Search | Genome Research

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

Method

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

Method

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

Resource

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

Research

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

Research

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

Resource

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

Resource

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

Research

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

Research

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

Research

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

Resource

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

Resource

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

LETTER

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

LETTER

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

ARTICLE

Targeting a Complex Transcriptome: The Construction of the Mouse Full-Length cDNA Encyclopedia

Piero Carninci
Kazunori Waki
Toshiyuki Shiraki
Hideaki Konno
Kazuhiro Shibata
Masayoshi Itoh Katsunori Aizawa Takahiro Arakawa Yoshiyuki Ishii Daisuke Sasaki Hidemasa Bono Shinji Kondo Yuichi Sugahara Rintaro Saito Naoki Osato Shiro Fukuda Kenjiro Sato Akira Watahiki Tomoko Hirozane-Kishikawa Mari Nakamura Yuko Shibata Ayako Yasunishi Noriko Kikuchi Atsushi Yoshiki Moriaki Kusakabe Stefano Gustincich Kirk Beisel William Pavan Vassilis Aidinis Akira Nakagawara William A. Held Hiroo Iwata Tomohiro Kono Hiromitsu Nakauchi Paul Lyons Christine Wells David A. Hume Michela Fagiolini Takao K. Hensch Michelle Brinkmeier Sally Camper Junji Hirota Peter Mombaerts
... [+38 authors] ...,
Masami Muramatsu
Yasushi Okazaki
Jun Kawai
Yoshihide Hayashizaki

First Published June 2, 2003

METHODS

A Computer-Based Method of Selecting Clones for a Full-Length cDNA Project: Simultaneous Collection of Negligibly Redundant and Variant cDNAs

Naoki Osato
Masayoshi Itoh
Hideaki Konno
Shinji Kondo
Kazuhiro Shibata
Piero Carninci Toshiyuki Shiraki Akira Shinagawa Takahiro Arakawa
... [+4 authors] ...,
Shoshi Kikuchi
Kouji Sato
Jun Kawai
Yoshihide Hayashizaki

First Published June 18, 2002

ARTICLE

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

METHODS

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

METHODS

Computer-Based Methods for the Mouse Full-Length cDNA Encyclopedia: Real-Time Sequence Clustering for Construction of a Nonredundant cDNA Library

Hideaki Konno
Yoshifumi Fukunishi
Kazuhiro Shibata
Masayoshi Itoh
Piero Carninci
Yuichi Sugahara
Yoshihide Hayashizaki

First Published January 18, 2001

LETTER

RIKEN Integrated Sequence Analysis (RISA) System—384-Format Sequencing Pipeline with 384 Multicapillary Sequencer

Kazuhiro Shibata
Masayoshi Itoh
Katsunori Aizawa
Sumiharu Nagaoka
Nobuya Sasaki
Piero Carninci Hideaki Konno Junichi Akiyama Katsuo Nishi Tokuji Kitsunai Hideo Tashiro Mari Itoh Noriko Sumi Yoshiyuki Ishii Shin Nakamura Makoto Hazama Tsutomu Nishine Akira Harada Rintaro Yamamoto Hiroyuki Matsumoto Sumito Sakaguchi Takashi Ikegami Katsuya Kashiwagi Syuji Fujiwake Kouji Inoue Yoshiyuki Togawa Masaki Izawa Eiji Ohara Masanori Watahiki Yuko Yoneda Tomokazu Ishikawa Kaori Ozawa Takumi Tanaka Shuji Matsuura Jun Kawai Yasushi Okazaki
... [+31 authors] ...,
Masami Muramatsu
Yorinao Inoue
Akira Kira
Yoshihide Hayashizaki

First Published November 1, 2000

METHODS

Normalization and Subtraction of Cap-Trapper-Selected cDNAs to Prepare Full-Length cDNA Libraries for Rapid Discovery of New Genes

Piero Carninci
Yuko Shibata
Norihito Hayatsu
Yuichi Sugahara
Kazuhiro Shibata
Masayoshi Itoh
... [+1 authors] ...,
Hideaki Konno
Yasushi Okazaki
Masami Muramatsu
Yoshihide Hayashizaki

First Published October 1, 2000

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