Search | Genome Research

Integrating short-read and long-read single-cell RNA sequencing for comprehensive transcriptome profiling in mouse retina

Meng Wang
Yumei Li
Jun Wang
Soo Hwan Oh
Yexuan Cao
Rui Chen

First Published March 6, 2025

Long-read genome sequencing and variant reanalysis increase diagnostic yield in neurodevelopmental disorders

Susan M. Hiatt
James M.J. Lawlor
Lori H. Handley
Donald R. Latner
Zachary T. Bonnstetter
Candice R. Finnila Michelle L. Thompson Lori Beth Boston Melissa Williams Ivan Rodriguez Nunez Jerry Jenkins Whitley V. Kelley E. Martina Bebin Michael A. Lopez Anna C.E. Hurst
... [+10 authors] ...,
Bruce R. Korf
Jeremy Schmutz
Jane Grimwood
Gregory M. Cooper

First Published September 19, 2024

Allele-specific transcription factor binding across human brain regions offers mechanistic insight into eQTLs

Ashlyn G. Anderson
Belle A. Moyers
Jacob M. Loupe
Ivan Rodriguez-Nunez
Stephanie A. Felker
James M.J. Lawlor William E. Bunney Blynn G. Bunney Preston M. Cartagena Adolfo Sequeira Stanley J. Watson
... [+6 authors] ...,
Huda Akil
Eric M. Mendenhall
Gregory M. Cooper
Richard M. Myers

First Published August 16, 2024

CodonBERT large language model for mRNA vaccines

Sizhen Li
Saeed Moayedpour
Ruijiang Li
Michael Bailey
Saleh Riahi
Lorenzo Kogler-Anele Milad Miladi Jacob Miner Fabien Pertuy Dinghai Zheng Jun Wang Akshay Balsubramani Khang Tran Minnie Zacharia Monica Wu Xiaobo Gu Ryan Clinton Carla Asquith Joseph Skaleski Lianne Boeglin Sudha Chivukula Anusha Dias Tod Strugnell
... [+18 authors] ...,
Fernando Ulloa Montoya
Vikram Agarwal
Ziv Bar-Joseph
Sven Jager

First Published July 1, 2024

cis-regulatory elements" > Probabilistic association of differentially expressed genes with cis-regulatory elements

Brian S. Roberts
Ashlyn G. Anderson
E. Christopher Partridge
Gregory M. Cooper
Richard M. Myers

First Published April 17, 2024

Genome-wide strand asymmetry in massively parallel reporter activity favors genic strands

Brian S. Roberts
E. Christopher Partridge
Bryan A. Moyers
Vikram Agarwal
Kimberly M. Newberry
Beth K. Martin
Jay Shendure
Richard M. Myers
Gregory M. Cooper

First Published April 20, 2021

Predicting unrecognized enhancer-mediated genome topology by an ensemble machine learning model

Li Tang
Matthew C. Hill
Jun Wang
Jianxin Wang
James F. Martin
Min Li

First Published November 12, 2020

Corrigendum: A systematic comparison reveals substantial differences in chromosomal versus episomal encoding of enhancer activity

Fumitaka Inoue
Martin Kircher
Beth Martin
Gregory M. Cooper
Daniela M. Witten
Michael T. McManus
Nadav Ahituv
Jay Shendure

First Published May 1, 2018

A genome-wide interactome of DNA-associated proteins in the human liver

Ryne C. Ramaker
Daniel Savic
Andrew A. Hardigan
Kimberly Newberry
Gregory M. Cooper
Richard M. Myers
Sara J. Cooper

First Published October 11, 2017

Assembly and analysis of 100 full MHC haplotypes from the Danish population

Jacob M. Jensen
Palle Villesen
Rune M. Friborg
Thomas Mailund
Søren Besenbacher
Mikkel H. Schierup Lasse Maretty Jacob Malte Jensen Bent Petersen Jonas Andreas Sibbesen Siyang Liu Palle Villesen Laurits Skov Kirstine Belling Christian Theil Have Jose M.G. Izarzugaza Marie Grosjean Jette Bork-Jensen Jakob Grove Thomas D. Als Shujia Huang Yuqi Chang Ruiqi Xu Weijian Ye Junhua Rao Xiaosen Guo Jihua Sun Hongzhi Cao Chen Ye Johan v Beusekom Thomas Espeseth Esben Flindt Rune M. Friborg Anders E. Halager Stephanie Le Hellard Christina M. Hultman Francesco Lescai Shengting Li Ole Lund Peter Løngren Thomas Mailund Maria Luisa Matey-Hernandez Ole Mors Christian N.S. Pedersen Thomas Sicheritz-Pontén Patrick Sullivan Ali Syed David Westergaard Rachita Yadav Ning Li Xun Xu Torben Hansen Anders Krogh Lars Bolund Thorkild I.A. Sørensen Oluf Pedersen Ramneek Gupta Simon Rasmussen Søren Besenbacher Anders D. Børglum Jun Wang
... [+56 authors] ...,
Hans Eiberg
Karsten Kristiansen
Søren Brunak
Mikkel Heide Schierup

First Published August 3, 2017

A systematic comparison reveals substantial differences in chromosomal versus episomal encoding of enhancer activity

Fumitaka Inoue
Martin Kircher
Beth Martin
Gregory M. Cooper
Daniela M. Witten
Michael T. McManus
Nadav Ahituv
Jay Shendure

First Published November 9, 2016

SCRaMbLE generates designed combinatorial stochastic diversity in synthetic chromosomes

Yue Shen
Giovanni Stracquadanio
Yun Wang
Kun Yang
Leslie A. Mitchell
Yaxin Xue Yizhi Cai Tai Chen Jessica S. Dymond Kang Kang Jianhui Gong Xiaofan Zeng Yongfen Zhang Yingrui Li Qiang Feng Xun Xu Jun Wang
... [+12 authors] ...,
Jian Wang
Huanming Yang
Jef D. Boeke
Joel S. Bader

First Published November 13, 2015

Promoter-distal RNA polymerase II binding discriminates active from inactive CCAAT/ enhancer-binding protein beta binding sites

Daniel Savic
Brian S. Roberts
Julia B. Carleton
E. Christopher Partridge
Michael A. White
Barak A. Cohen
Gregory M. Cooper
Jason Gertz
Richard M. Myers

First Published October 20, 2015

Parlez-vous VUS?

Gregory M. Cooper

First Published October 1, 2015

Epigenetic modification and inheritance in sexual reversal of fish

Changwei Shao
Qiye Li
Songlin Chen
Pei Zhang
Jinmin Lian
Qiaomu Hu Bing Sun Lijun Jin Shanshan Liu Zongji Wang Hongmei Zhao Zonghui Jin Zhuo Liang Yangzhen Li
... [+9 authors] ...,
Qiumei Zheng
Yong Zhang
Jun Wang
Guojie Zhang

First Published February 2, 2014

Whole-genome sequencing identifies recurrent mutations in hepatocellular carcinoma

Zhengyan Kan
Hancheng Zheng
Xiao Liu
Shuyu Li
Thomas D. Barber
Zhuolin Gong Huan Gao Ke Hao Melinda D. Willard Jiangchun Xu Robert Hauptschein Paul A. Rejto Julio Fernandez Guan Wang Qinghui Zhang Bo Wang Ronghua Chen Jian Wang Nikki P. Lee Wei Zhou Zhao Lin Zhiyu Peng Kang Yi Shengpei Chen Lin Li Xiaomei Fan Jie Yang Rui Ye Jia Ju Kai Wang Heather Estrella Shibing Deng Ping Wei Ming Qiu Isabella H. Wulur Jiangang Liu Mariam E. Ehsani Chunsheng Zhang Andrey Loboda Wing Kin Sung Amit Aggarwal Ronnie T. Poon Sheung Tat Fan Jun Wang James Hardwick Christoph Reinhard
... [+41 authors] ...,
Hongyue Dai
Yingrui Li
John M. Luk
Mao Mao

First Published June 20, 2013

Pyrus bretschneideri Rehd.)" > The genome of the pear (Pyrus bretschneideri Rehd.)

Jun Wu
Zhiwen Wang
Zebin Shi
Shu Zhang
Ray Ming
Shilin Zhu M. Awais Khan Shutian Tao Schuyler S. Korban Hao Wang Nancy J. Chen Takeshi Nishio Xun Xu Lin Cong Kaijie Qi Xiaosan Huang Yingtao Wang Xiang Zhao Juyou Wu Cao Deng Caiyun Gou Weili Zhou Hao Yin Gaihua Qin Yuhui Sha Ye Tao Hui Chen Yanan Yang Yue Song Dongliang Zhan Juan Wang Leiting Li Meisong Dai Chao Gu Yuezhi Wang Daihu Shi Xiaowei Wang Huping Zhang Liang Zeng Danman Zheng Chunlei Wang Maoshan Chen Guangbiao Wang Lin Xie Valpuri Sovero Shoufeng Sha Wenjiang Huang Shujun Zhang Mingyue Zhang Jiangmei Sun Linlin Xu Yuan Li Xing Liu Qingsong Li Jiahui Shen Junyi Wang
... [+51 authors] ...,
Robert E. Paull
Jeffrey L. Bennetzen
Jun Wang
Shaoling Zhang

First Published November 13, 2012

SOAPindel: Efficient identification of indels from short paired reads

Shengting Li
Ruiqiang Li
Heng Li
Jianliang Lu
Yingrui Li
Lars Bolund
Mikkel H. Schierup
Jun Wang

First Published September 12, 2012

Mycosphaerella graminicola and its wild sister species" > The making of a new pathogen: Insights from comparative population genomics of the domesticated wheat pathogen Mycosphaerella graminicola and its wild sister species

Eva H. Stukenbrock
Thomas Bataillon
Julien Y. Dutheil
Troels T. Hansen
Ruiqiang Li
Marcello Zala
Bruce A. McDonald
Jun Wang
Mikkel H. Schierup

First Published October 12, 2011

Acromyrmex echinatior suggests key adaptations to advanced social life and fungus farming" > The genome of the leaf-cutting ant Acromyrmex echinatior suggests key adaptations to advanced social life and fungus farming

Sanne Nygaard
Guojie Zhang
Morten Schiøtt
Cai Li
Yannick Wurm
Haofu Hu Jiajian Zhou Lu Ji Feng Qiu Morten Rasmussen Hailin Pan Frank Hauser
... [+7 authors] ...,
Anders Krogh
Cornelis J.P. Grimmelikhuijzen
Jun Wang
Jacobus J. Boomsma

First Published June 30, 2011

Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome

Guojie Zhang
Guangwu Guo
Xueda Hu
Yong Zhang
Qiye Li
Ruiqiang Li Ruhong Zhuang Zhike Lu Zengquan He Xiaodong Fang Li Chen Wei Tian Yong Tao Karsten Kristiansen Xiuqing Zhang
... [+10 authors] ...,
Songgang Li
Huanming Yang
Jian Wang
Jun Wang

First Published March 19, 2010

Evolutionary constraint facilitates interpretation of genetic variation in resequenced human genomes

David L. Goode
Gregory M. Cooper
Jeremy Schmutz
Mark Dickson
Eidelyn Gonzales
Ming Tsai Kalpana Karra
... [+2 authors] ...,
Eugene Davydov
Serafim Batzoglou
Richard M. Myers
Arend Sidow

First Published January 12, 2010

De novo assembly of human genomes with massively parallel short read sequencing

Ruiqiang Li
Hongmei Zhu
Jue Ruan
Wubin Qian
Xiaodong Fang
Zhongbin Shi Yingrui Li Shengting Li Gao Shan Karsten Kristiansen
... [+5 authors] ...,
Songgang Li
Huanming Yang
Jian Wang
Jun Wang

First Published December 17, 2009

A method for rapid, targeted CNV genotyping identifies rare variants associated with neurocognitive disease

Heather C. Mefford
Gregory M. Cooper
Troy Zerr
Joshua D. Smith
Carl Baker
Neil Shafer Erik C. Thorland
... [+2 authors] ...,
Cindy Skinner
Charles E. Schwartz
Deborah A. Nickerson
Evan E. Eichler

First Published June 8, 2009

SNP detection for massively parallel whole-genome resequencing

Ruiqiang Li
Yingrui Li
Xiaodong Fang
Huanming Yang
Jian Wang
Karsten Kristiansen
Jun Wang

First Published May 6, 2009

Qualifying the relationship between sequence conservation and molecular function

Gregory M. Cooper
Christopher D. Brown

First Published February 1, 2008

Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome

Elliott H. Margulies
Gregory M. Cooper
George Asimenos
Daryl J. Thomas
Colin N. Dewey
Adam Siepel Ewan Birney Damian Keefe Ariel S. Schwartz Minmei Hou James Taylor Sergey Nikolaev Juan I. Montoya-Burgos Ari Löytynoja Simon Whelan Fabio Pardi Tim Massingham James B. Brown Peter Bickel Ian Holmes James C. Mullikin Abel Ureta-Vidal Benedict Paten Eric A. Stone Kate R. Rosenbloom W. James Kent Gerard G. Bouffard Xiaobin Guan Nancy F. Hansen Jacquelyn R. Idol Valerie V.B. Maduro Baishali Maskeri Jennifer C. McDowell Morgan Park Pamela J. Thomas Alice C. Young Robert W. Blakesley Donna M. Muzny Erica Sodergren David A. Wheeler Kim C. Worley Huaiyang Jiang George M. Weinstock Richard A. Gibbs Tina Graves Robert Fulton Elaine R. Mardis Richard K. Wilson Michele Clamp James Cuff Sante Gnerre David B. Jaffe Jean L. Chang Kerstin Lindblad-Toh Eric S. Lander Angie Hinrichs Heather Trumbower Hiram Clawson Ann Zweig Robert M. Kuhn Galt Barber Rachel Harte Donna Karolchik Matthew A. Field Richard A. Moore Carrie A. Matthewson Jacqueline E. Schein Marco A. Marra Stylianos E. Antonarakis Serafim Batzoglou Nick Goldman Ross Hardison David Haussler
... [+68 authors] ...,
Webb Miller
Lior Pachter
Eric D. Green
Arend Sidow

First Published June 13, 2007

Arabidopsis" > A microarray analysis of the rice transcriptome and its comparison to Arabidopsis

Ligeng Ma
Chen Chen
Xigang Liu
Yuling Jiao
Ning Su
Lin Li Xiangfeng Wang Mengliang Cao Ning Sun Xiuqing Zhang Jingyue Bao Jian Li Soren Pedersen Lars Bolund Hongyu Zhao Longping Yuan
... [+11 authors] ...,
Gane Ka-Shu Wong
Jun Wang
Xing Wang Deng
Jian Wang

First Published September 1, 2005

Origin and evolution of new exons in rodents

Wen Wang
Hongkun Zheng
Shuang Yang
Haijing Yu
Jun Li
Huifeng Jiang Jianning Su Lei Yang Jianguo Zhang Jason McDermott Ram Samudrala Jian Wang Huanming Yang
... [+8 authors] ...,
Jun Yu
Karsten Kristiansen
Gane Ka-Shu Wong
Jun Wang

First Published August 18, 2005

Distribution and intensity of constraint in mammalian genomic sequence

Gregory M. Cooper
Eric A. Stone
George Asimenos
Eric D. Green
Serafim Batzoglou
Arend Sidow

First Published June 17, 2005

Automated Whole-Genome Multiple Alignment of Rat, Mouse, and Human

Michael Brudno
Alexander Poliakov
Asaf Salamov
Gregory M. Cooper
Arend Sidow
Edward M. Rubin
Victor Solovyev
Serafim Batzoglou
Inna Dubchak

First Published April 1, 2004

Characterization of Evolutionary Rates and Constraints in Three Mammalian Genomes

Gregory M. Cooper
Michael Brudno
Eric A. Stone
Inna Dubchak
Serafim Batzoglou
Arend Sidow

First Published April 1, 2004

Quantitative Estimates of Sequence Divergence for Comparative Analyses of Mammalian Genomes

Gregory M. Cooper
Michael Brudno
NISC Comparative Sequencing Program
Eric D. Green
Serafim Batzoglou
Arend Sidow

First Published May 1, 2003

LAGAN and Multi-LAGAN: Efficient Tools for Large-Scale Multiple Alignment of Genomic DNA

Michael Brudno
Chuong B. Do
Gregory M. Cooper
Michael F. Kim
Eugene Davydov
NISC Comparative Sequencing Program
Eric D. Green
Arend Sidow
Serafim Batzoglou

First Published March 12, 2003

Gramineae Genes" > Compositional Gradients in Gramineae Genes

Gane Ka-Shu Wong
Jun Wang
Lin Tao
Jun Tan
JianGuo Zhang
Douglas A. Passey
Jun Yu

First Published June 1, 2002

RePS: A Sequence Assembler That Masks Exact Repeats Identified from the Shotgun Data" > `RePS:` A Sequence Assembler That Masks Exact Repeats Identified from the Shotgun Data

Jun Wang
Gane Ka-Shu Wong
Peixiang Ni
Yujun Han
Xiangang Huang
Jianguo Zhang Chen Ye Yong Zhang Jianfei Hu Kunlin Zhang Xin Xu Lijuan Cong Hong Lu Xide Ren Xiaoyu Ren Jun He Lin Tao Douglas A. Passey
... [+13 authors] ...,
Jian Wang
Huanming Yang
Jun Yu
Songgang Li

First Published May 1, 2002

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Your search for returned 36 results

Integrating short-read and long-read single-cell RNA sequencing for comprehensive transcriptome profiling in mouse retina

Long-read genome sequencing and variant reanalysis increase diagnostic yield in neurodevelopmental disorders

Allele-specific transcription factor binding across human brain regions offers mechanistic insight into eQTLs

CodonBERT large language model for mRNA vaccines

cis-regulatory elements" > Probabilistic association of differentially expressed genes with cis-regulatory elements

Genome-wide strand asymmetry in massively parallel reporter activity favors genic strands

Predicting unrecognized enhancer-mediated genome topology by an ensemble machine learning model

Corrigendum: A systematic comparison reveals substantial differences in chromosomal versus episomal encoding of enhancer activity

A genome-wide interactome of DNA-associated proteins in the human liver

Assembly and analysis of 100 full MHC haplotypes from the Danish population

A systematic comparison reveals substantial differences in chromosomal versus episomal encoding of enhancer activity

SCRaMbLE generates designed combinatorial stochastic diversity in synthetic chromosomes

Promoter-distal RNA polymerase II binding discriminates active from inactive CCAAT/ enhancer-binding protein beta binding sites

Parlez-vous VUS?

Epigenetic modification and inheritance in sexual reversal of fish

Whole-genome sequencing identifies recurrent mutations in hepatocellular carcinoma

Pyrus bretschneideri Rehd.)" > The genome of the pear (Pyrus bretschneideri Rehd.)

SOAPindel: Efficient identification of indels from short paired reads

Mycosphaerella graminicola and its wild sister species" > The making of a new pathogen: Insights from comparative population genomics of the domesticated wheat pathogen Mycosphaerella graminicola and its wild sister species

Acromyrmex echinatior suggests key adaptations to advanced social life and fungus farming" > The genome of the leaf-cutting ant Acromyrmex echinatior suggests key adaptations to advanced social life and fungus farming

Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome

Evolutionary constraint facilitates interpretation of genetic variation in resequenced human genomes

De novo assembly of human genomes with massively parallel short read sequencing

A method for rapid, targeted CNV genotyping identifies rare variants associated with neurocognitive disease

SNP detection for massively parallel whole-genome resequencing

Qualifying the relationship between sequence conservation and molecular function

Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome

Arabidopsis" > A microarray analysis of the rice transcriptome and its comparison to Arabidopsis

Origin and evolution of new exons in rodents

Distribution and intensity of constraint in mammalian genomic sequence

Automated Whole-Genome Multiple Alignment of Rat, Mouse, and Human

Characterization of Evolutionary Rates and Constraints in Three Mammalian Genomes

Quantitative Estimates of Sequence Divergence for Comparative Analyses of Mammalian Genomes

LAGAN and Multi-LAGAN: Efficient Tools for Large-Scale Multiple Alignment of Genomic DNA

Gramineae Genes" > Compositional Gradients in Gramineae Genes

RePS: A Sequence Assembler That Masks Exact Repeats Identified from the Shotgun Data" > `RePS:` A Sequence Assembler That Masks Exact Repeats Identified from the Shotgun Data

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Your search for returned 36 results