My Publications
2025
Maimon, T., Trink, Y., Goldberger, J., & Kalisky, T. (2025). Unsupervised Machine Learning Reveals Temporal Components of Gene Expression in HeLa Cells Following Release from Cell Cycle Arrest. International Journal of Molecular Sciences, 26(19), Article 9491. https://doi.org/10.3390/ijms26199491
2024
Trink, Y., Urbach, A., Dekel, B., Hohenstein, P., Goldberger, J., & Kalisky, T. (2024). Characterization of Alternative Splicing in High-Risk Wilms’ Tumors. International Journal of Molecular Sciences, 25(8), Article 4520. https://doi.org/10.3390/ijms25084520
2023
Omer, D., Zontag, O. C., Gnatek, Y., Harari-Steinberg, O., Pleniceanu, O., Namestnikov, M., Cohen, A. H., Nissim-Rafinia, M., Tam, G., Kalisky, T., Meshorer, E., & Dekel, B. (2023). OCT4 induces long-lived dedifferentiated kidney progenitors poised to redifferentiate in 3D kidney spheroids. Molecular Therapy Methods and Clinical Development, 29, 329-346. https://doi.org/10.1016/j.omtm.2023.04.005
Trink, Y., Urbach, A., Dekel, B., Hohenstein, P., Goldberger, J., & Kalisky, T. (2023). Characterization of Continuous Transcriptional Heterogeneity in High-Risk Blastemal-Type Wilms’ Tumors Using Unsupervised Machine Learning. International Journal of Molecular Sciences, 24(4), Article 3532. https://doi.org/10.3390/ijms24043532
2022
Wineberg, Y., Kanter, I., Ben-Haim, N., Pode-Shakked, N., Bucris, E., Bar-Lev, T. H., Oriel, S., Reinus, H., Yehuda, Y., Gershon, R., Shukrun, R., Bar-Lev, D. D., Urbach, A., Dekel, B., & Kalisky, T. (2022). Characterization of alternative mRNA splicing in cultured cell populations representing progressive stages of human fetal kidney development. Scientific Reports, 12(1), Article 19548. https://doi.org/10.1038/s41598-022-24147-z
2021
Kanter, I., Yaari, G., & Kalisky, T. (2021). Applications of Community Detection Algorithms to Large Biological Datasets. In Methods in Molecular Biology (pp. 59-80). (Methods in Molecular Biology; Vol. 2243). Humana Press Inc.. https://doi.org/10.1007/978-1-0716-1103-6_3
Cohen-Zontag, O., Gershon, R., Harari-Steinberg, O., Kanter, I., Omer, D., Pleniceanu, O., Tam, G., Oriel, S., Ben-Hur, H., Katz, G., Dotan, Z., Kalisky, T., Dekel, B., & Pode-Shakked, N. (2021). Author Correction: Human kidney clonal proliferation disclose lineage-restricted precursor characteristics (Scientific Reports, (2020), 10, 1, (22097), 10.1038/s41598-020-78366-3). Scientific Reports, 11(1), Article 6970. https://doi.org/10.1038/s41598-021-86157-7
2020
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. (2020). Ex Vivo Expanded 3D Human Kidney Spheres Engraft Long Term and Repair Chronic Renal Injury in Mice. Cell Reports, 30(3), 852-869.e4. https://doi.org/10.1016/j.celrep.2019.12.047
Zabala, M., Lobo, N. A., Antony, J., Heitink, L. S., Gulati, G. S., Lam, J., Parashurama, N., Sanchez, K., Adorno, M., Sikandar, S. S., Kuo, A. H., Qian, D., Kalisky, T., Sim, S., Li, L., Dirbas, F. M., Somlo, G., Newman, A., Quake, S. R., & Clarke, M. F. (2020). LEFTY1 Is a Dual-SMAD Inhibitor that Promotes Mammary Progenitor Growth and Tumorigenesis. Cell Stem Cell, 27(2), 284-299.e8. https://doi.org/10.1016/j.stem.2020.06.017
Wineberg, Y., Bar-Lev, T. H., 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. (2020). Single-Cell RNA sequencing reveals mRNA splice isoform switching during kidney development. Journal of the American Society of Nephrology, 31(10), 2278-2291. https://doi.org/10.1681/ASN.2019080770
2019
Kanter, I., Dalerba, P., & Kalisky, T. (2019). A cluster robustness score for identifying cell subpopulations in single cell gene expression datasets from heterogeneous tissues and tumors. Bioinformatics, 35(6), 962-971. https://doi.org/10.1093/bioinformatics/bty708
Ling, T., Birger, Y., Stankiewicz, M. J., Ben-Haim, N., Kalisky, T., Rein, A., Kugler, E., Chen, W., Fu, C., Zhang, K., Patel, H., Sikora, J. W., Goo, Y. A., Kelleher, N., Zou, L., Izraeli, S., & Crispino, J. D. (2019). Chromatin occupancy and epigenetic analysis reveal new insights into the function of the GATA1 N terminus in erythropoiesis. Blood, 134(19), 1619-1631. https://doi.org/10.1182/blood.2019001234
Munro, D. A., Wineberg, Y., Tarnick, J., Vink, C. S., Li, Z., Pridans, C., Dzierzak, E., Kalisky, T., Hohenstein, P., & Davies, J. A. (2019). Macrophages restrict the nephrogenic field and promote endothelial connections during kidney development. eLife, 8, Article e43271. https://doi.org/10.7554/eLife.43271
2018
Kalisky, T., Oriel, S., Bar-Lev, T. H., Ben-Haim, N., Trink, A., Wineberg, Y., Kanter, I., Gilad, S., & Pyne, S. (2018). A brief review of single-cell transcriptomic technologies. Briefings in Functional Genomics, 17(1), 64-76. https://doi.org/10.1093/bfgp/elx019
Golan, H., Shukrun, R., Caspi, R., Vax, E., Pode-Shakked, N., Goldberg, S., Pleniceanu, O., Bar-Lev, D. D., 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. (2018). In Vivo Expansion of Cancer Stemness Affords Novel Cancer Stem Cell Targets: Malignant Rhabdoid Tumor as an Example. Stem Cell Reports, 11(3), 795-810. https://doi.org/10.1016/j.stemcr.2018.07.010
Kalisky, T. (2018). Talk. Paper presented at The 6th Annual Single Cell Analysis Congress, London, UK, November 8-9, 2018 (advisory board, invited talk), Israel.
Trink, A., Kanter, I., Pode-Shakked, N., Urbach, A., Dekel, B., & Kalisky, T. (2018). Geometry of Gene Expression Space of Wilms’ Tumors From Human Patients. Neoplasia (United States), 20(8), 871-881. https://doi.org/10.1016/j.neo.2018.06.006
2017
Pode-Shakked, N., Gershon, R., Tam, G., Omer, D., Gnatek, Y., Kanter, I., Oriel, S., Katz, G., Harari-Steinberg, O., Kalisky, T., & Dekel, B. (2017). Evidence of In Vitro Preservation of Human Nephrogenesis at the Single-Cell Level. Stem Cell Reports, 9(1), 279-291. https://doi.org/10.1016/j.stemcr.2017.04.026
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, D. D., Bollag, N., Shtainfeld, R., Armon, L., Urbach, A., Kalisky, T., Nagler, A., ... Dekel, B. (2017). Corrigendum to: Peroxisome proliferator-activated receptor gamma (PPARγ) is central to the initiation and propagation of human angiomyolipoma, suggesting its potential as a therapeutic target (EMBO Mol Med, (2017), 9, (508-530), 10.15252/emmm.201506111). EMBO Molecular Medicine, 9(12), 1763. https://doi.org/10.15252/emmm.201708507
Cai, S., Kalisky, T., Sahoo, D., Dalerba, P., Feng, W., Lin, Y., Qian, D., Kong, A., Yu, J., Wang, F., Chen, E. Y., Scheeren, F. A., Kuo, A. H., Sikandar, S. S., Hisamori, S., van Weele, L. J., Heiser, D., Sim, S., Lam, J., ... Clarke, M. F. (2017). A Quiescent Bcl11b High Stem Cell Population Is Required for Maintenance of the Mammary Gland. Cell Stem Cell, 20(2), 247-260.e5. https://doi.org/10.1016/j.stem.2016.11.007
Sikandar, S. S., Kuo, A. H., Kalisky, T., Cai, S., Zabala, M., Hsieh, R. W., Lobo, N. A., Scheeren, F. A., Sim, S., Qian, D., Dirbas, F. M., Somlo, G., Quake, S. R., & Clarke, M. F. (2017). Role of epithelial to mesenchymal transition associated genes in mammary gland regeneration and breast tumorigenesis. Nature Communications, 8(1), Article 1669. https://doi.org/10.1038/s41467-017-01666-2
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, D. D., Bollag, N., Shtainfeld, R., Armon, L., Urbach, A., Kalisky, T., Nagler, A., ... Dekel, B. (2017). PPARG is central to the initiation and propagation of human angiomyolipoma, suggesting its potential as a therapeutic target. EMBO Molecular Medicine, 9(4), 508-530. https://doi.org/10.15252/emmm.201506111
Zhao, C., Cai, S., Shin, K., Lim, A., Kalisky, T., Lu, W. J., Clarke, M. F., & Beachy, P. A. (2017). Stromal Gli2 activity coordinates a niche signaling program for mammary epithelial stem cells. Science, 356(6335), Article eaal3485. https://doi.org/10.1126/science.aal3485
2016
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. (2016). Dissecting Stages of Human Kidney Development and Tumorigenesis with Surface Markers Affords Simple Prospective Purification of Nephron Stem Cells. Scientific Reports, 6, Article 23562. https://doi.org/10.1038/srep23562
Dalerba, P., Sahoo, D., Paik, S., Guo, X., Yothers, G., Song, N., Wilcox-Fogel, N., Forgó, E., Rajendran, P. S., Miranda, S. P., Hisamori, S., Hutchison, J., Kalisky, T., Qian, D., Wolmark, N., Fisher, G. A., Van De Rijn, M., & Clarke, M. F. (2016). CDX2 as a Prognostic Biomarker in Stage II and Stage III Colon Cancer. New England Journal of Medicine, 374(3), 211-222. https://doi.org/10.1056/NEJMoa1506597
2015
Kanter, I., & Kalisky, T. (2015). Single cell transcriptomics: Methods and applications. Frontiers in Oncology, 5(FEB), Article 53. https://doi.org/10.3389/fonc.2015.00053
Korem, Y., Szekely, P., Hart, Y., Sheftel, H., Hausser, J., Mayo, A., Rothenberg, M. E., Kalisky, T., & Alon, U. (2015). Geometry of the Gene Expression Space of Individual Cells. PLoS Computational Biology, 11(7), Article e1004224. https://doi.org/10.1371/journal.pcbi.1004224
Chen, E. C., Karl, T. A., Kalisky, T., Gupta, S. K., O'Brien, C. A., Longacre, T. A., Van De Rijn, M., Quake, S. R., Clarke, M. F., & Rothenberg, M. E. (2015). KIT Signaling Promotes Growth of Colon Xenograft Tumors in Mice and Is Up-Regulated in a Subset of Human Colon Cancers. Gastroenterology, 149(3), 705e2-717.e2. https://doi.org/10.1053/j.gastro.2015.05.042
2014
Scheeren, F. A., Kuo, A. H., Van Weele, L. J., Cai, S., Glykofridis, I., Sikandar, S. S., Zabala, M., Qian, D., Lam, J. S., Johnston, D., Volkmer, J. P., Sahoo, D., Van De Rijn, M., Dirbas, F. M., Somlo, G., Kalisky, T., Rothenberg, M. E., Quake, S. R., & Clarke, M. F. (2014). A cell-intrinsic role for TLR2-MYD88 in intestinal and breast epithelia and oncogenesis. Nature Cell Biology, 16(12), 1238-1248. https://doi.org/10.1038/ncb3058
Wu, A. R., Neff, N. F., Kalisky, T., Dalerba, P., Treutlein, B., Rothenberg, M. E., Mburu, F. M., Mantalas, G. L., Sim, S., Clarke, M. F., & Quake, S. R. (2014). Quantitative assessment of single-cell RNA-sequencing methods. Nature Methods, 11(1), 41-46. https://doi.org/10.1038/nmeth.2694
Lawlor, P. N., Kalisky, T., Rosner, R., Rosner, M. R., & Kording, K. P. (2014). Conceptualizing cancer drugs as classifiers. PLoS ONE, 9(9), Article e106444. https://doi.org/10.1371/journal.pone.0106444
2012
Sen, A., Rothenberg, M. E., Mukherjee, G., Feng, N., Kalisky, T., Nair, N., Johnstone, I. M., Clarke, M. F., & Greenberg, H. B. (2012). Innate immune response to homologous rotavirus infection in the small intestinal villous epithelium at single-cell resolution. Proceedings of the National Academy of Sciences of the United States of America, 109(50), 20667-20672. https://doi.org/10.1073/pnas.1212188109
Sanchez-Freire, V., Ebert, A. D., Kalisky, T., Quake, S. R., & Wu, J. C. (2012). Microfluidic single-cell real-time PCR for comparative analysis of gene expression patterns. Nature Protocols, 7(5), 829-838. https://doi.org/10.1038/nprot.2012.021
Rothenberg, M. E., Nusse, Y., Kalisky, T., Lee, J. J., Dalerba, P., Scheeren, F., Lobo, N., Kulkarni, S., Sim, S., Qian, D., Beachy, P. A., Pasricha, P. J., Quake, S. R., & Clarke, M. F. (2012). Identification of a cKit+ colonic crypt base secretory cell that supports Lgr5+ stem cells in mice. Gastroenterology, 142(5), 1195-1205.e6. https://doi.org/10.1053/j.gastro.2012.02.006
2011
Dalerba, P., Kalisky, T., Sahoo, D., Rajendran, P. S., Rothenberg, M. E., Leyrat, A. A., Sim, S., Okamoto, J., Johnston, D. M., Qian, D., Zabala, M., Bueno, J., Neff, N. F., Wang, J., Shelton, A. A., Visser, B., Hisamori, S., Shimono, Y., Van De Wetering, M., ... Quake, S. R. (2011). Single-cell dissection of transcriptional heterogeneity in human colon tumors. Nature Biotechnology, 29(12), 1120-1127. https://doi.org/10.1038/nbt.2038
Glotzbach, J. P., Januszyk, M., Vial, I. N., Wong, V. W., Gelbard, A., Kalisky, T., Thangarajah, H., Longaker, M. T., Quake, S. R., Chu, G., & Gurtner, G. C. (2011). An information theoretic, microfluidic-based single cell analysis permits identification of subpopulations among putatively homogeneous stem cells. PLoS ONE, 6(6), Article e21211. https://doi.org/10.1371/journal.pone.0021211
Kalisky, T., & Quake, S. R. (2011). Single-cell genomics. Nature Methods, 8(4), 311-314. https://doi.org/10.1038/nmeth0411-311
Kalisky, T., Blainey, P., & Quake, S. R. (2011). Genomic analysis at the single-cell level. Annual Review of Genetics, 45, 431-445. https://doi.org/10.1146/annurev-genet-102209-163607
2009
Cohen, A. A., Kalisky, T., Mayo, A., Geva-Zatorsky, N., Danon, T., Issaeva, I., Kopito, R. B., Perzov, N., Milo, R., Sigal, A., & Alon, U. (2009). Protein dynamics in individual human cells: Experiment and theory. PLoS ONE, 4(4), Article e4901. https://doi.org/10.1371/journal.pone.0004901
Diehn, M., Cho, R. W., Lobo, N. A., Kalisky, T., Dorie, M. J., Kulp, A. N., Qian, D., Lam, J. S., Ailles, L. E., Wong, M., Joshua, B., Kaplan, M. J., Wapnir, I., Dirbas, F. M., Somlo, G., Garberoglio, C., Paz, B., Shen, J., Lau, S. K., ... Clarke, M. F. (2009). Association of reactive oxygen species levels and radioresistance in cancer stem cells. Nature, 458(7239), 780-783. https://doi.org/10.1038/nature07733
Kashtan, N., Mayo, A. E., Kalisky, T., & Alon, U. (2009). An Analytically Solvable Model for Rapid Evolution of Modular Structure. PLoS Computational Biology, 5(4). https://doi.org/10.1371/journal.pcbi.1000355
2008
Maruvka, Y. E., Kalisky, T., & Shnerb, N. M. (2008). Nonlocal competition and the speciation transition on random networks. Physical Review E, 78(3), Article 031920. https://doi.org/10.1103/physreve.78.031920
2007
Kalisky, T., Dekel, E., & Alon, U. (2007). Cost-benefit theory and optimal design of gene regulation functions. Physical Biology, 4(4), 229-245. https://doi.org/10.1088/1478-3975/4/4/001
Kalisky, T., Ashkenazy, Y., & Havlin, S. (2007). Volatility of fractal and multifractal time series. Israel Journal of Earth Sciences, 56(1), 47-56. https://doi.org/10.1560/ijes.56.1.47
Braunstein, L. A., Wu, Z., Chen, Y., Buldyrev, S. V., Kalisky, T., Sreenivasan, S., Cohen, R., López, E., Havlin, S., & Stanley, H. E. (2007). Optimal path and minimal spanning trees in random weighted networks. International Journal of Bifurcation and Chaos, 17(7), 2215-2255. https://doi.org/10.1142/S0218127407018361
2006
Kalisky, T., & Cohen, R. (2006). Width of percolation transition in complex networks. Physical Review E, 73(3), Article 035101. https://doi.org/10.1103/PhysRevE.73.035101
Kalisky, T., Sreenivasan, S., Braunstein, L. A., Buldyrev, S. V., Havlin, S., & Stanley, H. E. (2006). Scale-free networks emerging from weighted random graphs. Physical Review E, 73(2), Article 025103. https://doi.org/10.1103/PhysRevE.73.025103
Kalisky, T., Cohen, R., Mokryn, O., Dolev, D., Shavitt, Y., & Havlin, S. (2006). Tomography of scale-free networks and shortest path trees. Physical Review E, 74(6), Article 066108. https://doi.org/10.1103/PhysRevE.74.066108
2005
Kalisky, T., Braunstein, L. A., Buldyrev, S. V., Havlin, S., & Stanley, H. E. (2005). Scaling of optimal-path-lengths distribution in complex networks. Physical Review E, 72(2), Article 025102. https://doi.org/10.1103/physreve.72.025102
Kalisky, T., Ashkenazy, Y., & Havlin, S. (2005). Volatility of linear and nonlinear time series. Physical Review E, 72(1), Article 011913. https://doi.org/10.1103/PhysRevE.72.011913
Kalisky, T., Sreenivasan, S., Braunstein, L. A., Buldyrev, S. V., Havlin, S., & Stanley, H. E. (2005). Scale-free properties of weighted random graphs: Minimum Spanning trees and percolation. In SCIENCE OF COMPLEX NETWORKS: From Biology to the Internet and WWW, CNET 2004 (pp. 79-89). (AIP Conference Proceedings; Vol. 776). https://doi.org/10.1063/1.1985379
Sade, M., Kalisky, T., Havlin, S., & Berkovits, R. (2005). Localization transition on complex networks via spectral statistics. Physical Review E, 72(6), Article 066123. https://doi.org/10.1103/PhysRevE.72.066123
Sreenivasan, S., Kalisky, T., Braunstein, L. A., Buldyrev, S. V., Havlin, S., & Stanley, H. E. (2005). Transition between strong and weak disorder regimes for the optimal path. Physica A: Statistical Mechanics and its Applications, 346(1-2 SPEC. ISS.), 174-182. https://doi.org/10.1016/j.physa.2004.08.064
Havlin, S., Braunstein, L. A., Buldyrev, S. V., Cohen, R., Kalisky, T., Sreenivasan, S., & Stanley, H. E. (2005). Optimal path in random networks with disorder: A mini review. Physica A: Statistical Mechanics and its Applications, 346(1-2 SPEC. ISS.), 82-92. https://doi.org/10.1016/j.physa.2004.08.053
2004
Madar, N., Kalisky, T., Cohen, R., Ben-Avraham, D., & Havlin, S. (2004). Immunization and epidemic dynamics in complex networks. European Physical Journal B, 38(2), 269-276. https://doi.org/10.1140/epjb/e2004-00119-8
Sreenivasan, S., Kalisky, T., Braunstein, L. A., Buldyrev, S. V., Havlin, S., & Stanley, H. E. (2004). Effect of disorder strength on optimal paths in complex networks. Physical Review E, 70(4 2), 046133-1-046133-6. Article 046133. https://doi.org/10.1103/PhysRevE.70.046133
Kalisky, T., Cohen, R., ben-Avraham, D., & Havlin, S. (2004). Tomography and Stability of Complex Networks. In E. Ben-Naim, H. Frauenfelder, & Z. Toroczkai (Eds.), Complex Networks (Vol. 650, pp. 3-34). (Lecture Notes in Physics). Springer.
1996
Dana, I., & Kalisky, T. (1996). Symbolic dynamics for strong chaos on stochastic webs: General quasisymmetry. Physical Review E, 53(3), R2025-R2028. https://doi.org/10.1103/physreve.53.r2025