Selected Publications

Gal Yankovitz, Ofir Cohn, Eran Bacharach, Naama Peshes-Yaloz, Yael Steuerman, Fuad A Iraqi, Irit Gat-Viks.: Leveraging the cell lineage to predict cell-type specificity of regulatory variation from bulk genomics. Genetics 2021, 217 (4), iyab016.

Amit Frishberg, Inge van den Munckhof, Rob Ter Horst, Kiki Schraa, Leo AB Joosten, Joost HW Rutten, Adrian C Iancu, Ioana M Dregoesc, Bogdan A Tigu, Mihai G Netea, Niels P Riksen, Irit Gat-Viks.: An integrative model of cardiometabolic traits identifies two types of metabolic syndrome. Elife 2021, 10, e61710.

Iris Kamer, Yael Steuerman, Inbal Daniel-Meshulam, Gili Perry, Shai Izraeli, Marina Perelman, Nir Golan, David Simansky, Iris Barshack, Alon Ben Nun, Teodor Gottfried, Amir Onn, Irit Gat-Viks, Jair Bar.: Predicting brain metastasis in early stage non-small cell lung cancer patients by gene expression profiling. Translational Lung Cancer Research 2020, 9 (3), 682.

M Levy, A Frishberg, I Gat-Viks.: Inferring cellular heterogeneity of associations from single cell genomics. Bioinformatics 2020, 36 (11), 3466-3473.

R Wilentzik Müller, I Gat-Viks.: Exploring Neural Networks and Related Visualization Techniques in Gene Expression Data. Frontiers in Genetics 2020, 11, 402.

Bo Li, Sara M Clohisey, Bing Shao Chia, Bo Wang, Ang Cui, Thomas Eisenhaure, Lawrence D Schweitzer, Paul Hoover, Nicholas J Parkinson, Aharon Nachshon, Nikki Smith, Tim Regan, David Farr, Michael U Gutmann, Syed Irfan Bukhari, Andrew Law, Maya Sangesland, Irit Gat-Viks, Paul Digard, Shobha Vasudevan, Daniel Lingwood, David H Dockrell, John G Doench, J Kenneth Baillie, Nir Hacohen.: Genome-wide CRISPR screen identifies host dependency factors for influenza A virus infection. Nature communications 2020, 11, 1-18.

Yael Steuerman, Asaf Wasserman, David Zeltser, Itzhak Shapira, Daniel Trotzky, Pinchas Halpern, Ahuva Meilik, Eli Raykhshtat, Shlomo Berliner, Ori Rogowski, Irit Gat-Viks, Shani Shenhar-Tsarfaty.: Anemia measurements to distinguish between viral and bacterial infections in the emergency department. European Journal of Clinical Microbiology & Infectious Diseases 2019, 38 (12), 2331-2339.

Harel, T., Peshes-Yaloz, N., Bacharach, E., Gat-Viks I.: Predicting Phenotypic Diversity from Molecular and Genetic Data. Genetics 2019, 213, 297–311.

Frishberg, A., Peshes-Yaloz, N., Cohn, O., Rosentul, D., Steuerman, Y., Valadarsky, L., Yankovitz, G., Mandelboim, M., Iraqi, F.A., Amit, I., Mayo, L., Bacharach, E., Gat-Viks I.: Cell composition analysis of bulk genomics using single-cell data. Nature Methods 2019, 16, 327-332.

Botzman M, Gat-Viks I: Significant common environmental effects on leukocyte subpopulations. PLOS ONE 2018, 13 4 e0196193

Steuerman Y, Cohen M, Peshes-Yaloz N, Valadarsky L, Cohn O, David E, Frishberg A, Mayo L, Bacharach E, Amit I, Gat-Viks I: Dissection of Influenza Infection In Vivo by Single-Cell RNA Sequencing. Cell Syst. 2018, S2405-4712(18)30196-0.

Botzman M, Gat-Viks I: Significant common environmental effects on leukocyte subpopulations. PLOS ONE 2018, 13 4 e0196193

A. Nashef, R. Qabaja, Y. Salaymeh, M. Botzman, M. Munz, , H. Dommisch, B. Krone, P. Hoffmann, , J. Wellmann, M. Laudes, K. Berger, T. Kocher, B. Loos, N. van der Velde, , A.G. Uitterlinden, L.C.P.G.M. de Groot, A. Franke, S. Offenbacher, W. Lieb, K. Divaris, , R. Mott, I. Gat-Viks, E. Wiess, A. Schaefer, F.A. Iraqi, Y.H. Haddad: Integration of Murine and Human Studies for Mapping Periodontitis Susceptibility. Journal of Dental Research 2018.

Wilentzik R, C. J. Ye and Gat-Viks I: Reconstructing the Molecular Function of Genetic Variation in Regulatory Networks. GENETICS 2017, 207 4 1699-1709.

Talmi-Frank D, Altboum Z, Solomonov I, Udi Y, Adhemar Jaitin D, Klepfish M, David E, Zhuravlev A, Keren-Shaul H, R. Winter D, Gat-Viks I, Mandelboim M, Ziv T, Amit I, Sagi I: Extracellular Matrix Proteolysis by MT1-MMP Contributes to Influenza-Related Tissue Damage and Mortality. Cell Host & Microbe 2016, 20 , Issue 4, Pages 458-470

Nachshon A, Abu-Toamih Atamni HJ, Steuerman Y, Sheikh-Hamed R, Dorman A, Mott R, Dohm JC, Lehrach H, Sultan M, Shamir R, Sauer S, Himmelbauer H, Iraqi FA, Gat-Viks I: Dissecting the Effect of Genetic Variation on the Hepatic Expression of Drug Disposition Genes across the Collaborative Cross Mouse Strains. Front Genet. 2016, 7:172 eCollection 2016.

J. Abu-Toamih Atamni H, Botzman M, Mott R, Gat-Viks I, A. Iraqi F: Mapping liver fat female-dependent quantitative trait loci in collaborative cross mice.Mammalian Genome. 2016, 27 Issue 11–12, pp 565–573.

Frishberg A, Brodt A, Steuerman Y, Gat-Viks I: ImmQuant: a user-friendly tool for inferring immune cell-type composition from gene-expression data. Bioinformatics 2016, 32(24):3842-3843 – http://csgi.tau.ac.il/ImmQuant/.

Steuerman Y, Gat-Viks I: Exploiting Gene-Expression Deconvolution to Probe the Genetics of the Immune System. PLoS Comput Biol 2016, 12(4): e1004856.

Botzman M, Nachshon A, Brodt A and Gat-Viks I: POEM: Identifying Joint Additive Effects on Regulatory Circuits. Front. Genet. 2016, 7:48.

Frishberg A, Steuerman Y, Gat-Viks I: CoD: Inferring Immune-Cell Quantities Related to Disease States. Bioinformatics 2015, 31(24):3961-3919 –  http://csgi.tau.ac.il/CoD/.

Gat-Viks I, Geiger T, Barbi M, Raini G, Elroy-Stein O: Proteomics-level analysis of myelin formation and regeneration in a mouse model for Vanishing White Matter disease. J Neurochem 2015, 134(3):513-26.

Edri R, Yaffe Y, Ziller MJ, Mutukula N, Volkman R, David E, Jacob-Hirsch J, Malcov H, Levy C, Rechavi G, Gat-Viks I, Meissner A, Elkabetz Y: Analysing human neural stem cell ontogeny by consecutive isolation of Notch active neural progenitors. Nat Commun 2015, 6:6500.

Oren Y, Nachshon A, Frishberg A, Wilentzik R, Gat-Viks I: Linking traits based on their shared molecular mechanisms. Elife 2015, 4:e04346 – http://csgi.tau.ac.il/gemot/.

Wilentzik R, Gat-Viks I: A statistical framework for revealing signaling pathways perturbed by DNA variants. Nucleic Acids Res. 2015, 43(11):e74.

Brodt A, Botzman M, David E, Gat-Viks I: Dissecting dynamic genetic variation that controls temporal gene response in yeast. PLoS Comput Biol. 2014, 10(12):e1003984 – http://csgi.tau.ac.il/dyver/.

Altboum Z, Steuerman Y, David E, Barnett-Itzhaki Z, Valadarsky L, Keren-Shaul H, Meningher T, Mendelson E, Mandelboim M, Gat-Viks I, Amit I: Digital cell quantification identifies global immune cell dynamics during influenza infection. Molecular Systems Biology 2014, 10(2):720 – http://www.dcq.tau.ac.il.

Mazza A, Gat-Viks I, Farhan H, Sharan R: A minimum-labeling approach for reconstructing protein networks across multiple conditions. Algorithms for Molecular Biology 2014, 9(1):1.

Mazza A, Gat-Viks I, Sharan R: Elucidating influenza inhibition pathways via network reconstruction. Journal of Computational Biology 2014, doi:10.1089/cmb.2013.0147.

Irit Gat-Viks, Nicolas Chevrier, Roni Wilentzik, Thomas Eisenhaure, Raktima Raychowdhury, Yael Steuerman, Alex K Shalek, Nir Hacohen, Ido Amit & Aviv Regev: Deciphering molecular circuits from genetic variation underlying transcriptional responsiveness to stimuli. Nature Biotechnology 2013, 31(4): 342–349.

Kirby A, Gnirke A, Jaffe DB, Baresova V, Pochet N, Blumenstiel B, Ye C, Aird D, Stevens C, Robinson JT, Cabili MN, Gat-Viks I et al: Mutations causing medullary cystic kidney disease type 1 lie in a large VNTR in MUC1 missed by massively parallel sequencing. Nature Genetics 2013, 45(3):299-303.

Granit RZ, Gabai Y, Hadar T, Karamansha Y, Liberman L, Waldhorn I, Gat-Viks I, Regev A, Maly B, Darash-Yahana M, Peretz T, Ben-Porath I: EZH2 promotes a bi-lineage identity in basal-like breast cancer cells. Oncogene 2012, 32(33):3886-95.

Chevrier N, Mertins P, Artyomov MN, Shalek AK, Iannacone M, Ciaccio MF, Gat-Viks I, Tonti E, DeGrace MM, Clauser KR et al: Systematic discovery of TLR signaling components delineates viral-sensing circuits. Cell 2011, 147(4):853-67.

Szczurek E, Markowetz F, Gat-Viks I, Biecek P, Tiuryn J, Vingron M: Deregulation upon DNA damage revealed by joint analysis of context-specific perturbation data. BMC bioinformatics 2011, 12:249.

Ziv-Ukelson M, Gat-Viks I, Wexler Y, Shamir R: A faster algorithm for simultaneous alignment and folding of RNA. Journal of computational biology : a journal of computational molecular cell biology 2010, 17(8):1051-1065.

Gat-Viks I, Meller R, Kupiec M, Shamir R: Understanding gene sequence variation in the context of transcription regulation in yeast. PLoS genetics 2010, 6(1):e1000800. [software]

Shapira SD, Gat-Viks I, Shum BO, Dricot A, de Grace MM, Wu L, Gupta PB, Hao T, Silver SJ, Root DE et al: A physical and regulatory map of host-influenza interactions reveals pathways in H1N1 infection. Cell 2009, 139(7):1255-1267.

Bass AJ, Watanabe H, Mermel CH, Yu S, Perner S, Verhaak RG, Kim SY, Wardwell L, Tamayo P, Gat-Viks I et al: SOX2 is an amplified lineage-survival oncogene in lung and esophageal squamous cell carcinomas. Nature genetics 2009, 41(11):1238-1242.

Szczurek E, Gat-Viks I, Tiuryn J, Vingron M: Elucidating regulatory mechanisms downstream of a signaling pathway using informative experiments. Molecular systems biology 2009, 5:287. [software]

Gat-Viks I, Vingron M: Evidence for gene-specific rather than transcription rate-dependent histone H3 exchange in yeast coding regions. PLoS computational biology 2009, 5(2):e1000282.

Ulitsky I, Gat-Viks I, Shamir R: MetaReg: a platform for modeling, analysis and visualization of biological systems using large-scale experimental data. Genome biology 2008, 9(1):R1. [software]

Gat-Viks I, Shamir R: Refinement and expansion of signaling pathways: the osmotic response network in yeast. Genome research 2007, 17(3):358-367.

Gat-Viks I, Tanay A, Raijman D, Shamir R: A probabilistic methodology for integrating knowledge and experiments on biological networks. Journal of computational biology : a journal of computational molecular cell biology 2006, 13(2):165-181.

Gat-Viks I, Tanay A, Shamir R: Modeling and analysis of heterogeneous regulation in biological networks. Journal of computational biology : a journal of computational molecular cell biology 2004, 11(6):1034-1049.

Tanay A, Gat-Viks I, Shamir R: A global view of the selection forces in the evolution of yeast cis-regulation. Genome research 2004, 14(5):829-834.

Gat-Viks I, Shamir R, Karp RM, Sharan R: Reconstructing chain functions in genetic networks. Pacific Symposium on Biocomputing Pacific Symposium on Biocomputing 2004:498-509.

Gat-Viks I, Sharan R, Shamir R: Scoring clustering solutions by their biological relevance. Bioinformatics 2003, 19(18):2381-2389.

Gat-Viks I, Shamir R: Chain functions and scoring functions in genetic networks. Bioinformatics 2003, 19 Suppl 1:i108-117.