Volume 32, Issue 7 | July 2022

Perspective
- - Diversifying the genomic data science research community
    Rosa Alcazar
    Maria Alvarez
    Rachel Arnold
    Mentewab Ayalew
    Lyle G. Best
    Michael C. Campbell Kamal Chowdhury Katherine E.L. Cox Christina Daulton Youping Deng Carla Easter Karla Fuller Shazia Tabassum Hakim Ava M. Hoffman Natalie Kucher Andrew Lee Joslynn Lee Jeffrey T. Leek Robert Meller Loyda B. Méndez Miguel P. Méndez-González Stephen Mosher Michele Nishiguchi Siddharth Pratap Tiffany Rolle Sourav Roy Rachel Saidi Michael C. Schatz Shurjo K. Sen James Sniezek Edu Suarez Martinez Frederick J. Tan Jennifer Vessio Karriem Watson
    ...[+29 authors]...,
    Wendy Westbroek
    Joseph Wilcox
    Carrie Wright
    Xianfa Xie
    First Published July 20, 2022
Research
- - HDAC9 structural variants disrupting TWIST1 transcriptional regulation lead to craniofacial and limb malformations
    Naama Hirsch
    Idit Dahan
    Eva D'haene
    Matan Avni
    Sarah Vergult
    Marta Vidal-García Pamela Magini Claudio Graziano Giulia Severi Elena Bonora Anna Maria Nardone Francesco Brancati
    ...[+7 authors]...,
    Alberto Fernández-Jaén
    Olson J. Rory
    Benedikt Hallgrímsson
    Ramon Y. Birnbaum
    First Published June 16, 2022
  - Extensive protein dosage compensation in aneuploid human cancers
    Klaske M. Schukken
    Jason M. Sheltzer
    First Published June 14, 2022
  - Compartment-specific and ELAVL1-coordinated regulation of intronic polyadenylation isoforms by doxorubicin
    Alina Chakraborty
    Mandy Cadix
    Sébastien Relier
    Nicolò Taricco
    Tina Alaeitabar
    Alexandre Devaux Céline M. Labbé Sylvain Martineau Amélie Heneman-Masurel Pierre Gestraud
    ...[+5 authors]...,
    Alberto Inga
    Nicolas Servant
    Stéphan Vagner
    Martin Dutertre
    First Published July 20, 2022
  - Cell cycle arrest explains the observed bulk 3D genomic alterations in response to long-term heat shock in K562 cells
    Bingxiang Xu
    Xiaomeng Gao
    Xiaoli Li
    Yan Jia
    Feifei Li
    First Published July 14, 2022
  - Somatic retrotransposition in the developing rhesus macaque brain
    Victor Billon
    Francisco J. Sanchez-Luque
    Jay Rasmussen
    Gabriela O. Bodea
    Daniel J. Gerhardt
    Patricia Gerdes Seth W. Cheetham Stephanie N. Schauer Prabha Ajjikuttira Thomas J. Meyer Cora E. Layman Kimberly A. Nevonen Natasha Jansz Jose L. Garcia-Perez
    ...[+9 authors]...,
    Sandra R. Richardson
    Adam D. Ewing
    Lucia Carbone
    Geoffrey J. Faulkner
    First Published June 21, 2022
  - Multiple Pristionchus pacificus genomes reveal distinct evolutionary dynamics between de novo candidates and duplicated genes
    Neel Prabh
    Christian Rödelsperger
    First Published May 26, 2022
  - Dynamics of broad H3K4me3 domains uncover an epigenetic switch between cell identity and cancer-related genes
    Mohamed Belhocine
    Mathieu Simonin
    José David Abad Flores
    Agata Cieslak
    Iris Manosalva
    Lydie Pradel Charlotte Smith Eve-Lyne Mathieu Guillaume Charbonnier Joost H.A. Martens Hendrik G. Stunnenberg Muhammad Ahmad Maqbool Aneta Mikulasova Lisa J. Russell Daniel Rico
    ...[+10 authors]...,
    Denis Puthier
    Pierre Ferrier
    Vahid Asnafi
    Salvatore Spicuglia
    First Published June 23, 2021
  - Epigenomic translocation of H3K4me3 broad domains over oncogenes following hijacking of super-enhancers
    Aneta Mikulasova
    Daniel Kent
    Marco Trevisan-Herraz
    Nefeli Karataraki
    Kent T.M. Fung
    Cody Ashby Agata Cieslak Shmuel Yaccoby Frits van Rhee Maurizio Zangari Sharmilan Thanendrarajan Carolina Schinke Gareth J. Morgan Vahid Asnafi Salvatore Spicuglia Chris A. Brackley Anne E. Corcoran
    ...[+12 authors]...,
    Sophie Hambleton
    Brian A. Walker
    Daniel Rico
    Lisa J. Russell
    First Published December 21, 2021
Methods
- - High-resolution simulations of chromatin folding at genomic rearrangements in malignant B cells provide mechanistic insights into proto-oncogene deregulation
    Daniel Rico
    Daniel Kent
    Nefeli Karataraki
    Aneta Mikulasova
    Rolando Berlinguer-Palmini
    First Published July 21, 2022
  - Dynamic regulatory module networks for inference of cell type–specific transcriptional networks
    Alireza Fotuhi Siahpirani
    Sara Knaack
    Deborah Chasman
    Morten Seirup
    Rupa Sridharan
    First Published June 15, 2022
  - Identifying cell state–associated alternative splicing events and their coregulation
    Carlos F. Buen Abad Najar
    Prakruthi Burra
    Nir Yosef
    Liana F. Lareau
    First Published July 20, 2022
  - TransMeta simultaneously assembles multisample RNA-seq reads
    Ting Yu
    Xiaoyu Zhao
    Guojun Li
    First Published July 20, 2022
Resources
- - Zebrafish transposable elements show extensive diversification in age, genomic distribution, and developmental expression
    Ni-Chen Chang
    Quirze Rovira
    Jonathan Wells
    Cédric Feschotte
    Juan M. Vaquerizas
    First Published January 5, 2022
  - Epigenomic analysis reveals prevalent contribution of transposable elements to cis-regulatory elements, tissue-specific expression, and alternative promoters in zebrafish
    Hyung Joo Lee
    Yiran Hou
    Ju Heon Maeng
    Nakul M. Shah
    Yujie Chen
    First Published June 1, 2022

Table of Contents

Volume 32, Issue 7 | July 2022

Perspective

Diversifying the genomic data science research community

Research

HDAC9 structural variants disrupting TWIST1 transcriptional regulation lead to craniofacial and limb malformations

Extensive protein dosage compensation in aneuploid human cancers

Compartment-specific and ELAVL1-coordinated regulation of intronic polyadenylation isoforms by doxorubicin

Cell cycle arrest explains the observed bulk 3D genomic alterations in response to long-term heat shock in K562 cells

Somatic retrotransposition in the developing rhesus macaque brain

Multiple Pristionchus pacificus genomes reveal distinct evolutionary dynamics between de novo candidates and duplicated genes

Dynamics of broad H3K4me3 domains uncover an epigenetic switch between cell identity and cancer-related genes

Epigenomic translocation of H3K4me3 broad domains over oncogenes following hijacking of super-enhancers

Methods

High-resolution simulations of chromatin folding at genomic rearrangements in malignant B cells provide mechanistic insights into proto-oncogene deregulation

Dynamic regulatory module networks for inference of cell type–specific transcriptional networks

Identifying cell state–associated alternative splicing events and their coregulation

TransMeta simultaneously assembles multisample RNA-seq reads

Resources

Zebrafish transposable elements show extensive diversification in age, genomic distribution, and developmental expression

Epigenomic analysis reveals prevalent contribution of transposable elements to cis-regulatory elements, tissue-specific expression, and alternative promoters in zebrafish

Table of Contents

Volume 32, Issue 7 | July 2022

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Perspective

Research

Methods

Resources