Table of Contents

Research

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Genetic control of the dynamic transcriptional response to immune stimuli and glucocorticoids at single-cell resolution
- Justyna A. Resztak,
- Julong Wei,
- Samuele Zilioli,
- Edward Sendler,
- Adnan Alazizi,
- Henriette E. Mair-Meijers,
- Peijun Wu,
- Xiaoquan Wen,
- Richard B. Slatcher,
- Xiang Zhou,
- Francesca Luca,
- and Roger Pique-Regi
Genome Res. June 2023 33: 839-856; Published in Advance July 13, 2023, doi:10.1101/gr.276765.122
OPEN ACCESS ARTICLE
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Variation in histone configurations correlates with gene expression across nine inbred strains of mice
- Anna L. Tyler,
- Catrina Spruce,
- Romy Kursawe,
- Annat Haber,
- Robyn L. Ball,
- Wendy A. Pitman,
- Alexander D. Fine,
- Narayanan Raghupathy,
- Michael Walker,
- Vivek M. Philip,
- Christopher L. Baker,
- J. Matthew Mahoney,
- Gary A. Churchill,
- Jennifer J. Trowbridge,
- Michael L. Stitzel,
- Kenneth Paigen,
- Petko M. Petkov,
- and Gregory W. Carter
Genome Res. June 2023 33: 857-871; Published in Advance May 22, 2023, doi:10.1101/gr.277467.122
OPEN ACCESS ARTICLE
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Population genomics reveals mechanisms and dynamics of de novo expressed open reading frame emergence in Drosophila melanogaster
- Anna Grandchamp,
- Lucas Kühl,
- Marie Lebherz,
- Kathrin Brüggemann,
- John Parsch,
- and Erich Bornberg-Bauer
Genome Res. June 2023 33: 872-890; Published in Advance July 13, 2023, doi:10.1101/gr.277482.122
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Integration site–dependent HIV-1 promoter activity shapes host chromatin conformation
- Jack A. Collora and
- Ya-Chi Ho
Genome Res. June 2023 33: 891-906; Published in Advance June 9, 2023, doi:10.1101/gr.277698.123
OPEN ACCESS ARTICLE

Methods

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Accurate sequencing of DNA motifs able to form alternative (non-B) structures
- Matthias H. Weissensteiner,
- Marzia A. Cremona,
- Wilfried M. Guiblet,
- Nicholas Stoler,
- Robert S. Harris,
- Monika Cechova,
- Kristin A. Eckert,
- Francesca Chiaromonte,
- Yi-Fei Huang,
- and Kateryna D. Makova
Genome Res. June 2023 33: 907-922; Published in Advance July 11, 2023, doi:10.1101/gr.277490.122
OPEN ACCESS ARTICLE
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Efficient and accurate KIR and HLA genotyping with massively parallel sequencing data
- Li Song,
- Gali Bai,
- X. Shirley Liu,
- Bo Li,
- and Heng Li
Genome Res. June 2023 33: 923-931; Published in Advance May 11, 2023, doi:10.1101/gr.277585.122
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Debiased personalized gene coexpression networks for population-scale scRNA-seq data
- Shan Lu and
- Sündüz Keleş
Genome Res. June 2023 33: 932-947; Published in Advance June 9, 2023, doi:10.1101/gr.277363.122
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Genome skimming with nanopore sequencing precisely determines global and transposon DNA methylation in vertebrates
- Christopher Faulk
Genome Res. June 2023 33: 948-956; Published in Advance July 13, 2023, doi:10.1101/gr.277743.123
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Large-scale detection and characterization of interchromosomal rearrangements in normozoospermic bulls using massive genotype and phenotype data sets
- Jeanlin Jourdain,
- Harmonie Barasc,
- Thomas Faraut,
- Anne Calgaro,
- Nathalie Bonnet,
- Camille Marcuzzo,
- Amandine Suin,
- Anne Barbat,
- Chris Hozé,
- Florian Besnard,
- Sébastien Taussat,
- Cécile Grohs,
- Claire Kuchly,
- Carole Iampietro,
- Cécile Donnadieu,
- Alain Pinton,
- Didier Boichard,
- and Aurélien Capitan
Genome Res. June 2023 33: 957-971; Published in Advance July 6, 2023, doi:10.1101/gr.277787.123
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Inferring and comparing metabolism across heterogeneous sets of annotated genomes using AuCoMe
- Arnaud Belcour,
- Jeanne Got,
- Méziane Aite,
- Ludovic Delage,
- Jonas Collén,
- Clémence Frioux,
- Catherine Leblanc,
- Simon M. Dittami,
- Samuel Blanquart,
- Gabriel V. Markov,
- and Anne Siegel
Genome Res. June 2023 33: 972-987; Published in Advance July 19, 2023, doi:10.1101/gr.277056.122
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Genealogical inference and more flexible sequence clustering using iterative-PopPUNK
- Bin Zhao,
- John A. Lees,
- Hongjin Wu,
- Chao Yang,
- and Daniel Falush
Genome Res. June 2023 33: 988-998; Published in Advance May 30, 2023, doi:10.1101/gr.277395.122

Resource

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Discordant calls across genotype discovery approaches elucidate variants with systematic errors
- Elizabeth G. Atkinson,
- Mykyta Artomov,
- Alexander A. Loboda,
- Heidi L. Rehm,
- Daniel G. MacArthur,
- Konrad J. Karczewski,
- Benjamin M. Neale,
- and Mark J. Daly
Genome Res. June 2023 33: 999-1005; Published in Advance May 30, 2023, doi:10.1101/gr.277908.123

Research

Genetic control of the dynamic transcriptional response to immune stimuli and glucocorticoids at single-cell resolution

Variation in histone configurations correlates with gene expression across nine inbred strains of mice

Population genomics reveals mechanisms and dynamics of de novo expressed open reading frame emergence in Drosophila melanogaster

Integration site–dependent HIV-1 promoter activity shapes host chromatin conformation

Methods

Accurate sequencing of DNA motifs able to form alternative (non-B) structures

Efficient and accurate KIR and HLA genotyping with massively parallel sequencing data

Debiased personalized gene coexpression networks for population-scale scRNA-seq data

Genome skimming with nanopore sequencing precisely determines global and transposon DNA methylation in vertebrates

Large-scale detection and characterization of interchromosomal rearrangements in normozoospermic bulls using massive genotype and phenotype data sets

Inferring and comparing metabolism across heterogeneous sets of annotated genomes using AuCoMe

Genealogical inference and more flexible sequence clustering using iterative-PopPUNK

Resource

Discordant calls across genotype discovery approaches elucidate variants with systematic errors

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