Volume 29, Issue 6 | June 2019

In memoriam
- - Sydney Brenner—a personal perspective
    Byrappa Venkatesh
    First Published June 10, 2019
Research
- - 4q-D4Z4 chromatin architecture regulates the transcription of muscle atrophic genes in facioscapulohumeral muscular dystrophy
    Alice Cortesi
    Matthieu Pesant
    Shruti Sinha
    Federica Marasca
    Eleonora Sala
    Francesco Gregoretti Laura Antonelli
    ...[+2 authors]...,
    Gennaro Oliva
    Chiara Chiereghin
    Giulia Soldà
    Beatrice Bodega
    First Published May 16, 2019
  - A massively parallel 3′ UTR reporter assay reveals relationships between nucleotide content, sequence conservation, and mRNA destabilization
    Adam J. Litterman
    Robin Kageyama
    Olivier Le Tonqueze
    Wenxue Zhao
    John D. Gagnon
    First Published May 31, 2019
  - Systems analysis reveals complex biological processes during virus infection fate decisions
    Jordi Argilaguet
    Mireia Pedragosa
    Anna Esteve-Codina
    Graciela Riera
    Enric Vidal
    Cristina Peligero-Cruz Valentina Casella David Andreu Tsuneyasu Kaisho
    ...[+4 authors]...,
    Gennady Bocharov
    Burkhard Ludewig
    Simon Heath
    Andreas Meyerhans
    First Published May 28, 2019
  - Diversification and collapse of a telomere elongation mechanism
    Bastien Saint-Leandre
    Son C. Nguyen
    Mia T. Levine
    First Published May 28, 2019
  - Turnover of ribosome-associated transcripts from de novo ORFs produces gene-like characteristics available for de novo gene emergence in wild yeast populations
    Éléonore Durand
    Isabelle Gagnon-Arsenault
    Johan Hallin
    Isabelle Hatin
    Alexandre K. Dubé
    First Published May 31, 2019
  - Convergent recombination cessation between mating-type genes and centromeres in selfing anther-smut fungi
    Fantin Carpentier
    Ricardo C. Rodríguez de la Vega
    Sara Branco
    Alodie Snirc
    Marco A. Coelho
    First Published May 1, 2019
  - Human contamination in bacterial genomes has created thousands of spurious proteins
    Florian P. Breitwieser
    Mihaela Pertea
    Aleksey V. Zimin
    Steven L. Salzberg
    First Published May 7, 2019
Methods
- - Plasmid detection and assembly in genomic and metagenomic data sets
    Dmitry Antipov
    Mikhail Raiko
    Alla Lapidus
    Pavel A. Pevzner
    First Published May 2, 2019
  - methyl-ATAC-seq measures DNA methylation at accessible chromatin
    Roman Spektor
    Nathaniel D. Tippens
    Claudia A. Mimoso
    Paul D. Soloway
    First Published June 3, 2019
  - One minute analysis of 200 histone posttranslational modifications by direct injection mass spectrometry
    Simone Sidoli
    Yekaterina Kori
    Mariana Lopes
    Zuo-Fei Yuan
    Hee Jong Kim
    Katarzyna Kulej Kevin A. Janssen
    ...[+2 authors]...,
    Laura M. Agosto
    Julia Pinheiro Chagas da Cunha
    Andrew J. Andrews
    Benjamin A. Garcia
    First Published May 23, 2019
  - Genome-wide reconstitution of chromatin transactions reveals that RSC preferentially disrupts H2AZ-containing nucleosomes
    Aylin Cakiroglu
    Cedric R. Clapier
    Andreas H. Ehrensberger
    Elodie Darbo
    Bradley R. Cairns
    First Published May 16, 2019
  - Beta-binomial modeling of CRISPR pooled screen data identifies target genes with greater sensitivity and fewer false negatives
    Hyun-Hwan Jeong
    Seon Young Kim
    Maxime W.C. Rousseaux
    Huda Y. Zoghbi
    Zhandong Liu
    First Published April 23, 2019
Resources
- - Recompleting the Caenorhabditis elegans genome
    Jun Yoshimura
    Kazuki Ichikawa
    Massa J. Shoura
    Karen L. Artiles
    Idan Gabdank
    Lamia Wahba Cheryl L. Smith Mark L. Edgley
    ...[+3 authors]...,
    Ann E. Rougvie
    Andrew Z. Fire
    Shinichi Morishita
    Erich M. Schwarz
    First Published May 23, 2019
  - Long-read sequencing reveals intra-species tolerance of substantial structural variations and new subtelomere formation in C. elegans
    Chuna Kim
    Jun Kim
    Sunghyun Kim
    Daniel E. Cook
    Kathryn S. Evans
    First Published May 23, 2019
  - The C. elegans embryonic transcriptome with tissue, time, and alternative splicing resolution
    Adam D. Warner
    Louis Gevirtzman
    LaDeana W. Hillier
    Brent Ewing
    Robert H. Waterston
    First Published May 23, 2019

Table of Contents

Volume 29, Issue 6 | June 2019

In memoriam

Sydney Brenner—a personal perspective

Research

4q-D4Z4 chromatin architecture regulates the transcription of muscle atrophic genes in facioscapulohumeral muscular dystrophy

A massively parallel 3′ UTR reporter assay reveals relationships between nucleotide content, sequence conservation, and mRNA destabilization

Systems analysis reveals complex biological processes during virus infection fate decisions

Diversification and collapse of a telomere elongation mechanism

Turnover of ribosome-associated transcripts from de novo ORFs produces gene-like characteristics available for de novo gene emergence in wild yeast populations

Convergent recombination cessation between mating-type genes and centromeres in selfing anther-smut fungi

Human contamination in bacterial genomes has created thousands of spurious proteins

Methods

Plasmid detection and assembly in genomic and metagenomic data sets

methyl-ATAC-seq measures DNA methylation at accessible chromatin

One minute analysis of 200 histone posttranslational modifications by direct injection mass spectrometry

Genome-wide reconstitution of chromatin transactions reveals that RSC preferentially disrupts H2AZ-containing nucleosomes

Beta-binomial modeling of CRISPR pooled screen data identifies target genes with greater sensitivity and fewer false negatives

Resources

Recompleting the Caenorhabditis elegans genome

Long-read sequencing reveals intra-species tolerance of substantial structural variations and new subtelomere formation in C. elegans

The C. elegans embryonic transcriptome with tissue, time, and alternative splicing resolution

Table of Contents

Volume 29, Issue 6 | June 2019

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In memoriam

Research

Methods

Resources