, R; Barzilai, A; Bar-Ilan, D; Navon, R; Sidi, Y; Avni, D; and Leibowitz-Amit. R. “Silencing of a Large micro-RNA Cluster on Human Chromosome 14q32 in Melanoma: Biological Effects of mir-376a and mir-376c on Insulin Growth Factor 1 Receptor.” Molecular Cancer 11 (44), July 2, 2012. DOI:10.1186/1476-4598-11-44.

Sudmant, PH; Kitzman, JO; Antonacci, F; Alkan, C; Malig, M; Tsalenko, A; Sampas, N; Bruhn, L; Shendure, J; 1000 Genomes Project; Eichler, EE. "Diversity of Human Copy Number Variation and Multicopy Genes." Science 330 (6004), Oct. 29, 2010: 641 - 646. DOI: 10.1126/science.1197005

Kidd, JM; Sampas, N; Antonacci, F; Graves, T; Fulton, R; Hayden, HS; Alkan, C; Malig, M; Ventura, M; Giannuzzi, G; Kallicki, J; Anderson, P; Tsalenko, A; Yamada, NA; Tsang, P; Kaul, R; Wilson, RK; Bruhn, L.; Eichler, E.E. "Characterization of Missing Human Genome Sequences and Copy-Number Polymorphic Insertions." Nature Methods 7, May 2010: 365 - 371.

Perry, GH; Ben-Dor, A; Tsalenko, A; Sampas, N; Rodriguez-Revenga, L; Tran, CW; Scheffer, A; Steinfeld, I.; Tsang, P; Yamada, NA; Park, HS; Kim, JI; Seo, JS; Yakhini, Z; Laderman, S; Bruhn, L; and Lee, C. "The Fine-Scale and Complex Architecture of Human Copy-Number Variation." The Journal of Human Genetics 82, March 2008: 1-11. DOI:10.1016/j.ajhg.2007.12.010.

Ben-Dor, A; Lipson, D; Tsalenko, A; Reimers, M; Baumbusch, LO; Barrett, MT; Weinstein, JN; Børresen-Dale, AL; and Yakhini, Z. “Framework for Identifying Common Aberrations in DNA Copy Number Data.” RECOMB 2007: 122-136.

de Smith, AJ; Tsalenko, A; Sampas, N; Scheffer, A; Yamada, NA; Tsang, P; Ben-Dor, A; Yakhini, Z; Ellis, RJ; Bruhn, L; Laderman, S; Froguel, P; and Blakemore, AIF. “Array CGH Analysis of Copy Number Variation Identifies 1284 New Genes Variant in Healthy White Males: Implications for Association Studies of Complex Diseases.” Human Molecular Genetics, Advance Access, July 31, 2007: DOI:10.1093/hmg/ddm208.

Ashley, E; Ferrara, R; King, JY; Vailaya, A; Kuchinsky, A; He, X; Byers, B; Gerckens, U; Oblin, S; Tsalenko, A; Soito, A; Spin, JM; Tabibiazar, R; Connolly, AJ; Simpson, JB; Grube, E; and Quertermos, T. “Network Analysis of Human In-Stent Restenosis”, Circulation, Dec. 4, 2006: 2644-2654.

Kristensen, VN; Edvardsen, H; Tsalenko, A; Nordgard, SH; Sorlie, T; Sharan, R; Vailaya, A; Ben-Dor, A; Lonning, PE; Lien, S; Omholt, S; Syvanen, AC; Yakhini, Z; Borresen-Dale, AL. “Genetic variation in putative regulatory loci controlling gene expression in breast cancer.” Proc Natl Acad Sci. 20, May 16, 2006:7735-40.

Vailaya, A; Bluvas, P; Kincaid, R; Kuchinsky, A; Creech, M; and Adler, A. "An Architecture for Biological Information Extraction and Representation," Bioinformatics 21, 2005: 430-438.

Kincaid, R; Ben-Dor, A; and Yakhini, Z. "Exploratory Visualization of Array-based Comparative Genomic Hybridization," Information Visualization 4, 2005: 176-190.

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; and Laderman, S. "Comparative Genomic Hybridization Using Oligonucleotide Microarrays and Total Genomic DNA," Proceedings of the National Academy of Sciences of the United States of America 101, Dec. 10, 2004: 17765-17770.

Kincaid, R. "VistaClara: an Interactive Visualization for Exploratory Analysis of DNA Microarrays," in Proceedings of the 2004 ACM Symposium on Applied Computing. Nicosia, Cyprus: ACM Press, 2004: 167-174.

Complete list of publications at Agilent Labs Publications.