Search | Genome Research

Method

Incorporating valuable prior knowledge to improve deep learning prediction of genetic perturbation responses

Xiuhao Fu
Chao Yang
Chunyan Cui
Aoyun Geng
Yidi Sun
Chao Zha Feifei Cui
... [+2 authors] ...,
Leyi Wei
Quan Zou
Xin Gao
Zilong Zhang

First Published March 26, 2026

Research

Epigenetic drift score captures directional methylation variability and links aging to transcriptional, metabolic, and genetic alterations

Xiu Fan
Qili Qian
Wenran Li
Tianzi Liu
Changqing Zeng
Peilin Jia Huandong Lin Xin Gao
... [+3 authors] ...,
Li Jin
Mingfeng Xia
Sijia Wang
Fan Liu

First Published August 1, 2025

Method

A fast and adaptive detection framework for genome-wide chromatin loop mapping from Hi-C data

Siyuan Chen
Jiuming Wang
Inkyung Jung
Zhaowen Qiu
Xin Gao
Yu Li

First Published August 13, 2024

Method

Accurate transcriptome-wide identification and quantification of alternative polyadenylation from RNA-seq data with APAIQ

Yongkang Long
Bin Zhang
Shuye Tian
Jia Jia Chan
Juexiao Zhou
Zhongxiao Li Yisheng Li Zheng An Xingyu Liao Yu Wang Shiwei Sun
... [+6 authors] ...,
Ying Xu
Yvonne Tay
Wei Chen
Xin Gao

First Published April 28, 2023

Research

Enhancers with tissue-specific activity are enriched in intronic regions

Beatrice Borsari
Pablo Villegas-Mirón
Sílvia Pérez-Lluch
Isabel Turpin
Hafid Laayouni
Alba Segarra-Casas
Jaume Bertranpetit
Roderic Guigó
Sandra Acosta

First Published July 21, 2021

Corrigendum

Corrigendum: Functional annotation of human long noncoding RNAs via molecular phenotyping

Jordan A. Ramilowski
Chi Wai Yip
Saumya Agrawal
Jen-Chien Chang
Yari Ciani
Ivan V. Kulakovskiy Mickaël Mendez Jasmine Li Ching Ooi John F. Ouyang Nick Parkinson Andreas Petri Leonie Roos Jessica Severin Kayoko Yasuzawa Imad Abugessaisa Altuna Akalin Ivan V. Antonov Erik Arner Alessandro Bonetti Hidemasa Bono Beatrice Borsari Frank Brombacher Christopher J.F. Cameron Carlo Vittorio Cannistraci Ryan Cardenas Melissa Cardon Howard Chang Josée Dostie Luca Ducoli Alexander Favorov Alexandre Fort Diego Garrido Noa Gil Juliette Gimenez Reto Guler Lusy Handoko Jayson Harshbarger Akira Hasegawa Yuki Hasegawa Kosuke Hashimoto Norihito Hayatsu Peter Heutink Tetsuro Hirose Eddie L. Imada Masayoshi Itoh Bogumil Kaczkowski Aditi Kanhere Emily Kawabata Hideya Kawaji Tsugumi Kawashima S. Thomas Kelly Miki Kojima Naoto Kondo Haruhiko Koseki Tsukasa Kouno Anton Kratz Mariola Kurowska-Stolarska Andrew Tae Jun Kwon Jeffrey Leek Andreas Lennartsson Marina Lizio Fernando López-Redondo Joachim Luginbühl Shiori Maeda Vsevolod J. Makeev Luigi Marchionni Yulia A. Medvedeva Aki Minoda Ferenc Müller Manuel Muñoz-Aguirre Mitsuyoshi Murata Hiromi Nishiyori Kazuhiro R. Nitta Shuhei Noguchi Yukihiko Noro Ramil Nurtdinov Yasushi Okazaki Valerio Orlando Denis Paquette Callum J.C. Parr Owen J.L. Rackham Patrizia Rizzu Diego Fernando Sánchez Martinez Albin Sandelin Pillay Sanjana Colin A.M. Semple Youtaro Shibayama Divya M. Sivaraman Takahiro Suzuki Suzannah C. Szumowski Michihira Tagami Martin S. Taylor Chikashi Terao Malte Thodberg Supat Thongjuea Vidisha Tripathi Igor Ulitsky Roberto Verardo Ilya E. Vorontsov Chinatsu Yamamoto Robert S. Young J. Kenneth Baillie Alistair R.R. Forrest Roderic Guigó Michael M. Hoffman Chung Chau Hon Takeya Kasukawa Sakari Kauppinen Juha Kere Boris Lenhard Claudio Schneider Harukazu Suzuki
... [+107 authors] ...,
Ken Yagi
Michiel J.L. de Hoon
Jay W. Shin
Piero Carninci

First Published September 14, 2020

Method

TransBorrow: genome-guided transcriptome assembly by borrowing assemblies from different assemblers

Ting Yu
Zengchao Mu
Zhaoyuan Fang
Xiaoping Liu
Xin Gao
Juntao Liu

First Published August 17, 2020

Resource

A limited set of transcriptional programs define major cell types

Alessandra Breschi
Manuel Muñoz-Aguirre
Valentin Wucher
Carrie A. Davis
Diego Garrido-Martín
Sarah Djebali Jesse Gillis Dmitri D. Pervouchine Anna Vlasova Alexander Dobin Chris Zaleski Jorg Drenkow Cassidy Danyko Alexandra Scavelli
... [+9 authors] ...,
Ferran Reverter
Michael P. Snyder
Thomas R. Gingeras
Roderic Guigó

First Published July 29, 2020

Resource

Functional annotation of human long noncoding RNAs via molecular phenotyping

Jordan A. Ramilowski
Chi Wai Yip
Saumya Agrawal
Jen-Chien Chang
Yari Ciani
Ivan V. Kulakovskiy Mickaël Mendez Jasmine Li Ching Ooi John F. Ouyang Nick Parkinson Andreas Petri Leonie Roos Jessica Severin Kayoko Yasuzawa Imad Abugessaisa Altuna Akalin Ivan V. Antonov Erik Arner Alessandro Bonetti Hidemasa Bono Beatrice Borsari Frank Brombacher Christopher J.F. Cameron Carlo Vittorio Cannistraci Ryan Cardenas Melissa Cardon Howard Chang Josée Dostie Luca Ducoli Alexander Favorov Alexandre Fort Diego Garrido Noa Gil Juliette Gimenez Reto Guler Lusy Handoko Jayson Harshbarger Akira Hasegawa Yuki Hasegawa Kosuke Hashimoto Norihito Hayatsu Peter Heutink Tetsuro Hirose Eddie L. Imada Masayoshi Itoh Bogumil Kaczkowski Aditi Kanhere Emily Kawabata Hideya Kawaji Tsugumi Kawashima S. Thomas Kelly Miki Kojima Naoto Kondo Haruhiko Koseki Tsukasa Kouno Anton Kratz Mariola Kurowska-Stolarska Andrew Tae Jun Kwon Jeffrey Leek Andreas Lennartsson Marina Lizio Fernando López-Redondo Joachim Luginbühl Shiori Maeda Vsevolod J. Makeev Luigi Marchionni Yulia A. Medvedeva Aki Minoda Ferenc Müller Manuel Muñoz-Aguirre Mitsuyoshi Murata Hiromi Nishiyori Kazuhiro R. Nitta Shuhei Noguchi Yukihiko Noro Ramil Nurtdinov Yasushi Okazaki Valerio Orlando Denis Paquette Callum J.C. Parr Owen J.L. Rackham Patrizia Rizzu Diego Fernando Sánchez Martinez Albin Sandelin Pillay Sanjana Colin A.M. Semple Youtaro Shibayama Divya M. Sivaraman Takahiro Suzuki Suzannah C. Szumowski Michihira Tagami Martin S. Taylor Chikashi Terao Malte Thodberg Supat Thongjuea Vidisha Tripathi Igor Ulitsky Roberto Verardo Ilya E. Vorontsov Chinatsu Yamamoto Robert S. Young J. Kenneth Baillie Alistair R.R. Forrest Roderic Guigó Michael M. Hoffman Chung Chau Hon Takeya Kasukawa Sakari Kauppinen Juha Kere Boris Lenhard Claudio Schneider Harukazu Suzuki
... [+107 authors] ...,
Ken Yagi
Michiel J.L. de Hoon
Jay W. Shin
Piero Carninci

First Published July 27, 2020

Research

Megalobrama amblycephala × Culter alburnus" > The subgenomes show asymmetric expression of alleles in hybrid lineages of Megalobrama amblycephala × Culter alburnus

Li Ren
Wuhui Li
Qinbo Qin
He Dai
Fengming Han
Jun Xiao Xin Gao Jialin Cui Chang Wu Xiaojing Yan Guoliang Wang Guiming Liu Jia Liu Jiaming Li Zhong Wan Conghui Yang Chun Zhang Min Tao Jing Wang Kaikun Luo Shi Wang Fangzhou Hu Rurong Zhao Xuming Li Min Liu Hongkun Zheng Rong Zhou Yuqin Shu Yude Wang
... [+24 authors] ...,
Qinfeng Liu
Chenchen Tang
Wei Duan
Shaojun Liu

First Published October 24, 2019

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Your search for returned 33 results

Method

Incorporating valuable prior knowledge to improve deep learning prediction of genetic perturbation responses

Research

Epigenetic drift score captures directional methylation variability and links aging to transcriptional, metabolic, and genetic alterations

Method

A fast and adaptive detection framework for genome-wide chromatin loop mapping from Hi-C data

Method

Accurate transcriptome-wide identification and quantification of alternative polyadenylation from RNA-seq data with APAIQ

Research

Enhancers with tissue-specific activity are enriched in intronic regions

Corrigendum

Corrigendum: Functional annotation of human long noncoding RNAs via molecular phenotyping

Method

TransBorrow: genome-guided transcriptome assembly by borrowing assemblies from different assemblers

Resource

A limited set of transcriptional programs define major cell types

Resource

Functional annotation of human long noncoding RNAs via molecular phenotyping

Research

Megalobrama amblycephala × Culter alburnus" > The subgenomes show asymmetric expression of alleles in hybrid lineages of Megalobrama amblycephala × Culter alburnus

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