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Widespread specific intron retention events in nuclear RNA complexes identified by sedimentation analysis of pluripotent cellular extracts

Isabela T. Pereira
Izabela Mamede
Paulo P. Amaral
Gloria R. Franco
John L. Rinn

First Published August 26, 2025

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

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

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

RNA-seq as a tool for evaluating human embryo competence

Abigail F. Groff
Nina Resetkova
Francesca DiDomenico
Denny Sakkas
Alan Penzias
John L. Rinn
Kevin Eggan

First Published September 23, 2019

High-throughput functional analysis of lncRNA core promoters elucidates rules governing tissue specificity

Kaia Mattioli
Pieter-Jan Volders
Chiara Gerhardinger
James C. Lee
Philipp G. Maass
Marta Melé
John L. Rinn

First Published January 25, 2019

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

Chromatin environment, transcriptional regulation, and splicing distinguish lincRNAs and mRNAs

Marta Melé
Kaia Mattioli
William Mallard
David M. Shechner
Chiara Gerhardinger
John L. Rinn

First Published December 7, 2016

Basset: learning the regulatory code of the accessible genome with deep convolutional neural networks

David R. Kelley
Jasper Snoek
John L. Rinn

First Published May 3, 2016

Linking RNA biology to lncRNAs

Loyal A. Goff
John L. Rinn

First Published October 1, 2015

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