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Method

Accurate estimation of intraspecific microbial gene content variation in metagenomic data with MIDAS v3 and StrainPGC

Byron J. Smith
Chunyu Zhao
Veronika Dubinkina
Xiaofan Jin
Liron Zahavi
Saar Shoer
Jacqueline Moltzau-Anderson
Eran Segal
Katherine S. Pollard

First Published April 10, 2025

Resource

Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes

Guanjue Xiang
Xi He
Belinda M. Giardine
Kathryn J. Isaac
Dylan J. Taylor
Rajiv C. McCoy Camden Jansen Cheryl A. Keller Alexander Q. Wixom April Cockburn Amber Miller Qian Qi Yanghua He Yichao Li Jens Lichtenberg Elisabeth F. Heuston Stacie M. Anderson Jing Luan Marit W. Vermunt Feng Yue Michael E.G. Sauria Michael C. Schatz James Taylor Berthold Göttgens Jim R. Hughes Douglas R. Higgs Mitchell J. Weiss Yong Cheng Gerd A. Blobel David M. Bodine
... [+25 authors] ...,
Yu Zhang
Qunhua Li
Shaun Mahony
Ross C. Hardison

First Published July 1, 2024

Resource

The pig pangenome provides insights into the roles of coding structural variations in genetic diversity and adaptation

Zhengcao Li
Xiaohong Liu
Chen Wang
Zhenyang Li
Bo Jiang
Ruifeng Zhang Lu Tong Youping Qu Sheng He Haifan Chen Yafei Mao Qingnan Li Torsten Pook Yu Wu Yanjun Zan
... [+10 authors] ...,
Hui Zhang
Lu Li
Keying Wen
Yaosheng Chen

First Published November 1, 2023

Method

Domain-adaptive neural networks improve cross-species prediction of transcription factor binding

Kelly Cochran
Divyanshi Srivastava
Avanti Shrikumar
Akshay Balsubramani
Ross C. Hardison
Anshul Kundaje
Shaun Mahony

First Published January 18, 2022

Research

Diverse tumorigenic consequences of human papillomavirus integration in primary oropharyngeal cancers

David E. Symer
Keiko Akagi
Heather M. Geiger
Yang Song
Gaiyun Li
Anne-Katrin Emde Weihong Xiao Bo Jiang André Corvelo Nora C. Toussaint Jingfeng Li Amit Agrawal Enver Ozer Adel K. El-Naggar Zoe Du Jitesh B. Shewale Birgit Stache-Crain
... [+12 authors] ...,
Mark Zucker
Nicolas Robine
Kevin R. Coombes
Maura L. Gillison

First Published December 13, 2021

Resource

An integrative view of the regulatory and transcriptional landscapes in mouse hematopoiesis

Guanjue Xiang
Cheryl A. Keller
Elisabeth Heuston
Belinda M. Giardine
Lin An
Alexander Q. Wixom Amber Miller April Cockburn Michael E.G. Sauria Kathryn Weaver Jens Lichtenberg Berthold Göttgens Qunhua Li David Bodine Shaun Mahony James Taylor Gerd A. Blobel Mitchell J. Weiss Yong Cheng Feng Yue
... [+15 authors] ...,
Jim Hughes
Douglas R. Higgs
Yu Zhang
Ross C. Hardison

First Published March 4, 2020

Research

Sequence determinants of polyadenylation-mediated regulation

Ilya Vainberg Slutskin
Adina Weinberger
Eran Segal

First Published September 17, 2019

Research

Systematic interrogation of human promoters

Shira Weingarten-Gabbay
Ronit Nir
Shai Lubliner
Eilon Sharon
Yael Kalma
Adina Weinberger
Eran Segal

First Published January 8, 2019

Research

Human papillomavirus and the landscape of secondary genetic alterations in oral cancers

Maura L. Gillison
Keiko Akagi
Weihong Xiao
Bo Jiang
Robert K.L. Pickard
Jingfeng Li Benjamin J. Swanson Amit D. Agrawal Mark Zucker Birgit Stache-Crain Anne-Katrin Emde
... [+6 authors] ...,
Heather M. Geiger
Nicolas Robine
Kevin R. Coombes
David E. Symer

First Published December 18, 2018

Method

HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient

Tao Yang
Feipeng Zhang
Galip Gürkan Yardımcı
Fan Song
Ross C. Hardison
William Stafford Noble
Feng Yue
Qunhua Li

First Published August 30, 2017

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