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Research

Epigenetic characterization of pseudogenes across human tissues

  • Yunzhe Jiang
  • Beatrice Borsari
  • Mark Gerstein
  • First Published April 15, 2026
Research

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
Resource

Drosophila and C. elegans transcription factors reveal tissue-specific regulatory relationships" > Binding profiles for 961 Drosophila and C. elegans transcription factors reveal tissue-specific regulatory relationships

  • Michelle Kudron
  • Louis Gevirtzman
  • Alec Victorsen
  • Bridget C. Lear
  • Jiahao Gao
  • Jinrui Xu Swapna Samanta Emily Frink Adri Tran-Pearson Chau Huynh Dionne Vafeados Ann Hammonds William Fisher Martha Wall Greg Wesseling Vanessa Hernandez Zhichun Lin Mary Kasparian Kevin White Ravi Allada Mark Gerstein
  • ... [+16 authors] ...,
  • LaDeana Hillier
  • Susan E. Celniker
  • Valerie Reinke
  • Robert H. Waterston
  • First Published October 22, 2024
Method

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
Research

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
Research

Mus caroli and Mus pahari genomes" > Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes

  • David Thybert
  • Maša Roller
  • Fábio C.P. Navarro
  • Ian Fiddes
  • Ian Streeter
  • Christine Feig David Martin-Galvez Mikhail Kolmogorov Václav Janoušek Wasiu Akanni Bronwen Aken Sarah Aldridge Varshith Chakrapani William Chow Laura Clarke Carla Cummins Anthony Doran Matthew Dunn Leo Goodstadt Kerstin Howe Matthew Howell Ambre-Aurore Josselin Robert C. Karn Christina M. Laukaitis Lilue Jingtao Fergal Martin Matthieu Muffato Stefanie Nachtweide Michael A. Quail Cristina Sisu Mario Stanke Klara Stefflova Cock Van Oosterhout Frederic Veyrunes Ben Ward Fengtang Yang Golbahar Yazdanifar Amonida Zadissa David J. Adams Alvis Brazma Mark Gerstein Benedict Paten
  • ... [+37 authors] ...,
  • Son Pham
  • Thomas M. Keane
  • Duncan T. Odom
  • Paul Flicek
  • First Published March 21, 2018
Research

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
Method

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
Perspective

Linking RNA biology to lncRNAs

  • Loyal A. Goff
  • John L. Rinn
  • First Published October 1, 2015
Research

Analysis of variable retroduplications in human populations suggests coupling of retrotransposition to cell division

  • Alexej Abyzov
  • Rebecca Iskow
  • Omer Gokcumen
  • David W. Radke
  • Suganthi Balasubramanian
  • Baikang Pei
  • Lukas Habegger
  • Charles Lee
  • Mark Gerstein
  • First Published September 11, 2013
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