Tommy Kaplan - תומי קפלן

Senior Lecturer
School of Computer Science and Engineering
The Hebrew University of Jerusalem, Israel

Computational Biology

Enhancers, Genomics, Transcriptional regulation by distal enhancers,
Computational Epigenomics and Chromatin, Machine Learning

Now recruiting excellent students! (strong background in CS required)

Contact Information:

Dr. 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 profile


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

Shira is developing computational algorithms to analyze ChIA-PET data and integrate it with gene expression and ChIP-seq data

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

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

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

Inbar is developing Machine Learning classifiers to identify regulatory DNA regions in our genomes and decypher their function

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

Gil is using probabilistic models to analyzing Hi-C DNA-DNA interaction data and identify the hierarchical organization of our genome

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

Arbel is using our temporal chromatin data to study how enhancers are established during early Drosophila development

Joint Students:

Avital Sarusi Avital Sarusi
The Interplay between Genomic Architecture and Transcription Regulation during Differentiation - Adipogenesis as a Model
[PhD, with Dr. Ofir Hakim, Bar-Ilan University]


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]

Selected Publications:

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
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 | Genome Browser
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
[Supplemental data | GEO submission | Genome Browser]
Nature Tommy Kaplan and Nir Friedman
Gene Expression: Running to Stand Still
Nature, 2012, 484:171-172
[News and Views item of Lickwar, Lieb 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 | ZLD genome browser | 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 | SOM | Data | 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 | Data | 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.

Chromatin Domains: Genomic segmentation using accessibility and chromatin data:

Memberships and selected awards:


As a new faculty member, I organize two of the departmental seminars:

Conferences and Workshops:


Ariel Kaplan from Jerusalem

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