Tom Kalisky

Title(s)RSCH AND DEV ENGR 1 , Qualcomm Institute
SchoolVc-academic Affairs
Address9500 Gilman Drive #
La Jolla CA 92093
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. LEFTY1 Is a Dual-SMAD Inhibitor that Promotes Mammary Progenitor Growth and Tumorigenesis. Cell Stem Cell. 2020 Aug 06; 27(2):284-299.e8. Zabala M, Lobo NA, Antony J, Heitink LS, Gulati GS, Lam J, Parashurama N, Sanchez K, Adorno M, Sikandar SS, Kuo AH, Qian D, Kalisky T, Sim S, Li L, Dirbas FM, Somlo G, Newman A, Quake SR, Clarke MF. PMID: 32693087.
      View in: PubMed   Mentions:    Fields:    
    2. Single-Cell RNA Sequencing Reveals mRNA Splice Isoform Switching during Kidney Development. J Am Soc Nephrol. 2020 Oct; 31(10):2278-2291. Wineberg Y, Bar-Lev TH, Futorian A, Ben-Haim N, Armon L, Ickowicz D, Oriel S, Bucris E, Yehuda Y, Pode-Shakked N, Gilad S, Benjamin S, Hohenstein P, Dekel B, Urbach A, Kalisky T. PMID: 32651222.
      View in: PubMed   Mentions:    Fields:    
    3. Ex Vivo Expanded 3D Human Kidney Spheres Engraft Long Term and Repair Chronic Renal Injury in Mice. Cell Rep. 2020 01 21; 30(3):852-869.e4. Harari-Steinberg O, Omer D, Gnatek Y, Pleniceanu O, Goldberg S, Cohen-Zontag O, Pri-Chen S, Kanter I, Ben Haim N, Becker E, Ankawa R, Fuchs Y, Kalisky T, Dotan Z, Dekel B. PMID: 31968258.
      View in: PubMed   Mentions: 1     Fields:    
    4. Chromatin occupancy and epigenetic analysis reveal new insights into the function of the GATA1 N terminus in erythropoiesis. Blood. 2019 11 07; 134(19):1619-1631. 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. PMID: 31409672.
      View in: PubMed   Mentions: 3     Fields:    Translation:AnimalsCells
    5. Biometric recognition of newborns and infants by non-contact fingerprinting: lessons learned. Gates Open Res. 2019; 3:1477. Saggese S, Zhao Y, Kalisky T, Avery C, Forster D, Edith Duarte-Vera L, Almada-Salazar LA, Perales-Gonzalez D, Hubenko A, Kleeman M, Chacon-Cruz E, Aronoff-Spencer E. PMID: 31410396.
      View in: PubMed   Mentions:
    6. A cluster robustness score for identifying cell subpopulations in single cell gene expression datasets from heterogeneous tissues and tumors. Bioinformatics. 2019 03 15; 35(6):962-971. Kanter I, Dalerba P, Kalisky T. PMID: 30165506.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    7. Macrophages restrict the nephrogenic field and promote endothelial connections during kidney development. Elife. 2019 02 13; 8. Munro DAD, Wineberg Y, Tarnick J, Vink CS, Li Z, Pridans C, Dzierzak E, Kalisky T, Hohenstein P, Davies JA. PMID: 30758286.
      View in: PubMed   Mentions: 5     Fields:    Translation:AnimalsCells
    8. In Vivo Expansion of Cancer Stemness Affords Novel Cancer Stem Cell Targets: Malignant Rhabdoid Tumor as an Example. Stem Cell Reports. 2018 09 11; 11(3):795-810. Golan H, Shukrun R, Caspi R, Vax E, Pode-Shakked N, Goldberg S, Pleniceanu O, Bar-Lev DD, Mark-Danieli M, Pri-Chen S, Jacob-Hirsch J, Kanter I, Trink A, Schiby G, Bilik R, Kalisky T, Harari-Steinberg O, Toren A, Dekel B. PMID: 30122444.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansAnimalsCells
    9. Geometry of Gene Expression Space of Wilms' Tumors From Human Patients. Neoplasia. 2018 08; 20(8):871-881. Trink A, Kanter I, Pode-Shakked N, Urbach A, Dekel B, Kalisky T. PMID: 30029183.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    10. A brief review of single-cell transcriptomic technologies. Brief Funct Genomics. 2018 01 01; 17(1):64-76. Kalisky T, Oriel S, Bar-Lev TH, Ben-Haim N, Trink A, Wineberg Y, Kanter I, Gilad S, Pyne S. PMID: 28968725.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansCells
    11. Peroxisome proliferator-activated receptor gamma (PPAR?) is central to the initiation and propagation of human angiomyolipoma, suggesting its potential as a therapeutic target. EMBO Mol Med. 2017 12; 9(12):1763. Pleniceanu O, Shukrun R, Omer D, Vax E, Kanter I, Dziedzic K, Pode-Shakked N, Mark-Daniei M, Pri-Chen S, Gnatek Y, Alfandary H, Varda-Bloom N, Bar-Lev DD, Bollag N, Shtainfeld R, Armon L, Urbach A, Kalisky T, Nagler A, Harari-Steinberg O, Arbiser JL, Dekel B. PMID: 29196313.
      View in: PubMed   Mentions: 1     Fields:    
    12. Role of epithelial to mesenchymal transition associated genes in mammary gland regeneration and breast tumorigenesis. Nat Commun. 2017 11 21; 8(1):1669. Sikandar SS, Kuo AH, Kalisky T, Cai S, Zabala M, Hsieh RW, Lobo NA, Scheeren FA, Sim S, Qian D, Dirbas FM, Somlo G, Quake SR, Clarke MF. PMID: 29162812.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansAnimalsCells
    13. Evidence of In Vitro Preservation of Human Nephrogenesis at the Single-Cell Level. Stem Cell Reports. 2017 07 11; 9(1):279-291. Pode-Shakked N, Gershon R, Tam G, Omer D, Gnatek Y, Kanter I, Oriel S, Katz G, Harari-Steinberg O, Kalisky T, Dekel B. PMID: 28552604.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansCells
    14. Peroxisome proliferator-activated receptor gamma (PPAR?) is central to the initiation and propagation of human angiomyolipoma, suggesting its potential as a therapeutic target EMBO Mol Med. 2017 04; 9(4):508-530. Pleniceanu O, Shukrun R, Omer D, Vax E, Kanter I, Dziedzic K, Pode-Shakked N, Mark-Daniei M, Pri-Chen S, Gnatek Y, Alfandary H, Varda-Bloom N, Bar-Lev DD, Bollag N, Shtainfeld R, Armon L, Urbach A, Kalisky T, Nagler A, Harari-Steinberg O, Arbiser JL, Dekel B. PMID: 28275008.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansAnimalsCells
    15. Stromal Gli2 activity coordinates a niche signaling program for mammary epithelial stem cells. Science. 2017 04 21; 356(6335). Zhao C, Cai S, Shin K, Lim A, Kalisky T, Lu WJ, Clarke MF, Beachy PA. PMID: 28280246.
      View in: PubMed   Mentions: 14     Fields:    Translation:AnimalsCells
    16. A Quiescent Bcl11b High Stem Cell Population Is Required for Maintenance of the Mammary Gland. Cell Stem Cell. 2017 02 02; 20(2):247-260.e5. Cai S, Kalisky T, Sahoo D, Dalerba P, Feng W, Lin Y, Qian D, Kong A, Yu J, Wang F, Chen EY, Scheeren FA, Kuo AH, Sikandar SS, Hisamori S, van Weele LJ, Heiser D, Sim S, Lam J, Quake S, Clarke MF. PMID: 28041896.
      View in: PubMed   Mentions: 15     Fields:    Translation:AnimalsCells
    17. Dissecting Stages of Human Kidney Development and Tumorigenesis with Surface Markers Affords Simple Prospective Purification of Nephron Stem Cells. Sci Rep. 2016 Mar 29; 6:23562. 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, Dekel B. PMID: 27020553.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansAnimalsCells
    18. CDX2 as a Prognostic Biomarker in Stage II and Stage III Colon Cancer. N Engl J Med. 2016 Jan 21; 374(3):211-22. Dalerba P, Sahoo D, Paik S, Guo X, Yothers G, Song N, Wilcox-Fogel N, Forgó E, Rajendran PS, Miranda SP, Hisamori S, Hutchison J, Kalisky T, Qian D, Wolmark N, Fisher GA, van de Rijn M, Clarke MF. PMID: 26789870.
      View in: PubMed   Mentions: 104     Fields:    Translation:Humans
    19. Geometry of the Gene Expression Space of Individual Cells. PLoS Comput Biol. 2015 Jul; 11(7):e1004224. Korem Y, Szekely P, Hart Y, Sheftel H, Hausser J, Mayo A, Rothenberg ME, Kalisky T, Alon U. PMID: 26161936.
      View in: PubMed   Mentions: 15     Fields:    Translation:HumansAnimalsCells
    20. KIT Signaling Promotes Growth of Colon Xenograft Tumors in Mice and Is Up-Regulated in a Subset of Human Colon Cancers. Gastroenterology. 2015 Sep; 149(3):705-17.e2. Chen EC, Karl TA, Kalisky T, Gupta SK, O'Brien CA, Longacre TA, van de Rijn M, Quake SR, Clarke MF, Rothenberg ME. PMID: 26026391.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansAnimalsCells
    21. Single cell transcriptomics: methods and applications. Front Oncol. 2015; 5:53. Kanter I, Kalisky T. PMID: 25806353.
      View in: PubMed   Mentions:
    22. A cell-intrinsic role for TLR2-MYD88 in intestinal and breast epithelia and oncogenesis. Nat Cell Biol. 2014 Dec; 16(12):1238-48. 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, Rothenberg ME, Quake SR, Clarke MF. PMID: 25362351.
      View in: PubMed   Mentions: 36     Fields:    Translation:HumansAnimalsCells
    23. Conceptualizing cancer drugs as classifiers. PLoS One. 2014; 9(9):e106444. Lawlor PN, Kalisky T, Rosner R, Rosner MR, Kording KP. PMID: 25248130.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    24. Quantitative assessment of single-cell RNA-sequencing methods. Nat Methods. 2014 Jan; 11(1):41-6. Wu AR, Neff NF, Kalisky T, Dalerba P, Treutlein B, Rothenberg ME, Mburu FM, Mantalas GL, Sim S, Clarke MF, Quake SR. PMID: 24141493.
      View in: PubMed   Mentions: 227     Fields:    Translation:HumansCells
    25. 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 Dec 11; 109(50):20667-72. Sen A, Rothenberg ME, Mukherjee G, Feng N, Kalisky T, Nair N, Johnstone IM, Clarke MF, Greenberg HB. PMID: 23188796.
      View in: PubMed   Mentions: 30     Fields:    Translation:AnimalsCells
    26. Microfluidic single-cell real-time PCR for comparative analysis of gene expression patterns. Nat Protoc. 2012 Apr 05; 7(5):829-38. Sanchez-Freire V, Ebert AD, Kalisky T, Quake SR, Wu JC. PMID: 22481529.
      View in: PubMed   Mentions: 62     Fields:    Translation:HumansCells
    27. Identification of a cKit(+) colonic crypt base secretory cell that supports Lgr5(+) stem cells in mice. Gastroenterology. 2012 May; 142(5):1195-1205.e6. Rothenberg ME, Nusse Y, Kalisky T, Lee JJ, Dalerba P, Scheeren F, Lobo N, Kulkarni S, Sim S, Qian D, Beachy PA, Pasricha PJ, Quake SR, Clarke MF. PMID: 22333952.
      View in: PubMed   Mentions: 68     Fields:    Translation:AnimalsCells
    28. Single-cell dissection of transcriptional heterogeneity in human colon tumors. Nat Biotechnol. 2011 Nov 13; 29(12):1120-7. Dalerba P, Kalisky T, 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. PMID: 22081019.
      View in: PubMed   Mentions: 251     Fields:    Translation:HumansAnimalsCells
    29. Genomic analysis at the single-cell level. Annu Rev Genet. 2011; 45:431-45. Kalisky T, Blainey P, Quake SR. PMID: 21942365.
      View in: PubMed   Mentions: 60     Fields:    Translation:HumansCells
    30. An information theoretic, microfluidic-based single cell analysis permits identification of subpopulations among putatively homogeneous stem cells. PLoS One. 2011; 6(6):e21211. Glotzbach JP, Januszyk M, Vial IN, Wong VW, Gelbard A, Kalisky T, Thangarajah H, Longaker MT, Quake SR, Chu G, Gurtner GC. PMID: 21731674.
      View in: PubMed   Mentions: 39     Fields:    Translation:AnimalsCells
    31. Single-cell genomics. Nat Methods. 2011 Apr; 8(4):311-4. Kalisky T, Quake SR. PMID: 21451520.
      View in: PubMed   Mentions: 96     Fields:    Translation:AnimalsCells
    32. Protein dynamics in individual human cells: experiment and theory. PLoS One. 2009; 4(4):e4901. Cohen AA, Kalisky T, Mayo A, Geva-Zatorsky N, Danon T, Issaeva I, Kopito RB, Perzov N, Milo R, Sigal A, Alon U. PMID: 19381343.
      View in: PubMed   Mentions: 33     Fields:    Translation:Humans
    33. An analytically solvable model for rapid evolution of modular structure. PLoS Comput Biol. 2009 Apr; 5(4):e1000355. Kashtan N, Mayo AE, Kalisky T, Alon U. PMID: 19360090.
      View in: PubMed   Mentions: 11     Fields:    
    34. Association of reactive oxygen species levels and radioresistance in cancer stem cells. Nature. 2009 Apr 09; 458(7239):780-3. Diehn M, Cho RW, Lobo NA, Kalisky T, Dorie MJ, Kulp AN, Qian D, Lam JS, Ailles LE, Wong M, Joshua B, Kaplan MJ, Wapnir I, Dirbas FM, Somlo G, Garberoglio C, Paz B, Shen J, Lau SK, Quake SR, Brown JM, Weissman IL, Clarke MF. PMID: 19194462.
      View in: PubMed   Mentions: 737     Fields:    Translation:HumansAnimalsCells
    35. Nonlocal competition and the speciation transition on random networks. Phys Rev E Stat Nonlin Soft Matter Phys. 2008 Sep; 78(3 Pt 1):031920. Maruvka YE, Kalisky T, Shnerb NM. PMID: 18851078.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimals
    36. Cost-benefit theory and optimal design of gene regulation functions. Phys Biol. 2007 Nov 07; 4(4):229-45. Kalisky T, Dekel E, Alon U. PMID: 17991990.
      View in: PubMed   Mentions: 27     Fields:    Translation:Cells
    37. Tomography of scale-free networks and shortest path trees. Phys Rev E Stat Nonlin Soft Matter Phys. 2006 Dec; 74(6 Pt 2):066108. Kalisky T, Cohen R, Mokryn O, Dolev D, Shavitt Y, Havlin S. PMID: 17280122.
      View in: PubMed   Mentions:    Fields:    
    38. Width of percolation transition in complex networks. Phys Rev E Stat Nonlin Soft Matter Phys. 2006 Mar; 73(3 Pt 2):035101. Kalisky T, Cohen R. PMID: 16605583.
      View in: PubMed   Mentions: 1     Fields:    
    39. Scale-free networks emerging from weighted random graphs. Phys Rev E Stat Nonlin Soft Matter Phys. 2006 Feb; 73(2 Pt 2):025103. Kalisky T, Sreenivasan S, Braunstein LA, Buldyrev SV, Havlin S, Stanley HE. PMID: 16605380.
      View in: PubMed   Mentions:    Fields:    
    40. Localization transition on complex networks via spectral statistics. Phys Rev E Stat Nonlin Soft Matter Phys. 2005 Dec; 72(6 Pt 2):066123. Sade M, Kalisky T, Havlin S, Berkovits R. PMID: 16486026.
      View in: PubMed   Mentions: 1     Fields:    
    41. Scaling of optimal-path-lengths distribution in complex networks. Phys Rev E Stat Nonlin Soft Matter Phys. 2005 Aug; 72(2 Pt 2):025102. Kalisky T, Braunstein LA, Buldyrev SV, Havlin S, Stanley HE. PMID: 16196625.
      View in: PubMed   Mentions:    Fields:    
    42. Volatility of linear and nonlinear time series. Phys Rev E Stat Nonlin Soft Matter Phys. 2005 Jul; 72(1 Pt 1):011913. Kalisky T, Ashkenazy Y, Havlin S. PMID: 16090007.
      View in: PubMed   Mentions: 3     Fields:    
    43. Effect of disorder strength on optimal paths in complex networks. Phys Rev E Stat Nonlin Soft Matter Phys. 2004 Oct; 70(4 Pt 2):046133. Sreenivasan S, Kalisky T, Braunstein LA, Buldyrev SV, Havlin S, Stanley HE. PMID: 15600486.
      View in: PubMed   Mentions: 2     Fields:    
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