Search | Genome Research

Discovery of high-confidence human protein-coding genes and exons by whole-genome PhyloCSF helps elucidate 118 GWAS loci

Jonathan M. Mudge
Irwin Jungreis
Toby Hunt
Jose Manuel Gonzalez
James C. Wright
Mike Kay Claire Davidson Stephen Fitzgerald Ruth Seal Susan Tweedie Liang He Robert M. Waterhouse Yue Li
... [+8 authors] ...,
Elspeth Bruford
Jyoti S. Choudhary
Adam Frankish
Manolis Kellis

First Published September 19, 2019

An AR-ERG transcriptional signature defined by long-range chromatin interactomes in prostate cancer cells

Zhizhuo Zhang
Kern Rei Chng
Shreyas Lingadahalli
Zikai Chen
Mei Hui Liu
Huy Hoang Do Shaojiang Cai Nicola Rinaldi Huay Mei Poh Guoliang Li Ying Ying Sung Charlie L. Heng Leighton J. Core Si Kee Tan Xiaoan Ruan John T. Lis
... [+11 authors] ...,
Manolis Kellis
Yijun Ruan
Wing-Kin Sung
Edwin Cheung

First Published January 3, 2019

cis-mediators for trans-eQTLs across many human tissues using genomic mediation analysis" > Identifying cis-mediators for trans-eQTLs across many human tissues using genomic mediation analysis

Fan Yang
Jiebiao Wang
Brandon L. Pierce
Lin S. Chen
François Aguet
Kristin G. Ardlie Beryl B. Cummings Ellen T. Gelfand Gad Getz Kane Hadley Robert E. Handsaker Katherine H. Huang Seva Kashin Konrad J. Karczewski Monkol Lek Xiao Li Daniel G. MacArthur Jared L. Nedzel Duyen T. Nguyen Michael S. Noble Ayellet V. Segrè Casandra A. Trowbridge Taru Tukiainen Nathan S. Abell Brunilda Balliu Ruth Barshir Omer Basha Alexis Battle Gireesh K. Bogu Andrew Brown Christopher D. Brown Stephane E. Castel Lin S. Chen Colby Chiang Donald F. Conrad Nancy J. Cox Farhan N. Damani Joe R. Davis Olivier Delaneau Emmanouil T. Dermitzakis Barbara E. Engelhardt Eleazar Eskin Pedro G. Ferreira Laure Frésard Eric R. Gamazon Diego Garrido-Martín Ariel D.H. Gewirtz Genna Gliner Michael J. Gloudemans Roderic Guigo Ira M. Hall Buhm Han Yuan He Farhad Hormozdiari Cedric Howald Hae Kyung Im Brian Jo Eun Yong Kang Yungil Kim Sarah Kim-Hellmuth Tuuli Lappalainen Gen Li Xin Li Boxiang Liu Serghei Mangul Mark I. McCarthy Ian C. McDowell Pejman Mohammadi Jean Monlong Stephen B. Montgomery Manuel Muñoz-Aguirre Anne W. Ndungu Dan L. Nicolae Andrew B. Nobel Meritxell Oliva Halit Ongen John J. Palowitch Nikolaos Panousis Panagiotis Papasaikas YoSon Park Princy Parsana Anthony J. Payne Christine B. Peterson Jie Quan Ferran Reverter Chiara Sabatti Ashis Saha Michael Sammeth Alexandra J. Scott Andrey A. Shabalin Reza Sodaei Matthew Stephens Barbara E. Stranger Benjamin J. Strober Jae Hoon Sul Emily K. Tsang Sarah Urbut Martijn van de Bunt Gao Wang Xiaoquan Wen Fred A. Wright Hualin S. Xi Esti Yeger-Lotem Zachary Zappala Judith B. Zaugg Yi-Hui Zhou Joshua M. Akey Daniel Bates Joanne Chan Lin S. Chen Melina Claussnitzer Kathryn Demanelis Morgan Diegel Jennifer A. Doherty Andrew P. Feinberg Marian S. Fernando Jessica Halow Kasper D. Hansen Eric Haugen Peter F. Hickey Lei Hou Farzana Jasmine Ruiqi Jian Lihua Jiang Audra Johnson Rajinder Kaul Manolis Kellis Muhammad G. Kibriya Kristen Lee Jin Billy Li Qin Li Xiao Li Jessica Lin Shin Lin Sandra Linder Caroline Linke Yaping Liu Matthew T. Maurano Benoit Molinie Stephen B. Montgomery Jemma Nelson Fidencio J. Neri Meritxell Oliva Yongjin Park Brandon L. Pierce Nicola J. Rinaldi Lindsay F. Rizzardi Richard Sandstrom Andrew Skol Kevin S. Smith Michael P. Snyder John Stamatoyannopoulos Barbara E. Stranger Hua Tang Emily K. Tsang Li Wang Meng Wang Nicholas Van Wittenberghe Fan Wu Rui Zhang Concepcion R. Nierras Philip A. Branton Latarsha J. Carithers Ping Guan Helen M. Moore Abhi Rao Jimmie B. Vaught Sarah E. Gould Nicole C. Lockart Casey Martin Jeffery P. Struewing Simona Volpi Anjene M. Addington Susan E. Koester A. Roger Little Lori E. Brigham Richard Hasz Marcus Hunter Christopher Johns Mark Johnson Gene Kopen William F. Leinweber John T. Lonsdale Alisa McDonald Bernadette Mestichelli Kevin Myer Brian Roe Michael Salvatore Saboor Shad Jeffrey A. Thomas Gary Walters Michael Washington Joseph Wheeler Jason Bridge Barbara A. Foster Bryan M. Gillard Ellen Karasik Rachna Kumar Mark Miklos Michael T. Moser Scott D. Jewell Robert G. Montroy Daniel C. Rohrer Dana R. Valley David A. Davis Deborah C. Mash Anita H. Undale Anna M. Smith David E. Tabor Nancy V. Roche Jeffrey A. McLean Negin Vatanian Karna L. Robinson Leslie Sobin Mary E. Barcus Kimberly M. Valentino Liqun Qi Steven Hunter Pushpa Hariharan Shilpi Singh Ki Sung Um Takunda Matose Maria M. Tomaszewski Laura K. Barker Maghboeba Mosavel Laura A. Siminoff Heather M. Traino Paul Flicek Thomas Juettemann Magali Ruffier Dan Sheppard Kieron Taylor Stephen J. Trevanion Daniel R. Zerbino Brian Craft Mary Goldman Maximilian Haeussler W. James Kent Christopher M. Lee
... [+234 authors] ...,
Benedict Paten
Kate R. Rosenbloom
John Vivian
Jingchun Zhu

First Published October 11, 2017

Co-expression networks reveal the tissue-specific regulation of transcription and splicing

Ashis Saha
Yungil Kim
Ariel D.H. Gewirtz
Brian Jo
Chuan Gao
Ian C. McDowell Barbara E. Engelhardt Alexis Battle François Aguet Kristin G. Ardlie Beryl B. Cummings Ellen T. Gelfand Gad Getz Kane Hadley Robert E. Handsaker Katherine H. Huang Seva Kashin Konrad J. Karczewski Monkol Lek Xiao Li Daniel G. MacArthur Jared L. Nedzel Duyen T. Nguyen Michael S. Noble Ayellet V. Segrè Casandra A. Trowbridge Taru Tukiainen Nathan S. Abell Brunilda Balliu Ruth Barshir Omer Basha Alexis Battle Gireesh K. Bogu Andrew Brown Christopher D. Brown Stephane E. Castel Lin S. Chen Colby Chiang Donald F. Conrad Nancy J. Cox Farhan N. Damani Joe R. Davis Olivier Delaneau Emmanouil T. Dermitzakis Barbara E. Engelhardt Eleazar Eskin Pedro G. Ferreira Laure Frésard Eric R. Gamazon Diego Garrido-Martín Ariel D.H. Gewirtz Genna Gliner Michael J. Gloudemans Roderic Guigo Ira M. Hall Buhm Han Yuan He Farhad Hormozdiari Cedric Howald Hae Kyung Im Brian Jo Eun Yong Kang Yungil Kim Sarah Kim-Hellmuth Tuuli Lappalainen Gen Li Xin Li Boxiang Liu Serghei Mangul Mark I. McCarthy Ian C. McDowell Pejman Mohammadi Jean Monlong Stephen B. Montgomery Manuel Muñoz-Aguirre Anne W. Ndungu Dan L. Nicolae Andrew B. Nobel Meritxell Oliva Halit Ongen John J. Palowitch Nikolaos Panousis Panagiotis Papasaikas YoSon Park Princy Parsana Anthony J. Payne Christine B. Peterson Jie Quan Ferran Reverter Chiara Sabatti Ashis Saha Michael Sammeth Alexandra J. Scott Andrey A. Shabalin Reza Sodaei Matthew Stephens Barbara E. Stranger Benjamin J. Strober Jae Hoon Sul Emily K. Tsang Sarah Urbut Martijn van de Bunt Gao Wang Xiaoquan Wen Fred A. Wright Hualin S. Xi Esti Yeger-Lotem Zachary Zappala Judith B. Zaugg Yi-Hui Zhou Joshua M. Akey Daniel Bates Joanne Chan Lin S. Chen Melina Claussnitzer Kathryn Demanelis Morgan Diegel Jennifer A. Doherty Andrew P. Feinberg Marian S. Fernando Jessica Halow Kasper D. Hansen Eric Haugen Peter F. Hickey Lei Hou Farzana Jasmine Ruiqi Jian Lihua Jiang Audra Johnson Rajinder Kaul Manolis Kellis Muhammad G. Kibriya Kristen Lee Jin Billy Li Qin Li Xiao Li Jessica Lin Shin Lin Sandra Linder Caroline Linke Yaping Liu Matthew T. Maurano Benoit Molinie Stephen B. Montgomery Jemma Nelson Fidencio J. Neri Meritxell Oliva Yongjin Park Brandon L. Pierce Nicola J. Rinaldi Lindsay F. Rizzardi Richard Sandstrom Andrew Skol Kevin S. Smith Michael P. Snyder John Stamatoyannopoulos Barbara E. Stranger Hua Tang Emily K. Tsang Li Wang Meng Wang Nicholas Van Wittenberghe Fan Wu Rui Zhang Concepcion R. Nierras Philip A. Branton Latarsha J. Carithers Ping Guan Helen M. Moore Abhi Rao Jimmie B. Vaught Sarah E. Gould Nicole C. Lockart Casey Martin Jeffery P. Struewing Simona Volpi Anjene M. Addington Susan E. Koester A. Roger Little Lori E. Brigham Richard Hasz Marcus Hunter Christopher Johns Mark Johnson Gene Kopen William F. Leinweber John T. Lonsdale Alisa McDonald Bernadette Mestichelli Kevin Myer Brian Roe Michael Salvatore Saboor Shad Jeffrey A. Thomas Gary Walters Michael Washington Joseph Wheeler Jason Bridge Barbara A. Foster Bryan M. Gillard Ellen Karasik Rachna Kumar Mark Miklos Michael T. Moser Scott D. Jewell Robert G. Montroy Daniel C. Rohrer Dana R. Valley David A. Davis Deborah C. Mash Anita H. Undale Anna M. Smith David E. Tabor Nancy V. Roche Jeffrey A. McLean Negin Vatanian Karna L. Robinson Leslie Sobin Mary E. Barcus Kimberly M. Valentino Liqun Qi Steven Hunter Pushpa Hariharan Shilpi Singh Ki Sung Um Takunda Matose Maria M. Tomaszewski Laura K. Barker Maghboeba Mosavel Laura A. Siminoff Heather M. Traino Paul Flicek Thomas Juettemann Magali Ruffier Dan Sheppard Kieron Taylor Stephen J. Trevanion Daniel R. Zerbino Brian Craft Mary Goldman Maximilian Haeussler W. James Kent Christopher M. Lee
... [+238 authors] ...,
Benedict Paten
Kate R. Rosenbloom
John Vivian
Jingchun Zhu

First Published October 11, 2017

D. melanogaster modENCODE transcriptome annotation" > Comparative validation of the D. melanogaster modENCODE transcriptome annotation

Zhen-Xia Chen
David Sturgill
Jiaxin Qu
Huaiyang Jiang
Soo Park
Nathan Boley Ana Maria Suzuki Anthony R. Fletcher David C. Plachetzki Peter C. FitzGerald Carlo G. Artieri Joel Atallah Olga Barmina James B. Brown Kerstin P. Blankenburg Emily Clough Abhijit Dasgupta Sai Gubbala Yi Han Joy C. Jayaseelan Divya Kalra Yoo-Ah Kim Christie L. Kovar Sandra L. Lee Mingmei Li James D. Malley John H. Malone Tittu Mathew Nicolas R. Mattiuzzo Mala Munidasa Donna M. Muzny Fiona Ongeri Lora Perales Teresa M. Przytycka Ling-Ling Pu Garrett Robinson Rebecca L. Thornton Nehad Saada Steven E. Scherer Harold E. Smith Charles Vinson Crystal B. Warner Kim C. Worley Yuan-Qing Wu Xiaoyan Zou Peter Cherbas Manolis Kellis Michael B. Eisen Fabio Piano Karin Kionte David H. Fitch Paul W. Sternberg Asher D. Cutter Michael O. Duff Roger A. Hoskins Brenton R. Graveley Richard A. Gibbs Peter J. Bickel Artyom Kopp
... [+54 authors] ...,
Piero Carninci
Susan E. Celniker
Brian Oliver
Stephen Richards

First Published July 1, 2014

Drosophila melanogaster" > Diverse patterns of genomic targeting by transcriptional regulators in Drosophila melanogaster

Matthew Slattery
Lijia Ma
Rebecca F. Spokony
Robert K. Arthur
Pouya Kheradpour
Anshul Kundaje Nicolas Nègre Alex Crofts Ryan Ptashkin Jennifer Zieba Alexander Ostapenko Sarah Suchy Alec Victorsen Nader Jameel A. Jason Grundstad Wenxuan Gao Jennifer R. Moran
... [+12 authors] ...,
E. Jay Rehm
Robert L. Grossman
Manolis Kellis
Kevin P. White

First Published July 1, 2014

Evolutionary dynamics and tissue specificity of human long noncoding RNAs in six mammals

Stefan Washietl
Manolis Kellis
Manuel Garber

First Published January 15, 2014

Most parsimonious reconciliation in the presence of gene duplication, loss, and deep coalescence using labeled coalescent trees

Yi-Chieh Wu
Matthew D. Rasmussen
Mukul S. Bansal
Manolis Kellis

First Published December 5, 2013

Integrating and mining the chromatin landscape of cell-type specificity using self-organizing maps

Ali Mortazavi
Shirley Pepke
Camden Jansen
Georgi K. Marinov
Jason Ernst
Manolis Kellis
Ross C. Hardison
Richard M. Myers
Barbara J. Wold

First Published October 29, 2013

Arboretum: Reconstruction and analysis of the evolutionary history of condition-specific transcriptional modules

Sushmita Roy
Ilan Wapinski
Jenna Pfiffner
Courtney French
Amanda Socha
Jay Konieczka
... [+1 authors] ...,
Naomi Habib
Manolis Kellis
Dawn Thompson
Aviv Regev

First Published May 2, 2013

Interplay between chromatin state, regulator binding, and regulatory motifs in six human cell types

Jason Ernst
Manolis Kellis

First Published April 17, 2013

Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay

Pouya Kheradpour
Jason Ernst
Alexandre Melnikov
Peter Rogov
Li Wang
Xiaolan Zhang
Jessica Alston
Tarjei S. Mikkelsen
Manolis Kellis

First Published March 19, 2013

Constitutive nuclear lamina–genome interactions are highly conserved and associated with A/T-rich sequence

Wouter Meuleman
Daan Peric-Hupkes
Jop Kind
Jean-Bernard Beaudry
Ludo Pagie
Manolis Kellis
Marcel Reinders
Lodewyk Wessels
Bas van Steensel

First Published November 2, 2012

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

Drosophila melanogaster by integrative inference of transcriptional networks" > Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks

Daniel Marbach
Sushmita Roy
Ferhat Ay
Patrick E. Meyer
Rogerio Candeias
Tamer Kahveci
Christopher A. Bristow
Manolis Kellis

First Published March 28, 2012

Unified modeling of gene duplication, loss, and coalescence using a locus tree

Matthew D. Rasmussen
Manolis Kellis

First Published January 23, 2012

Drosophila and other metazoa" > Evidence of abundant stop codon readthrough in Drosophila and other metazoa

Irwin Jungreis
Michael F. Lin
Rebecca Spokony
Clara S. Chan
Nicolas Negre
Alec Victorsen
Kevin P. White
Manolis Kellis

First Published October 12, 2011

Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes

Michael F. Lin
Pouya Kheradpour
Stefan Washietl
Brian J. Parker
Jakob S. Pedersen
Manolis Kellis

First Published October 12, 2011

New families of human regulatory RNA structures identified by comparative analysis of vertebrate genomes

Brian J. Parker
Ida Moltke
Adam Roth
Stefan Washietl
Jiayu Wen
Manolis Kellis
Ronald Breaker
Jakob Skou Pedersen

First Published October 12, 2011

Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration

Weisheng Wu
Yong Cheng
Cheryl A. Keller
Jason Ernst
Swathi Ashok Kumar
Tejaswini Mishra Christapher Morrissey Christine M. Dorman Kuan-Bei Chen Daniela Drautz Belinda Giardine Yoichiro Shibata Lingyun Song Max Pimkin Gregory E. Crawford Terrence S. Furey Manolis Kellis Webb Miller James Taylor Stephan C. Schuster Yu Zhang
... [+16 authors] ...,
Francesca Chiaromonte
Gerd A. Blobel
Mitchell J. Weiss
Ross C. Hardison

First Published July 27, 2011

The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes

Kim D. Pruitt
Jennifer Harrow
Rachel A. Harte
Craig Wallin
Mark Diekhans
Donna R. Maglott Steve Searle Catherine M. Farrell Jane E. Loveland Barbara J. Ruef Elizabeth Hart Marie-Marthe Suner Melissa J. Landrum Bronwen Aken Sarah Ayling Robert Baertsch Julio Fernandez-Banet Joshua L. Cherry Val Curwen Michael DiCuccio Manolis Kellis Jennifer Lee Michael F. Lin Michael Schuster Andrew Shkeda Clara Amid Garth Brown Oksana Dukhanina Adam Frankish Jennifer Hart Bonnie L. Maidak Jonathan Mudge Michael R. Murphy Terence Murphy Jeena Rajan Bhanu Rajput Lillian D. Riddick Catherine Snow Charles Steward David Webb Janet A. Weber Laurens Wilming Wenyu Wu Ewan Birney David Haussler
... [+40 authors] ...,
Tim Hubbard
James Ostell
Richard Durbin
David Lipman

First Published June 4, 2009

Conservation of small RNA pathways in platypus

Elizabeth P. Murchison
Pouya Kheradpour
Ravi Sachidanandam
Carly Smith
Emily Hodges
Zhenyu Xuan
... [+1 authors] ...,
Manolis Kellis
Frank Grützner
Alexander Stark
Gregory J. Hannon

First Published May 7, 2008

Drosophila genomes" > Reliable prediction of regulator targets using 12 Drosophila genomes

Pouya Kheradpour
Alexander Stark
Sushmita Roy
Manolis Kellis

First Published November 7, 2007

Drosophila melanogaster using 12 fly genomes" > Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes

Michael F. Lin
Joseph W. Carlson
Madeline A. Crosby
Beverley B. Matthews
Charles Yu
Soo Park Kenneth H. Wan Andrew J. Schroeder L. Sian Gramates Susan E. St. Pierre Margaret Roark Kenneth L. Wiley Rob J. Kulathinal Peili Zhang Kyl V. Myrick
... [+10 authors] ...,
Jerry V. Antone
Susan E. Celniker
William M. Gelbart
Manolis Kellis

First Published November 7, 2007

Drosophila microRNAs" > Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs

J. Graham Ruby
Alexander Stark
Wendy K. Johnston
Manolis Kellis
David P. Bartel
Eric C. Lai

First Published November 7, 2007

Drosophila genomes" > Systematic discovery and characterization of fly microRNAs using 12 Drosophila genomes

Alexander Stark
Pouya Kheradpour
Leopold Parts
Julius Brennecke
Emily Hodges
Gregory J. Hannon
Manolis Kellis

First Published November 7, 2007

Accurate gene-tree reconstruction by learning gene- and species-specific substitution rates across multiple complete genomes

Matthew D. Rasmussen
Manolis Kellis

First Published November 7, 2007

The Secreted Protein Discovery Initiative (SPDI), a Large-Scale Effort to Identify Novel Human Secreted and Transmembrane Proteins: A Bioinformatics Assessment

Hilary F. Clark
Austin L. Gurney
Evangeline Abaya
Kevin Baker
Daryl Baldwin
Jennifer Brush Jian Chen Bernard Chow Clarissa Chui Craig Crowley Bridget Currell Bethanne Deuel Patrick Dowd Dan Eaton Jessica Foster Christopher Grimaldi Qimin Gu Philip E. Hass Sherry Heldens Arthur Huang Hok Seon Kim Laura Klimowski Yisheng Jin Stephanie Johnson James Lee Lhney Lewis Dongzhou Liao Melanie Mark Edward Robbie Celina Sanchez Jill Schoenfeld Somasekar Seshagiri Laura Simmons Jennifer Singh Victoria Smith Jeremy Stinson Alicia Vagts Richard Vandlen Colin Watanabe David Wieand Kathryn Woods Ming-Hong Xie Daniel Yansura Sothy Yi Guoying Yu Jean Yuan Min Zhang
... [+42 authors] ...,
Zemin Zhang
Audrey Goddard
William I. Wood
Paul Godowski

First Published January 1, 2003

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Your search for returned 29 results

Discovery of high-confidence human protein-coding genes and exons by whole-genome PhyloCSF helps elucidate 118 GWAS loci

An AR-ERG transcriptional signature defined by long-range chromatin interactomes in prostate cancer cells

cis-mediators for trans-eQTLs across many human tissues using genomic mediation analysis" > Identifying cis-mediators for trans-eQTLs across many human tissues using genomic mediation analysis

Co-expression networks reveal the tissue-specific regulation of transcription and splicing

D. melanogaster modENCODE transcriptome annotation" > Comparative validation of the D. melanogaster modENCODE transcriptome annotation

Drosophila melanogaster" > Diverse patterns of genomic targeting by transcriptional regulators in Drosophila melanogaster

Evolutionary dynamics and tissue specificity of human long noncoding RNAs in six mammals

Most parsimonious reconciliation in the presence of gene duplication, loss, and deep coalescence using labeled coalescent trees

Integrating and mining the chromatin landscape of cell-type specificity using self-organizing maps

Arboretum: Reconstruction and analysis of the evolutionary history of condition-specific transcriptional modules

Interplay between chromatin state, regulator binding, and regulatory motifs in six human cell types

Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay

Constitutive nuclear lamina–genome interactions are highly conserved and associated with A/T-rich sequence

GENCODE: The reference human genome annotation for The ENCODE Project

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

Drosophila melanogaster by integrative inference of transcriptional networks" > Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks

Unified modeling of gene duplication, loss, and coalescence using a locus tree

Drosophila and other metazoa" > Evidence of abundant stop codon readthrough in Drosophila and other metazoa

Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes

New families of human regulatory RNA structures identified by comparative analysis of vertebrate genomes

Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration

The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes

Conservation of small RNA pathways in platypus

Drosophila genomes" > Reliable prediction of regulator targets using 12 Drosophila genomes

Drosophila melanogaster using 12 fly genomes" > Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes

Drosophila microRNAs" > Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs

Drosophila genomes" > Systematic discovery and characterization of fly microRNAs using 12 Drosophila genomes

Accurate gene-tree reconstruction by learning gene- and species-specific substitution rates across multiple complete genomes

The Secreted Protein Discovery Initiative (SPDI), a Large-Scale Effort to Identify Novel Human Secreted and Transmembrane Proteins: A Bioinformatics Assessment

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