Tommy Kaplan - תומי קפלן

Prof. Tommy Kaplan - פרופ׳ תומי קפלן

Tommy Kaplan
פרופסור, ראש החוג לביולוגיה חישובית
בית הספר להנדסה ולמדעי המחשב, בית הספר לרפואה
האוניברסיטה העברית בירושלים

Professor, Head of the Computational Biology Program
School of Computer Science and Engineering, Faculty of Medicine
The Hebrew University of Jerusalem, Israel

Computational Biology

DNA Methylation of cell-free DNA, Computational Epigenomics, Enhancers and Gene Regulation, Machine Learning

Contact Information:

Prof. Tommy Kaplan
School of Computer Science and Engineering
The Hebrew University
Jerusalem 9190401
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:

Nature 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 Grinbaum, 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 DNA methylation atlas of normal human cell types
Nature, 2023 [GEO GSE186458 | poster | הארץ | הידען | Research Highlight]
Genome browser sessions: hg19 | hg38
Software: wgbstools | UXM fragment-level deconvolution
Cell Reports Methods Miri Varshavsky, Gil Harari, Benjamin Glaser, Yuval Dor, Ruth Shemer, and Tommy Kaplan
Accurate age prediction from blood using a small set of DNA methylation sites and a cohort-based machine learning algorithm
Cell Reports Methods, 2023 [GP-age epigenetic clock | poster | GEO GSE207605]
eLife Megan E. McNamara*, Netanel Loyfer*, Amber J. Kiliti, Marcel O. Schmidt, Sapir Shabi-Porat, Sidharth Jain, Sarah Martinez Roth, A. Patrick McDeed IV, Nesreen Shahrour, Elizabeth Ballew, Yun-Tien Lin, Heng-Hong Li, Anne Deslattes Mays, Sonali Rudra, Anna T. Riegel, Keith Unger*, Tommy Kaplan*, and Anton Wellstein*
Circulating cell-free methylated DNA reveals tissue-specific, cellular damage from radiation treatment
JCI Insight, 2023
Software: wgbstools | fragment-level Markov-model deconvolution
Med Ayelet Peretz*, Netanel Loyfer*, Sheina Piyanzin, Bracha Lea Ochana, Daniel Neiman, Judith Magenheim, Agnes Klochendler, Zeina Drawshy, Ilana Fox-Fisher, Ori Fridlich, Joshua Moss, Daniel Cohen, Hai Zemmour, Gordon Cann, Joerg Bredno, Oliver Venn, Batia Avni, Tural Alekberli, Yaacov Samet, Amit Korach, Ori Wald, Vladimir Yutkin, Uzi Izhar, Nir Pillar, Markus Grompe, Zvi Fridlender, Ariel Rokach, David Planer, Giora Landesberg, Benjamin Glaser, Ruth Shemer, Tommy Kaplan and Yuval Dor
The DNA methylome of human vascular endothelium and its use in liquid biopsies
Med, 2023
BMC Medical Genomics Jonathan Rosenski, Sagiv Shifman, and Tommy Kaplan
Predicting gene knockout effects from expression data
BMC Medical Genomics, 2023 [github]
bioRxiv Aleks Danov, Ofir Segev, Avi Bograd, Yedidya Ben Eliyahu, Noam Dotan, Tommy Kaplan*, and Asaf Levy*
Toxinome - The Bacterial Protein Toxin Database
mBio, 2023 [Toxinome: the Bacterial toxin database]
Nature Communications 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 GSE171127 | הארץ | הידען ]
eLife 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
eLife 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
Frontiers in Genetics 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
Nature Neuroscience 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 GSE143758]
Science Advances 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 GSE137316, GSE135193]
Nature Biotechnology 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 [הארץ]
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 ]
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 | github meth atlas]
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 ]
PNAS Michael Klutstein*, Joshua Moss*, Tommy Kaplan, and Howard Cedar
Contribution of epigenetic mechanisms to variation in cancer risk among tissues
PNAS, 2017
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 | 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
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]
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
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.

Students:

Netanel Loyfer 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 Jonathan Rosenski
Machine learning analysis of parental imprinting in DNA methylation data
[PhD]
Roy Mizrachi Roy Mizrachi
DNA methylation in forensics sciences
[MSc]
Mika Schechter Mika Schechter
Predicting 3D genome folding using computational methods
[MSc]
Roni Schwartz Roni Schwartz
DNA methylation hotspots and nucleosomes
[MSc]
Daniel Nudelman Daniel Nudelman
Deep learning predictions of age from DNA methylation
[MSc]

Alumni:

Miri Varshavsky Miri Varshavsky
GP-Age: Accurate age prediction from blood using few methylation sites [Poster]
(Best Poster Award in Ilanit 2023)
[MSc]
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
(Best Poster Award at the Broad-ISF conference 2019)
[MSc, CS/LS program]
Noam Glausiusz Noam Glausiusz
Modeling dependencies in DNA methylation sequencing data
[MSc, CS program, with Prof. Gal Elidan]
Ido Lokay Ido Lokay
Phylogenetic Mixture Model for DNA Methylation Patterns Formation During Cell Differentiation
[MSc, CSE program]
Josh Moss Josh Moss
Computational Aspects of Cell-Free DNA (Kaye Innovation Award, 2019)
[MD/PhD program, with Prof. Yuval Dor]
Lior Ziv Lior Ziv
Computational analysis of short- and long-read genomics in the brain
[MSc, CS/LS program, with Dr. Ami Citri]
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)
[Postdoc]

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

David Taub 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 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]

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.

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.

Software:

Memberships and selected awards:

Conferences, Workshops and Public Talks:

Teaching:

Ariel Kaplan from Jerusalem בית ספר כרמים גבעת רם