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Items: 41

1.

Biometric identification of newborns and infants by non-contact fingerprinting: lessons learned.

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.

Gates Open Res. 2019 May 29;3:1477. doi: 10.12688/gatesopenres.12914.1. eCollection 2019.

2.

Chromatin occupancy and epigenetic analysis reveal new insights into the function of the GATA1 N terminus in erythropoiesis.

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.

Blood. 2019 Nov 7;134(19):1619-1631. doi: 10.1182/blood.2019001234.

PMID:
31409672
3.

Macrophages restrict the nephrogenic field and promote endothelial connections during kidney development.

Munro DAD, Wineberg Y, Tarnick J, Vink CS, Li Z, Pridans C, Dzierzak E, Kalisky T, Hohenstein P, Davies JA.

Elife. 2019 Feb 13;8. pii: e43271. doi: 10.7554/eLife.43271.

4.

A cluster robustness score for identifying cell subpopulations in single cell gene expression datasets from heterogeneous tissues and tumors.

Kanter I, Dalerba P, Kalisky T.

Bioinformatics. 2019 Mar 15;35(6):962-971. doi: 10.1093/bioinformatics/bty708.

PMID:
30165506
5.

In Vivo Expansion of Cancer Stemness Affords Novel Cancer Stem Cell Targets: Malignant Rhabdoid Tumor as an Example.

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.

Stem Cell Reports. 2018 Sep 11;11(3):795-810. doi: 10.1016/j.stemcr.2018.07.010. Epub 2018 Aug 16.

6.

Geometry of Gene Expression Space of Wilms' Tumors From Human Patients.

Trink A, Kanter I, Pode-Shakked N, Urbach A, Dekel B, Kalisky T.

Neoplasia. 2018 Aug;20(8):871-881. doi: 10.1016/j.neo.2018.06.006. Epub 2018 Jul 18.

7.

Peroxisome proliferator-activated receptor gamma (PPARγ) is central to the initiation and propagation of human angiomyolipoma, suggesting its potential as a therapeutic target.

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.

EMBO Mol Med. 2017 Dec;9(12):1763. doi: 10.15252/emmm.201708507. No abstract available.

8.

Role of epithelial to mesenchymal transition associated genes in mammary gland regeneration and breast tumorigenesis.

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.

Nat Commun. 2017 Nov 21;8(1):1669. doi: 10.1038/s41467-017-01666-2.

9.

A brief review of single-cell transcriptomic technologies.

Kalisky T, Oriel S, Bar-Lev TH, Ben-Haim N, Trink A, Wineberg Y, Kanter I, Gilad S, Pyne S.

Brief Funct Genomics. 2018 Jan 1;17(1):64-76. doi: 10.1093/bfgp/elx019. Review.

PMID:
28968725
10.

Evidence of In Vitro Preservation of Human Nephrogenesis at the Single-Cell Level.

Pode-Shakked N, Gershon R, Tam G, Omer D, Gnatek Y, Kanter I, Oriel S, Katz G, Harari-Steinberg O, Kalisky T, Dekel B.

Stem Cell Reports. 2017 Jul 11;9(1):279-291. doi: 10.1016/j.stemcr.2017.04.026. Epub 2017 May 25.

11.

Stromal Gli2 activity coordinates a niche signaling program for mammary epithelial stem cells.

Zhao C, Cai S, Shin K, Lim A, Kalisky T, Lu WJ, Clarke MF, Beachy PA.

Science. 2017 Apr 21;356(6335). pii: eaal3485. doi: 10.1126/science.aal3485. Epub 2017 Mar 9.

PMID:
28280246
12.

Peroxisome proliferator-activated receptor gamma (PPARγ) is central to the initiation and propagation of human angiomyolipoma, suggesting its potential as a therapeutic target

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.

EMBO Mol Med. 2017 Apr;9(4):508-530. doi: 10.15252/emmm.201506111. Erratum in: EMBO Mol Med. 2017 Dec;9(12 ):1763.

13.

A Quiescent Bcl11b High Stem Cell Population Is Required for Maintenance of the Mammary Gland.

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.

Cell Stem Cell. 2017 Feb 2;20(2):247-260.e5. doi: 10.1016/j.stem.2016.11.007. Epub 2016 Dec 29.

14.

Dissecting Stages of Human Kidney Development and Tumorigenesis with Surface Markers Affords Simple Prospective Purification of Nephron Stem Cells.

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.

Sci Rep. 2016 Mar 29;6:23562. doi: 10.1038/srep23562.

15.

CDX2 as a Prognostic Biomarker in Stage II and Stage III Colon Cancer.

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.

N Engl J Med. 2016 Jan 21;374(3):211-22. doi: 10.1056/NEJMoa1506597.

16.

Geometry of the Gene Expression Space of Individual Cells.

Korem Y, Szekely P, Hart Y, Sheftel H, Hausser J, Mayo A, Rothenberg ME, Kalisky T, Alon U.

PLoS Comput Biol. 2015 Jul 10;11(7):e1004224. doi: 10.1371/journal.pcbi.1004224. eCollection 2015 Jul.

17.

KIT Signaling Promotes Growth of Colon Xenograft Tumors in Mice and Is Up-Regulated in a Subset of Human Colon Cancers.

Chen EC, Karl TA, Kalisky T, Gupta SK, O'Brien CA, Longacre TA, van de Rijn M, Quake SR, Clarke MF, Rothenberg ME.

Gastroenterology. 2015 Sep;149(3):705-17.e2. doi: 10.1053/j.gastro.2015.05.042. Epub 2015 May 28.

18.

Single cell transcriptomics: methods and applications.

Kanter I, Kalisky T.

Front Oncol. 2015 Mar 10;5:53. doi: 10.3389/fonc.2015.00053. eCollection 2015. Review.

19.

A cell-intrinsic role for TLR2-MYD88 in intestinal and breast epithelia and oncogenesis.

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.

Nat Cell Biol. 2014 Dec;16(12):1238-48. doi: 10.1038/ncb3058. Epub 2014 Nov 2.

PMID:
25362351
20.

Conceptualizing cancer drugs as classifiers.

Lawlor PN, Kalisky T, Rosner R, Rosner MR, Kording KP.

PLoS One. 2014 Sep 23;9(9):e106444. doi: 10.1371/journal.pone.0106444. eCollection 2014.

21.

Quantitative assessment of single-cell RNA-sequencing methods.

Wu AR, Neff NF, Kalisky T, Dalerba P, Treutlein B, Rothenberg ME, Mburu FM, Mantalas GL, Sim S, Clarke MF, Quake SR.

Nat Methods. 2014 Jan;11(1):41-6. doi: 10.1038/nmeth.2694. Epub 2013 Oct 20.

22.

Innate immune response to homologous rotavirus infection in the small intestinal villous epithelium at single-cell resolution.

Sen A, Rothenberg ME, Mukherjee G, Feng N, Kalisky T, Nair N, Johnstone IM, Clarke MF, Greenberg HB.

Proc Natl Acad Sci U S A. 2012 Dec 11;109(50):20667-72. doi: 10.1073/pnas.1212188109. Epub 2012 Nov 27.

23.

Microfluidic single-cell real-time PCR for comparative analysis of gene expression patterns.

Sanchez-Freire V, Ebert AD, Kalisky T, Quake SR, Wu JC.

Nat Protoc. 2012 Apr 5;7(5):829-38. doi: 10.1038/nprot.2012.021.

24.

Identification of a cKit(+) colonic crypt base secretory cell that supports Lgr5(+) stem cells in mice.

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.

Gastroenterology. 2012 May;142(5):1195-1205.e6. doi: 10.1053/j.gastro.2012.02.006. Epub 2012 Feb 11.

25.

Single-cell dissection of transcriptional heterogeneity in human colon tumors.

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.

Nat Biotechnol. 2011 Nov 13;29(12):1120-7. doi: 10.1038/nbt.2038.

26.

Genomic analysis at the single-cell level.

Kalisky T, Blainey P, Quake SR.

Annu Rev Genet. 2011;45:431-45. doi: 10.1146/annurev-genet-102209-163607. Epub 2011 Sep 19. Review.

27.

An information theoretic, microfluidic-based single cell analysis permits identification of subpopulations among putatively homogeneous stem cells.

Glotzbach JP, Januszyk M, Vial IN, Wong VW, Gelbard A, Kalisky T, Thangarajah H, Longaker MT, Quake SR, Chu G, Gurtner GC.

PLoS One. 2011;6(6):e21211. doi: 10.1371/journal.pone.0021211. Epub 2011 Jun 22.

28.

Single-cell genomics.

Kalisky T, Quake SR.

Nat Methods. 2011 Apr;8(4):311-4. doi: 10.1038/nmeth0411-311.

PMID:
21451520
29.

Protein dynamics in individual human cells: experiment and theory.

Cohen AA, Kalisky T, Mayo A, Geva-Zatorsky N, Danon T, Issaeva I, Kopito RB, Perzov N, Milo R, Sigal A, Alon U.

PLoS One. 2009;4(4):e4901. doi: 10.1371/journal.pone.0004901. Epub 2009 Apr 17.

30.

An analytically solvable model for rapid evolution of modular structure.

Kashtan N, Mayo AE, Kalisky T, Alon U.

PLoS Comput Biol. 2009 Apr;5(4):e1000355. doi: 10.1371/journal.pcbi.1000355. Epub 2009 Apr 10.

31.

Association of reactive oxygen species levels and radioresistance in cancer stem cells.

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.

Nature. 2009 Apr 9;458(7239):780-3. doi: 10.1038/nature07733.

32.

Nonlocal competition and the speciation transition on random networks.

Maruvka YE, Kalisky T, Shnerb NM.

Phys Rev E Stat Nonlin Soft Matter Phys. 2008 Sep;78(3 Pt 1):031920. Epub 2008 Sep 24.

PMID:
18851078
33.

Cost-benefit theory and optimal design of gene regulation functions.

Kalisky T, Dekel E, Alon U.

Phys Biol. 2007 Nov 7;4(4):229-45.

PMID:
17991990
34.

Tomography of scale-free networks and shortest path trees.

Kalisky T, Cohen R, Mokryn O, Dolev D, Shavitt Y, Havlin S.

Phys Rev E Stat Nonlin Soft Matter Phys. 2006 Dec;74(6 Pt 2):066108. Epub 2006 Dec 15.

PMID:
17280122
35.

Width of percolation transition in complex networks.

Kalisky T, Cohen R.

Phys Rev E Stat Nonlin Soft Matter Phys. 2006 Mar;73(3 Pt 2):035101. Epub 2006 Mar 7.

PMID:
16605583
36.

Scale-free networks emerging from weighted random graphs.

Kalisky T, Sreenivasan S, Braunstein LA, Buldyrev SV, Havlin S, Stanley HE.

Phys Rev E Stat Nonlin Soft Matter Phys. 2006 Feb;73(2 Pt 2):025103. Epub 2006 Feb 10.

PMID:
16605380
37.

Localization transition on complex networks via spectral statistics.

Sade M, Kalisky T, Havlin S, Berkovits R.

Phys Rev E Stat Nonlin Soft Matter Phys. 2005 Dec;72(6 Pt 2):066123. Epub 2005 Dec 23.

PMID:
16486026
38.

Scaling of optimal-path-lengths distribution in complex networks.

Kalisky T, Braunstein LA, Buldyrev SV, Havlin S, Stanley HE.

Phys Rev E Stat Nonlin Soft Matter Phys. 2005 Aug;72(2 Pt 2):025102. Epub 2005 Aug 10.

PMID:
16196625
39.

Volatility of linear and nonlinear time series.

Kalisky T, Ashkenazy Y, Havlin S.

Phys Rev E Stat Nonlin Soft Matter Phys. 2005 Jul;72(1 Pt 1):011913. Epub 2005 Jul 21.

PMID:
16090007
40.

Effect of disorder strength on optimal paths in complex networks.

Sreenivasan S, Kalisky T, Braunstein LA, Buldyrev SV, Havlin S, Stanley HE.

Phys Rev E Stat Nonlin Soft Matter Phys. 2004 Oct;70(4 Pt 2):046133. Epub 2004 Oct 29.

PMID:
15600486
41.

Symbolic dynamics for strong chaos on stochastic webs: General quasisymmetry.

Dana I I, Kalisky T.

Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics. 1996 Mar;53(3):R2025-R2028. No abstract available.

PMID:
9964598

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