Table of Contents

Review

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Advancing genomic technologies and clinical awareness accelerates discovery of disease-associated tandem repeat sequences
- Terence Gall-Duncan,
- Nozomu Sato,
- Ryan K.C. Yuen,
- and Christopher E. Pearson
Genome Res. January 2022 32: 1-27; Published in Advance December 29, 2021, doi:10.1101/gr.269530.120

Research

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Spatial organization of chromosomes leads to heterogeneous chromatin motion and drives the liquid- or gel-like dynamical behavior of chromatin
- Hossein Salari,
- Marco Di Stefano,
- and Daniel Jost
Genome Res. January 2022 32: 28-43; Published in Advance December 28, 2021, doi:10.1101/gr.275827.121
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Low-frequency somatic copy number alterations in normal human lymphocytes revealed by large-scale single-cell whole-genome profiling
- Lu Liu,
- He Chen,
- Cheng Sun,
- Jianyun Zhang,
- Juncheng Wang,
- Meijie Du,
- Jie Li,
- Lin Di,
- Jie Shen,
- Shuang Geng,
- Yuhong Pang,
- Yingying Luo,
- Chen Wu,
- Yusi Fu,
- Zhe Zheng,
- Jianbin Wang,
- and Yanyi Huang
Genome Res. January 2022 32: 44-54; Published in Advance December 28, 2021, doi:10.1101/gr.275453.121
OPEN ACCESS ARTICLE
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Diverse tumorigenic consequences of human papillomavirus integration in primary oropharyngeal cancers
- David E. Symer,
- Keiko Akagi,
- Heather M. Geiger,
- Yang Song,
- Gaiyun Li,
- Anne-Katrin Emde,
- Weihong Xiao,
- Bo Jiang,
- André Corvelo,
- Nora C. Toussaint,
- Jingfeng Li,
- Amit Agrawal,
- Enver Ozer,
- Adel K. El-Naggar,
- Zoe Du,
- Jitesh B. Shewale,
- Birgit Stache-Crain,
- Mark Zucker,
- Nicolas Robine,
- Kevin R. Coombes,
- and Maura L. Gillison
Genome Res. January 2022 32: 55-70; Published in Advance December 13, 2021, doi:10.1101/gr.275911.121
OPEN ACCESS ARTICLE
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Meta-analysis of human and mouse ALS astrocytes reveals multi-omic signatures of inflammatory reactive states
- Oliver J. Ziff,
- Benjamin E. Clarke,
- Doaa M. Taha,
- Hamish Crerar,
- Nicholas M. Luscombe,
- and Rickie Patani
Genome Res. January 2022 32: 71-84; Published in Advance December 28, 2021, doi:10.1101/gr.275939.121
OPEN ACCESS ARTICLE
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Genomic environments scale the activities of diverse core promoters
- Clarice K.Y. Hong and
- Barak A. Cohen
Genome Res. January 2022 32: 85-96; Published in Advance December 27, 2021, doi:10.1101/gr.276025.121
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Cell type–specific analysis by single-cell profiling identifies a stable mammalian tRNA–mRNA interface and increased translation efficiency in neurons
- William Gao,
- Carlos J. Gallardo-Dodd,
- and Claudia Kutter
Genome Res. January 2022 32: 97-110; Published in Advance December 2, 2021, doi:10.1101/gr.275944.121
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Mediator dynamics during heat shock in budding yeast
- Debasish Sarkar,
- Z. Iris Zhu,
- Elizabeth R. Knoll,
- Emily Paul,
- David Landsman,
- and Randall H. Morse
Genome Res. January 2022 32: 111-123; Published in Advance November 16, 2021, doi:10.1101/gr.275750.121

Methods

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De novo individualized disease modules reveal the synthetic penetrance of genes and inform personalized treatment regimens
- Taylor M. Weiskittel,
- Choong Y. Ung,
- Cristina Correia,
- Cheng Zhang,
- and Hu Li
Genome Res. January 2022 32: 124-134; Published in Advance December 7, 2021, doi:10.1101/gr.275889.121
OPEN ACCESS ARTICLE
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A full-proteome, interaction-specific characterization of mutational hotspots across human cancers
- Siwei Chen,
- Yuan Liu,
- Yingying Zhang,
- Shayne D. Wierbowski,
- Steven M. Lipkin,
- Xiaomu Wei,
- and Haiyuan Yu
Genome Res. January 2022 32: 135-149; Published in Advance December 28, 2021, doi:10.1101/gr.275437.121
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Profiling chromatin accessibility in formalin-fixed paraffin-embedded samples
- Hua Zhang,
- Vamsi Krishna Polavarapu,
- Pengwei Xing,
- Miao Zhao,
- Lucy Mathot,
- Linxuan Zhao,
- Gabriela Rosen,
- Fredrik J. Swartling,
- Tobias Sjöblom,
- and Xingqi Chen
Genome Res. January 2022 32: 150-161; Published in Advance July 14, 2021, doi:10.1101/gr.275269.121
OPEN ACCESS ARTICLE
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Comprehensive determination of transcription start sites derived from all RNA polymerases using ReCappable-seq
- Bo Yan,
- George Tzertzinis,
- Ira Schildkraut,
- and Laurence Ettwiller
Genome Res. January 2022 32: 162-174; Published in Advance November 23, 2021, doi:10.1101/gr.275784.121
OPEN ACCESS ARTICLE

Resources

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RefSeq Functional Elements as experimentally assayed nongenic reference standards and functional interactions in human and mouse
- Catherine M. Farrell,
- Tamara Goldfarb,
- Sanjida H. Rangwala,
- Alexander Astashyn,
- Olga D. Ermolaeva,
- Vichet Hem,
- Kenneth S. Katz,
- Vamsi K. Kodali,
- Frank Ludwig,
- Craig L. Wallin,
- Kim D. Pruitt,
- and Terence D. Murphy
Genome Res. January 2022 32: 175-188; Published in Advance December 7, 2021, doi:10.1101/gr.275819.121
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Transposable element variants and their potential adaptive impact in urban populations of the malaria vector Anopheles coluzzii
- Carlos Vargas-Chavez,
- Neil Michel Longo Pendy,
- Sandrine E. Nsango,
- Laura Aguilera,
- Diego Ayala,
- and Josefa González
Genome Res. January 2022 32: 189-202; Published in Advance December 29, 2021, doi:10.1101/gr.275761.121
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Long-read assembly and comparative evidence-based reanalysis of Cryptosporidium genome sequences reveal expanded transporter repertoire and duplication of entire chromosome ends including subtelomeric regions
- Rodrigo P. Baptista,
- Yiran Li,
- Adam Sateriale,
- Mandy J. Sanders,
- Karen L. Brooks,
- Alan Tracey,
- Brendan R.E. Ansell,
- Aaron R. Jex,
- Garrett W. Cooper,
- Ethan D. Smith,
- Rui Xiao,
- Jennifer E. Dumaine,
- Peter Georgeson,
- Bernard J. Pope,
- Matthew Berriman,
- Boris Striepen,
- James A. Cotton,
- and Jessica C. Kissinger
Genome Res. January 2022 32: 203-213; Published in Advance November 11, 2021, doi:10.1101/gr.275325.121
OPEN ACCESS ARTICLE

Review

Advancing genomic technologies and clinical awareness accelerates discovery of disease-associated tandem repeat sequences

Research

Spatial organization of chromosomes leads to heterogeneous chromatin motion and drives the liquid- or gel-like dynamical behavior of chromatin

Low-frequency somatic copy number alterations in normal human lymphocytes revealed by large-scale single-cell whole-genome profiling

Diverse tumorigenic consequences of human papillomavirus integration in primary oropharyngeal cancers

Meta-analysis of human and mouse ALS astrocytes reveals multi-omic signatures of inflammatory reactive states

Genomic environments scale the activities of diverse core promoters

Cell type–specific analysis by single-cell profiling identifies a stable mammalian tRNA–mRNA interface and increased translation efficiency in neurons

Mediator dynamics during heat shock in budding yeast

Methods

De novo individualized disease modules reveal the synthetic penetrance of genes and inform personalized treatment regimens

A full-proteome, interaction-specific characterization of mutational hotspots across human cancers

Profiling chromatin accessibility in formalin-fixed paraffin-embedded samples

Comprehensive determination of transcription start sites derived from all RNA polymerases using ReCappable-seq

Resources

RefSeq Functional Elements as experimentally assayed nongenic reference standards and functional interactions in human and mouse

Transposable element variants and their potential adaptive impact in urban populations of the malaria vector Anopheles coluzzii

Long-read assembly and comparative evidence-based reanalysis of Cryptosporidium genome sequences reveal expanded transporter repertoire and duplication of entire chromosome ends including subtelomeric regions

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