Works by Kaplan, Tommy

Results: 36

Nucleosome positioning from tiling microarray data.

Published in:

Bioinformatics, 2008, v. 24, n. 13, p. i139, doi. 10.1093/bioinformatics/btn151

By:

Moran Yassour;
Tommy Kaplan;
Ariel Jaimovich;
Nir Friedman

Publication type:

Article

Large-scale discovery of enhancers from human heart tissue.

Published in:

Nature Genetics, 2012, v. 44, n. 1, p. 89, doi. 10.1038/ng.1006

By:

May, Dalit;
Blow, Matthew J;
Kaplan, Tommy;
McCulley, David J;
Jensen, Brian C;
Akiyama, Jennifer A;
Holt, Amy;
Plajzer-Frick, Ingrid;
Shoukry, Malak;
Wright, Crystal;
Afzal, Veena;
Simpson, Paul C;
Rubin, Edward M;
Black, Brian L;
Bristow, James;
Pennacchio, Len A;
Visel, Axel

Publication type:

Article

Structure and function of a transcriptional network activated by the MAPK Hog1.

Published in:

Nature Genetics, 2008, v. 40, n. 11, p. 1300, doi. 10.1038/ng.235

By:

Capaldi, Andrew P;
Kaplan, Tommy;
Liu, Ying;
Habib, Naomi;
Regev, Aviv;
Friedman, Nir;
O'Shea, Erin K

Publication type:

Article

Remote immune processes revealed by immune-derived circulating cell-free DNA.

Published in:

eLife, 2021, p. 1, doi. 10.7554/eLife.70520

By:

Fox-Fisher, Ilana;
Piyanzin, Sheina;
Ochana, Bracha Lea;
Klochendler, Agnes;
Magenheim, Judith;
Peretz, Ayelet;
Loyfer, Netanel;
Moss, Joshua;
Cohen, Daniel;
Drori, Yaron;
Friedman, Nehemya;
Mandelboim, Michal;
Rothenberg, Marc E.;
Caldwell, Julie M.;
Rochman, Mark;
Jamshidi, Arash;
Cann, Gordon;
Lavi, David;
Kaplan, Tommy;
Glaser, Benjamin

Publication type:

Article

Comparative parallel multi-omics analysis during the induction of pluripotent and trophectoderm states.

Published in:

Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-31131-8

By:

Jaber, Mohammad;
Radwan, Ahmed;
Loyfer, Netanel;
Abdeen, Mufeed;
Sebban, Shulamit;
Khatib, Areej;
Yassen, Hazar;
Kolb, Thorsten;
Zapatka, Marc;
Makedonski, Kirill;
Ernst, Aurelie;
Kaplan, Tommy;
Buganim, Yosef

Publication type:

Article

Genome-wide search for Zelda-like chromatin signatures identifes GAF as a pioneer factor in early fy development.

Published in:

Epigenetics & Chromatin, 2017, v. 10, p. 1, doi. 10.1186/s13072-017-0141-5

By:

Moshe, Arbel;
Kaplan, Tommy

Publication type:

Article

Genome-Wide Analysis of Androgen Receptor Targets Reveals COUP-TF1 as a Novel Player in Human Prostate Cancer.

Published in:

PLoS ONE, 2012, v. 7, n. 10, p. 1, doi. 10.1371/journal.pone.0046467

By:

Perets, Ruth;
Kaplan, Tommy;
Stein, Ilan;
Hidas, Guy;
Tayeb, Shay;
Avraham, Eti;
Ben-Neriah, Yinon;
Simon, Itamar;
Pikarsky, Eli

Publication type:

Article

High Throughput Determination of TGFβ1/SMAD3 Targets in A549 Lung Epithelial Cells.

Published in:

PLoS ONE, 2011, v. 6, n. 5, p. 1, doi. 10.1371/journal.pone.0020319

By:

Zhang, Yingze;
Handley, Daniel;
Kaplan, Tommy;
Yu, Haiying;
Bais, Abha S.;
Richards, Thomas;
Pandit, Kusum V.;
Zeng, Qilu;
Benos, Panayiotis V.;
Friedman, Nir;
Eickelberg, Oliver;
Kaminski, Naftali

Publication type:

Article

Functional characterization of the ZEB2 regulatory landscape.

Published in:

Human Molecular Genetics, 2019, v. 28, n. 9, p. 1487, doi. 10.1093/hmg/ddy440

By:

Yaacov, Reut Bar;
Eshel, Reut;
Farhi, Einan;
Shemuluvich, Fania;
Kaplan, Tommy;
Birnbaum, Ramon Y

Publication type:

Article

Identification of novel toxins associated with the extracellular contractile injection system using machine learning.

Published in:

Molecular Systems Biology, 2024, v. 20, n. 8, p. 859, doi. 10.1038/s44320-024-00053-6

By:

Danov, Aleks;
Pollin, Inbal;
Moon, Eric;
Ho, Mengfei;
Wilson, Brenda A;
Papathanos, Philippos A;
Kaplan, Tommy;
Levy, Asaf

Publication type:

Article

A Novel Bayesian DNA Motif Comparison Method for Clustering and Retrieval.

Published in:

PLoS Computational Biology, 2008, v. 4, n. 2, p. 1, doi. 10.1371/journal.pcbi.1000010

By:

Habib, Naomi;
Kaplan, Tommy;
Margalit, Hanah;
Friedman, Nir

Publication type:

Article

Ab Initio Prediction of Transcription Factor Targets Using Structural Knowledge.

Published in:

PLoS Computational Biology, 2005, v. 1, n. 1, p. 5, doi. 10.1371/journal.pcbi.0010001

By:

Kaplan, Tommy;
Friedman, Nir;
Margalit, Hanah;
Sali, Andrej

Publication type:

Article

Stable Binding of the Conserved Transcription Factor Grainy Head to its Target Genes Throughout Drosophila melanogaster Development.

Published in:

Genetics, 2017, v. 205, n. 2, p. 605, doi. 10.1534/genetics.116.195685

By:

Nevil, Markus;
Bondra, Eliana R.;
Schulz, Katharine N.;
Kaplan, Tommy;
Harrison, Melissa M.

Publication type:

Article

Promoter-enhancer interactions identified from Hi-C data using probabilistic models and hierarchical topological domains.

Published in:

Nature Communications, 2017, v. 8, n. 1, p. 1, doi. 10.1038/s41467-017-02386-3

By:

Ron, Gil;
Globerson, Yuval;
Moran, Dror;
Kaplan, Tommy

Publication type:

Article

Post-transcriptional 3´-UTR cleavage of mRNA transcripts generates thousands of stable uncapped autonomous RNA fragments.

Published in:

Nature Communications, 2017, v. 8, n. 1, p. 1, doi. 10.1038/s41467-017-02099-7

By:

Malka, Yuval;
Steiman-Shimony, Avital;
Rosenthal, Eran;
Argaman, Liron;
Cohen-Daniel, Leonor;
Arbib, Eliran;
Margalit, Hanah;
Kaplan, Tommy;
Berger, Michael

Publication type:

Article

Hierarchical role for transcription factors and chromatin structure in genome organization along adipogenesis.

Published in:

FEBS Journal, 2017, v. 284, n. 19, p. 3230, doi. 10.1111/febs.14183

By:

Sarusi Portuguez, Avital;
Schwartz, Michal;
Siersbaek, Rasmus;
Nielsen, Ronni;
Sung, Myong‐Hee;
Mandrup, Susanne;
Kaplan, Tommy;
Hakim, Ofir

Publication type:

Article

Roles for H2A.Z and Its Acetylation in GAL1 Transcription and Gene Induction, but Not GAL1-Transcriptional Memory.

Published in:

PLoS Biology, 2010, v. 8, n. 6, p. 1, doi. 10.1371/journal.pbio.1000401

By:

Halley, Jeffrey E.;
Kaplan, Tommy;
Wang, Alice Y.;
Kobor, Michael S.;
Rine, Jasper

Publication type:

Article

Single-Nucleosome Mapping of Histone Modifications in S. cerevisiae.

Published in:

PLoS Biology, 2005, v. 3, n. 10, p. 1753, doi. 10.1371/journal.pbio.0030328

By:

Chih Long Liu;
Kaplan, Tommy;
Minkyu Kim;
Buratowski, Stephen;
Schreiber, Stuart L.;
Friedman, Nir;
Rando, Oliver J.

Publication type:

Article

Single-Nucleosome Mapping of Histone Modifications in S. cerevisiae.

Published in:

PLoS Biology, 2005, v. 3, n. 8, p. 1, doi. 10.1371/journal.pbio.0030328

By:

Liu, Chih Long;
Kaplan, Tommy;
Kim, Minkyu;
Buratowski, Stephen;
Schreiber, Stuart L;
Friedman, Nir;
Rando, Oliver J

Publication type:

Article

Detection of Cell Types Contributing to Cancer From Circulating, Cell-Free Methylated DNA.

Published in:

Frontiers in Genetics, 2021, v. 12, p. 1, doi. 10.3389/fgene.2021.671057

By:

Barefoot, Megan E.;
Loyfer, Netanel;
Kiliti, Amber J.;
McDeed IV, A. Patrick;
Kaplan, Tommy;
Wellstein, Anton

Publication type:

Article

Atlas of imprinted and allele-specific DNA methylation in the human body.

Published in:

Nature Communications, 2025, v. 16, n. 1, p. 1, doi. 10.1038/s41467-025-57433-1

By:

Rosenski, Jonathan;
Peretz, Ayelet;
Magenheim, Judith;
Loyfer, Netanel;
Shemer, Ruth;
Glaser, Benjamin;
Dor, Yuval;
Kaplan, Tommy

Publication type:

Article

Determining time since deposition of latent fingerprints on forensic adhesive tape using ultrafast DESI-MS and machine learning.

Published in:

Scientific Reports, 2025, v. 15, n. 1, p. 1, doi. 10.1038/s41598-025-02639-y

By:

Rajs, Nora;
Harush-Brosh, Yinon;
Raisch, Ron;
Yakobi Arancibia, Ravit;
Zoabi, Amani;
Golan, Guy Nevet;
Shpitzen, Moshe;
Wiesner, Sarena;
Levin-Elad, Michal;
Kaplan, Tommy;
Margulis, Katherine

Publication type:

Article

Ep300 sequestration to functionally distinct glucocorticoid receptor binding loci underlie rapid gene activation and repression.

Published in:

Nucleic Acids Research, 2022, v. 50, n. 12, p. 6702, doi. 10.1093/nar/gkac488

By:

Portuguez, Avital Sarusi;
Grbesa, Ivana;
Tal, Moran;
Deitch, Rachel;
Raz, Dana;
Kliker, Limor;
Weismann, Ran;
Schwartz, Michal;
Loza, Olga;
Cohen, Leslie;
Marchenkov-Flam, Libi;
Sung, Myong-Hee;
Kaplan, Tommy;
Hakim, Ofir

Publication type:

Article

Reconstructing spatial organizations of chromosomes through manifold learning.

Published in:

Nucleic Acids Research, 2018, v. 46, n. 8, p. 1, doi. 10.1093/nar/gky065

By:

Zhu, Guangxiang;
Deng, Wenxuan;
Hu, Hailin;
Ma, Rui;
Zhang, Sai;
Yang, Jinglin;
Peng, Jian;
Kaplan, Tommy;
Zeng, Jianyang

Publication type:

Article

A hyperdynamic H3.3 nucleosome marks promoter regions in pluripotent embryonic stem cells.

Published in:

Nucleic Acids Research, 2017, v. 45, n. 21, p. 12181, doi. 10.1093/nar/gkx817

By:

Schlesinger, Sharon;
Kaffe, Binyamin;
Melcer, Shai;
Aguilera, Jose D.;
Sivaraman, Divya M.;
Kaplan, Tommy;
Meshorer, Eran

Publication type:

Article

DNA Methylation-Based Assessment of Cell Composition in Human Pancreas and Islets.

Published in:

Diabetes, 2024, v. 73, n. 4, p. 554, doi. 10.2337/db23-0704

By:

Drawshy, Zeina;
Neiman, Daniel;
Fridlich, Ori;
Peretz, Ayelet;
Magenheim, Judith;
Rozo, Andrea V.;
Doliba, Nicolai M.;
Stoffers, Doris A.;
Kaestner, Klaus H.;
Schatz, Desmond A.;
Wasserfall, Clive;
Campbell-Thompson, Martha;
Shapiro, James;
Kaplan, Tommy;
Shemer, Ruth;
Glaser, Benjamin;
Klochendler, Agnes;
Dor, Yuval

Publication type:

Article

A standardized framework for robust fragmentomic feature extraction from cell-free DNA sequencing data.

Published in:

Genome Biology, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s13059-025-03607-5

By:

Wang, Haichao;
Mennea, Paulius D.;
Chan, Yu Kiu Elkie;
Cheng, Zhao;
Neofytou, Maria C.;
Surani, Arif Anwer;
Vijayaraghavan, Aadhitthya;
Ditter, Emma-Jane;
Bowers, Richard;
Eldridge, Matthew D.;
Shcherbo, Dmitry S.;
Smith, Christopher G.;
Markowetz, Florian;
Cooper, Wendy N.;
Kaplan, Tommy;
Rosenfeld, Nitzan;
Zhao, Hui

Publication type:

Article

Unraveling the transcriptional regulation of TWIST1 in limb development.

Published in:

PLoS Genetics, 2018, v. 14, n. 10, p. 1, doi. 10.1371/journal.pgen.1007738

By:

Hirsch, Naama;
Eshel, Reut;
Bar Yaacov, Reut;
Shahar, Tal;
Shmulevich, Fania;
Dahan, Idit;
Levaot, Noam;
Kaplan, Tommy;
Lupiáñez, Darío G.;
Birnbaum, Ramon Y.

Publication type:

Article

Gene expression: Running to stand still.

Published in:

Nature, 2012, v. 484, n. 7393, p. 171, doi. 10.1038/484171a

By:

Kaplan, Tommy;
Friedman, Nir

Publication type:

Article

Genomic retargeting of p53 and CTCF is associated with transcriptional changes during oncogenic HRas-induced transformation.

Published in:

Communications Biology, 2020, v. 3, n. 1, p. N.PAG, doi. 10.1038/s42003-020-01398-y

By:

Schwartz, Michal;
Portugez, Avital Sarusi;
Attia, Bracha Zukerman;
Tannenbaum, Miriam;
Cohen, Leslie;
Loza, Olga;
Chase, Emily;
Turman, Yousef;
Kaplan, Tommy;
Salah, Zaidoun;
Hakim, Ofir

Publication type:

Article

Predicting gene knockout effects from expression data.

Published in:

BMC Medical Genomics, 2023, v. 16, n. 1, p. 1, doi. 10.1186/s12920-023-01446-6

By:

Rosenski, Jonathan;
Shifman, Sagiv;
Kaplan, Tommy

Publication type:

Article

Evaluation of PSI-BLAST alignment accuracy in comparison to structural alignments.

Published in:

Protein Science: A Publication of the Protein Society, 2000, v. 9, n. 11, p. 2278

By:

FRIEDBERG, IDDO;
KAPLAN, TOMMY;
MARGALIT, HANAH

Publication type:

Article

Extensive Divergence of Transcription Factor Binding in <i>Drosophila</i> Embryos with Highly Conserved Gene Expression.

Published in:

PLoS Genetics, 2013, v. 9, n. 9, p. 1, doi. 10.1371/journal.pgen.1003748

By:

Paris, Mathilde;
Kaplan, Tommy;
Li, Xiao Yong;
Villalta, Jacqueline E.;
Lott, Susan E.;
Eisen, Michael B.

Publication type:

Article

Zelda Binding in the Early Drosophila melanogaster Embryo Marks Regions Subsequently Activated at the Maternal-to-Zygotic Transition.

Published in:

PLoS Genetics, 2011, v. 7, n. 10, p. 1, doi. 10.1371/journal.pgen.1002266

By:

Harrison, Melissa M.;
Li, Xiao-Yong;
Kaplan, Tommy;
Botchan, Michael R.;
Eisen, Michael B.

Publication type:

Article

Quantitative Models of the Mechanisms That Control Genome-Wide Patterns of Transcription Factor Binding during Early Drosophila Development.

Published in:

PLoS Genetics, 2011, v. 7, n. 2, p. 1, doi. 10.1371/journal.pgen.1001290

By:

Kaplan, Tommy;
Xiao-Yong Li;
Sabo, Peter J.;
Thomas, Sean;
Stamatoyannopoulos, John A.;
Biggin, Mark D.;
Eisen, Michael B.

Publication type:

Article

Cell Cycle- and Chaperone-Mediated Regulation of H3K56ac Incorporation in Yeast.

Published in:

PLoS Genetics, 2008, v. 4, n. 11, p. 1, doi. 10.1371/journal.pgen.1000270

By:

Kaplan, Tommy;
Chih Long Liu;
Erkmann, Judith A.;
Holik, John;
Grunstein, Michael;
Kaufman, Paul D.;
Friedman, Nir;
Rando, Oliver J.

Publication type:

Article