Publications: PROF Tommy Kaplan

Mizrachi R, Neiman D, Rosenski J, Loyfer N, Share D, Adjedj C, Glaser B, Shpitzen M et al. ( 2025 ) . Genetic/epigenetic DNA markers for linking suspects and tissues in complex crime scenes . Briefings in Bioinformatics vol. 26 , ( 4 )

Ben-Ami R, Loyfer N, Cohen E, Fialkoff G, Sharkia I, Piyanzin S, Bogot N, Kochan D et al. ( 2025 ) . Epigenetic liquid biopsies reveal endothelial turnover and erythropoiesis in asymptomatic COVID-19 . Life Science Alliance vol. 8 , ( 10 )

Ochana B-L, Nudelman D, Cohen D, Peretz A, Piyanzin S, Gal Rosenberg O, Horn A, Loyfer N et al. ( 2025 ) . Time is encoded by methylation changes at clustered CpG sites . Cell Reports vol. 44 , ( 7 )

Rajs N, Harush-Brosh Y, Raisch R, Yakobi Arancibia R, Zoabi A, Golan GN, Shpitzen M, Wiesner S et al. ( 2025 ) . Determining time since deposition of latent fingerprints on forensic adhesive tape using ultrafast DESI-MS and machine learning . Scientific Reports vol. 15 , ( 1 )

Wang H, Mennea PD, Chan YKE, Cheng Z, Neofytou MC, Surani AA, Vijayaraghavan A, Ditter E-J et al. ( 2025 ) . A standardized framework for robust fragmentomic feature extraction from cell-free DNA sequencing data . Genome Biology vol. 26 , ( 1 )

Rosenski J, Peretz A, Magenheim J, Loyfer N, Shemer R, Glaser B, Dor Y, Kaplan T ( 2025 ) . Atlas of imprinted and allele-specific DNA methylation in the human body . Nature Communications vol. 16 , ( 1 )

Ochana B-L, Nudelman D, Cohen D, Peretz A, Piyanzin S, Gal O, Horn A, Loyfer N et al. ( 2024 ) . Time is encoded by methylation changes at clustered CpG sites .

Danov A, Pollin I, Moon E, Ho M, Wilson BA, Papathanos PA, Kaplan T, Levy A ( 2024 ) . Identification of novel toxins associated with the extracellular contractile injection system using machine learning . Molecular Systems Biology vol. 20 , ( 8 ) 859 - 879 .

Goldstein Y, Cohen OT, Wald O, Bavli D, Kaplan T, Benny O ( 2024 ) . Particle uptake in cancer cells can predict malignancy and drug resistance using machine learning . Science Advances vol. 10 , ( 22 )

Drawshy Z, Neiman D, Fridlich O, Peretz A, Magenheim J, Rozo AV, Doliba NM, Stoffers DA et al. ( 2024 ) . DNA Methylation-Based Assessment of Cell Composition in Human Pancreas and Islets . Diabetes vol. 73 , ( 4 ) 554 - 564 .

Danov A, Segev O, Bograd A, Eliyahu YB, Dotan N, Kaplan T, Levy A ( 2023 ) . Toxinome—the bacterial protein toxin database . mBio vol. 15 , ( 1 ) e01911 - e01923 .

Varshavsky M, Harari G, Glaser B, Dor Y, Shemer R, Kaplan T ( 2023 ) . Accurate age prediction from blood using a small set of DNA methylation sites and a cohort-based machine learning algorithm . Cell Reports Methods vol. 3 , ( 9 )

McNamara ME, Loyfer N, Kiliti AJ, Schmidt MO, Shabi-Porat S, Jain SS, Roth SM, McDeed AP et al. ( 2023 ) . Circulating cell-free methylated DNA reveals tissue-specific, cellular damage from radiation treatment . JCI Insight vol. 8 , ( 14 )

Fridlich O, Peretz A, Fox-Fisher I, Pyanzin S, Dadon Z, Shcolnik E, Sadeh R, Fialkoff G et al. ( 2023 ) . Elevated cfDNA after exercise is derived primarily from mature polymorphonuclear neutrophils, with a minor contribution of cardiomyocytes . Cell Reports Medicine vol. 4 , ( 6 )

Peretz A, Loyfer N, Piyanzin S, Ochana BL, Neiman D, Magenheim J, Klochendler A, Drawshy Z et al. ( 2023 ) . The DNA methylome of human vascular endothelium and its use in liquid biopsies . Med vol. 4 , ( 4 ) 263 - 281.e4 .

Rosenski J, Shifman S, Kaplan T ( 2023 ) . Predicting gene knockout effects from expression data . BMC Medical Genomics vol. 16 , ( 1 )

Loyfer N, Magenheim J, Peretz A, Cann G, Bredno J, Klochendler A, Fox-Fisher I, Shabi-Porat S et al. ( 2023 ) . A DNA methylation atlas of normal human cell types . Nature vol. 613 , ( 7943 ) 355 - 364 .

Jaber M, Radwan A, Loyfer N, Abdeen M, Sebban S, Khatib A, Yassen H, Kolb T et al. ( 2022 ) . Comparative parallel multi-omics analysis during the induction of pluripotent and trophectoderm states . Nature Communications vol. 13 , ( 1 )

Portuguez AS, Grbesa I, Tal M, Deitch R, Raz D, Kliker L, Weismann R, Schwartz M et al. ( 2022 ) . Ep300 sequestration to functionally distinct glucocorticoid receptor binding loci underlie rapid gene activation and repression . Nucleic Acids Research vol. 50 , ( 12 ) 6702 - 6714 .

Magenheim J, Rokach A, Peretz A, Loyfer N, Cann G, Amini H, Moradi P, Nagaraju S et al. ( 2022 ) . Universal lung epithelium DNA methylation markers for detection of lung damage in liquid biopsies . European Respiratory Journal vol. 60 , ( 5 )

Lubotzky A, Zemmour H, Neiman D, Gotkine M, Loyfer N, Piyanzin S, Ochana B-L, Lehmann-Werman R et al. ( 2022 ) . Liquid biopsy reveals collateral tissue damage in cancer . JCI Insight vol. 7 , ( 2 )

Fox-Fisher I, Piyanzin S, Ochana BL, Klochendler A, Magenheim J, Peretz A, Loyfer N, Moss J et al. ( 2021 ) . Remote immune processes revealed by immune-derived circulating cell-free DNA . eLife vol. 10 ,

Barefoot ME, Loyfer N, Kiliti AJ, McDeed AP, Kaplan T, Wellstein A ( 2021 ) . Detection of Cell Types Contributing to Cancer From Circulating, Cell-Free Methylated DNA . Frontiers in Genetics vol. 12 ,

Sadeh R, Sharkia I, Fialkoff G, Rahat A, Gutin J, Chappleboim A, Nitzan M, Fox-Fisher I et al. ( 2021 ) . Author Correction: ChIP-seq of plasma cell-free nucleosomes identifies gene expression programs of the cells of origin . Nature Biotechnology vol. 39 , ( 5 ) 642 - 642 .

Sadeh R, Sharkia I, Fialkoff G, Rahat A, Gutin J, Chappleboim A, Nitzan M, Fox-Fisher I et al. ( 2021 ) . Author Correction: ChIP-seq of plasma cell-free nucleosomes identifies gene expression programs of the cells of origin . Nature Biotechnology vol. 39 , ( 5 ) 642 - 642 .

Sadeh R, Sharkia I, Fialkoff G, Rahat A, Gutin J, Chappleboim A, Nitzan M, Fox-Fisher I et al. ( 2021 ) . ChIP-seq of plasma cell-free nucleosomes identifies gene expression programs of the cells of origin . Nature Biotechnology vol. 39 , ( 5 ) 586 - 598 .

Schwartz M, Portugez AS, Attia BZ, Tannenbaum M, Cohen L, Loza O, Chase E, Turman Y et al. ( 2020 ) . Genomic retargeting of p53 and CTCF is associated with transcriptional changes during oncogenic HRas-induced transformation . Communications Biology vol. 3 , ( 1 )

Habib N, McCabe C, Medina S, Varshavsky M, Kitsberg D, Dvir-Szternfeld R, Green G, Dionne D et al. ( 2020 ) . Disease-associated astrocytes in Alzheimer’s disease and aging . Nature Neuroscience vol. 23 , ( 6 ) 701 - 706 .

Brill-Karniely Y, Dror D, Duanis-Assaf T, Goldstein Y, Schwob O, Millo T, Orehov N, Stern T et al. ( 2020 ) . Triangular correlation (TrC) between cancer aggressiveness, cell uptake capability, and cell deformability . Science Advances vol. 6 , ( 3 )

Benchetrit H, Jaber M, Zayat V, Sebban S, Pushett A, Makedonski K, Zakheim Z, Radwan A et al. ( 2019 ) . Direct Induction of the Three Pre-implantation Blastocyst Cell Types from Fibroblasts . Cell Stem Cell vol. 24 , ( 6 ) 983 - 994.e7 .

Yaacov RB, Eshel R, Farhi E, Shemuluvich F, Kaplan T, Birnbaum RY ( 2018 ) . Functional characterization of the ZEB2 regulatory landscape . Human Molecular Genetics vol. 28 , ( 9 ) 1487 - 1497 .

Moss J, Magenheim J, Neiman D, Zemmour H, Loyfer N, Korach A, Samet Y, Maoz M et al. ( 2018 ) . Comprehensive human cell-type methylation atlas reveals origins of circulating cell-free DNA in health and disease . Nature Communications vol. 9 , ( 1 )

Hirsch N, Eshel R, Yaacov RB, Shahar T, Shmulevich F, Dahan I, Levaot N, Kaplan T et al. ( 2018 ) . Unraveling the transcriptional regulation of TWIST1 in limb development . PLOS Genetics vol. 14 , ( 10 )

Schwartz M, Sarusi A, Deitch RT, Tal M, Raz D, Sung M-H, Kaplan T, Hakim O ( 2018 ) . Comparative analysis of T4 DNA ligases and DNA polymerases used in chromosome conformation capture assays . BioTechniques vol. 58 , ( 4 ) 195 - 199 .

Zhu G, Deng W, Hu H, Ma R, Zhang S, Yang J, Peng J, Kaplan T et al. ( 2018 ) . Reconstructing spatial organizations of chromosomes through manifold learning . Nucleic Acids Research vol. 46 , ( 8 ) e50 - e50 .

Ron G, Globerson Y, Moran D, Kaplan T ( 2017 ) . Promoter-enhancer interactions identified from Hi-C data using probabilistic models and hierarchical topological domains . Nature Communications vol. 8 , ( 1 )

Malka Y, Steiman-Shimony A, Rosenthal E, Argaman L, Cohen-Daniel L, Arbib E, Margalit H, Kaplan T et al. ( 2017 ) . Post-transcriptional 3´-UTR cleavage of mRNA transcripts generates thousands of stable uncapped autonomous RNA fragments . Nature Communications vol. 8 , ( 1 )

Schlesinger S, Kaffe B, Melcer S, Aguilera JD, Sivaraman DM, Kaplan T, Meshorer E ( 2017 ) . A hyperdynamic H3.3 nucleosome marks promoter regions in pluripotent embryonic stem cells . Nucleic Acids Research vol. 45 , ( 21 ) 12181 - 12194 .

Portuguez AS, Schwartz M, Siersbaek R, Nielsen R, Sung M, Mandrup S, Kaplan T, Hakim O ( 2017 ) . Hierarchical role for transcription factors and chromatin structure in genome organization along adipogenesis . The FEBS Journal vol. 284 , ( 19 ) 3230 - 3244 .

Moshe A, Kaplan T ( 2017 ) . Genome-wide search for Zelda-like chromatin signatures identifies GAF as a pioneer factor in early fly development . Epigenetics & Chromatin vol. 10 , ( 1 )

Klutstein M, Moss J, Kaplan T, Cedar H ( 2017 ) . Contribution of epigenetic mechanisms to variation in cancer risk among tissues . Proceedings of the National Academy of Sciences of the United States of America vol. 114 , ( 9 ) 2230 - 2234 .

Nevil M, Bondra ER, Schulz KN, Kaplan T, Harrison MM ( 2017 ) . Stable Binding of the Conserved Transcription Factor Grainy Head to its Target Genes Throughout Drosophila melanogaster Development . Genetics vol. 205 , ( 2 ) 605 - 620 .

Schulz KN, Bondra ER, Moshe A, Villalta JE, Lieb JD, Kaplan T, McKay DJ, Harrison MM ( 2015 ) . Zelda is differentially required for chromatin accessibility, transcription factor binding, and gene expression in the early Drosophila embryo . Genome Research vol. 25 , ( 11 ) 1715 - 1726 .

Li X-Y, Harrison MM, Villalta JE, Kaplan T, Eisen MB ( 2014 ) . Establishment of regions of genomic activity during the Drosophila maternal to zygotic transition . eLife vol. 3 ,

Zhou H, Wan B, Grubisic I, Kaplan T, Tjian R ( 2014 ) . TAF7L modulates brown adipose tissue formation . eLife vol. 3 ,

Zhou H, Grubisic I, Zheng K, He Y, Wang PJ, Kaplan T, Tjian R ( 2013 ) . Taf7l cooperates with Trf2 to regulate spermiogenesis . Proceedings of the National Academy of Sciences of the United States of America vol. 110 , ( 42 ) 16886 - 16891 .

Paris M, Kaplan T, Li XY, Villalta JE, Lott SE, Eisen MB ( 2013 ) . Extensive Divergence of Transcription Factor Binding in Drosophila Embryos with Highly Conserved Gene Expression . PLOS Genetics vol. 9 , ( 9 )

Paris M, Kaplan T, Li XY, Villalta JE, Lott SE, Eisen MB ( 2013 ) . Extensive divergence of transcription factor binding in Drosophila embryos with highly conserved gene expression .

Visel A, Taher L, Girgis H, May D, Golonzhka O, Hoch RV, McKinsey GL, Pattabiraman K et al. ( 2013 ) . A High-Resolution Enhancer Atlas of the Developing Telencephalon . Cell vol. 152 , ( 4 ) 895 - 908 .

Zhou H, Kaplan T, Li Y, Grubisic I, Zhang Z, Wang PJ, Eisen MB, Tjian R ( 2013 ) . Dual functions of TAF7L in adipocyte differentiation . eLife vol. 2 ,

Perets R, Kaplan T, Stein I, Hidas G, Tayeb S, Avraham E, Ben-Neriah Y, Simon I et al. ( 2012 ) . Genome-Wide Analysis of Androgen Receptor Targets Reveals COUP-TF1 as a Novel Player in Human Prostate Cancer . PLOS ONE vol. 7 , ( 10 )

Kaplan T, Friedman N ( 2012 ) . Running to stand still . Nature vol. 484 , ( 7393 ) 171 - 172 .

Kaplan T, Biggin MD ( 2012 ) . Chapter 11 Quantitative Models of the Mechanisms that Control Genome-Wide Patterns of Animal Transcription Factor Binding . Computational Methods in Cell Biology , vol. 110 , Elsevier

Kaplan T, Biggin MD ( 2012 ) . Quantitative Models of the Mechanisms that Control Genome-Wide Patterns of Animal Transcription Factor Binding . Methods in Cell Biology , vol. 110 ,

May D, Blow MJ, Kaplan T, McCulley DJ, Jensen BC, Akiyama JA, Holt A, Plajzer-Frick I et al. ( 2011 ) . Large-scale discovery of enhancers from human heart tissue . Nature Genetics vol. 44 , ( 1 ) 89 - 93 .

Harrison MM, Li X-Y, Kaplan T, Botchan MR, Eisen MB ( 2011 ) . Zelda Binding in the Early Drosophila melanogaster Embryo Marks Regions Subsequently Activated at the Maternal-to-Zygotic Transition . PLOS Genetics vol. 7 , ( 10 )

Zhang Y, Handley D, Kaplan T, Yu H, Bais AS, Richards T, Pandit KV, Zeng Q et al. ( 2011 ) . High Throughput Determination of TGFβ1/SMAD3 Targets in A549 Lung Epithelial Cells . PLOS ONE vol. 6 , ( 5 )

Kaplan T, Li X-Y, Sabo PJ, Thomas S, Stamatoyannopoulos JA, Biggin MD, Eisen MB ( 2011 ) . Quantitative Models of the Mechanisms That Control Genome-Wide Patterns of Transcription Factor Binding during Early Drosophila Development . PLOS Genetics vol. 7 , ( 2 )

Halley JE, Kaplan T, Wang AY, Kobor MS, Rine J ( 2010 ) . Roles for H2A.Z and Its Acetylation in GAL1 Transcription and Gene Induction, but Not GAL1-Transcriptional Memory . PLOS Biology vol. 8 , ( 6 )

Yassour M, Kaplan T, Fraser HB, Levin JZ, Pfiffner J, Adiconis X, Schroth G, Luo S et al. ( 2009 ) . Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing . Proceedings of the National Academy of Sciences of the United States of America vol. 106 , ( 9 ) 3264 - 3269 .

Friedberg I, Kaplan T, Margalit H ( 2008 ) . Evaluation of PSI‐BLAST alignment accuracy in comparison to structural alignments . Protein Science vol. 9 , ( 11 ) 2278 - 2284 .

Kaplan T, Liu CL, Erkmann JA, Holik J, Grunstein M, Kaufman PD, Friedman N, Rando OJ ( 2008 ) . Cell Cycle– and Chaperone-Mediated Regulation of H3K56ac Incorporation in Yeast . PLOS Genetics vol. 4 , ( 11 )

Capaldi AP, Kaplan T, Liu Y, Habib N, Regev A, Friedman N, O'Shea EK ( 2008 ) . Structure and function of a transcriptional network activated by the MAPK Hog1 . Nature Genetics vol. 40 , ( 11 ) 1300 - 1306 .

Yassour M, Kaplan T, Jaimovich A, Friedman N ( 2008 ) . Nucleosome positioning from tiling microarray data . Bioinformatics vol. 24 , ( 13 ) i139 - i146 .

Habib N, Kaplan T, Margalit H, Friedman N ( 2008 ) . A Novel Bayesian DNA Motif Comparison Method for Clustering and Retrieval . PLOS Computational Biology vol. 4 , ( 2 )

Dion MF, Kaplan T, Kim M, Buratowski S, Friedman N, Rando OJ ( 2007 ) . Dynamics of Replication-Independent Histone Turnover in Budding Yeast . Science vol. 315 , ( 5817 ) 1405 - 1408 .

Liu CL, Kaplan T, Kim M, Buratowski S, Schreiber SL, Friedman N, Rando OJ ( 2005 ) . Single-Nucleosome Mapping of Histone Modifications in S. cerevisiae . PLOS Biology vol. 3 , ( 10 )

Kaplan T, Friedman N, Margalit H ( 2005 ) . Ab Initio Prediction of Transcription Factor Targets Using Structural Knowledge . PLOS Computational Biology vol. 1 , ( 1 )

Kaplan T, Friedman N, Margalit H ( 2005 ) . Predicting Transcription Factor Binding Sites Using Structural Knowledge . Lecture Notes in Computer Science . vol. 3500 , 522 - 537 .

Barash Y, Elidan G, Kaplan T, Friedman N ( 2004 ) . CIS: compound importance sampling method for protein–DNA binding site p-value estimation . Bioinformatics vol. 21 , ( 5 ) 596 - 600 .

Barash Y, Elidan G, Friedman N, Kaplan T ( 2003 ) . Modeling dependencies in protein-DNA binding sites . Conference: Proceedings of the seventh annual international conference on Research in computational molecular biology28 - 37 .

Friedberg I, Kaplan T, Margalit H ( 2000 ) . Glimmers in the midnight zone: characterization of aligned identical residues in sequence-dissimilar proteins sharing a common fold . Bioinformatics . vol. 8 , 162 - 170 .

Loyfer N, Magenheim J, Peretz A, Cann G, Bredno J, Klochendler A, Fox-Fisher I, Shabi-Porat S et al. . A human DNA methylation atlas reveals principles of cell type-specific methylation and identifies thousands of cell type-specific regulatory elements .

Varshavsky M, Harari G, Glaser B, Dor Y, Shemer R, Kaplan T . Accurate age prediction from blood using of small set of DNA methylation sites and a cohort-based machine learning algorithm .

Patel T, Schwarz R, Riege K, Varshavsky M, Kestler HA, Kaplan T, Hoffmann S, van Bömmel A . An improved epigenetic age estimation with TFMethyl Clock reveals DNA methylation changes during aging in transcription factor binding sites .

Rosenski J, Peretz A, Magenheim J, Loyfer N, Shemer R, Glaser B, Dor Y, Kaplan T . Atlas of imprinted and allele-specific DNA methylation in the human body .

Barefoot ME, Loyfer N, Kiliti AJ, Schmidt MO, Shabi-Porat S, Jain S, Roth SM, McDeed AP et al. . Cell-free, methylated DNA in blood samples reveals tissue-specific, cellular damage from radiation treatment .

Sadeh R, Sharkia I, Fialkoff G, Rahat A, Gutin J, Chappleboim A, Nitzan M, Fox-Fisher I et al. . ChIP-seq of plasma cell-free nucleosomes identifies cell-of-origin gene expression programs .

Jaber M, Radwan A, Loyfer N, Abdeen M, Sebban S, Kolb T, Zapatka M, Makedonski K et al. . Comparative Parallel Multi-Omics Analysis During the Induction of Pluripotent and Trophectoderm States .

Moss J, Magenheim J, Neiman D, Zemmour H, Loyfer N, Korach A, Samet Y, Maoz M et al. . Comprehensive human cell-type methylation atlas reveals origins of circulating cell-free DNA in health and disease .

Cohn D, Zuk O, Kaplan T . Enhancer Identification using Transfer and Adversarial Deep Learning of DNA Sequences .

Ben-Ami R, Loyfer N, Cohen E, Fialkoff G, Sharkia I, Bogot N, Kochan D, Kalak G et al. . Epigenetic liquid biopsies reveal elevated vascular endothelial cell turnover and erythropoiesis in asymptomatic COVID-19 patients .

Li X-Y, Harrison MM, Kaplan T, Eisen MB . Establishment of regions of genomic activity during the Drosophila maternal to zygotic transition .

Zhu G, Deng W, Hu H, Ma R, Zhang S, Yang J, Peng J, Kaplan T et al. . GEM: A manifold learning based framework for reconstructing spatial organizations of chromosomes .

Portuguez AS, Grbesa I, Tal M, Deitch R, Raz D, Weismann R, Schwartz M, Loza O et al. . Gene activation and repression by the glucocorticoid receptor are mediated by sequestering Ep300 and two modes of chromatin binding .

Fuchs G, Rosenthal E, Bublik D-R, Kaplan T, Oren M . Gene body H2B monoubiquitylation regulates gene-selective RNA Polymerase II pause release and is not rate limiting for transcription elongation .

Moshe A, Kaplan T . Genome-wide Search for Zelda-like Chromatin Signatures Identifies GAF as a Pioneer Factor in Early Fly Development .

Schwartz M, Portugez AS, Attia BZ, Tannenbaum M, Loza O, Chase A, Turman Y, Kaplan T et al. . Genomic Retargeting of Tumor Suppressors p53 and CTCF Promotes Oncogenesis .

Ron G, Moran D, Kaplan T . Promoter-Enhancer Interactions Identified from Hi-C Data using Probabilistic Models and Hierarchical Topological Domains .

Fox-Fisher I, Piyanzin S, Ochana B-L, Klochendler A, Magenheim J, Peretz A, Loyfer N, Moss J et al. . Remote immune processes revealed by immune-derived circulating cell-free DNA .

Mandel T, Landau U, Kaplan T, Williams LE . The H3K27me3 epigenetic mark is crucial for callus cell identity and for the acquisition of new fate during root and shoot regeneration .

Rosenski J, Sabag O, Marcus E, Loyfer N, Dor Y, Cedar H, Kaplan T . The genetic basis for DNA methylation variation across tissues and development .

Danov A, Segev O, Bograd A, Eliyahu YB, Dotan N, Kaplan T, Levy A . Toxinome - The Bacterial Protein Toxin Database .

Loyfer N, Rosenski J, Kaplan T . wgbstools: A computational suite for DNA methylation sequencing data representation, visualization, and analysis .