J. Rozowsky

发表

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

William Stafford Noble, Nancy R. Zhang, Stephen C. J. Parker, 2007, Nature.

PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls

Raymond K. Auerbach, M. Gerstein, N. Carriero, 2009, Nature Biotechnology.

Diverse Roles and Interactions of the SWI/SNF Chromatin Remodeling Complex Revealed Using Global Approaches

Raymond K. Auerbach, M. Gerstein, J. Rozowsky, 2011, PLoS genetics.

Landscape of transcription in human cells

Nadav S. Bar, Pedro G. Ferreira, Morgan C. Giddings, 2012, Nature.

Corrigendum: Diverse human extracellular RNAs are widely detected in human plasma

D. Levy, M. Gerstein, J. Rozowsky, 2016, Nature Communications.

Architecture of the human regulatory network derived from ENCODE data

David Z. Chen, Kevin Y. Yip, Timothy E. Reddy, 2012, Nature.

AlleleSeq: analysis of allele-specific expression and binding in a network framework

M. Gerstein, M. Rubin, A. Abyzov, 2011, Molecular systems biology.

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

Marc D. Perry, James B. Brown, Timothy E. Reddy, 2012, Genome research.

An Integrated Encyclopedia of DNA Elements in the Human Genome

Raymond K. Auerbach, William Stafford Noble, Stephen C. J. Parker, 2012, Nature.

The ENCODE (ENCyclopedia Of DNA Elements) Project

Paul T. Groth, William Stafford Noble, Colin N. Dewey, 2004, Science.

Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project

Raymond K. Auerbach, Kevin Y. Yip, Stefan R. Henz, 2010, Science.

Expanded encyclopaedias of DNA elements in the human and mouse genomes

Michael J. Purcaro, Gene W. Yeo, M. Gerstein, 2020, Nature.

Major molecular differences between mammalian sexes are involved in drug metabolism and renal function.

J. Rinn, M. Gerstein, M. Snyder, 2004, Developmental cell.

A statistical framework for modeling gene expression using chromatin features and application to modENCODE datasets

Kevin Y. Yip, M. Gerstein, J. Rozowsky, 2011, Genome Biology.

Extending gene ontology in the context of extracellular RNA and vesicle communication

Kei-Hoi Cheung, Andrew I. Su, Kasey Vickers, 2016, Journal of biomedical semantics.

Mapping accessible chromatin regions using Sono-Seq

Raymond K. Auerbach, M. Gerstein, K. Struhl, 2009, Proceedings of the National Academy of Sciences.

A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

Raymond K. Auerbach, William Stafford Noble, Stephen C. J. Parker, 2011, PLoS biology.

Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors

Kevin Y. Yip, James B. Brown, P. Bickel, 2012, Genome Biology.

Mapping of transcription factor binding regions in mammalian cells by ChIP: comparison of array- and sequencing-based technologies.

Yijun Ruan, Chia-Lin Wei, Mark B Gerstein, 2007, Genome research.

Global Identification of Human Transcribed Sequences with Genome Tiling Arrays

Thomas E. Royce, J. Rinn, M. Gerstein, 2004, Science.

Understanding transcriptional regulation by integrative analysis of transcription factor binding data

Kevin Y. Yip, E. Birney, M. Gerstein, 2012, Genome research.

Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping.

Mark Gerstein, Paul Bertone, Thomas E. Royce, 2005, Trends in genetics : TIG.

The real cost of sequencing: scaling computation to keep pace with data generation

Jing Zhang, Mark Gerstein, Farren J. Isaacs, 2016, Genome biology.

Supervised enhancer prediction with epigenetic pattern recognition and targeted validation

Kevin Y. Yip, Tyler H. Garvin, M. Gerstein, 2018, Nature Methods.

Comparative Analysis of the Transcriptome across Distant Species

Peter J. Bickel, Raymond K. Auerbach, Peter J. Park, 2014, Nature.

Divergence of transcription factor binding sites across related yeast species.

Mark Gerstein, Haiyuan Yu, Michael R. Seringhaus, 2007, Science.

Annotating non-coding regions of the genome

M. Gerstein, J. Rozowsky, Roger Alexander, 2010, Nature Reviews Genetics.

Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets.

Mark Gerstein, Kevin Struhl, Zhiping Weng, 2008, Genome research.

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

Thomas E. Royce, M. Gerstein, J. Rozowsky, 2007, Nucleic acids research.

Comparison and calibration of transcriptome data from RNA-Seq and tiling arrays

M. Gerstein, L. Hillier, R. Waterston, 2010, BMC Genomics.

METHOD Open Access

David Z. Chen, M. Gerstein, M. Rubin, 2014 .

Variation in Transcription Factor Binding Among Humans

M. Gerstein, Fabian Grubert, Michael P. Snyder, 2010, Science.

The Reality of Pervasive Transcription

Paulo P. Amaral, J. Rinn, M. Gerstein, 2011, PLoS biology.

exRNA Atlas Analysis Reveals Distinct Extracellular RNA Cargo Types and Their Carriers Present across Human Biofluids

Alexander R. Pico, Andrew R. Jackson, James A. Diao, 2019, Cell.

exceRpt: A Comprehensive Analytic Platform for Extracellular RNA Profiling.

M. Gerstein, A. Milosavljevic, J. Rozowsky, 2019, Cell systems.

Total Extracellular Small RNA Profiles from Plasma, Saliva, and Urine of Healthy Subjects

Rebecca A. Reiman, J. Rozowsky, R. Kitchen, 2017, Scientific Reports.

What is a gene, post-ENCODE? History and updated definition.

M. Gerstein, J. Korbel, Zhengdong D. Zhang, 2007, Genome research.

Design optimization methods for genomic DNA tiling arrays.

M. Gerstein, V. Trifonov, J. Karro, 2005, Genome research.

A myelopoiesis-associated regulatory intergenic noncoding RNA transcript within the human HOXA cluster.

M. Gerstein, Michael P. Snyder, S. Weissman, 2009, Blood.

A uniform survey of allele-specific binding and expression over 1000-Genomes-Project individuals

M. Gerstein, A. Abyzov, L. Regan, 2016, Nature Communications.

Decoding neuroproteomics: integrating the genome, translatome and functional anatomy

M. Gerstein, A. Nairn, J. Rozowsky, 2014, Nature Neuroscience.

Systematic analysis of transcribed loci in ENCODE regions using RACE sequencing reveals extensive transcription in the human genome

Mark Gerstein, Joel Rozowsky, Alexander E Urban, 2008, Genome Biology.

Comparative analysis of pseudogenes across three phyla

Yan Zhang, Mark Diekhans, Jennifer Harrow, 2014, Proceedings of the National Academy of Sciences.

Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing

Raymond K. Auerbach, Mark Gerstein, Joel Rozowsky, 2009 .

Tilescope: online analysis pipeline for high-density tiling microarray data

Mark Gerstein, Hugo Y. K. Lam, Joel Rozowsky, 2007, Genome Biology.

Mismatch oligonucleotides in human and yeast: guidelines for probe design on tiling microarrays

Mark Gerstein, Justin Jee, Michael R. Seringhaus, 2008, BMC Genomics.

Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome.

Deyou Zheng, Mark B Gerstein, Alexander E Urban, 2007, Genome research.

The DART classification of unannotated transcription within the ENCODE regions: associating transcription with known and novel loci.

Daniel E. Newburger, M. Gerstein, R. Guigó, 2007, Genome research.

Novel transcribed regions in the human genome.

J. Korbel, M. Snyder, T. Gingeras, 2006, Cold Spring Harbor Symposia on Quantitative Biology.

On perturbative gravity and gauge theory

J. Rozowsky, M. Perelstein, L. Dixon, 2000, hep-th/0002078.

Perturbative relations between gravity and gauge theory

J. Rozowsky, M. Perelstein, L. Dixon, 1999, hep-th/9911194.

Identification and analysis of functional elements in 1 % of the human genome by the ENCODE pilot project The ENCODE Project Consortium *

Colin N. Dewey, James B. Brown, Anason S. Halees, 2007 .

Allele-specific epigenome maps reveal sequence-dependent stochastic switching at regulatory loci

Robert C. Altshuler, M. Gerstein, Manolis Kellis, 2018, Science.

throughput sequencing and array data by integrating conservation , secondary structure and high Prediction and characterization of non-coding RNAs in C . elegans

Raymond K. Auerbach, Kevin Y. Yip, M. Gerstein, 2010 .

Extending gene ontology in the context of extracellular RNA and vesicle communication

M. Gerstein, D. Galas, A. Su, 2016, Journal of biomedical semantics.

Phase 2 of extracellular RNA communication consortium charts next-generation approaches for extracellular RNA research

Jennifer C. Jones, Betty Y. S. Kim, M. Gerstein, 2022, iScience.

Appearance of beta cephei pulsations in the Be star 27 CMa

J. Rozowsky, L. Balona, 1991 .

ONE-LOOP N-POINT HELICITY AMPLITUDES IN (SELF-DUAL) GRAVITY

J. Rozowsky, M. Perelstein, L. Dixon, 1998, hep-th/9809160.

Multi-leg one-loop gravity amplitudes from gauge theory

J. Rozowsky, M. Perelstein, L. Dixon, 1998, hep-th/9811140.

Revisiting the bad luck hypothesis: Cancer risk and aging are linked to replication-driven changes to the epigenome

M. Levine, M. Gerstein, L. Pusztai, 2022, bioRxiv.

On perturbative gravity and gauge theory

J. Rozowsky, M. Perelstein, L. Dixon, 2000, hep-th/0002078.

On the relationship between Yang-Mills theory and gravity and its implication for ultraviolet divergences

J. Rozowsky, M. Perelstein, L. Dixon, 1998, hep-th/9802162.

The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models

William Stafford Noble, James C. Wright, Jacob M. Schreiber, 2022, Cell.

Feynman Diagrams and Cutting Rules

J. Rozowsky, 1997, hep-ph/9709423.

QCD fishnets revisited

J. Rozowsky, K. Bering, C. Thorn, 1999, hep-th/9909141.

Two-loop four-gluon amplitudes in N = 4 super-Yang-Mills

J. Rozowsky, Z. Bern, B. Yan, 1997, hep-ph/9702424.

loci ENCODE regions : Associating transcription with known and novel The DART classification of unannotated transcription within the Material Supplemental

Daniel E. Newburger, M. Gerstein, R. Guigó, 2007 .

A Novel Tissue Atlas and Online Tool for the Interrogation of Small RNA Expression in Human Tissues and Biofluids

Rebecca A. Reiman, J. Rozowsky, L. Laurent, 2022, Frontiers in Cell and Developmental Biology.

Diverse human extracellular RNAs are widely detected in human plasma

Mark Gerstein, Robert Kitchen, Daniel Levy, 2016, Nature Communications.

Systematic evaluation of variability in ChIP-chip experiments using data

Jun S. Song, Xiaoqin, Xiao-qin, 2008 .

A cross-organism framework for supervised enhancer prediction with epigenetic pattern recognition and targeted validation

Mark Gerstein, Chengfei Yan, Axel Visel, 2018, bioRxiv.

Comparative analysis of regulatory information and circuits across distant species

Peter J. Bickel, Mark Gerstein, Philip Cayting, 2014, Nature.

Multi-tissue integrative analysis of personal epigenomes

William Stafford Noble, James C. Wright, Jacob M. Schreiber, 2021 .

Bioinformatics Applications Note Gene Expression Rseqtools: a Modular Framework to Analyze Rna-seq Data Using Compact, Anonymized Data Summaries

Mark Gerstein, Ashish Agarwal, Michael Snyder, 2022 .

Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data.

Raymond K. Auerbach, Kevin Y Yip, Zhi John Lu, 2011, Genome research.

Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data

Wei Niu, Mark Gerstein, Jiang Qian, 2011, PLoS Comput. Biol..

Transcription factor binding site identification in yeast: a comparison of high-density oligonucleotide and PCR-based microarray platforms

Mark Gerstein, Michael R. Seringhaus, Anthony R. Borneman, 2007, Functional & Integrative Genomics.

transcript within the human HOXA cluster A myelopoiesis-associated regulatory intergenic non-coding RNA

M. Gerstein, Michael P. Snyder, S. Weissman, 2009 .

ACT: aggregation and correlation toolbox for analyses of genome tracks

Lucas Lochovsky, Mark Gerstein, Jie Wang, 2011, Bioinform..

Open Problems in Extracellular RNA Data Analysis: Insights From an ERCC Online Workshop

Ryan M Spengler, J. Rozowsky, G. Stolovitzky, 2022, Frontiers in Genetics.

The Extracellular RNA Communication Consortium: Establishing Foundational Knowledge and Technologies for Extracellular RNA Research

Nikita A. Sakhanenko, Michael T. McManus, Andrew R. Jackson, 2019, Cell.

Multi-tissue integrative analysis of personal epigenomes [preprint] Multi-tissue integrative analysis of personal epigenomes [preprint] you.

Lei, James C. Wright, Jacob M. Schreiber, 2021 .

Bioinformatics Original Paper a Supervised Hidden Markov Model Framework for Efficiently Segmenting Tiling Array Data in Transcriptional and Chip-chip Experiments: Systematically Incorporating Validated Biological Knowledge

Mark Gerstein, Jan O. Korbel, Michael Snyder, 2022 .

Pollen-derived RNAs Are Found in the Human Circulation

D. Levy, M. Gerstein, J. Rozowsky, 2019, iScience.

Integration of extracellular RNA profiling data using metadata, biomedical ontologies and Linked Data technologies

Kei-Hoi Cheung, Andrew I. Su, Bob S. Carter, 2015, Journal of extracellular vesicles.

An approach to compare genome tiling microarray and MPSS sequencing data for transcript mapping

Mark Gerstein, Joel Rozowsky, Rajkumar Sasidharan, 2009, BMC Research Notes.

An approach to comparing tiling array and high throughput sequencing technologies for genomic transcript mapping

Mark Gerstein, Ashish Agarwal, Joel Rozowsky, 2009, BMC Research Notes.

Assessing the need for sequence-based normalization in tiling microarray experiments

Mark Gerstein, Thomas E. Royce, Joel S. Rozowsky, 2007, Bioinform..

An integrative ENCODE resource for cancer genomics

Jie Xu, Lucas Lochovsky, Donghoon Lee, 2019, Nature Communications.

MUSIC: identification of enriched regions in ChIP-Seq experiments using a mappability-corrected multiscale signal processing framework

Mark Gerstein, Arif Harmanci, Joel Rozowsky, 2014, Genome Biology.

Modeling ChIP Sequencing In Silico with Applications

Mark Gerstein, Michael Snyder, Joel S. Rozowsky, 2008, PLoS Comput. Biol..

Loregic: A Method to Characterize the Cooperative Logic of Regulatory Factors

Mark Gerstein, Chao Cheng, Daifeng Wang, 2015, PLoS Comput. Biol..

OrthoClust: an orthology-based network framework for clustering data across multiple species

Mark Gerstein, Daifeng Wang, Koon-Kiu Yan, 2014, Genome Biology.

Erratum to: The real cost of sequencing: scaling computation to keep pace with data generation

Farren J. Isaacs, M. Gerstein, G. Weinstock, 2016, Genome Biology.

VAT: a computational framework to functionally annotate variants in personal genomes within a cloud-computing environment

Mark Gerstein, David Z. Chen, Michael Snyder, 2012, Bioinform..

Extrapolating traditional DNA microarray statistics to tiling and protein microarray technologies.

Michael Snyder, Haiyuan Yu, Xiaowei Zhu, 2006, Methods in enzymology.

Evaluation of commercially available small RNASeq library preparation kits using low input RNA

J. Rozowsky, Ravi V. Shah, K. Danielson, 2018, BMC Genomics.

Isoform-Level Interpretation of High-Throughput Proteomics Data Enabled by Deep Integration with RNA-seq.

M. Gerstein, A. Nairn, J. Rozowsky, 2018, Journal of proteome research.

Tiling array data analysis: a multiscale approach using wavelets

Mark Gerstein, Joel S. Rozowsky, Alexander Karpikov, 2011, BMC Bioinformatics.

Structuring supplemental materials in support of reproducibility

Mark Gerstein, Victoria Stodden, Dov Greenbaum, 2017, Genome Biology.

modENCODE Project Genome by the Caenorhabditis elegans Integrative Analysis of the

Raymond K. Auerbach, Kevin Y. Yip, Stefan R. Henz, 2011 .

Novel approaches for bioinformatic analysis of salivary RNA sequencing data for development

Mark Gerstein, Sung Kim, Xiaoyan Wang, 2018, Bioinform..

Whole-genome sequencing of phenotypically distinct inflammatory breast cancers reveals similar genomic alterations to non-inflammatory breast cancers

M. Gerstein, W. Woodward, L. Pusztai, 2021, Genome medicine.

Analysis of Genomic Tiling Microarrays for Transcript Mapping and the Identification of Transcription Factor Binding Sites

Mark Gerstein, Michael Snyder, Paul Bertone, 2005, BSB.

Perspectives on ENCODE

Xintao Wei, Christopher B. Burge, Jason Liu, 2020, Nature.

modENCODE consortia ChIP-seq guidelines and practices of the ENCODE and Material Supplemental

James B. Brown, Timothy E. Reddy, P. Bickel, 2012 .

Stroke and Circulating Extracellular RNAs

D. Levy, M. Gerstein, J. Rozowsky, 2017, Stroke.

Landscape of transcription in human cells

Nadav S. Bar, Pedro G. Ferreira, Morgan C. Giddings, 2012, Nature.

Discordant Expression of Circulating microRNA from Cellular and Extracellular Sources

D. Levy, M. Gerstein, J. Rozowsky, 2016, PloS one.

Electromagnetic pion form factor at finite temperature

J. Rozowsky, M. Loewe, C. Dominguez, 1994 .

exRNA-eCLIP intersection analysis reveals a map of extracellular RNA binding proteins and associated RNAs across major human biofluids and carriers

Andrew R. Jackson, A. Milosavljevic, J. Rozowsky, 2023, Cell genomics.

Defining the force between separated sources on a light front

J. Rozowsky, C. Thorn, 1999, hep-th/9902145.

Perturbative relations between gravity and gauge theory

J. Rozowsky, M. Perelstein, L. Dixon, 1999, hep-th/9911194.

Evaluation of commercially available small RNASeq library preparation kits using low input RNA

J. Rozowsky, Saumya Das, K. Danielson, 2018, BMC Genomics.

Author Correction: Expanded encyclopaedias of DNA elements in the human and mouse genomes

M. Gerstein, Z. Weng, Manolis Kellis, 2022, Nature.

OrthoClust: an orthology-based network framework for clustering data across multiple species

M. Gerstein, J. Rozowsky, Koon-Kiu Yan, 2014, Genome Biology.

Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors

Kevin Y. Yip, James B. Brown, E. Birney, 2012, Genome Biology.

Divergence of transcription factor binding sites across related yeast species.

Michael R. Seringhaus, M. Gerstein, Haiyuan Yu, 2007, Science.

More than bad luck: Cancer and aging are linked to replication-driven changes to the epigenome

M. Levine, M. Gerstein, L. Pusztai, 2023, Science advances.

Structuring supplemental materials in support of reproducibility

M. Gerstein, V. Stodden, J. Rozowsky, 2017, Genome Biology.

Erratum to: The real cost of sequencing: scaling computation to keep pace with data generation

Farren J. Isaacs, M. Gerstein, G. Weinstock, 2016, Genome Biology.

FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data

David Z. Chen, M. Gerstein, M. Rubin, 2010, Genome Biology.

A statistical framework for modeling gene expression using chromatin features and application to modENCODE datasets

Kevin Y. Yip, M. Gerstein, J. Rozowsky, 2011, Genome Biology.

Variation in Transcription Factor Binding Among Humans

M. Gerstein, Fabian Grubert, Michael P. Snyder, 2010, Science.

The Extracellular RNA Communication Consortium: Establishing Foundational Knowledge and Technologies for Extracellular RNA Research

Nikita A. Sakhanenko, Michael T. McManus, Andrew R. Jackson, 2019, Cell.

Open Access Research Article Comparison and Calibration of Transcriptome Data from Rna-seq and Tiling Arrays

M. Gerstein, L. Hillier, R. Waterston, 2022 .

The real cost of sequencing: scaling computation to keep pace with data generation

Farren J. Isaacs, M. Gerstein, G. Weinstock, 2016, Genome Biology.

Tilescope: online analysis pipeline for high-density tiling microarray data

Hugo Y. K. Lam, M. Gerstein, Zhengdong D. Zhang, 2007, Genome Biology.

Transcription Factor Binding Site Identification in Yeast: a Comparison of High-density Oligonucleotide and Pcr-based Microarray Platforms

Michael R. Seringhaus, J. Rozowsky, A. Borneman, 2007 .

Comparative Analysis of the Transcriptome across Distant Species

Dmitri D. Pervouchine, Gennifer E. Merrihew, Benjamin W. Booth, 2014, Nature.

Temporal Dynamics of Collaborative Networks in Large Scientific Consortia.

Mark Gerstein, Daifeng Wang, Koon-Kiu Yan, 2016, Trends in genetics : TIG.

Multi-tissue integrative analysis of personal epigenomes

Rachel M. Sherman, C. Nusbaum, R. Guigó, 2021 .

Multi-tissue integrative analysis of personal epigenomes

Rachel M. Sherman, R. Guigó, A. Mortazavi, 2021 .

exRNA Atlas Analysis Reveals Distinct Extracellular RNA Cargo Types and Their Carriers Present across Human Biofluids

Alexander R. Pico, Andrew R. Jackson, James A. Diao, 2019, Cell.

Domain wall solutions with Abelian gauge fields

J. Rozowsky, R. Volkas, K. Wali, 2003, hep-th/0305232.

Understanding transcriptional regulation by integrative analysis of Understanding transcriptional regulation by integrative analysis of transcription factor binding data transcription factor binding data

E. Birney, Jing Leng, J. Rozowsky, 2022 .

transcription factor binding data Understanding transcriptional regulation by integrative analysis of

E. Birney, M. Gerstein, Jing Leng, 2012 .

Single-cell multi-cohort dissection of the schizophrenia transcriptome

Kelsey S. Montgomery, Annie W Shieh, Alex A. Pollen, 2022, Science.

FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data

David Z. Chen, M. Gerstein, M. Rubin, 2010, Genome Biology.

Allele-specific epigenome maps reveal sequence-dependent stochastic switching at regulatory loci

Robert C. Altshuler, M. Gerstein, Manolis Kellis, 2018, Science.

Deciphering the impact of genomic variation on function.

William H. Majoros, Neva C. Durand, Alan F. Rubin, 2024, Nature.