Tommy Kaplan - תומי קפלן

Associate Professor
School of Computer Science and Engineering
The Hebrew University of Jerusalem, Israel

Program for Computer Science and Computational Biology (CSLS)
(jointly with Prof. Michal Linial)

Computational Biology

Enhancers, Genomics, cell-free DNA methylation,
Computational Epigenomics and Chromatin, Machine Learning

Open positions for excellent PhD/postdoc candidates! See project ideas.

Contact Information:

Prof. Tommy Kaplan
School of Computer Science and Engineering
The Hebrew University
Jerusalem 91904

Office: Rothberg B-529
Phone/Fax: +972-2-5494506

  CV of Tommy Kaplan | Google Scholar | ORCiD

Selected Publications:

bioRxiv Ronen Sadeh, Gavriel Fialkoff, Israa Sharkia, Ayelet Rahat, Mor Nitzan, Ilana Fox-Fisher, Daniel Neiman, Guy Meler, Zahala Kamari, Dayana Yaish, Samir Abu-Gazala, Tommy Kaplan, Ruth Shemer, David Planer, Aviad Zik, Eithan Galun, Benjamin Glaser, Yuval Dor, and Nir Friedman
ChIP-seq of plasma cell-free nucleosomes identifies cell-of-origin gene expression programs
bioRxiv, 2019
Cell Stem Cell Hana Benchetrit, Mohammad Jaber, Valery Zayat, Shulamit Sebban, Avital Pushett, Kirill Makedonski, Zvi Zakheim, Ahmed Radwan, Noam Maoz, Rachel Lasry, Noa Renous, Michal Inbar, Oren Ram, Tommy Kaplan, and Yosef Buganim
Direct Induction of the Three Pre-implantation Blastocyst Cell Types from Fibroblasts
Cell Stem Cell, 2019, 10.1016/j.stem.2019.03.018 [GEO submission]
Human Molecular Genetics Reut Bar Yaacov, Reut Eshel, Fania Shemuluvich, Tommy Kaplan, and Ramon Birnbaum
Functional characterization of the ZEB2 regulatory landscape
Human Molecular Genetics, 2018, ddy440
Nature Communications Joshua Moss, Judith Magenheim, Daniel Neiman, Hai Zemmour, Netanel Loyfer, Amit Korach, Yaacov Samet, Myriam Maoz, Henrik Druid, Peter Arner, Keng-Yeh Fu, Endre Kiss, Kirsty L. Spalding, Giora Landesberg, Aviad Zick, Albert Grinshpun, AM James Shapiro, Markus Grompe, Avigail Dreazan Wittenberg, Benjamin Glaser, Ruth Shemer*, Tommy Kaplan*, and Yuval Dor*
Comprehensive human cell-type methylation atlas reveals origins of circulating cell-free DNA in health and disease
Nature Communications, 2018, 9:5068 [GEO submission | github meth atlas]
PLoS Genetics Naama Hirsch, Reut Eshel, Reut Bar Yaacov, Tal Shahar, Fania Shemuluvich, Idit Dahan, Noam Levaot, Tommy Kaplan, Dario Lupianez, and Ramon Birnbaum
Unraveling the transcriptional regulation of TWIST1 in limb development
PLoS Genetics, 2018, 14(10):e1007738
bioRxiv Dikla Cohn, Or Zuk*, and Tommy Kaplan*
Enhancer Identification using Transfer and Adversarial Deep Learning of DNA Sequences
bioRxiv, 2018 [enhancer_CNN github | enhancer datasets]
Nature Communications Gil Ron, Yuval Globerson, Dror Moran, and Tommy Kaplan
Promoter-Enhancer Interactions Identified from Hi-C Data using Probabilistic Models and Hierarchical Topological Domains
Nature Communications, 2017, 8(1):2237 [PSYCHIC github | poster]
Nature Communications Yuval Malka, Avital Steiman-Shimony, Eran Rosenthal, Leonor Cohen-Daniel, Eliran Arbib, Liron Argaman, Hanah Margalit, Tommy Kaplan* and Michael Berger*
Post-transcriptional 3'-UTR cleavage of mRNA transcripts generates thousands of stable uncapped autonomous RNA fragments
Nature Communications, 2017, 8(1):2029 [GEO submission]
NAR Sharon Schlesinger, Binyamin Kaffe, Shai Melcer, Jose D. Aguilera, Divya M. Sivaraman, Tommy Kaplan* and Eran Meshorer*
A hyperdynamic H3.3 nucleosome marks promoter regions in pluripotent embryonic stem cells
NAR, 2017, 45(21):12181-94 [GEO submission]
FEBS Avital Sarusi Portuguez, Michal Schwartz, Rasmus Siersbaek, Ronni Nielsen, Myong-Hee Sung, Susanne Mandrup, Tommy Kaplan, and Ofir Hakim
Hierarchical role for transcription factors and chromatin structure in genome organization along adipogenesis
FEBS, 2017 [GEO submission]
PNAS Michael Klutstein*, Joshua Moss*, Tommy Kaplan, and Howard Cedar
Contribution of epigenetic mechanisms to variation in cancer risk among tissues
PNAS, 2017
EPCH Arbel Moshe and Tommy Kaplan
Genome-wide Search for Zelda-like Chromatin Signatures Identifies GAF as a Pioneer Factor in Early Fly Development
Epigenetics & Chromatin, 2017, 10(1):33 [Data | ChromSig github]
Genetics Markus Nevil, Eliana R. Bondra, Katharine N. Schulz, Tommy Kaplan, and Melissa M. Harrison
Stable Binding of the Conserved Transcription Factor Grainy Head to Its Target Genes Throughout Drosophila melanogaster Development
Genetics, 2016, 205(2):605-20 [GEO submission]
Genome Research Katharine N. Schulz, Eliana R. Bondra, Arbel Moshe, Jacqueline E. Villalta, Jason D. Lieb, Tommy Kaplan, Daniel J. McKay, and Melissa M. Harrison
Zelda is differentially required for chromatin accessibility, transcription-factor binding and gene expression in the early Drosophila embryo
Genome Research, 2015, 25(11):1715-26 [GEO submission]
eLife Xiao-Yong Li, Melissa M. Harrison, Jacqueline E. Villalta, Tommy Kaplan*, and Michael B. Eisen*
Establishment of regions of genomic activity during the Drosophila maternal to zygotic transition
eLife, 2014;3:e03737 [Digest | GEO submission | Genome Browser]
eLife Haiying Zhou, Bo Wan, Ivan Grubisic, Tommy Kaplan, and Robert Tjian
TAF7L modulates brown adipose tissue formation
eLife, 2014;3:e02811 [Digest | GEO submission | eLife Insight coverage]
PNAS Haiying Zhou, Ivan Grubisic, Ke Zheng, Ying He, P. Jeremy Wang, Tommy Kaplan, and Robert Tjian
Taf7l cooperates with Trf2 to regulate spermiogenesis
PNAS, 2013, 1317034110v1-201317034
PLoS Genetics Mathilde Paris, Tommy Kaplan, Xiao-Yong Li, Jacqueline E. Villalta, Susan E. Lott, and Michael B. Eisen
Extensive Divergence of Transcription Factor Binding in Drosophila Embryos with Highly Conserved Gene Expression
PLoS Genetics, 2013, 9(9):e1003748
Cell Axel Visel,... Dalit May,... Tommy Kaplan,... Edward M. Rubin, Ivan Ovcharenko, Len A. Pennacchio, John L. R. Rubenstein
A High-Resolution Enhancer Atlas of the Developing Telencephalon
Cell, 2013, 10.1016/j.cell.2012.12.041
eLife Haiying Zhou, Tommy Kaplan, Yan Li, Ivan Grubisic, Zhengjian Zhang, P. Jeremy Wang, Michael B. Eisen and Robert Tjian
Dual Functions of TAF7L in Adipocyte Differentiation
eLife, 2013;2:e00170
Nature Tommy Kaplan and Nir Friedman
Gene Expression: Running to Stand Still
Nature, 2012, 484:171-172
[News and Views item of Lickwar et al's Genome-wide protein-DNA binding dynamics suggest a molecular clutch for transcription factor function]
Nature Genetics Dalit May, Matthew J. Blow, Tommy Kaplan, David J. McCulley, Brian C. Jensen, Jennifer A. Akiyama, Amy Holt, Ingrid Plajzer-Frick, Malak Shoukry, Crystal Wright, Veena Afzal, Paul C. Simpson, Edward M. Rubin, Brian L. Black, James Bristow, Len A. Pennacchio, and Axel Visel
Large-Scale Discovery of Enhancers from Human Heart Tissue
Nature Genetics, 2012, 44:89-93 [ Abstract | Supp. Information ]
PLoS Genetics Melissa M. Harrison*, Xiao-Yong Li*, Tommy Kaplan*, Michael R. Botchan and Michael B. Eisen
Zelda binding in the early Drosophila melanogaster embryo marks regions subsequently activated at the maternal-to-zygotic transition
PLoS Genetics, 2011, 7(10): e1002266 [ Why Zelda is cool? | HHMI news | Grizzly Peak fitting | Nat. Rev. Gen In Brief | F1000 ]
PLoS Genetics Tommy Kaplan, Xiao-Yong Li, Peter Sabo, John A. Stamatoyannopoulos, Mark D. Biggin, and Michael B. Eisen
Quantitative Models of the Mechanisms that Control Genome-Wide Patterns of Transcription Factor Binding During Early Drosophila Development
PLoS Genetics, 2011, 7(2): e1001290 [Book chapter]
PLoS Biology Jeffrey E. Halley, Tommy Kaplan, Alice Y. Wang, Michael S. Kobor, and Jasper Rine
Roles for H2A.Z and Its Acetylation in GAL1 Transcription and Gene Induction, but Not GAL1-Transcriptional Memory
PLoS Biology, 2010, 8(6):e1000401 [F1000]
PNAS Moran Yassour*, Tommy Kaplan*, Hunter B. Fraser, Joshua Z. Levine, Jenna Pfiffner, Xian Adiconis, Gary Schroth, Shujun Luo, Irina Khrebtukova, Andreas Gnirke, Chad Nusbaum, Dawn-Anne Thompson, Nir Friedman, and Aviv Regev
Ab initio Construction of a Eukaryotic Transcriptome by Massively Parallel mRNA Sequencing [Supp. Data]
PNAS, 2009, 106(9):3264-9
PLoS Genetics Tommy Kaplan*, Chih Long Liu*, Judith A. Erkmann*, John Holik, Michael Grunstein, Paul D. Kaufman, Nir Friedman and Oliver J. Rando
Cell Cycle- and Chaperone-Mediated Regulation of H3K56ac Incorporation in Yeast
PLoS Genetics, 2008, 4(11):e1000270 [F1000]
Nature Genetics Andrew P. Capaldi, Tommy Kaplan, Ying Liu, Naomi Habib, Aviv Regev, Nir Friedman and Erin K. O'Shea
Structure and Function of a Transcriptional Network Activated by the MAPK Hog1
Nature Genetics, 2008, 40:1300-6 [Abstract | Supp. information | Supp. webpage | ChIP-chip Peak Fitting Algorithm | F1000 | NBT's news and views ]
Science Micheal F Dion*, Tommy Kaplan*, Minkyu Kim, Stephen Buratowski, Nir Friedman, and Oliver J. Rando
Dynamics of Replication-Independent Histone Turnover in Budding Yeast
Science, 2007, 315(5817):1405-8 [ Abstract | Poster | F1000 ]
PLoS Biology Chih Long Liu*, Tommy Kaplan*, Minkyu Kim, Stephen Buratowski, Stuart L. Schreiber, Nir Friedman, and Oliver J. Rando
Single-Nucleosome Mapping of Histone Modifications in S. cerevisiae
PLoS Biology, 2005, 3(10):e328 [ Interactive Map | F1000 ]
PLoS Comp Biol Tommy Kaplan, Nir Friedman and Hanah Margalit
ab initio Prediction of Transcription Factor Targets using Structural Knowledge
PLoS Comp. Biol., 2005, 1(1):e1
RECOMB 2003 Yoseph Barash, Gal Elidan, Nir Friedman, and Tommy Kaplan
Modeling Dependencies in Protein-DNA Binding Sites
Proc 7th Ann Int Conf in Comp Mol Bio (RECOMB), 2003

  A full list of publications via PubMed, Google Scholar.


Netanel Loyfer Netanel Loyfer
Computational Analysis of whole-genome bisulfite-seq DNA methylation data (Best Poster Award in Hebrew University's Open Day 2019)

Josh Moss Josh Moss
Computational Aspects of Cell-Free DNA (Kaye Innovation Award, 2019)
[MD/PhD program, with Prof. Yuval Dor]

Ido Lokay Ido Lokay
Feature Selection and Deconvolution of cell-free DNA methylation data
[MSc, CSE program]

Lior Ziv Lior Ziv
Computational analysis of short- and long-read genomics in the brain
[MSc, CS/LS program, with Dr. Ami Citri]

Hadar Mulian Hadar Mulian
Semi-constrained non-negative matrix factorization models for cell-free DNA data
[MSc, CS/LS program]

Sapir Shabi Sapir Shabi
Modeling dependencies in cell-free DNA methylation data
[MSc, CS/LS program]

Noam Glausiusz Noam Glausiusz
Modeling dependencies in DNA methylation sequencing data
[MSc, CS program, with Prof. Gal Elidan]


Guy Kelman Guy Kelman, PhD
Comparative analysis in Bat and Mouse identifies wing-specific genes and regulatory regions (Best Poster Awards in IBS 2017 and Hebrew University's Open Day 2017)

Guy is our local Batman, using mRNA-seq and ChIP-seq data to indentify Enhancers in developing Bat wings.

David Ariel David Ariel
Classification of Enhancer sequencing in multiple tissues using k-order Markovian models
[MSc, CS program]

David is developing structured Hidden Markov Models (sHMMs) of DNA sequences, using high-order probabilistic emission models.

Yuval Globerson Yuval Globerson
Analyzing 3D genomic data using Spectral methods and other Computational models
[MSc, CS program]

Paz Bunis Paz Bunis
Deep Learning models of DNA sequences for multi-label multi-class Enhancer classification
[MSc, CS program]

Paz is developing Convolutional Neural Networks for Enhancer classification based on DNA shape and seqeunce.

Dikla Cohn Dikla Cohn
Enhancer Identification using Transfer and Adversarial Deep Learning of DNA Sequences [github enhancer_CNN]
[MSc, CS]

Comparative Deep Learning of Regulatory DNA Sequences

Yuval Cantor Yuval Cantor
Detecting Cancer by Methylation Patterns
[BSc, CS/LS program]

Gil Ron Gil Ron
Finding Hierarchies in Topological Domains using a Unified Bayesian Interaction Model
[MSc, CS]

Probabilistic models to hierarchically analyzing Hi-C DNA-DNA interaction data and identify Promoter-Enhancer interactions in multiple species and cell types.

Eran Rosenthal Eran Rosenthal
Computational models of large-scale genomics data
[MSc, CS/LS program]

Hidden Markov Models (HMMs) for the segmentation of the genome into chromatin and trancriptional domains.

Shira Ginzburg Shira (Strauss) Ginzburg, MSc
Genome-wide 3D maps of regulatory interactions in the mouse developing forebrain
[MSc, CS/LS program]

Computational algorithms to analyze ChIA-PET data and integrate it with gene expression and ChIP-seq data, to identify Enhancer and their Promoter targets.

Inbar Naor Inbar Naor, MSc
Classification of Putative Regulatory Enhancers from DNA sequences
[MSc, CS]

Machine Learning sequence classifiers to identify regulatory DNA regions and decypher their function.

Arbel Moshe Arbel Moshe, MSc
Chromatin-based Temporal Clustering of Enhancers in Developing Fly Embryos
[MSc, CS]

Temporal chromatin data to study how enhancers are established during early Drosophila development.

Dror Moran Dror Moran
Finding enhancer-promoter interactions from Hi-C data
[BSc, CS/LS program]

Rom Shenhav Rom Shenhav
Role of Distal Enhancers in Regulation of Gene Expression in a Mouse Model for Chronic Cardiac Ischemia
[BSc, CS/LS program]

Elkana Baris Elkana Baris
Automated Computational Analysis of ChIA-PET DNA-DNA Interaction Data
[BSc, CS/LS program]

Chromatin Domains: Genomic segmentation using accessibility and chromatin data:

Memberships and selected awards:


Conferences, Workshops and Public Talks:


Ariel Kaplan from Jerusalem

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