Search | Genome Research

Precision environmental health monitoring by longitudinal exposome and multi-omics profiling

Peng Gao
Xiaotao Shen
Xinyue Zhang
Chao Jiang
Sai Zhang
Xin Zhou
Sophia Miryam Schüssler-Fiorenza Rose
Michael Snyder

First Published June 6, 2022

Microfluidic isoform sequencing shows widespread splicing coordination in the human transcriptome

Hagen Tilgner
Fereshteh Jahanbani
Ishaan Gupta
Paul Collier
Eric Wei
Morten Rasmussen
Michael Snyder

First Published December 1, 2017

Diurnal regulation of RNA polymerase III transcription is under the control of both the feeding–fasting response and the circadian clock

François Mange
Viviane Praz
Eugenia Migliavacca
Ian M. Willis
Frédéric Schütz
Nouria Hernandez Nouria Hernandez Mauro Delorenzi Bart Deplancke Béatrice Desvergne Nicolas Guex Winship Herr Felix Naef Jacques Rougemont Ueli Schibler Teemu Andersin Pascal Cousin Federica Gilardi Fabienne Lammers François Mange Dominic Villeneuve Fabrice David Roberto Fabbretti Philippe Jacquet Irina Krier Dmitry Kuznetsov Marion Leleu Robin Liechti Olivier Martin Eugenia Migliavacca Aurélien Naldi Viviane Praz
... [+27 authors] ...,
Leonor Rib
Jonathan Sobel
Volker Vlegel
Ioannis Xenarios

First Published March 24, 2017

Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization

Nicolas Bonhoure
Gergana Bounova
David Bernasconi
Viviane Praz
Fabienne Lammers
Donatella Canella Ian M. Willis Winship Herr Nouria Hernandez Mauro Delorenzi Nouria Hernandez Mauro Delorenzi Bart Deplancke Béatrice Desvergne Nicolas Guex Winship Herr Felix Naef Jacques Rougemont Ueli Schibler Teemu Andersin Pascal Cousin Federica Gilardi Pascal Gos Fabienne Lammers Sunil Raghav Dominic Villeneuve Roberto Fabbretti Volker Vlegel Ioannis Xenarios Eugenia Migliavacca Viviane Praz Fabrice David Yohan Jarosz Dmitry Kuznetsov Robin Liechti Olivier Martin Julien Delafontaine Julia Cajan Kyle Gustafson Irina Krier Marion Leleu Nacho Molina
... [+37 authors] ...,
Aurélien Naldi
Leonor Rib
Laura Symul
Gergana Bounova

First Published April 7, 2014

Linking disease associations with regulatory information in the human genome

Marc A. Schaub
Alan P. Boyle
Anshul Kundaje
Serafim Batzoglou
Michael Snyder

First Published September 5, 2012

Annotation of functional variation in personal genomes using RegulomeDB

Alan P. Boyle
Eurie L. Hong
Manoj Hariharan
Yong Cheng
Marc A. Schaub
Maya Kasowski Konrad J. Karczewski Julie Park
... [+3 authors] ...,
Benjamin C. Hitz
Shuai Weng
J. Michael Cherry
Michael Snyder

First Published September 5, 2012

Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors

Jie Wang
Jiali Zhuang
Sowmya Iyer
XinYing Lin
Troy W. Whitfield
Melissa C. Greven Brian G. Pierce Xianjun Dong Anshul Kundaje Yong Cheng Oliver J. Rando Ewan Birney
... [+7 authors] ...,
Richard M. Myers
William S. Noble
Michael Snyder
Zhiping Weng

First Published September 5, 2012

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

Stephen G. Landt
Georgi K. Marinov
Anshul Kundaje
Pouya Kheradpour
Florencia Pauli
Serafim Batzoglou Bradley E. Bernstein Peter Bickel James B. Brown Philip Cayting Yiwen Chen Gilberto DeSalvo Charles Epstein Katherine I. Fisher-Aylor Ghia Euskirchen Mark Gerstein Jason Gertz Alexander J. Hartemink Michael M. Hoffman Vishwanath R. Iyer Youngsook L. Jung Subhradip Karmakar Manolis Kellis Peter V. Kharchenko Qunhua Li Tao Liu X. Shirley Liu Lijia Ma Aleksandar Milosavljevic Richard M. Myers Peter J. Park Michael J. Pazin Marc D. Perry Debasish Raha Timothy E. Reddy Joel Rozowsky Noam Shoresh Arend Sidow Matthew Slattery John A. Stamatoyannopoulos Michael Y. Tolstorukov Kevin P. White Simon Xi
... [+38 authors] ...,
Peggy J. Farnham
Jason D. Lieb
Barbara J. Wold
Michael Snyder

First Published September 5, 2012

$Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs$

Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs

Hagen Tilgner
David G. Knowles
Rory Johnson
Carrie A. Davis
Sudipto Chakrabortty
Sarah Djebali
... [+1 authors] ...,
João Curado
Michael Snyder
Thomas R. Gingeras
Roderic Guigó

First Published September 5, 2012

Understanding transcriptional regulation by integrative analysis of transcription factor binding data

Chao Cheng
Roger Alexander
Renqiang Min
Jing Leng
Kevin Y. Yip
Joel Rozowsky Koon-Kiu Yan Xianjun Dong Sarah Djebali Yijun Ruan Carrie A. Davis Piero Carninci Timo Lassman Thomas R. Gingeras Roderic Guigó
... [+10 authors] ...,
Ewan Birney
Zhiping Weng
Michael Snyder
Mark Gerstein

First Published September 5, 2012

A highly integrated and complex PPARGC1A transcription factor binding network in HepG2 cells

Alexandra E. Charos
Brian D. Reed
Debasish Raha
Anna M. Szekely
Sherman M. Weissman
Michael Snyder

First Published September 5, 2012

Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements

Anshul Kundaje
Sofia Kyriazopoulou-Panagiotopoulou
Max Libbrecht
Cheryl L. Smith
Debasish Raha
Elliott E. Winters
... [+1 authors] ...,
Steven M. Johnson
Michael Snyder
Serafim Batzoglou
Arend Sidow

First Published September 5, 2012

A multiplicity of factors contributes to selective RNA polymerase III occupancy of a subset of RNA polymerase III genes in mouse liver

Donatella Canella
David Bernasconi
Federica Gilardi
Gwendal LeMartelot
Eugenia Migliavacca
Viviane Praz Pascal Cousin Mauro Delorenzi Nouria Hernandez Nouria Hernandez Mauro Delorenzi Bart Deplancke Béatrice Desvergne Nicolas Guex Winship Herr Felix Naef Jacques Rougemont Ueli Schibler Bart Deplancke Nicolas Guex Winship Herr Nicolas Guex Teemu Andersin Pascal Cousin Federica Gilardi Pascal Gos Gwendal Le Martelot Fabienne Lammers Donatella Canella Federica Gilardi Sunil Raghav Roberto Fabbretti Arnaud Fortier Li Long Volker Vlegel Ioannis Xenarios Eugenia Migliavacca Viviane Praz Nicolas Guex Felix Naef Jacques Rougemont Fabrice David Yohan Jarosz Dmitry Kuznetsov Robin Liechti Olivier Martin Frederick Ross Lucas Sinclair Julia Cajan Irina Krier Marion Leleu Eugenia Migliavacca Nacho Molina Aurélien Naldi Guillaume Rey Laura Symul Nicolas Guex Felix Naef Jacques Rougemont David Bernasconi Mauro Delorenzi Teemu Andersin Donatella Canella
... [+58 authors] ...,
Federica Gilardi
Gwendal Le Martelot
Fabienne Lammers
Sunil Raghav

First Published January 27, 2012

CNVnator: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing

Alexej Abyzov
Alexander E. Urban
Michael Snyder
Mark Gerstein

First Published February 7, 2011

C. elegans" > Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans

Wei Niu
Zhi John Lu
Mei Zhong
Mihail Sarov
John I. Murray
Cathleen M. Brdlik Judith Janette Chao Chen Pedro Alves Elicia Preston Cindie Slightham Lixia Jiang Anthony A. Hyman Stuart K. Kim
... [+9 authors] ...,
Robert H. Waterston
Mark Gerstein
Michael Snyder
Valerie Reinke

First Published December 22, 2010

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

Zhi John Lu
Kevin Y. Yip
Guilin Wang
Chong Shou
LaDeana W. Hillier
Ekta Khurana Ashish Agarwal Raymond Auerbach Joel Rozowsky Chao Cheng Masaomi Kato David M. Miller Frank Slack
... [+8 authors] ...,
Michael Snyder
Robert H. Waterston
Valerie Reinke
Mark B. Gerstein

First Published December 22, 2010

Candida albicans using RNA-seq" > Comprehensive annotation of the transcriptome of the human fungal pathogen Candida albicans using RNA-seq

Vincent M. Bruno
Zhong Wang
Sadie L. Marjani
Ghia M. Euskirchen
Jeffrey Martin
Gavin Sherlock
Michael Snyder

First Published September 1, 2010

Defining the RNA polymerase III transcriptome: Genome-wide localization of the RNA polymerase III transcription machinery in human cells

Donatella Canella
Viviane Praz
Jaime H. Reina
Pascal Cousin
Nouria Hernandez

First Published April 22, 2010

MSB: A mean-shift-based approach for the analysis of structural variation in the genome

Lu-yong Wang
Alexej Abyzov
Jan O. Korbel
Michael Snyder
Mark Gerstein

First Published November 26, 2008

Analysis of copy number variants and segmental duplications in the human genome: Evidence for a change in the process of formation in recent evolutionary history

Philip M. Kim
Hugo Y.K. Lam
Alexander E. Urban
Jan O. Korbel
Jason Affourtit
Fabian Grubert
... [+1 authors] ...,
Xueying Chen
Sherman Weissman
Michael Snyder
Mark B. Gerstein

First Published October 8, 2008

Genome-wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor binding

A. Gordon Robertson
Mikhail Bilenky
Angela Tam
Yongjun Zhao
Thomas Zeng
Nina Thiessen Timothee Cezard Anthony P. Fejes Elizabeth D. Wederell Rebecca Cullum Ghia Euskirchen Martin Krzywinski Inanc Birol Michael Snyder
... [+9 authors] ...,
Pamela A. Hoodless
Martin Hirst
Marco A. Marra
Steven J.M. Jones

First Published September 11, 2008

A genomic analysis of RNA polymerase II modification and chromatin architecture related to 3′ end RNA polyadenylation

Zheng Lian
Alexander Karpikov
Jin Lian
Milind C. Mahajan
Stephen Hartman
Mark Gerstein
Michael Snyder
Sherman M. Weissman

First Published May 16, 2008

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

David S. Johnson
Wei Li
D. Benjamin Gordon
Arindam Bhattacharjee
Bo Curry
Jayati Ghosh Leonardo Brizuela Jason S. Carroll Myles Brown Paul Flicek Christoph M. Koch Ian Dunham Mark Bieda Xiaoqin Xu Peggy J. Farnham Philipp Kapranov David A. Nix Thomas R. Gingeras Xinmin Zhang Heather Holster Nan Jiang Roland D. Green Jun S. Song Scott A. McCuine Elizabeth Anton Loan Nguyen Nathan D. Trinklein Zhen Ye Keith Ching David Hawkins Bing Ren Peter C. Scacheri Joel Rozowsky Alexander Karpikov Ghia Euskirchen Sherman Weissman Mark Gerstein Michael Snyder Annie Yang Zarmik Moqtaderi Heather Hirsch Hennady P. Shulha Yutao Fu Zhiping Weng
... [+39 authors] ...,
Kevin Struhl
Richard M. Myers
Jason D. Lieb
X. Shirley Liu

First Published February 7, 2008

Integrated analysis of experimental data sets reveals many novel promoters in 1% of the human genome

Nathan D. Trinklein
Ulaş Karaöz
Jiaqian Wu
Anason Halees
Shelley Force Aldred
Patrick J. Collins Deyou Zheng Zhengdong D. Zhang
... [+3 authors] ...,
Mark B. Gerstein
Michael Snyder
Richard M. Myers
Zhiping Weng

First Published June 13, 2007

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

Joel S. Rozowsky
Daniel Newburger
Fred Sayward
Jiaqian Wu
Greg Jordan
Jan O. Korbel Ugrappa Nagalakshmi Jin Yang Deyou Zheng Roderic Guigó Thomas R. Gingeras
... [+6 authors] ...,
Sherman Weissman
Perry Miller
Michael Snyder
Mark B. Gerstein

First Published June 13, 2007

Statistical analysis of the genomic distribution and correlation of regulatory elements in the ENCODE regions

Zhengdong D. Zhang
Alberto Paccanaro
Yutao Fu
Sherman Weissman
Zhiping Weng
Joseph Chang
Michael Snyder
Mark B. Gerstein

First Published June 13, 2007

Pseudogenes in the ENCODE regions: Consensus annotation, analysis of transcription, and evolution

Deyou Zheng
Adam Frankish
Robert Baertsch
Philipp Kapranov
Alexandre Reymond
Siew Woh Choo Yontao Lu France Denoeud Stylianos E. Antonarakis Michael Snyder Yijun Ruan Chia-Lin Wei
... [+7 authors] ...,
Thomas R. Gingeras
Roderic Guigó
Jennifer Harrow
Mark B. Gerstein

First Published June 13, 2007

Structured RNAs in the ENCODE selected regions of the human genome

Stefan Washietl
Jakob S. Pedersen
Jan O. Korbel
Claudia Stocsits
Andreas R. Gruber
Jörg Hackermüller Jana Hertel Manja Lindemeyer Kristin Reiche Andrea Tanzer Catherine Ucla Carine Wyss Stylianos E. Antonarakis France Denoeud Julien Lagarde Jorg Drenkow Philipp Kapranov Thomas R. Gingeras Roderic Guigó Michael Snyder
... [+15 authors] ...,
Mark B. Gerstein
Alexandre Reymond
Ivo L. Hofacker
Peter F. Stadler

First Published June 13, 2007

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

Ghia M. Euskirchen
Joel S. Rozowsky
Chia-Lin Wei
Wah Heng Lee
Zhengdong D. Zhang
Stephen Hartman Olof Emanuelsson Viktor Stolc
... [+3 authors] ...,
Sherman Weissman
Mark B. Gerstein
Yijun Ruan
Michael Snyder

First Published June 13, 2007

Mapping the chromosomal targets of STAT1 by Sequence Tag Analysis of Genomic Enrichment (STAGE)

Akshay A. Bhinge
Jonghwan Kim
Ghia M. Euskirchen
Michael Snyder
Vishwanath R. Iyer

First Published June 13, 2007

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

Mark B. Gerstein
Can Bruce
Joel S. Rozowsky
Deyou Zheng
Jiang Du
Jan O. Korbel
... [+1 authors] ...,
Olof Emanuelsson
Zhengdong D. Zhang
Sherman Weissman
Michael Snyder

First Published June 13, 2007

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

Olof Emanuelsson
Ugrappa Nagalakshmi
Deyou Zheng
Joel S. Rozowsky
Alexander E. Urban
Jiang Du Zheng Lian
... [+2 authors] ...,
Viktor Stolc
Sherman Weissman
Michael Snyder
Mark B. Gerstein

First Published November 21, 2006

Predicting essential genes in fungal genomes

Michael Seringhaus
Alberto Paccanaro
Anthony Borneman
Michael Snyder
Mark Gerstein

First Published August 9, 2006

Design optimization methods for genomic DNA tiling arrays

Paul Bertone
Valery Trifonov
Joel S. Rozowsky
Falk Schubert
Olof Emanuelsson
John Karro
Ming-Yang Kao
Michael Snyder
Mark Gerstein

First Published December 19, 2005

Large-Scale Mutagenesis of the Yeast Genome Using a Tn7-Derived Multipurpose Transposon

Anuj Kumar
Michael Seringhaus
Matthew C. Biery
Robert J. Sarnovsky
Lara Umansky
Stacy Piccirillo Matthew Heidtman Kei-Hoi Cheung
... [+3 authors] ...,
Craig J. Dobry
Mark B. Gerstein
Nancy L. Craig
Michael Snyder

First Published October 1, 2004

Filter results by:

Your search for returned 35 results

Precision environmental health monitoring by longitudinal exposome and multi-omics profiling

Microfluidic isoform sequencing shows widespread splicing coordination in the human transcriptome

Diurnal regulation of RNA polymerase III transcription is under the control of both the feeding–fasting response and the circadian clock

Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization

Linking disease associations with regulatory information in the human genome

Annotation of functional variation in personal genomes using RegulomeDB

Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors

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

Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs

Understanding transcriptional regulation by integrative analysis of transcription factor binding data

A highly integrated and complex PPARGC1A transcription factor binding network in HepG2 cells

Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements

A multiplicity of factors contributes to selective RNA polymerase III occupancy of a subset of RNA polymerase III genes in mouse liver

CNVnator: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing

C. elegans" > Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans

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

Candida albicans using RNA-seq" > Comprehensive annotation of the transcriptome of the human fungal pathogen Candida albicans using RNA-seq

Defining the RNA polymerase III transcriptome: Genome-wide localization of the RNA polymerase III transcription machinery in human cells

MSB: A mean-shift-based approach for the analysis of structural variation in the genome

Analysis of copy number variants and segmental duplications in the human genome: Evidence for a change in the process of formation in recent evolutionary history

Genome-wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor binding

A genomic analysis of RNA polymerase II modification and chromatin architecture related to 3′ end RNA polyadenylation

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

Integrated analysis of experimental data sets reveals many novel promoters in 1% of the human genome

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

Statistical analysis of the genomic distribution and correlation of regulatory elements in the ENCODE regions

Pseudogenes in the ENCODE regions: Consensus annotation, analysis of transcription, and evolution

Structured RNAs in the ENCODE selected regions of the human genome

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

Mapping the chromosomal targets of STAT1 by Sequence Tag Analysis of Genomic Enrichment (STAGE)

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

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

Predicting essential genes in fungal genomes

Design optimization methods for genomic DNA tiling arrays

Large-Scale Mutagenesis of the Yeast Genome Using a Tn7-Derived Multipurpose Transposon

Filter results by:

Filter by Author

Filter by Article type

Your search for returned 35 results