Search | Genome Research

Epigenetic characterization of pseudogenes across human tissues

Yunzhe Jiang
Beatrice Borsari
Mark Gerstein

First Published April 15, 2026

A map of enhancer regions in primary human neural progenitor cells using capture STARR-seq

Sophia C. Gaynor-Gillett
Lijun Cheng
Manman Shi
Jason Liu
Gaoyuan Wang
Megan Spector Qiuyu Guo Le Qi Mary Flaherty Martha Wall Ahyeon Hwang Mengting Gu Zhanlin Chen Yuhang Chen Jennifer R. Moran Jing Zhang
... [+11 authors] ...,
Donghoon Lee
Mark Gerstein
Daniel Geschwind
Kevin P. White

First Published July 11, 2025

Drosophila and C. elegans transcription factors reveal tissue-specific regulatory relationships" > Binding profiles for 961 Drosophila and C. elegans transcription factors reveal tissue-specific regulatory relationships

Michelle Kudron
Louis Gevirtzman
Alec Victorsen
Bridget C. Lear
Jiahao Gao
Jinrui Xu Swapna Samanta Emily Frink Adri Tran-Pearson Chau Huynh Dionne Vafeados Ann Hammonds William Fisher Martha Wall Greg Wesseling Vanessa Hernandez Zhichun Lin Mary Kasparian Kevin White Ravi Allada Mark Gerstein
... [+16 authors] ...,
LaDeana Hillier
Susan E. Celniker
Valerie Reinke
Robert H. Waterston

First Published October 22, 2024

The circular RNome of primary breast cancer

Marcel Smid
Saskia M. Wilting
Katharina Uhr
F. Germán Rodríguez-González
Vanja de Weerd
Wendy J.C. Prager-Van der Smissen Michelle van der Vlugt-Daane Anne van Galen Serena Nik-Zainal Adam Butler Sancha Martin Helen R. Davies Johan Staaf Marc J. van de Vijver Andrea L. Richardson Gaëten MacGrogan Roberto Salgado Gert G.G.M. van den Eynden Colin A. Purdie Alastair M. Thompson Carlos Caldas Paul N. Span Fred C.G.J. Sweep Peter T. Simpson Sunil R. Lakhani Steven Van Laere Christine Desmedt Angelo Paradiso Jorunn Eyfjord Annegien Broeks Anne Vincent-Salomon Andrew P. Futreal Stian Knappskog Tari King Alain Viari Anne-Lise Børresen-Dale Hendrik G. Stunnenberg
... [+32 authors] ...,
Mike Stratton
John A. Foekens
Anieta M. Sieuwerts
John W.M. Martens

First Published January 28, 2019

Mus caroli and Mus pahari genomes" > Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes

David Thybert
Maša Roller
Fábio C.P. Navarro
Ian Fiddes
Ian Streeter
Christine Feig David Martin-Galvez Mikhail Kolmogorov Václav Janoušek Wasiu Akanni Bronwen Aken Sarah Aldridge Varshith Chakrapani William Chow Laura Clarke Carla Cummins Anthony Doran Matthew Dunn Leo Goodstadt Kerstin Howe Matthew Howell Ambre-Aurore Josselin Robert C. Karn Christina M. Laukaitis Lilue Jingtao Fergal Martin Matthieu Muffato Stefanie Nachtweide Michael A. Quail Cristina Sisu Mario Stanke Klara Stefflova Cock Van Oosterhout Frederic Veyrunes Ben Ward Fengtang Yang Golbahar Yazdanifar Amonida Zadissa David J. Adams Alvis Brazma Mark Gerstein Benedict Paten
... [+37 authors] ...,
Son Pham
Thomas M. Keane
Duncan T. Odom
Paul Flicek

First Published March 21, 2018

One thousand somatic SNVs per skin fibroblast cell set baseline of mosaic mutational load with patterns that suggest proliferative origin

Alexej Abyzov
Livia Tomasini
Bo Zhou
Nikolaos Vasmatzis
Gianfilippo Coppola
Mariangela Amenduni Reenal Pattni Michael Wilson
... [+3 authors] ...,
Mark Gerstein
Sherman Weissman
Alexander E. Urban
Flora M. Vaccarino

First Published February 24, 2017

Analysis of variable retroduplications in human populations suggests coupling of retrotransposition to cell division

Alexej Abyzov
Rebecca Iskow
Omer Gokcumen
David W. Radke
Suganthi Balasubramanian
Baikang Pei
Lukas Habegger
Charles Lee
Mark Gerstein

First Published September 11, 2013

The origin, evolution, and functional impact of short insertion–deletion variants identified in 179 human genomes

Stephen B. Montgomery
David L. Goode
Erika Kvikstad
Cornelis A. Albers
Zhengdong D. Zhang
Xinmeng Jasmine Mu Guruprasad Ananda Bryan Howie Konrad J. Karczewski Kevin S. Smith Vanessa Anaya Rhea Richardson Joe Davis Daniel G. MacArthur Arend Sidow Laurent Duret Mark Gerstein
... [+12 authors] ...,
Kateryna D. Makova
Jonathan Marchini
Gil McVean
Gerton Lunter

First Published March 11, 2013

GENCODE: The reference human genome annotation for The ENCODE Project

Jennifer Harrow
Adam Frankish
Jose M. Gonzalez
Electra Tapanari
Mark Diekhans
Felix Kokocinski Bronwen L. Aken Daniel Barrell Amonida Zadissa Stephen Searle If Barnes Alexandra Bignell Veronika Boychenko Toby Hunt Mike Kay Gaurab Mukherjee Jeena Rajan Gloria Despacio-Reyes Gary Saunders Charles Steward Rachel Harte Michael Lin Cédric Howald Andrea Tanzer Thomas Derrien Jacqueline Chrast Nathalie Walters Suganthi Balasubramanian Baikang Pei Michael Tress Jose Manuel Rodriguez Iakes Ezkurdia Jeltje van Baren Michael Brent David Haussler Manolis Kellis Alfonso Valencia
... [+32 authors] ...,
Alexandre Reymond
Mark Gerstein
Roderic Guigó
Tim J. Hubbard

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

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

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

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

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

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

Assessing the limits of genomic data integration for predicting protein networks

Long J. Lu
Yu Xia
Alberto Paccanaro
Haiyuan Yu
Mark Gerstein

First Published July 5, 2005

Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles

Yoav Gilad
Scott A. Rifkin
Paul Bertone
Mark Gerstein
Kevin P. White

First Published May 2, 2005

Annotation Transfer Between Genomes: Protein–Protein Interologs and Protein–DNA Regulogs

Haiyuan Yu
Nicholas M. Luscombe
Hao Xin Lu
Xiaowei Zhu
Yu Xia
Jing-Dong J. Han
... [+1 authors] ...,
Nicolas Bertin
Sambath Chung
Marc Vidal
Mark Gerstein

First Published June 1, 2004

Millions of Years of Evolution Preserved: A Comprehensive Catalog of the Processed Pseudogenes in the Human Genome

Zhaolei Zhang
Paul M. Harrison
Yin Liu
Mark Gerstein

First Published December 1, 2003

Spectral Biclustering of Microarray Data: Coclustering Genes and Conditions

Yuval Kluger
Ronen Basri
Joseph T. Chang
Mark Gerstein

First Published April 1, 2003

Systematic Learning of Gene Functional Classes From DNA Array Expression Data by Using Multilayer Perceptrons

Alvaro Mateos
Joaquı́n Dopazo
Ronald Jansen
Yuhai Tu
Mark Gerstein
Gustavo Stolovitzky

First Published November 1, 2002

Identification and Analysis of Over 2000 Ribosomal Protein Pseudogenes in the Human Genome

Zhaolei Zhang
Paul Harrison
Mark Gerstein

First Published October 1, 2002

Molecular Fossils in the Human Genome: Identification and Analysis of the Pseudogenes in Chromosomes 21 and 22

Paul M. Harrison
Hedi Hegyi
Suganthi Balasubramanian
Nicholas M. Luscombe
Paul Bertone
Nathaniel Echols
Ted Johnson
Mark Gerstein

First Published February 1, 2002

Relating Whole-Genome Expression Data with Protein-Protein Interactions

Ronald Jansen
Dov Greenbaum
Mark Gerstein

First Published January 1, 2002

Annotation Transfer for Genomics: Measuring Functional Divergence in Multi-Domain Proteins

Hedi Hegyi
Mark Gerstein

First Published October 1, 2001

Interrelating Different Types of Genomic Data, from Proteome to Secretome: 'Oming in on Function

Dov Greenbaum
Nicholas M. Luscombe
Ronald Jansen
Jiang Qian
Mark Gerstein

First Published September 1, 2001

Whole-genome Trees Based on the Occurrence of Folds and Orthologs: Implications for Comparing Genomes on Different Levels

Jimmy Lin
Mark Gerstein

First Published June 1, 2000

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Your search for returned 30 results

Epigenetic characterization of pseudogenes across human tissues

A map of enhancer regions in primary human neural progenitor cells using capture STARR-seq

Drosophila and C. elegans transcription factors reveal tissue-specific regulatory relationships" > Binding profiles for 961 Drosophila and C. elegans transcription factors reveal tissue-specific regulatory relationships

The circular RNome of primary breast cancer

Mus caroli and Mus pahari genomes" > Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes

One thousand somatic SNVs per skin fibroblast cell set baseline of mosaic mutational load with patterns that suggest proliferative origin

Analysis of variable retroduplications in human populations suggests coupling of retrotransposition to cell division

The origin, evolution, and functional impact of short insertion–deletion variants identified in 179 human genomes

GENCODE: The reference human genome annotation for The ENCODE Project

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

Understanding transcriptional regulation by integrative analysis of transcription factor binding data

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

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

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

Predicting essential genes in fungal genomes

Design optimization methods for genomic DNA tiling arrays

Assessing the limits of genomic data integration for predicting protein networks

Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles

Annotation Transfer Between Genomes: Protein–Protein Interologs and Protein–DNA Regulogs

Millions of Years of Evolution Preserved: A Comprehensive Catalog of the Processed Pseudogenes in the Human Genome

Spectral Biclustering of Microarray Data: Coclustering Genes and Conditions

Systematic Learning of Gene Functional Classes From DNA Array Expression Data by Using Multilayer Perceptrons

Identification and Analysis of Over 2000 Ribosomal Protein Pseudogenes in the Human Genome

Molecular Fossils in the Human Genome: Identification and Analysis of the Pseudogenes in Chromosomes 21 and 22

Relating Whole-Genome Expression Data with Protein-Protein Interactions

Annotation Transfer for Genomics: Measuring Functional Divergence in Multi-Domain Proteins

Interrelating Different Types of Genomic Data, from Proteome to Secretome: 'Oming in on Function

Whole-genome Trees Based on the Occurrence of Folds and Orthologs: Implications for Comparing Genomes on Different Levels

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Your search for returned 30 results