Prof. Tommy Kaplan - פרופ׳ תומי קפלן

ראש החוג לביולוגיה חישובית בית הספר להנדסה ולמדעי המחשב, בית הספר לרפואה Associate Professor School of Computer Science and Engineering, Faculty of Medicine The Hebrew University of Jerusalem, Israel Head Computer Science and Computational Biology program (jointly with Prof. Michal Linial)

Contact Information:

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

E-mail: tommy.kaplan@mail.huji.ac.il
Office: Rothberg B-529
Phone/Fax: +972-2-5494506

  CV of Tommy Kaplan | Google Scholar | ORCiD

Selected Publications:

Netanel Loyfer*, Judith Magenheim*, Ayelet Peretz*, Gordon Cann, Joerg Bredno, Agnes Klochendler, Ilana Fox-Fisher, Sapir Shabi-Porat, Merav Hecht, Tsuria Pelet, Joshua Moss, Zeina Drawshy, Hamed Amini, Patriss Moradi, Sudharani Nagaraju, Dvora Bauman, David Shveiky, Shay Porat, Gurion Rivkin, Omer Or, Nir Hirshoren, Einat Carmon, Alon Pikarsky, Abed Khalaileh, Gideon Zamir, Ronit Grinboim, Machmud Abu Gazala, Ido Mizrahi, Noam Shussman, Amit Korach, Ori Wald, Uzi Izhar, Eldad Erez, Vladimir Yutkin, Yaacov Samet, Devorah Rotnemer Golinkin, Kirsty L. Spalding, Henrik Druid, Peter Arner, A.M. James Shapiro, Markus Grompe, Alex Aravanis, Oliver Venn, Arash Jamshidi, Ruth Shemer, Yuval Dor*, Benjamin Glaser*, and Tommy Kaplan* A human DNA methylation atlas reveals principles of cell type-specific methylation and identifies thousands of cell type-specific regulatory elements bioRxiv, 2022 [GEO submission GSE186458 | poster]

Mohammad Jaber*, Ahmed Radwan*, Netanel Loyfer*, Mufeed Abdeen, Shulamit Sebban, Thorsten Kolb, Marc Zapatka, Kirill Makedonski, Aurelie Ernst, Tommy Kaplan*, and Yossi Buganim* Comparative Parallel Multi-Omics Analysis During the Induction of Pluripotent and Trophectoderm States Nature Communications, 2022 [GEO submission GSE171127]

Asael Lubotzky, Hai Zemmour, Daniel Neiman, Marc Gotkine, Netanel Loyfer, Sheina Piyanzin, Bracha-Lea Ochana, Roni Lehmann-Werman, Daniel Cohen, Joshua Moss, Judith Magenheim, Maureen F. Loftus, Lauren Brais, Kimmie Ng, Raul Mostoslavsky, Brian M. Wolpin, Aviad Zick, Myriam Maoz, Albert Grinshpun, Anatoli Kustanovich, Chen Makranz, Jonathan E. Cohen, Tamar Peretz, Ayala Hubert, Mark Temper, Azzam Salah, Shani Avniel-Polak, Simona Grozinsky-Glasberg, Kirsty L. Spalding, Ariel Rokach, Tommy Kaplan, Benjamin Glaser, Ruth Shemer, and Yuval Dor Liquid biopsy reveals collateral tissue damage in cancer JCI Insight, 2022

Ilana Fox-Fisher, Sheina Piyanzin, Bracha Lea Ochana, Agnes Klochendler, Judith Magenheim, Ayelet Peretz, Netanel Loyfer, Joshua Moss, Daniel Cohen, Yaron Drori, Nehemya Friedman, Michal Mandelboim, Marc E Rothenberg, Julie M Caldwell, Mark Rochman, Arash Jamshidi, Gordon Cann, David Lavi, Tommy Kaplan, Benjamin Glaser, Ruth Shemer, and Yuval Dor Remote immune processes revealed by immune-derived circulating cell-free DNA eLife, 2021

Megan E. Barefoot, Netanel Loyfer, Amber J. Kiliti, A. Patrick McDeed IV, Tommy Kaplan, and Anton Wellstein Detection of Cell Types Contributing to Cancer From Circulating, Cell-Free Methylated DNA Frontiers in Genetics, 2021

Naomi Habib, Cristin McCabe, Sedi Medina, Miriam Varshavsky, Daniel Kitsberg, Raz Dvir-Szternfeld, Gilad Green, Danielle Dionne, Lan Nguyen, Jamie L. Marshall, Fei Chen, Feng Zhang, Tommy Kaplan, Aviv Regev, and Michal Schwartz Disease-associated astrocytes in Alzheimer’s disease and aging Nature Neuroscience, 2020 [GEO submission GSE143758]

Yifat Brill-Karniely, Dvir Dror, Tal Duanis-Assaf, Yoel Goldstein, Ouri Schwob, Talya Millo, Natalie Orehov, Tal Stern, Mohammad Jaber, Netanel Loyfer, Margarita Vosk-Artzi, Hadar Benyamini, Diane Bielenberg, Tommy Kaplan, Yosef Buganim, Meital Reches and Ofra Benny Triangular correlation (TrC) between cancer aggressiveness, cell uptake capability, and cell deformability Science Advances, 6(3):eaax2861, 10.1126/sciadv.aax2861 [GEO submissions GSE137316, GSE135193]

Ronen Sadeh, Israa Sharkia, ... , Tommy Kaplan, Ruth Shemer, David Planer, Eithan Galun, Benjamin Glaser, Aviad Zik, Yuval Dor, and Nir Friedman ChIP-seq of plasma cell-free nucleosomes identifies gene expression programs of the cells of origin Nature Biotechnology, 2021

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]

Reut Bar Yaacov, Reut Eshel, Fania Shemuluvich, Tommy Kaplan, and Ramon Birnbaum Functional characterization of the ZEB2 regulatory landscape Human Molecular Genetics, 2018, ddy440

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]

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

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]

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]

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]

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]

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]

Michael Klutstein*, Joshua Moss*, Tommy Kaplan, and Howard Cedar Contribution of epigenetic mechanisms to variation in cancer risk among tissues PNAS, 2017

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]

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]

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]

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]

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]

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

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

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

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

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]

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 ]

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 ]

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]

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]

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

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]

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 ]

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 ]

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 ]

Tommy Kaplan, Nir Friedman and Hanah Margalit ab initio Prediction of Transcription Factor Targets using Structural Knowledge PLoS Comp. Biol., 2005, 1(1):e1

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.

Students:

Netanel Loyfer Computational Analysis of whole-genome bisulfite-seq DNA methylation data (Best Poster Awards in Hebrew University's Open Day 2019, Broad-ISF conference 2019) [PhD]

Jonathan Rosenski Machine learning analysis of parental imprinting in DNA methylation data [PhD]

Roy Mizrachi DNA methylation in forensics sciences [MSc]

Itay Gera Optimal loss functions for DNA methylation deconvolution algorithms [MSc]

Miri Varshavsky Machine learning-based DNA methylation age predictions [MSc]

Mika Schechter Predicting 3D genome folding using computational methods [MSc]

Alumni:

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

Sapir Shabi Modeling dependencies in cell-free DNA methylation data (Best Poster Award at the Broad-ISF conference 2019) [MSc, CS/LS program]

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

Ido Lokay Phylogenetic Mixture Model for DNA Methylation Patterns Formation During Cell Differentiation [MSc, CSE program]

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

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

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

David Taub 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 Analyzing 3D genomic data using Spectral methods and other Computational models. [MSc, CS program]

Paz Bunis Deep Learning models of DNA sequences for multi-label multi-class Enhancer classification [MSc, CS program] Convolutional Neural Networks for Enhancer classification based on DNA shape and seqeunce.

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.

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 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 (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, 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, 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.

Software:

• wgbstools - A computational suite for DNA methylation sequencing data representation, visualization, and analysis
  
  By Netanel Loyfer et al.

Memberships and selected awards:

• 2009 GE & Science Prize for Young Life Scientists [Haaretz, (הארץ) | Israel21C]
• Member, I-CORE center for Gene Regulation in Complex Human Diseases (Headed by Prof. Howard Cedar)
  
• Member, I-CORE center for Chromatin and RNA in Gene Regulation (Headed by Prof. Nir Friedman)
  

Seminars:

• Bioclub - Computational Biology, Systems Biology, Genomics, Proteomics, Epigenetics, and additional areas of modern biology.
• Computer Science Departmental Colloquium

Conferences, Workshops and Public Talks:

• International Conference on Genome Regulation in 3D, 28-30/6/2015, Weizmann Inst.
• I-CORE workshop on Transcriptional circuitry and the regulatory conformation of the genome, 1/2/2015, Hebrew Univ.
• Hebrew University Gender Committee workshop on - How to Choose a Postdoc Position - איך לבחור מקום לפוסטדוק - Watch on YouTube
  
• Women in Science 2019
• Popular talk on Regulatory Regions in the Human Genome - מדוע תשע"ו | פרופ׳ תומי קפלן | הגנום הלא-מקודד: מציאת ופענוח אזורי הבקרה בגנום האדם
• Popular talk on Computer Science and Genomics - פרופ׳ תומי קפלן | גנומיקה וביולוגיה חישובית

Teaching:

• Research Methods in Computational Biology (2nd year seminar) [2014-present]
• Algorithms in Computational Biology (CBIO) [2015-present]
• Computational Genomics [2014-present]
• Advanced topics in Computational Biology (MSc seminar) [2013-present]
• Advanced Practical Machine Learning [2013-2018]
• Systems Biology of Transcription [2013-2019]
• High-Throughput Methods in Biology [2012-2014]

Ariel Kaplan from Jerusalem בית ספר כרמים גבעת רם