{"id":26,"date":"2012-12-04T14:21:41","date_gmt":"2012-12-04T12:21:41","guid":{"rendered":"http:\/\/www.eng.biu.ac.il\/kaliskt\/?page_id=26"},"modified":"2019-09-23T23:32:38","modified_gmt":"2019-09-23T20:32:38","slug":"publications","status":"publish","type":"page","link":"https:\/\/www.eng.biu.ac.il\/kaliskt\/publications\/","title":{"rendered":"Publications"},"content":{"rendered":"

Ling T, Birger Y, Stankiewicz MJ, Ben-Haim N, Kalisky T<\/span>, Rein A, Kugler E, Chen W, Fu C, Zhang K, Patel H, Sikora JW, Goo YA, Kelleher N, Zou L, Izraeli S, Crispino JD.,\u00a0\"Chromatin occupancy and epigenetic analysis reveal new insights into the function of GATA1 N-terminus in erythropoiesis.\", Blood. 2019 Aug 13. pii: blood.2019001234. doi: 10.1182\/blood.2019001234.<\/p>\n

Munro DAD, Wineberg Y, Tarnick J, Vink CS, Li Z, Pridans C, Dzierzak E,\u00a0Kalisky T<\/span>, Hohenstein P, and Davies JA.,\u00a0 \"Macrophages restrict the nephrogenic field and promote endothelial connections during kidney development.\",\u00a0Elife. 2019 Feb 13;8. pii: e43271. doi: 10.7554\/eLife.43271.<\/p>\n

Itamar Kanter, Piero Dalerba, and Tomer Kalisky<\/u>, \u201cA cluster robustness score for identifying cell subpopulations in single cell gene expression datasets from heterogeneous tissues and tumors\u201d, Bioinformatics<\/span>. 2019 Mar 15;35(6):962-971. doi: 10.1093\/bioinformatics\/bty708.<\/p>\n

Ariel Trink, Itamar Kanter, Naomi Pode-Shakked, Achia Urbach, Benjamin Dekel*, and Tomer Kalisky<\/u>*, \u201cGeometry of gene expression space of Wilms' tumors from human patients\u201d (*Co-senior authorship), Neoplasia. 2018 Aug;20(8):871-881. doi: 10.1016\/j.neo.2018.06.006<\/p>\n

Hana Golan, Rachel Shukrun, Revital Caspi, Einav Vax, Naomi Pode-Shakked, Sanja Goldberg, Oren Pleniceanu, Dekel D. Bar-Lev, Michal Mark Danieli, Sara Pri-Chen, Jasmine Jacob-Hirsch, Itamar Kanter, Ariel Trink, Ginette Schiby, Ron Bilik, Tomer Kalisky<\/u>, Orit Harari-Steinberg, Amos Toren, and Benjamin Dekel, \u201cA Platform to Discover Therapeutic Cancer Stem Cell Antigens Using Patient Derived Xenografts: Malignant Rhabdoid Tumor as an Example\u201d. Stem Cell Reports. 2018 Aug 13. pii: S2213-6711(18)30315-1. doi: 10.1016\/j.stemcr.2018.07.010<\/p>\n

Shaheen Sikandar, Angera Kuo, Tomer Kalisky<\/u>, Shang Cai, Maider Zabala, Robert Hsieh, Ferenc Scheeren, Neethan Lobo, Sopheak Sim, Dalong Qian, Frederick Dirbas, George Somlo, Stephen Quake, and Michael Clarke, \"Role of epithelial to mesenchymal transition associated genes in mammary gland regeneration and breast tumorigenesis\", Nature Communications. 2017 Nov 21; 8(1):1669. doi: 10.1038\/s41467-017-01666-2.<\/p>\n

Kalisky T<\/span>*, Oriel S, Bar-Lev TH, Ben-Haim N, Trink A, Wineberg Y, Kanter I, Gilad S, and Pyne S*, \"A brief review of single-cell transcriptomic technologies\". Brief. Funct. Genomics 2017; 1\u201313, doi:\u00a010.1093\/bfgp\/elx019\u00a0(*Co-senior authorship)\u00a0pdf<\/a><\/p>\n

Pode-Shakked N, Gershon R, Tam G, Omer D, Gnatek Y, Kanter I, Oriel S, Katz G, Harari-Steinberg O, Kalisky T*<\/span>, and Dekel B*, \"Evidence of In\u00a0Vitro Preservation of Human Nephrogenesis at the Single-Cell Level\",\u00a0Stem Cell Reports<\/span>. 2017 May 25. pii: S2213-6711(17)30180-7. doi: 10.1016\/j.stemcr.2017.04.026. (*Co-senior author) \u00a0pdf<\/a><\/p>\n

Chen Zhao, Shang Cai, Kunyoo Shin, Agnes Lim, Tomer Kalisky<\/span>, Wan-Jin Lu, Michael F. Clarke, Philip A. Beachy, \u201cStromal Gli2 activity coordinates a niche signaling program for mammary epithelial stem cells\u201d, Science. 2017 Mar 9. pii: eaal3485. doi: 10.1126\/science.aal3485. pdf<\/a>, supplementary_info<\/a><\/p>\n

Pleniceanu O, Shukrun R, Omer D, Vax E, Kanter I, Dziedzic K, Pode-Shaked N, Mark-Daniei M, Pri-Chen S, Gnatek Y, Alfandary H, Varda-Bloom N, Bar-Lev D, Bollag N, Shtainfeld R, Armon L, Urbach A, Kalisky T<\/span>, Nagler A, Harari-Steinberg O, Arbiser JL, and Dekel B: \u201cPPARG is central to the initiation and propagation of human angiomyolipoma, suggesting its potential as a therapeutic target\u201d. EMBO Mol Med. 2017 Mar 8. pii: e201506111. doi: 10.15252\/emmm.201506111. pdf<\/a>, supplementary_info<\/a>, Haaretz_story<\/a><\/p>\n

Shang Cai, Tomer Kalisky<\/span>, Debashis Sahoo, Piero Dalerba, Weiguo Feng, Yuan Lin, Dalong Qian, Angela Kong, Jeffrey Yu, Flora Wang, Elizabeth Y. Chen, Ferenc A.Scheeren, Angera H. Kuo, Shaheen S. Sikandar, Shigeo Hisamori, Linda J. van Weele, Diane Heiser, Sopheak Sim, Jessica Lam, Stephen Quake, and Michael F. Clarke, \u201cA Quiescent Bcl11b High Stem Cell Population is Required for Mammary Gland Regeneration\u201d, Cell Stem Cell, 2016 Dec 19. pii: S1934-5909(16)30403-9. doi: 10.1016\/j.stem.2016.11.007. pdf<\/a><\/p>\n

Pode-Shakked N, Pleniceanu O, Gershon R, Shukrun R, Kanter I, Bucris E, Pode-Shakked B, Tam G, Tam H, Caspi R, Pri-Chen S, Vax E, Katz G, Omer D, Harari-Steinberg O, Kalisky T<\/span>, Dekel B., \"Dissecting Stages of Human Kidney Development and Tumorigenesis with Surface Markers Affords Simple Prospective Purification of Nephron Stem Cells\",\u00a0Sci Rep<\/span>. 2016 Mar 29;6:23562. doi: 10.1038\/srep23562. pdf<\/a>, supplementary_info<\/a><\/p>\n

Piero Dalerba., Debashis Sahoo, Soonmyung Paik, Xiangqian Guo, Greg Yothers, Nan Song, \u00a0Nate Wilcox-Fogel, Erna Forg\u00f3, Pradeep S. Rajendran, Stephen P. Miranda, Shigeo Hisamori, Jacqueline Hutchison, Tomer Kalisky<\/span>, Dalong Qian, Norman Wolmark, George A. Fisher, Matt van de Rijn, and Michael F. Clarke, \"CDX2 as a Prognostic Biomarker in Stage II and Stage III Colon Cancer\", N. Engl. J. Med. 374, 211\u2013222 (2016).\u00a0editorial<\/a>, pdf<\/a>, supplementary_info<\/a><\/p>\n

Yael Korem, Pablo Szekely, Yuval Hart, Hila Sheftel, Jean Hausser, Avi Mayo, Michael E Rothenberg, Tomer Kalisky<\/u>, Uri Alon, \u201cGeometry of the Gene Expression Space of Individual Cells\u201d, PLoS Comput Biol. 2015 Jul 10;11(7):e1004224. doi: 10.1371\/journal.pcbi.1004224.\u00a0pdf<\/a><\/p>\n

Chen EC, Karl TA, Kalisky T<\/u>, Gupta SK, O'Brien CA, Longacre TA, van de Rijn M, Quake SR, Clarke MF, Rothenberg ME, \u201cKIT Signaling Promotes Growth of Colon Xenograft Tumors in Mice and is Upregulated in a Subset of Human Colon Cancers\u201d, 2015 May 27. doi: 10.1053\/j.gastro.2015.05.042. pdf<\/a><\/p>\n

Kanter I and Kalisky T<\/u>, \u201cSingle cell transcriptomics: methods and applications\u201d. Front. Oncol. 2015 Mar 10;5:53. doi: 10.3389\/fonc.2015.00053. Review. pdf<\/a><\/p>\n

Scheeren FA, Kuo AH, van Weele LJ, Cai S, Glykofridis I, Sikandar SS, Zabala M, Qian D, Lam JS, Johnston D, Volkmer JP, Sahoo D, van de Rijn M, Dirbas FM, Somlo G, Kalisky T<\/span>, Rothenberg ME, Quake SR, Clarke MF, \u201cA cell-intrinsic role for TLR2-MYD88 in intestinal and breast epithelia and oncogenesis\u201d, Nat Cell Biol. 2014 Nov 2. doi: 10.1038\/ncb3058. pdf<\/a>,\u00a0supplementary_info<\/a><\/span><\/p>\n

Lawlor PN, Kalisky T<\/span>, Rosner R, Rosner MR, Kording KP, \"Conceptualizing cancer drugs as classifiers<\/a>\",\u00a0PLoS One<\/span>. 2014 Sep 23;9(9):e106444.\u00a0pdf<\/a><\/span><\/p>\n

Wu AR, Neff NF,\u00a0Kalisky T<\/span>, Dalerba P, Treutlein B, Rothenberg ME, Mburu FM, Mantalas GL, Sim S, Clarke MF, Quake SR, \"Quantitative assessment of single-cell RNA-sequencing methods\", Nat Methods. 2013 Oct 20; doi: 10.1038\/nmeth.2694. [Epub ahead of print].pdf<\/a>,\u00a0supplementary_info<\/a><\/span><\/p>\n

Sen A, Rothenberg ME, Mukherjee G, Feng N, Kalisky T<\/span>, Nair N, Johnstone IM, Clarke MF, Greenberg HB, \"Innate immune response to homologous rotavirus infection in the small intestinal villous epithelium at single-cell resolution\", Proc Natl Acad Sci U S A. 2012 Nov 27. pdf<\/a><\/p>\n

Veronica Sanchez-Freire, Antje D. Ebert, Tomer Kalisky<\/span>, Stephen R. Quake, Joseph C. Wu, \u201cMicrofluidic single cell real-time PCR for comparative analysis of gene expression patterns\u201d, Nature Protocols 2012;7(5):829-38. pdf<\/a><\/p>\n

Rothenberg ME, Nusse Y, Kalisky T<\/span>, Lee JJ, Dalerba P, Scheeren F, Lobo N, Kulkarni S, Sim S, Qian D, Beachy PA, Pasricha PJ, Quake SR, and Clarke MF, \u201cIdentification of a cKit(+) Colonic Crypt Base Secretory Cell That Supports Lgr5(+) Stem Cells in Mice\u201d, Gastroenterology 2012;142(5):1195-1205. pdf<\/a>\u00a0
\n<\/a><\/p>\n

Dalerba P*, Kalisky T<\/span>*, Sahoo D*, Rajendran PS, Rothenberg ME, Leyrat AA, Sim S, Okamoto J, Johnston DM, Qian D, Zabala M, Bueno J, Neff NF, Wang J, Shelton AA, Visser B, Hisamori S, Shimono Y, van de Wetering M, Clevers H, Clarke MF, Quake SR. \u201cSingle-cell dissection of transcriptional heterogeneity in human colon tumors\u201d, Nature Biotechnology 2011; 29(12):1120-7 (*Equal contribution) pdf<\/a>\u00a0,\u00a0supplementary_info<\/a>
\n<\/a><\/p>\n

T. Kalisky<\/span>, P. Blainey, and S.R. Quake, \u201cGenomic Analysis at the Single Cell Level\u201d, Annual Review of Genetics, Vol. 45 (2011) pdf<\/a><\/p>\n

T. Kalisky<\/span> and S.R. Quake, \u201cSingle-Cell Genomics\u201d, Nat Methods. 2011 Apr;8(4):311-4. pdf<\/a><\/p>\n

Jason P. Glotzbach, Michael Januszyk, Ivan N. Vial, Victor W. Wong, Alexander Gelbard, Tomer Kalisky<\/span>, Hariharan Thangarajah, Michael T. Longaker, Stephen R. Quake, Gilbert Chu, Geoffrey C. Gurtner, \u201cAn Information Theoretic, Microfluidic-Based Single Cell Analysis Permits Identification of Subpopulations among Putatively Homogeneous Stem Cells\u201d, PLoS ONE 2011, 6(6): e21211. pdf<\/a><\/p>\n

Diehn M, Cho RW, Lobo NA, Kalisky T<\/span>, Dorie MJ, Kulp AN, Qian D, Lam JS, Ailles LE, Wong M, Joshua B, Kaplan MJ, Wapnir I, Dirbas F, Somlo G, Garberoglio C, Paz B, Shen J, Lau SK, Quake SR, Brown JM, Weissman IL, Clarke MF, \u201cAssociation of reactive oxygen species levels and radioresistance in cancer stem cells\u201d, Nature 2009; 458 (7239), pp. 780-783. pdf<\/a>,\u00a0supplementary_figures<\/a>, supplementary_methods<\/a><\/p>\n

Kashtan N, Mayo AE, Kalisky T<\/span>, Alon U, \"An Analytically Solvable Model for Rapid Evolution of Modular Structure\", PLoS Computational Biology 2009; 5(4): e1000355. pdf<\/a><\/p>\n

Cohen AA*, Kalisky T<\/span>*, Mayo A*, Geva-Zatorsky N, Danon T, Issaeva I, Kopito RB, Perzov N, Milo R, Sigal A, Alon U, \"Protein Dynamics in Individual Human Cells: Experiment and Theory\", PLoS One. 2009; 4(4): e4901. (*Equal contribution) pdf<\/a><\/p>\n

Y. E. Maruvka, T. Kalisky<\/span>, and N. Shnerb, \"Nonlocal competition and the speciation transition on random networks\", Physical Review E 78, 031920 (2008). Also selected for the October 1, 2008 issue of Virtual Journal of Biological Physics Research. pdf<\/a><\/p>\n

T. Kalisky<\/span>, E. Dekel, and U. Alon, \"Cost\u2013benefit theory and optimal design of gene regulation functions\", Physical Biology 4, 229-245 (2007). Also selected for \u201cPhysical Biology, Highlights of 2007\u201d. pdf<\/a><\/p>\n

T. Kalisky<\/span>, R. Cohen, O. Mokryn, D. Dolev, Y. Shavitt, and S. Havlin \"Tomography of scale-free networks and shortest-path trees\", Phys. Rev. E 74, 066108 (2006). pdf<\/a><\/p>\n

T. Kalisky<\/span> and R. Cohen, \u201cWidth of percolation transition in complex networks\u201d, Phys. Rev. E (RC) 73, 035101 (2006). pdf<\/a><\/p>\n

T. Kalisky<\/span>, S. Sreenivasan, L. A. Braunstein, S. V. Buldyrev, S. Havlin and H. E. Stanley, \u201cScale-free networks emerging from weighted random graphs\u201d, Phys. Rev. E (RC) 73, 025103 (2006) pdf<\/a><\/p>\n

M. Sade, T. Kalisky<\/span>, S. Havlin and R. Berkovits, \u201cStudy of localization transition on complex networks via spectral statistics\u201d, Phys. Rev. E 72, 066123 (2005). pdf<\/a><\/p>\n

T. Kalisky<\/span>, L. A. Braunstein, S. V. Buldyrev, S. Havlin and H. E. Stanley, \u201cScaling of optimal-path-lengths distribution in complex networks\u201d, Phys. Rev. E (RC) 72, R025102 (2005). pdf<\/a><\/p>\n

T. Kalisky<\/span>, Y. Ashkenazy and S. Havlin, \u201cVolatility of Linear and Nonlinear Time Series\u201d, Phys. Rev. E 72, 011913 (2005). Also selected for publication in the virtual journal for biological physics research (August 2005). pdf<\/a><\/p>\n

S. Sreenivasan, T. Kalisky<\/span>, L. A. Braunstein, S. V. Buldyrev, S. Havlin and H. E. Stanley, \u201cEffect of disorder strength on optimal paths in complex networks\u201d, Phys. Rev. E 70, 046133 (2004). pdf<\/a><\/p>\n

I. Dana and T. Kalisky<\/span>, \u201cSymbolic dynamics for strong chaos on stochastic webs: General quasisymmetry\u201d, Phys. Rev. E (RC) 53, R2025\u2013R2028 (1996). pdf<\/a><\/p>\n

Patents:<\/strong><\/span><\/p>\n

Michael F. Clarke, Stephen R. Quake, Piero D. Dalerba, Huiping Liu, Anne Leyrat, Tomer Kalisky<\/u>, and Maximilian Diehn, Patent Application #US-20100255471 - \"Single cell gene expression for diagnosis, prognosis and identification of drug targets\".<\/p>\n

Michael F. Clarke, Stephen R. Quake, Piero D. Dalerba, Huiping Liu, Anne A. Leyrat, Tomer Kalisky<\/u>, Maximilian Diehn, Michael Rothenberg, Jianbin Wang, and Neethan Lobo, Patent Application #US-20130225435 - \"Methods and systems for analysis of single cells\".<\/p>\n","protected":false},"excerpt":{"rendered":"

Ling T, Birger Y, Stankiewicz MJ, Ben-Haim N, Kalisky T, Rein A, Kugler E, Chen W, Fu C, Zhang K, Patel H, Sikora JW, Goo YA, Kelleher N, Zou L, Izraeli S, Crispino JD.,\u00a0“Chromatin occupancy and epigenetic analysis reveal new insights into the function of GATA1 N-terminus in erythropoiesis.”, Blood. 2019 Aug 13. pii: blood.2019001234. … Continue reading Publications<\/span> →<\/span><\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"open","template":"","meta":{"footnotes":""},"class_list":["post-26","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/www.eng.biu.ac.il\/kaliskt\/wp-json\/wp\/v2\/pages\/26"}],"collection":[{"href":"https:\/\/www.eng.biu.ac.il\/kaliskt\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.eng.biu.ac.il\/kaliskt\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.eng.biu.ac.il\/kaliskt\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.eng.biu.ac.il\/kaliskt\/wp-json\/wp\/v2\/comments?post=26"}],"version-history":[{"count":90,"href":"https:\/\/www.eng.biu.ac.il\/kaliskt\/wp-json\/wp\/v2\/pages\/26\/revisions"}],"predecessor-version":[{"id":647,"href":"https:\/\/www.eng.biu.ac.il\/kaliskt\/wp-json\/wp\/v2\/pages\/26\/revisions\/647"}],"wp:attachment":[{"href":"https:\/\/www.eng.biu.ac.il\/kaliskt\/wp-json\/wp\/v2\/media?parent=26"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}