Works by Gerstein, Mark

Results: 292

The Reality of Pervasive Transcription.

Published in:

2011

By:

Clark, Michael B.;
Amaral, Paulo P.;
Schlesinger, Felix J.;
Dinger1, Marcel E.;
Taft, Ryan J.;
Rinn, John L.;
Ponting, Chris P.;
Stadler, Peter F.;
Morris, Kevin V.;
Morillon, Antonin;
Rozowsky, Joel S.;
Gerstein, Mark B.;
Wahlestedt, Claes;
Hayashizaki, Yoshihide;
Carninci, Piero;
Gingeras, Thomas R.;
Mattick, John S.

Publication type:

Opinion

Bayesian Modeling of the Yeast SH3 Domain Interactome Predicts Spatiotemporal Dynamics of Endocytosis Proteins.

Published in:

PLoS Biology, 2009, v. 7, n. 10, p. 1, doi. 10.1371/journal.pbio.1000218

By:

Tonikian, Raffi;
Xiaofeng Xin;
Toret, Christopher P.;
Gfeller, David;
Landgraf, Christiane;
Panni, Simona;
Paoluzi, Serena;
Castagnoli, Luisa;
Currell, Bridget;
Seshagiri, Somasekar;
Haiyuan Yu;
Winsor, Barbara;
Vidal, Marc;
Gerstein, Mark B.;
Bader, Gary D.;
Volkmer, Rudolf;
Cesareni, Gianni;
Drubin, David G.;
Kim, Philip M.;
Sidhu, Sachdev S.

Publication type:

Article

REliable PIcking by Consensus (REPIC): a consensus methodology for harnessing multiple cryo-EM particle pickers.

Published in:

Communications Biology, 2024, v. 7, n. 1, p. 1, doi. 10.1038/s42003-024-07045-0

By:

Cameron, Christopher J. F.;
Seager, Sebastian J. H.;
Sigworth, Fred J.;
Tagare, Hemant D.;
Gerstein, Mark B.

Publication type:

Article

Annual Research Review: The promise of stem cell research for neuropsychiatric disorders.

Published in:

Journal of Child Psychology & Psychiatry, 2011, v. 52, n. 4, p. 504, doi. 10.1111/j.1469-7610.2010.02348.x

By:

Vaccarino, Flora M.;
Urban, Alexander Eckehart;
Stevens, Hanna E.;
Szekely, Anna;
Abyzov, Alexej;
Grigorenko, Elena L.;
Gerstein, Mark;
Weissman, Sherman

Publication type:

Article

The Role of Cloud Computing in Managing the Deluge of Potentially Private Genetic Data.

Published in:

American Journal of Bioethics, 2011, v. 11, n. 11, p. 39, doi. 10.1080/15265161.2011.608242

By:

Greenbaum, Dov;
Gerstein, Mark

Publication type:

Article

Social Considerations in Research: Consider Them but Don't Use Them.

Published in:

2011

By:

Greenbaum, Dov;
Gerstein, Mark

Publication type:

Opinion

Social Networking and Personal Genomics: Suggestions for Optimizing the Interaction.

Published in:

American Journal of Bioethics, 2009, v. 9, n. 6/7, p. 15, doi. 10.1080/15265160902894039

By:

Greenbaum, Dov;
Gerstein, Mark

Publication type:

Article

Genomic Anonymity: Have We Already Lost It?

Published in:

American Journal of Bioethics, 2008, v. 8, n. 10, p. 71, doi. 10.1080/15265160802478560

By:

Greenbaum, Dov;
Du, Jiang;
Gerstein, Mark

Publication type:

Article

Large-scale atlas of microarray data reveals the distinct expression landscape of different tissues in Arabidopsis.

Published in:

Plant Journal, 2016, v. 86, n. 6, p. 472, doi. 10.1111/tpj.13175

By:

He, Fei;
Yoo, Shinjae;
Wang, Daifeng;
Kumari, Sunita;
Gerstein, Mark;
Ware, Doreen;
Maslov, Sergei

Publication type:

Article

Characterization of stress-responsive lnc RNAs in Arabidopsis thaliana by integrating expression, epigenetic and structural features.

Published in:

Plant Journal, 2014, v. 80, n. 5, p. 848, doi. 10.1111/tpj.12679

By:

Di, Chao;
Yuan, Jiapei;
Wu, Yue;
Li, Jingrui;
Lin, Huixin;
Hu, Long;
Zhang, Ting;
Qi, Yijun;
Gerstein, Mark B.;
Guo, Yan;
Lu, Zhi John

Publication type:

Article

Child Development and Structural Variation in the Human Genome.

Published in:

Child Development, 2013, v. 84, n. 1, p. 34, doi. 10.1111/cdev.12051

By:

Zhang, Ying;
Haraksingh, Rajini;
Grubert, Fabian;
Abyzov, Alexej;
Gerstein, Mark;
Weissman, Sherman;
Urban, Alexander E.

Publication type:

Article

Impact and characterization of serial structural variations across humans and great apes.

Published in:

Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-52027-9

By:

Höps, Wolfram;
Rausch, Tobias;
Jendrusch, Michael;
Human Genome Structural Variation Consortium (HGSVC);
Ashraf, Hufsah;
Audano, Peter A.;
Austine, Ola;
Basile, Anna O.;
Beck, Christine R.;
Jan Bonder, Marc;
Byrska-Bishop, Marta;
Chaisson, Mark J. P.;
Chong, Zechen;
Corvelo, André;
Devine, Scott E.;
Ebert, Peter;
Ebler, Jana;
Eichler, Evan E.;
Gerstein, Mark B.;
Hallast, Pille

Publication type:

Article

STARRPeaker: uniform processing and accurate identification of STARR-seq active regions.

Published in:

Genome Biology, 2020, v. 21, n. 1, p. 1, doi. 10.1186/s13059-020-02194-x

By:

Lee, Donghoon;
Shi, Manman;
Moran, Jennifer;
Wall, Martha;
Zhang, Jing;
Liu, Jason;
Fitzgerald, Dominic;
Kyono, Yasuhiro;
Ma, Lijia;
White, Kevin P.;
Gerstein, Mark

Publication type:

Article

SVFX: a machine learning framework to quantify the pathogenicity of structural variants.

Published in:

Genome Biology, 2020, v. 21, n. 1, p. N.PAG, doi. 10.1186/s13059-020-02178-x

By:

Kumar, Sushant;
Harmanci, Arif;
Vytheeswaran, Jagath;
Gerstein, Mark B.

Publication type:

Article

RADAR: annotation and prioritization of variants in the post-transcriptional regulome of RNA-binding proteins.

Published in:

Genome Biology, 2020, v. 21, n. 1, p. 1, doi. 10.1186/s13059-020-01979-4

By:

Zhang, Jing;
Liu, Jason;
Lee, Donghoon;
Feng, Jo-Jo;
Lochovsky, Lucas;
Lou, Shaoke;
Rutenberg-Schoenberg, Michael;
Gerstein, Mark

Publication type:

Article

Approaches for integrating heterogeneous RNA-seq data reveal cross-talk between microbes and genes in asthmatic patients.

Published in:

Genome Biology, 2020, v. 21, n. 1, p. 1, doi. 10.1186/s13059-020-02033-z

By:

Spakowicz, Daniel;
Lou, Shaoke;
Barron, Brian;
Gomez, Jose L.;
Li, Tianxiao;
Liu, Qing;
Grant, Nicole;
Yan, Xiting;
Hoyd, Rebecca;
Weinstock, George;
Chupp, Geoffrey L.;
Gerstein, Mark

Publication type:

Article

Approaches for integrating heterogeneous RNA-seq data reveal cross-talk between microbes and genes in asthmatic patients.

Published in:

Genome Biology, 2020, v. 21, n. 1, p. 1, doi. 10.1186/s13059-020-02033-z

By:

Spakowicz, Daniel;
Lou, Shaoke;
Barron, Brian;
Gomez, Jose L.;
Li, Tianxiao;
Liu, Qing;
Grant, Nicole;
Yan, Xiting;
Hoyd, Rebecca;
Weinstock, George;
Chupp, Geoffrey L.;
Gerstein, Mark

Publication type:

Article

Genomics and data science: an application within an umbrella.

Published in:

Genome Biology, 2019, v. 20, n. 1, p. N.PAG, doi. 10.1186/s13059-019-1724-1

By:

Navarro, Fábio C. P.;
Mohsen, Hussein;
Yan, Chengfei;
Li, Shantao;
Gu, Mengting;
Meyerson, William;
Gerstein, Mark

Publication type:

Article

Measuring the reproducibility and quality of Hi-C data.

Published in:

Genome Biology, 2019, v. 20, n. 1, p. N.PAG, doi. 10.1186/s13059-019-1658-7

By:

Yardımcı, Galip Gürkan;
Ozadam, Hakan;
Sauria, Michael E. G.;
Ursu, Oana;
Yan, Koon-Kiu;
Yang, Tao;
Chakraborty, Abhijit;
Kaul, Arya;
Lajoie, Bryan R.;
Song, Fan;
Zhan, Ye;
Ay, Ferhat;
Gerstein, Mark;
Kundaje, Anshul;
Li, Qunhua;
Taylor, James;
Yue, Feng;
Dekker, Job;
Noble, William S.

Publication type:

Article

Computer security in academia-a potential roadblock to distributed annotation of the human genome.

Published in:

Nature Biotechnology, 2004, v. 22, n. 6, p. 771, doi. 10.1038/nbt0604-771

By:

Greenbaum, Dov;
Douglas, Shawn M;
Smith, Andrew;
Lim, Joanna;
Fischer, Michael;
Schultz, Martin;
Gerstein, Mark

Publication type:

Article

Reconstructing genetic networks in yeast.

Published in:

Nature Biotechnology, 2003, v. 21, n. 11, p. 1295, doi. 10.1038/nbt1103-1295

By:

Zhaolei Zhang, Charles;
Gerstein, Mark

Publication type:

Article

A universal legal framework as a prerequisite for database interoperability.

Published in:

Nature Biotechnology, 2003, v. 21, n. 9, p. 979, doi. 10.1038/nbt0903-979

By:

Greenbaum, Dov;
Gerstein, Mark

Publication type:

Article

An integrated approach for finding overlooked genes in yeast.

Published in:

Nature Biotechnology, 2002, v. 20, n. 1, p. 58, doi. 10.1038/nbt0102-58

By:

Kumar, Anuj;
Harrison, Paul M.;
Cheung, Kei-Hoi;
Lan, Ning;
Echols, Nathaniel;
Bertone, Paul;
Miller, Perry;
Gerstein, Mark B.;
Snyder, Michael

Publication type:

Article

GRAM: A GeneRAlized Model to predict the molecular effect of a non-coding variant in a cell-type specific manner.

Published in:

PLoS Genetics, 2019, v. 15, n. 8, p. 1, doi. 10.1371/journal.pgen.1007860

By:

Lou, Shaoke;
Cotter, Kellie A.;
Li, Tianxiao;
Liang, Jin;
Mohsen, Hussein;
Liu, Jason;
Zhang, Jing;
Cohen, Sandra;
Xu, Jinrui;
Yu, Haiyuan;
Rubin, Mark A.;
Gerstein, Mark

Publication type:

Article

Rapid Evolution by Positive Darwinian Selection in T-Cell Antigen CD4 in Primates.

Published in:

Journal of Molecular Evolution, 2008, v. 66, n. 5, p. 446, doi. 10.1007/s00239-008-9097-1

By:

Zhang, Zhengdong D.;
Weinstock, George;
Gerstein, Mark

Publication type:

Article

Measuring Shifts in Function and Evolutionary Opportunity Using Variability Profiles: A Case Study of the Globins.

Published in:

Journal of Molecular Evolution, 2000, v. 51, n. 3, p. 223, doi. 10.1007/s002390010084

By:

Naylor, Gavin J. P.;
Gerstein, Mark

Publication type:

Article

Genomics: Protein fossils live on as RNA.

Published in:

Nature, 2008, v. 453, n. 7196, p. 729, doi. 10.1038/453729a

By:

Sasidharan, Rajkumar;
Gerstein, Mark

Publication type:

Article

Structured digital abstract makes text mining easy.

Published in:

2007

By:

Gerstein, Mark;
Seringhaus, Michael;
Fields, Stanley

Publication type:

Letter

Tools needed to navigate landscape of the genome.

Published in:

2006

By:

Gerstein, Mark

Publication type:

Letter

Genomic analysis of regulatory network dynamics reveals large topological changes.

Published in:

Nature, 2004, v. 431, n. 7006, p. 308, doi. 10.1038/nature02782

By:

Luscombe, Nicholas M.;
Babu, M. Madan;
Yu, Haiyuan;
Snyder, Michael;
Teichmann, Sarah A.;
Gerstein, Mark

Publication type:

Article

Predicting spatially resolved gene expression via tissue morphology using adaptive spatial GNNs.

Published in:

Bioinformatics, 2024, v. 40, p. ii111, doi. 10.1093/bioinformatics/btae383

By:

Song, Tianci;
Cosatto, Eric;
Wang, Gaoyuan;
Kuang, Rui;
Gerstein, Mark;
Min, Martin Renqiang;
Warrell, Jonathan

Publication type:

Article

Representing core gene expression activity relationships using the latent structure implicit in Bayesian networks.

Published in:

Bioinformatics, 2024, v. 40, n. 8, p. 1, doi. 10.1093/bioinformatics/btae463

By:

Gao, Jiahao;
Gerstein, Mark

Publication type:

Article

MolLM: a unified language model for integrating biomedical text with 2D and 3D molecular representations.

Published in:

Bioinformatics, 2024, v. 40, p. i357, doi. 10.1093/bioinformatics/btae260

By:

Tang, Xiangru;
Tran, Andrew;
Tan, Jeffrey;
Gerstein, Mark B

Publication type:

Article

BioCoder: a benchmark for bioinformatics code generation with large language models.

Published in:

Bioinformatics, 2024, v. 40, p. i266, doi. 10.1093/bioinformatics/btae230

By:

Tang, Xiangru;
Qian, Bill;
Gao, Rick;
Chen, Jiakang;
Chen, Xinyun;
Gerstein, Mark B

Publication type:

Article

Binding peptide generation for MHC Class I proteins with deep reinforcement learning.

Published in:

Bioinformatics, 2023, v. 39, n. 2, p. 1, doi. 10.1093/bioinformatics/btad055

By:

Chen, Ziqi;
Zhang, Baoyi;
Guo, Hongyu;
Emani, Prashant;
Clancy, Trevor;
Jiang, Chongming;
Gerstein, Mark;
Ning, Xia;
Cheng, Chao;
Min, Martin Renqiang

Publication type:

Article

Gene Tracer: a smart, interactive, voice-controlled Alexa skill For gene information retrieval and browsing, mutation annotation and network visualization.

Published in:

Bioinformatics, 2021, v. 37, n. 18, p. 2998, doi. 10.1093/bioinformatics/btab107

By:

Lou, Shaoke;
Li, Tianxiao;
Liu, Jason;
Gerstein, Mark

Publication type:

Article

DECODE: a Deep-learning framework for Condensing enhancers and refining boundaries with large-scale functional assays.

Published in:

Bioinformatics, 2021, v. 37, p. i280, doi. 10.1093/bioinformatics/btab283

By:

Chen, Zhanlin;
Zhang, Jing;
Liu, Jason;
Dai, Yi;
Lee, Donghoon;
Min, Martin Renqiang;
Xu, Min;
Gerstein, Mark

Publication type:

Article

SCAN-ATAC-Sim: a scalable and efficient method for simulating single-cell ATAC-seq data from bulk-tissue experiments.

Published in:

Bioinformatics, 2021, v. 37, n. 12, p. 1756, doi. 10.1093/bioinformatics/btaa1039

By:

Chen, Zhanlin;
Zhang, Jing;
Liu, Jason;
Zhang, Zixuan;
Zhu, Jiangqi;
Lee, Donghoon;
Xu, Min;
Gerstein, Mark

Publication type:

Article

FANCY: fast estimation of privacy risk in functional genomics data.

Published in:

Bioinformatics, 2020, v. 36, n. 21, p. 5145, doi. 10.1093/bioinformatics/btaa661

By:

Gürsoy, Gamze;
Brannon, Charlotte M;
Navarro, Fabio C P;
Gerstein, Mark

Publication type:

Article

Modeling the relative relationship of transcription factor binding and histone modifications to gene expression levels in mouse embryonic stem cells.

Published in:

Nucleic Acids Research, 2012, v. 40, n. 2, p. 553, doi. 10.1093/nar/gkr752

By:

Cheng, Chao;
Gerstein, Mark

Publication type:

Article

Analysis of genomic variation in non-coding elements using population-scale sequencing data from the 1000 Genomes Project.

Published in:

Nucleic Acids Research, 2011, v. 39, n. 16, p. 7058, doi. 10.1093/nar/gkr342

By:

Mu, Xinmeng Jasmine;
Lu, Zhi John;
Kong, Yong;
Lam, Hugo Y. K.;
Gerstein, Mark B.

Publication type:

Article

Segmental duplications in the human genome reveal details of pseudogene formation.

Published in:

Nucleic Acids Research, 2010, v. 38, n. 20, p. 6997, doi. 10.1093/nar/gkq587

By:

Khurana, Ekta;
Lam, Hugo Y. K.;
Cheng, Chao;
Carriero, Nicholas;
Cayting, Philip;
Gerstein, Mark B.

Publication type:

Article

3V: cavity, channel and cleft volume calculator and extractor.

Published in:

Nucleic Acids Research, 2010, v. 38, n. suppl_2, p. W555, doi. 10.1093/nar/gkq395

By:

Voss, Neil R.;
Gerstein, Mark

Publication type:

Article

Pseudofam: the pseudogene families database.

Published in:

Nucleic Acids Research, 2009, v. 37, n. suppl_1, p. D738, doi. 10.1093/nar/gkn758

By:

Lam, Hugo Y. K.;
Khurana, Ekta;
Fang, Gang;
Cayting, Philip;
Carriero, Nicholas;
Cheung, Kei-Hoi;
Gerstein, Mark B.

Publication type:

Article

Toward a universal microarray: prediction of gene expression through nearest-neighbor probe sequence identification.

Published in:

Nucleic Acids Research, 2007, v. 35, n. 15, p. e99, doi. 10.1093/nar/gkm549

By:

Royce, Thomas E.;
Rozowsky, Joel S.;
Gerstein, Mark B.

Publication type:

Article

Positional artifacts in microarrays: experimental verification and construction of COP, an automated detection tool.

Published in:

Nucleic Acids Research, 2007, v. 35, n. 2, p. e8

By:

Yu, Haiyuan;
Nguyen, Katherine;
Royce, Tom;
Qian, Jiang;
Nelson, Kenneth;
Snyder, Michael;
Gerstein, Mark

Publication type:

Article

Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation.

Published in:

Nucleic Acids Research, 2007, v. 35, p. d55, doi. 10.1093/nar/gkl851

By:

Karro, John E.;
Yan, Yangpan;
Zheng, Deyou;
Zhang, Zhaolei;
Carriero, Nicholas;
Cayting, Philip;
Harrrison, Paul;
Gerstein, Mark

Publication type:

Article

Genomic analysis of insertion behavior and target specificity of mini-Tn7 and Tn3 transposons in Saccharomyces cerevisiae.

Published in:

Nucleic Acids Research, 2006, v. 34, n. 8, p. e57, doi. 10.1093/nar/gkl184

By:

Seringhaus, Michael;
Kumar, Anuj;
Hartigan, John;
Snyder, Michael;
Gerstein, Mark

Publication type:

Article

The Database of Macromolecular Motions: new features added at the decade mark.

Published in:

Nucleic Acids Research, 2006, v. 34, n. suppl 1, p. d296, doi. 10.1093/nar/gkj046

By:

Flores, Samuel;
Echols, Nathaniel;
Milburn, Duncan;
Hespenheide, Brandon;
Keating, Kevin;
Lu, Jason;
Wells, Stephen;
Yu, Eric Z.;
Thorpe, Michael;
Gerstein, Mark

Publication type:

Article

Transcribed processed pseudogenes in the human genome: an intermediate form of expressed retrosequence lacking protein-coding ability.

Published in:

Nucleic Acids Research, 2005, v. 33, n. 8, p. 2374, doi. 10.1093/nar/gki531

By:

Harrison, Paul M.;
Zheng, Deyou;
Zhang, Zhaolei;
Carriero, Nicholas;
Gerstein, Mark

Publication type:

Article