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The Faculty of Medicine - Developmental Biology and Cancer Research: Kaplan Tommy


 Last updated June 2021 - School of Pharmacy

List of Publications

(1) Sadeh R, Sharkia I, Fialkoff G, Rahat A, Gutin J, Chappleboim A, et al. Author Correction: ChIP-seq of plasma cell-free nucleosomes identifies gene expression programs of the cells of origin (Nature Biotechnology, (2021), 39, 5, (586-598), 10.1038/s41587-020-00775-6). Nat Biotechnol 2021;39(5):642.

(2) Sadeh R, Sharkia I, Fialkoff G, Rahat A, Gutin J, Chappleboim A, et al. ChIP-seq of plasma cell-free nucleosomes identifies gene expression programs of the cells of origin. Nat Biotechnol 2021;39(5):586-598.

(3) Schwartz M, Portugez AS, Attia BZ, Tannenbaum M, Cohen L, Loza O, et al. Genomic retargeting of p53 and CTCF is associated with transcriptional changes during oncogenic HRas-induced transformation. Commun Biolog 2020;3(1).

(4) Habib N, McCabe C, Medina S, Varshavsky M, Kitsberg D, Dvir-Szternfeld R, et al. Disease-associated astrocytes in Alzheimer’s disease and aging. Nat Neurosci 2020;23(6):701-706.

(5) Brill-Karniely Y, Dror D, Duanis-Assaf T, Goldstein Y, Schwob O, Millo T, et al. Triangular correlation (TrC) between cancer aggressiveness, cell uptake capability, and cell deformability. Sci Adv 2020;6(3).

(6) Benchetrit H, Jaber M, Zayat V, Sebban S, Pushett A, Makedonski K, et al. Direct Induction of the Three Pre-implantation Blastocyst Cell Types from Fibroblasts. Cell Stem Cell 2019;24(6):983-994.e7.

(7) Bar Yaacov R, Eshel R, Farhi E, Shemuluvich F, Kaplan T, Birnbaum RY. Functional characterization of the ZEB2 regulatory landscape. Hum Mol Genet 2019;28(9):1487-1497.

(8) Moss J, Magenheim J, Neiman D, Zemmour H, Loyfer N, Korach A, et al. Comprehensive human cell-type methylation atlas reveals origins of circulating cell-free DNA in health and disease. Nat Commun 2018;9(1).

(9) Hirsch N, Eshel R, Bar Yaacov R, Shahar T, Shmulevich F, Dahan I, et al. Unraveling the transcriptional regulation of TWIST1 in limb development. PLoS Genet 2018;14(10).

(10) Zhu G, Deng W, Hu H, Ma R, Zhang S, Yang J, et al. Reconstructing spatial organizations of chromosomes through manifold learning. Nucleic Acids Res 2018;46(8):e50.

(11) Ron G, Globerson Y, Moran D, Kaplan T. Promoter-enhancer interactions identified from Hi-C data using probabilistic models and hierarchical topological domains. Nat Commun 2017;8(1).

(12) Schlesinger S, Kaffe B, Melcer S, Aguilera JD, Sivaraman DM, Kaplan T, et al. A hyperdynamic H3.3 nucleosome marks promoter regions in pluripotent embryonic stem cells. Nucleic Acids Res 2017;45(21):12181-12194.

(13) Malka Y, Steiman-Shimony A, Rosenthal E, Argaman L, Cohen-Daniel L, Arbib E, et al. Post-transcriptional 3´-UTR cleavage of mRNA transcripts generates thousands of stable uncapped autonomous RNA fragments. Nat Commun 2017;8(1).

(14) Sarusi Portuguez A, Schwartz M, Siersbaek R, Nielsen R, Sung M-, Mandrup S, et al. Hierarchical role for transcription factors and chromatin structure in genome organization along adipogenesis. FEBS J 2017;284(19):3230-3244.

(15) Moshe A, Kaplan T. Genome-wide search for Zelda-like chromatin signatures identifies GAF as a pioneer factor in early fly development. Epigenetics Chromatin 2017;10(1).

(16) Klutstein M, Moss J, Kaplan T, Cedar H. Contribution of epigenetic mechanisms to variation in cancer risk among tissues. Proc Natl Acad Sci U S A 2017;114(9):2230-2234.

(17) Klutstein M, Moss J, Kaplan T, Cedar H. Contribution of epigenetic mechanisms to variation in cancer risk among tissues. Proc Natl Acad Sci U S A 2017;114(9):2230-2234.

(18) Nevil M, Bondra ER, Schulz KN, Kaplan T, Harrison MM. Stable binding of the conserved transcription factor grainy head to its target genes throughout Drosophila melanogaster development. Genetics 2017;205(2):605-620.

(19) Schulz KN, Bondra ER, Moshe A, Villalta JE, Lieb JD, Kaplan T, et al. Zelda is differentially required for chromatin accessibility, transcription factor binding, and gene expression in the early Drosophila embryo. Genome Res 2015;25(11):1715-1726.

(20) Schwartz M, Sarusi A, Deitch RT, Tal M, Raz D, Sung M-, et al. Comparative analysis of T4 DNA ligases and DNA polymerases used in chromosome conformation capture assays. BioTechniques 2015;58(4):195-199.

(21) Zhou H, Wan B, Grubisic I, Kaplan T, Tjian R. TAF7L modulates brown adipose tissue formation. eLife 2014;2014(3).

(22) Li X-, Harrison MM, Villalta JE, Kaplan T, Eisen MB. Establishment of regions of genomic activity during the Drosophila maternal to zygotic transition. Elife 2014;3.

(23) Zhou H, Grubisic I, Zheng K, He Y, Wang PJ, Kaplan T, et al. Taf7l cooperates with Trf2 to regulate spermiogenesis. Proc Natl Acad Sci U S A 2013;110(42):16886-16891.

(24) Paris M, Kaplan T, Li XY, Villalta JE, Lott SE, Eisen MB. Extensive Divergence of Transcription Factor Binding in Drosophila Embryos with Highly Conserved Gene Expression. PLoS Genet 2013;9(9).

(25) Visel A, Taher L, Girgis H, May D, Golonzhka O, Hoch RV, et al. A high-resolution enhancer atlas of the developing telencephalon. Cell 2013;152(4):895-908.

(26) Zhou H, Kaplan T, Li Y, Grubisic I, Zhang Z, Wang PJ, et al. Dual functions of TAF7L in adipocyte differentiation. eLife 2013;2013(2).

(27) Perets R, Kaplan T, Stein I, Hidas G, Tayeb S, Avraham E, et al. Genome-Wide Analysis of Androgen Receptor Targets Reveals COUP-TF1 as a Novel Player in Human Prostate Cancer. PLoS ONE 2012;7(10).

(28) Kaplan T, Friedman N. Gene expression: Running to stand still. Nature 2012;484(7393):171-172.

(29) Kaplan T, Biggin MD. Quantitative Models of the Mechanisms that Control Genome-Wide Patterns of Animal Transcription Factor Binding. Methods Cell Biol 2012;110:263-283.

(30) May D, Blow MJ, Kaplan T, McCulley DJ, Jensen BC, Akiyama JA, et al. Large-scale discovery of enhancers from human heart tissue. Nat Genet 2012;44(1):89-93.

(31) Harrison MM, Li X-, Kaplan T, Botchan MR, Eisen MB. Zelda binding in the early Drosophila melanogaster embryo marks regions subsequently activated at the maternal-to-zygotic transition. PLoS Genet 2011;7(10).

(32) Zhang Y, Handley D, Kaplan T, Yu H, Bais AS, Richards T, et al. High throughput determination of TGFβ1/SMAD3 targets in A549 lung epithelial cells. PLoS ONE 2011;6(5).

(33) Kaplan T, Li X-, Sabo PJ, Thomas S, Stamatoyannopoulos JA, Biggin MD, et al. Quantitative models of the mechanisms that control genome-wide patterns of transcription factor binding during early drosophila development. PLoS Genet 2011;7(2).

(34) Halley JE, Kaplan T, Wang AY, Kobor MS, Rine J. Roles for H2A.Z and its acetylation in GAL1 transcription and gene induction, but not GAL1-transcriptional memory. PloS Biol 2010;8(6).

(35) Kaplan T, Liu CL, Erkmann JA, Holik J, Grunstein M, Kaufman PD, et al. Cell cycle- and chaperone-mediated regulation of H3K56ac incorporation in yeast. PLoS Genet 2008;4(11).

(36) Yassour M, Kaplan T, Jaimovich A, Friedman N. Nucleosome positioning from tiling microarray data. Bioinformatics 2008;24(13):i139-i146.

(37) Habib N, Kaplan T, Margalit H, Friedman N. A novel Bayesian DNA motif comparison method for clustering and retrieval. PLoS Comput Biol 2008;4(2).

(38) Capaldi AP, Kaplan T, Liu Y, Habib N, Regev A, Friedman N, et al. Structure and function of a transcriptional network activated by the MAPK Hog1. Nat Genet 2008;40(11):1300-1306.

(39) Dion MF, Kaplan T, Kim M, Buratowski S, Friedman N, Rando OJ. Dynamics of replication-independent histone turnover in budding yeast. Science 2007;315(5817):1405-1408.

(40) Chih LL, Kaplan T, Kim M, Buratowski S, Schreiber SL, Friedman N, et al. Single-nucleosome mapping of histone modifications in S. cerevisiae. PloS Biol 2005;3(10).

(41) Barash Y, Elidan G, Kaplan T, Friedman N. CIS: Compound importance sampling method for protein-DNA binding site p-value estimation. Bioinformatics 2005;21(5):596-600.

(42) Kaplan T, Friedman N, Margalit H. Ab initio prediction of transcription factor targets using structural knowledge. PLoS Comput Biol 2005;1(1):0005-0013.

(43) Predicting transcription factor binding sites using structural knowledge. Lecture Notes in Bioinformatics (Subseries of Lecture Notes in Computer Science); 2005.

(44) Modeling dependencies in protein-DNA binding sites. Proceedings of the Annual International Conference on Computational Molecular Biology, RECOMB; 2003.

(45) Friedberg I, Kaplan T, Margalit H. Glimmers in the midnight zone: characterization of aligned identical residues in sequence-dissimilar proteins sharing a common fold. Proc Int Conf Intell Syst Mol Biol 2000;8:162-170.

(46) Friedberg I, Kaplan T, Margalit H. Evaluation of PSI-BLAST alignment accuracy in comparison to structural alignments. Protein Sci 2000;9(11):2278-2284.