Table of Contents

Research

Select this article
Synchronized replication of genes encoding the same protein complex in fast-proliferating cells
- Ying Chen,
- Ke Li,
- Xiao Chu,
- Lucas B. Carey,
- and Wenfeng Qian
Genome Res. December 2019 29: 1929-1938; Published in Advance October 29, 2019, doi:10.1101/gr.254342.119
Select this article
Promoter-specific dynamics of TATA-binding protein association with the human genome
- Yuko Hasegawa and
- Kevin Struhl
Genome Res. December 2019 29: 1939-1950; Published in Advance November 15, 2019, doi:10.1101/gr.254466.119
Select this article
Clonal copy-number mosaicism in autoreactive T lymphocytes in diabetic NOD mice
- Maha Alriyami,
- Luc Marchand,
- Quan Li,
- Xiaoyu Du,
- Martin Olivier,
- and Constantin Polychronakos
Genome Res. December 2019 29: 1951-1961; Published in Advance November 6, 2019, doi:10.1101/gr.247882.118
OPEN ACCESS ARTICLE
Select this article
A high-resolution gene expression atlas links dedicated meristem genes to key architectural traits
- Steffen Knauer,
- Marie Javelle,
- Lin Li,
- Xianran Li,
- Xiaoli Ma,
- Kokulapalan Wimalanathan,
- Sunita Kumari,
- Robyn Johnston,
- Samuel Leiboff,
- Robert Meeley,
- Patrick S. Schnable,
- Doreen Ware,
- Carolyn Lawrence-Dill,
- Jianming Yu,
- Gary J. Muehlbauer,
- Michael J. Scanlon,
- and Marja C.P. Timmermans
Genome Res. December 2019 29: 1962-1973; Published in Advance November 19, 2019, doi:10.1101/gr.250878.119
OPEN ACCESS ARTICLE
Select this article
Chromatin-sensitive cryptic promoters putatively drive expression of alternative protein isoforms in yeast
- Wu Wei,
- Bianca P. Hennig,
- Jingwen Wang,
- Yujie Zhang,
- Ilaria Piazza,
- Yerma Pareja Sanchez,
- Christophe D. Chabbert,
- Sophie H. Adjalley,
- Lars M. Steinmetz,
- and Vicent Pelechano
Genome Res. December 2019 29: 1974-1984; Published in Advance November 18, 2019, doi:10.1101/gr.243378.118
Select this article
Accessibility of promoter DNA is not the primary determinant of chromatin-mediated gene regulation
- Răzvan V. Chereji,
- Peter R. Eriksson,
- Josefina Ocampo,
- Hemant K. Prajapati,
- and David J. Clark
Genome Res. December 2019 29: 1985-1995; Published in Advance September 11, 2019, doi:10.1101/gr.249326.119

Methods

Select this article
Absolute nucleosome occupancy map for the Saccharomyces cerevisiae genome
- Elisa Oberbeckmann,
- Michael Wolff,
- Nils Krietenstein,
- Mark Heron,
- Jessica L. Ellins,
- Andrea Schmid,
- Stefan Krebs,
- Helmut Blum,
- Ulrich Gerland,
- and Philipp Korber
Genome Res. December 2019 29: 1996-2009; Published in Advance November 6, 2019, doi:10.1101/gr.253419.119
Select this article
Modeling Niemann–Pick disease type C in a human haploid cell line allows for patient variant characterization and clinical interpretation
- Steven Erwood,
- Reid A. Brewer,
- Teija M.I. Bily,
- Eleonora Maino,
- Liangchi Zhou,
- Ronald D. Cohn,
- and Evgueni A. Ivakine
Genome Res. December 2019 29: 2010-2019; Published in Advance November 21, 2019, doi:10.1101/gr.250720.119
Select this article
Network-based hierarchical population structure analysis for large genomic data sets
- Gili Greenbaum,
- Amir Rubin,
- Alan R. Templeton,
- and Noah A. Rosenberg
Genome Res. December 2019 29: 2020-2033; Published in Advance November 6, 2019, doi:10.1101/gr.250092.119
Select this article
Identifying gene function and module connections by the integration of multispecies expression compendia
- Hao Li,
- Daria Rukina,
- Fabrice P.A. David,
- Terytty Yang Li,
- Chang-Myung Oh,
- Arwen W. Gao,
- Elena Katsyuba,
- Maroun Bou Sleiman,
- Andrea Komljenovic,
- Qingyao Huang,
- Robert W. Williams,
- Marc Robinson-Rechavi,
- Kristina Schoonjans,
- Stephan Morgenthaler,
- and Johan Auwerx
Genome Res. December 2019 29: 2034-2045; Published in Advance November 21, 2019, doi:10.1101/gr.251983.119
OPEN ACCESS ARTICLE
Select this article
Deep profiling and custom databases improve detection of proteoforms generated by alternative splicing
- Laura M. Agosto,
- Matthew R. Gazzara,
- Caleb M. Radens,
- Simone Sidoli,
- Josue Baeza,
- Benjamin A. Garcia,
- and Kristen W. Lynch
Genome Res. December 2019 29: 2046-2055; Published in Advance November 14, 2019, doi:10.1101/gr.248435.119
Select this article
AIDE: annotation-assisted isoform discovery with high precision
- Wei Vivian Li,
- Shan Li,
- Xin Tong,
- Ling Deng,
- Hubing Shi,
- and Jingyi Jessica Li
Genome Res. December 2019 29: 2056-2072; Published in Advance November 6, 2019, doi:10.1101/gr.251108.119

Resources

Select this article
Discovery of high-confidence human protein-coding genes and exons by whole-genome PhyloCSF helps elucidate 118 GWAS loci
- Jonathan M. Mudge,
- Irwin Jungreis,
- Toby Hunt,
- Jose Manuel Gonzalez,
- James C. Wright,
- Mike Kay,
- Claire Davidson,
- Stephen Fitzgerald,
- Ruth Seal,
- Susan Tweedie,
- Liang He,
- Robert M. Waterhouse,
- Yue Li,
- Elspeth Bruford,
- Jyoti S. Choudhary,
- Adam Frankish,
- and Manolis Kellis
Genome Res. December 2019 29: 2073-2087; Published in Advance September 19, 2019, doi:10.1101/gr.246462.118
OPEN ACCESS ARTICLE
Select this article
Murine single-cell RNA-seq reveals cell-identity- and tissue-specific trajectories of aging
- Jacob C. Kimmel,
- Lolita Penland,
- Nimrod D. Rubinstein,
- David G. Hendrickson,
- David R. Kelley,
- and Adam Z. Rosenthal
Genome Res. December 2019 29: 2088-2103; Published in Advance November 21, 2019, doi:10.1101/gr.253880.119
OPEN ACCESS ARTICLE
Select this article
The C. elegans 3′ UTRome v2 resource for studying mRNA cleavage and polyadenylation, 3′-UTR biology, and miRNA targeting
- Hannah S. Steber,
- Christina Gallante,
- Shannon O'Brien,
- Po-Lin Chiu,
- and Marco Mangone
Genome Res. December 2019 29: 2104-2116; Published in Advance November 19, 2019, doi:10.1101/gr.254839.119
OPEN ACCESS ARTICLE

Reviewer Index

Select this article

Reviewer Index, Volume 29, 2019
Genome Res. December 2019 29: 2117-2121

Research

Synchronized replication of genes encoding the same protein complex in fast-proliferating cells

Promoter-specific dynamics of TATA-binding protein association with the human genome

Clonal copy-number mosaicism in autoreactive T lymphocytes in diabetic NOD mice

A high-resolution gene expression atlas links dedicated meristem genes to key architectural traits

Chromatin-sensitive cryptic promoters putatively drive expression of alternative protein isoforms in yeast

Accessibility of promoter DNA is not the primary determinant of chromatin-mediated gene regulation

Methods

Absolute nucleosome occupancy map for the Saccharomyces cerevisiae genome

Modeling Niemann–Pick disease type C in a human haploid cell line allows for patient variant characterization and clinical interpretation

Network-based hierarchical population structure analysis for large genomic data sets

Identifying gene function and module connections by the integration of multispecies expression compendia

Deep profiling and custom databases improve detection of proteoforms generated by alternative splicing

AIDE: annotation-assisted isoform discovery with high precision

Resources

Discovery of high-confidence human protein-coding genes and exons by whole-genome PhyloCSF helps elucidate 118 GWAS loci

Murine single-cell RNA-seq reveals cell-identity- and tissue-specific trajectories of aging

The C. elegans 3′ UTRome v2 resource for studying mRNA cleavage and polyadenylation, 3′-UTR biology, and miRNA targeting

Reviewer Index

Reviewer Index, Volume 29, 2019

This Issue

Preprint Server

Current Issue

In This Issue