Tommy Kaplan

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Nir FriedmanProfessor of Computer Science and Medicine, Hebrew UniversityVerified email at mail.huji.ac.il
Netanel LoyferPhD candidate, Hebrew Unviersity of JerusalemVerified email at mail.huji.ac.il
Michael B. EisenInvestigator, HHMI and Associate Professor of Molecular and Cell Biology, UC BerkeleyVerified email at berkeley.edu
Yuval DorProfessor of Biology, Hebrew University of JerusalemVerified email at ekmd.huji.ac.il
Benjamin GlaserHadassah-Hebrew University Medical CenterVerified email at mail.huji.ac.il
Ruth ShemerVerified email at mail.huji.ac.il
Melissa HarrisonProfessorVerified email at wisc.edu
Oliver RandoProfessor of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical SchoolVerified email at umassmed.edu
Joshua MossHadassah Hebrew University Medical CenterVerified email at mail.huji.ac.il
michal schwartzprofessorVerified email at weizmann.ac.il
Hanah MargalitThe Hebrew University of JerusalemVerified email at ekmd.huji.ac.il
Naomi HabibHebrew University of Jerusalem IsraelVerified email at elsc.huji.ac.il
Minkyu KimUniversity of Texas Health Science Center San AntonioVerified email at uthscsa.edu
Miri Varshavsky HassidComputer Science and Computational Biology, Hebrew University of JerusalemVerified email at mail.huji.ac.il
Len A. PennacchioSenior Staff Scientist, Lawrence Berkeley National LaboratoryVerified email at lbl.gov
Axel ViselLawrence Berkeley National LaboratoryVerified email at lbl.gov
Dalit MayMD/PhD, Consultant Clinical Genetics, Shaare Zedek Medical Center. GP Clalit Health ServicesVerified email at clalit.org.il
Matthew BlowResearch scientist, Joint Genome InstituteVerified email at lbl.gov
Edward M RubinScience CorpsVerified email at science-corps.org
Mike BotchanProfessor of Molecular and Cell BiologyVerified email at berkeley.edu

Tommy Kaplan

Professor of Computer Science and Computational Biology, The Hebrew University

Verified email at cs.huji.ac.il - Homepage

Computational Biology Genomics DNA methylation Machine Learning cell-free DNA


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Comprehensive human cell-type methylation atlas reveals origins of circulating cell-free DNA in health and disease J Moss, J Magenheim, D Neiman, H Zemmour, N Loyfer, A Korach, ... Nature communications 9 (1), 5068, 2018	780	2018
Disease-associated astrocytes in Alzheimer’s disease and aging N Habib, C McCabe, S Medina, M Varshavsky, D Kitsberg, ... Nature neuroscience 23 (6), 701-706, 2020	665	2020
Single-nucleosome mapping of histone modifications in S. cerevisiae CL Liu, T Kaplan, M Kim, S Buratowski, SL Schreiber, N Friedman, ... PLoS biology 3 (10), e328, 2005	663	2005
Dynamics of replication-independent histone turnover in budding yeast MF Dion, T Kaplan, M Kim, S Buratowski, N Friedman, OJ Rando Science 315 (5817), 1405, 2007	659	2007
Zelda Binding in the Early Drosophila melanogaster Embryo Marks Regions Subsequently Activated at the Maternal-to-Zygotic Transition MM Harrison, XY Li, T Kaplan, MR Botchan, MB Eisen PLoS genetics 7 (10), e1002266, 2011	381	2011
Modeling dependencies in protein-DNA binding sites Y Barash, G Elidan, N Friedman, T Kaplan Proceedings of the seventh annual international conference on Research in …, 2003	321	2003
Large-scale discovery of enhancers from human heart tissue D May, MJ Blow, T Kaplan, DJ McCulley, BC Jensen, JA Akiyama, A Holt, ... Nature genetics 44 (1), 89-93, 2012	313	2012
Structure and function of a transcriptional network activated by the MAPK Hog1 AP Capaldi, T Kaplan, Y Liu, N Habib, A Regev, N Friedman, EK O'Shea Nature genetics 40 (11), 1300-1306, 2008	279	2008
A high-resolution enhancer atlas of the developing telencephalon A Visel, L Taher, H Girgis, D May, O Golonzhka, RV Hoch, GL McKinsey, ... Cell 152 (4), 895-908, 2013	278	2013
Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing M Yassour, T Kaplan, HB Fraser, JZ Levin, J Pfiffner, X Adiconis, ... Proceedings of the National Academy of Sciences 106 (9), 3264-3269, 2009	273	2009
A DNA methylation atlas of normal human cell types N Loyfer, J Magenheim, A Peretz, G Cann, J Bredno, A Klochendler, ... Nature 613 (7943), 355-364, 2023	241	2023
Quantitative Models of the Mechanisms That Control Genome-Wide Patterns of Transcription Factor Binding during Early Drosophila Development T Kaplan, XY Li, PJ Sabo, S Thomas, JA Stamatoyannopoulos, MD Biggin, ... PLoS genetics 7 (2), e1001290, 2011	219	2011
Establishment of regions of genomic activity during the Drosophila maternal to zygotic transition XY Li, MM Harrison, JE Villalta, T Kaplan, MB Eisen Elife 3, e03737, 2014	218	2014
Zelda is differentially required for chromatin accessibility, transcription factor binding, and gene expression in the early Drosophila embryo KN Schulz, ER Bondra, A Moshe, JE Villalta, JD Lieb, T Kaplan, ... Genome research 25 (11), 1715-1726, 2015	186	2015
Cell cycle–and chaperone-mediated regulation of H3K56ac incorporation in yeast T Kaplan, CL Liu, JA Erkmann, J Holik, M Grunstein, PD Kaufman, ... PLoS genetics 4 (11), e1000270, 2008	180	2008
Promoter-enhancer interactions identified from Hi-C data using probabilistic models and hierarchical topological domains G Ron, Y Globerson, D Moran, T Kaplan Nature Communications 8 (1), 2237, 2017	164	2017
Ab initio prediction of transcription factor targets using structural knowledge T Kaplan, N Friedman, H Margalit PLoS computational biology 1 (1), e1, 2005	149	2005
ChIP-seq of plasma cell-free nucleosomes identifies gene expression programs of the cells of origin R Sadeh, I Sharkia, G Fialkoff, A Rahat, J Gutin, A Chappleboim, M Nitzan, ... Nature Biotechnology, 1-13, 2021	120	2021
Extensive Divergence of Transcription Factor Binding in Drosophila Embryos with Highly Conserved Gene Expression M Paris, T Kaplan, XY Li, JE Villalta, SE Lott, MB Eisen PLoS genetics 9 (9), e1003748, 2013	118	2013
Roles for H2A.Z and Its Acetylation in GAL1 Transcription and Gene Induction, but Not GAL1-Transcriptional Memory JE Halley, T Kaplan, AY Wang, MS Kobor, J Rine PLoS biology 8 (6), e1000401, 2010	110	2010

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