Table of Contents

In memoriam

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C. Thomas Caskey (1938–2022)
- Richard A. Gibbs,
- Aravinda Chakravarti,
- Evan E. Eichler,
- Eric D. Green,
- Richard M. Myers,
- Anne C. Ferguson-Smith,
- Kateryna D. Makova,
- and Hillary E. Sussman
Genome Res. March 2022 32: vii-viii; Published in Advance February 17, 2022, doi:10.1101/gr.276658.122
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Research

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Functional noncoding SNPs in human endothelial cells fine-map vascular trait associations
- Anu Toropainen,
- Lindsey K. Stolze,
- Tiit Örd,
- Michael B. Whalen,
- Paula Martí Torrell,
- Verena M. Link,
- Minna U. Kaikkonen,
- and Casey E. Romanoski
Genome Res. March 2022 32: 409-424; Published in Advance February 22, 2022, doi:10.1101/gr.276064.121
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Genomic context sensitivity of insulator function
- André M. Ribeiro-dos-Santos,
- Megan S. Hogan,
- Raven D. Luther,
- Ran Brosh,
- and Matthew T. Maurano
Genome Res. March 2022 32: 425-436; Published in Advance January 26, 2022, doi:10.1101/gr.276449.121
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Enhancer–silencer transitions in the human genome
- Di Huang and
- Ivan Ovcharenko
Genome Res. March 2022 32: 437-448; Published in Advance February 1, 2022, doi:10.1101/gr.275992.121
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Whole-genome resequencing of temporally stratified samples reveals substantial loss of haplotype diversity in the highly inbred Scandinavian wolf population
- Agnese Viluma,
- Øystein Flagstad,
- Mikael Åkesson,
- Camilla Wikenros,
- Håkan Sand,
- Petter Wabakken,
- and Hans Ellegren
Genome Res. March 2022 32: 449-458; Published in Advance February 8, 2022, doi:10.1101/gr.276070.121
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Joint actions of diverse transcription factor families establish neuron-type identities and promote enhancer selectivity
- Angela Jimeno-Martín,
- Erick Sousa,
- Rebeca Brocal-Ruiz,
- Noemi Daroqui,
- Miren Maicas,
- and Nuria Flames
Genome Res. March 2022 32: 459-473; Published in Advance January 24, 2022, doi:10.1101/gr.275623.121
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Distal regulation, silencers, and a shared combinatorial syntax are hallmarks of animal embryogenesis
- Paola Cornejo-Páramo,
- Kathrein Roper,
- Sandie M. Degnan,
- Bernard M. Degnan,
- and Emily S. Wong
Genome Res. March 2022 32: 474-487; Published in Advance January 19, 2022, doi:10.1101/gr.275864.121

Methods

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De novo mutation rates at the single-mutation resolution in a human HBB gene region associated with adaptation and genetic disease
- Daniel Melamed,
- Yuval Nov,
- Assaf Malik,
- Michael B. Yakass,
- Evgeni Bolotin,
- Revital Shemer,
- Edem K. Hiadzi,
- Karl L. Skorecki,
- and Adi Livnat
Genome Res. March 2022 32: 488-498; Published in Advance January 14, 2022, doi:10.1101/gr.276103.121
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Discovery of an unusually high number of de novo mutations in sperm of older men using duplex sequencing
- Renato Salazar,
- Barbara Arbeithuber,
- Maja Ivankovic,
- Monika Heinzl,
- Sofia Moura,
- Ingrid Hartl,
- Theresa Mair,
- Angelika Lahnsteiner,
- Thomas Ebner,
- Omar Shebl,
- Johannes Pröll,
- and Irene Tiemann-Boege
Genome Res. March 2022 32: 499-511; Published in Advance February 24, 2022, doi:10.1101/gr.275695.121
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Domain-adaptive neural networks improve cross-species prediction of transcription factor binding
- Kelly Cochran,
- Divyanshi Srivastava,
- Avanti Shrikumar,
- Akshay Balsubramani,
- Ross C. Hardison,
- Anshul Kundaje,
- and Shaun Mahony
Genome Res. March 2022 32: 512-523; Published in Advance January 18, 2022, doi:10.1101/gr.275394.121
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Predicting genotype-specific gene regulatory networks
- Deborah Weighill,
- Marouen Ben Guebila,
- Kimberly Glass,
- John Quackenbush,
- and John Platig
Genome Res. March 2022 32: 524-533; Published in Advance February 22, 2022, doi:10.1101/gr.275107.120
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NicE-C efficiently reveals open chromatin–associated chromosome interactions at high resolution
- Zhengyu Luo,
- Ran Zhang,
- Tengfei Hu,
- Yuting Zhu,
- Yueming Wu,
- Wenfei Li,
- Zhi Zhang,
- Xuebiao Yao,
- Haiyi Liang,
- and Xiaoyuan Song
Genome Res. March 2022 32: 534-544; Published in Advance February 1, 2022, doi:10.1101/gr.275986.121
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Low-input RNase footprinting for simultaneous quantification of cytosolic and mitochondrial translation
- Qianru Li,
- Haiwang Yang,
- Emily K. Stroup,
- Hongbin Wang,
- and Zhe Ji
Genome Res. March 2022 32: 545-557; Published in Advance February 22, 2022, doi:10.1101/gr.276139.121
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Accurate and robust inference of microbial growth dynamics from metagenomic sequencing reveals personalized growth rates
- Tyler A. Joseph,
- Philippe Chlenski,
- Aviya Litman,
- Tal Korem,
- and Itsik Pe'er
Genome Res. March 2022 32: 558-568; Published in Advance January 5, 2022, doi:10.1101/gr.275533.121

Resources

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Mitochondrial DNA variation across 56,434 individuals in gnomAD
- Kristen M. Laricchia,
- Nicole J. Lake,
- Nicholas A. Watts,
- Megan Shand,
- Andrea Haessly,
- Laura Gauthier,
- David Benjamin,
- Eric Banks,
- Jose Soto,
- Kiran Garimella,
- James Emery,
- Genome Aggregation Database Consortium,
- Heidi L. Rehm,
- Daniel G. MacArthur,
- Grace Tiao,
- Monkol Lek,
- Vamsi K. Mootha,
- and Sarah E. Calvo
Genome Res. March 2022 32: 569-582; Published in Advance January 24, 2022, doi:10.1101/gr.276013.121
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Genome biology of the darkedged splitfin, Girardinichthys multiradiatus, and the evolution of sex chromosomes and placentation
- Kang Du,
- Martin Pippel,
- Susanne Kneitz,
- Romain Feron,
- Irene da Cruz,
- Sylke Winkler,
- Brigitta Wilde,
- Edgar G. Avila Luna,
- Gene Myers,
- Yann Guiguen,
- Constantino Macias Garcia,
- and Manfred Schartl
Genome Res. March 2022 32: 583-594; Published in Advance January 26, 2022, doi:10.1101/gr.275826.121

In memoriam

C. Thomas Caskey (1938–2022)

Research

Functional noncoding SNPs in human endothelial cells fine-map vascular trait associations

Genomic context sensitivity of insulator function

Enhancer–silencer transitions in the human genome

Whole-genome resequencing of temporally stratified samples reveals substantial loss of haplotype diversity in the highly inbred Scandinavian wolf population

Joint actions of diverse transcription factor families establish neuron-type identities and promote enhancer selectivity

Distal regulation, silencers, and a shared combinatorial syntax are hallmarks of animal embryogenesis

Methods

De novo mutation rates at the single-mutation resolution in a human HBB gene region associated with adaptation and genetic disease

Discovery of an unusually high number of de novo mutations in sperm of older men using duplex sequencing

Domain-adaptive neural networks improve cross-species prediction of transcription factor binding

Predicting genotype-specific gene regulatory networks

NicE-C efficiently reveals open chromatin–associated chromosome interactions at high resolution

Low-input RNase footprinting for simultaneous quantification of cytosolic and mitochondrial translation

Accurate and robust inference of microbial growth dynamics from metagenomic sequencing reveals personalized growth rates

Resources

Mitochondrial DNA variation across 56,434 individuals in gnomAD

Genome biology of the darkedged splitfin, Girardinichthys multiradiatus, and the evolution of sex chromosomes and placentation

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