Table of Contents

Research

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Complex mosaic structural variations in human fetal brains
- Shobana Sekar,
- Livia Tomasini,
- Christos Proukakis,
- Taejeong Bae,
- Logan Manlove,
- Yeongjun Jang,
- Soraya Scuderi,
- Bo Zhou,
- Maria Kalyva,
- Anahita Amiri,
- Jessica Mariani,
- Fritz J. Sedlazeck,
- Alexander E. Urban,
- Flora M. Vaccarino,
- and Alexej Abyzov
Genome Res. December 2020 30: 1695-1704; Published in Advance October 29, 2020, doi:10.1101/gr.262667.120
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Widespread intron retention impairs protein homeostasis in C9orf72 ALS brains
- Qingqing Wang,
- Erin G. Conlon,
- James L. Manley,
- and Donald C. Rio
Genome Res. December 2020 30: 1705-1715; Published in Advance October 14, 2020, doi:10.1101/gr.265298.120
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Sequence analysis in Bos taurus reveals pervasiveness of X–Y arms races in mammalian lineages
- Jennifer F. Hughes,
- Helen Skaletsky,
- Tatyana Pyntikova,
- Natalia Koutseva,
- Terje Raudsepp,
- Laura G. Brown,
- Daniel W. Bellott,
- Ting-Jan Cho,
- Shannon Dugan-Rocha,
- Ziad Khan,
- Colin Kremitzki,
- Catrina Fronick,
- Tina A. Graves-Lindsay,
- Lucinda Fulton,
- Wesley C. Warren,
- Richard K. Wilson,
- Elaine Owens,
- James E. Womack,
- William J. Murphy,
- Donna M. Muzny,
- Kim C. Worley,
- Bhanu P. Chowdhary,
- Richard A. Gibbs,
- and David C. Page
Genome Res. December 2020 30: 1716-1726; Published in Advance November 18, 2020, doi:10.1101/gr.269902.120
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Tissue-specific patterns of regulatory changes underlying gene expression differences among Ficedula flycatchers and their naturally occurring F₁ hybrids
- Carina F. Mugal,
- Mi Wang,
- Niclas Backström,
- David Wheatcroft,
- Murielle Ålund,
- Marie Sémon,
- S. Eryn McFarlane,
- Ludovic Dutoit,
- Anna Qvarnström,
- and Hans Ellegren
Genome Res. December 2020 30: 1727-1739; Published in Advance November 3, 2020, doi:10.1101/gr.254508.119
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Loss of histone H3.3 results in DNA replication defects and altered origin dynamics in C. elegans
- Maude Strobino,
- Joanna M. Wenda,
- Laura Padayachy,
- and Florian A. Steiner
Genome Res. December 2020 30: 1740-1751; Published in Advance November 10, 2020, doi:10.1101/gr.260794.120
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Distinctive regulatory architectures of germline-active and somatic genes in C. elegans
- Jacques Serizay,
- Yan Dong,
- Jürgen Jänes,
- Michael Chesney,
- Chiara Cerrato,
- and Julie Ahringer
Genome Res. December 2020 30: 1752-1765; Published in Advance October 22, 2020, doi:10.1101/gr.265934.120
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Global regulatory features of alternative splicing across tissues and within the nervous system of C. elegans
- Bina Koterniak,
- Pallavi P. Pilaka,
- Xicotencatl Gracida,
- Lisa-Marie Schneider,
- Iva Pritišanac,
- Yun Zhang,
- and John A. Calarco
Genome Res. December 2020 30: 1766-1780; Published in Advance October 30, 2020, doi:10.1101/gr.267328.120
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Sequencing identifies multiple early introductions of SARS-CoV-2 to the New York City region
- Matthew T. Maurano,
- Sitharam Ramaswami,
- Paul Zappile,
- Dacia Dimartino,
- Ludovic Boytard,
- André M. Ribeiro-dos-Santos,
- Nicholas A. Vulpescu,
- Gael Westby,
- Guomiao Shen,
- Xiaojun Feng,
- Megan S. Hogan,
- Manon Ragonnet-Cronin,
- Lily Geidelberg,
- Christian Marier,
- Peter Meyn,
- Yutong Zhang,
- John Cadley,
- Raquel Ordoñez,
- Raven Luther,
- Emily Huang,
- Emily Guzman,
- Carolina Arguelles-Grande,
- Kimon V. Argyropoulos,
- Margaret Black,
- Antonio Serrano,
- Melissa E. Call,
- Min Jae Kim,
- Brendan Belovarac,
- Tatyana Gindin,
- Andrew Lytle,
- Jared Pinnell,
- Theodore Vougiouklakis,
- John Chen,
- Lawrence H. Lin,
- Amy Rapkiewicz,
- Vanessa Raabe,
- Marie I. Samanovic,
- George Jour,
- Iman Osman,
- Maria Aguero-Rosenfeld,
- Mark J. Mulligan,
- Erik M. Volz,
- Paolo Cotzia,
- Matija Snuderl,
- and Adriana Heguy
Genome Res. December 2020 30: 1781-1788; Published in Advance October 22, 2020, doi:10.1101/gr.266676.120
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Methods

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Ultrafast and scalable variant annotation and prioritization with big functional genomics data
- Dandan Huang,
- Xianfu Yi,
- Yao Zhou,
- Hongcheng Yao,
- Hang Xu,
- Jianhua Wang,
- Shijie Zhang,
- Wenyan Nong,
- Panwen Wang,
- Lei Shi,
- Chenghao Xuan,
- Miaoxin Li,
- Junwen Wang,
- Weidong Li,
- Hoi Shan Kwan,
- Pak Chung Sham,
- Kai Wang,
- and Mulin Jun Li
Genome Res. December 2020 30: 1789-1801; Published in Advance October 15, 2020, doi:10.1101/gr.267997.120
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Identifying chromosomal subpopulations based on their recombination histories advances the study of the genetic basis of phenotypic traits
- Carlos Ruiz-Arenas,
- Alejandro Cáceres,
- Marcos López,
- Dolors Pelegrí-Sisó,
- Josefa González,
- and Juan R. González
Genome Res. December 2020 30: 1802-1814; Published in Advance November 17, 2020, doi:10.1101/gr.258301.119
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Cross-species analysis of enhancer logic using deep learning
- Liesbeth Minnoye,
- Ibrahim Ihsan Taskiran,
- David Mauduit,
- Maurizio Fazio,
- Linde Van Aerschot,
- Gert Hulselmans,
- Valerie Christiaens,
- Samira Makhzami,
- Monika Seltenhammer,
- Panagiotis Karras,
- Aline Primot,
- Edouard Cadieu,
- Ellen van Rooijen,
- Jean-Christophe Marine,
- Giorgia Egidy,
- Ghanem-Elias Ghanem,
- Leonard Zon,
- Jasper Wouters,
- and Stein Aerts
Genome Res. December 2020 30: 1815-1834; Published in Advance July 30, 2020, doi:10.1101/gr.260844.120
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Predicting unrecognized enhancer-mediated genome topology by an ensemble machine learning model
- Li Tang,
- Matthew C. Hill,
- Jun Wang,
- Jianxin Wang,
- James F. Martin,
- and Min Li
Genome Res. December 2020 30: 1835-1845; Published in Advance November 12, 2020, doi:10.1101/gr.264606.120
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Pooled protein tagging, cellular imaging, and in situ sequencing for monitoring drug action in real time
- Andreas Reicher,
- Anna Koren,
- and Stefan Kubicek
Genome Res. December 2020 30: 1846-1855; Published in Advance November 17, 2020, doi:10.1101/gr.261503.120
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Corrigendum

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Corrigendum: Transcriptome evidence reveals enhanced autophagy-lysosomal function in centenarians
Genome Res. December 2020 30: 1856; doi:10.1101/gr.273623.120
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Reviewer Index

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Reviewer Index, Volume 30, 2020
Genome Res. December 2020 30: 1857-1861

Research

Complex mosaic structural variations in human fetal brains

Widespread intron retention impairs protein homeostasis in C9orf72 ALS brains

Sequence analysis in Bos taurus reveals pervasiveness of X–Y arms races in mammalian lineages

Tissue-specific patterns of regulatory changes underlying gene expression differences among Ficedula flycatchers and their naturally occurring F₁ hybrids

Loss of histone H3.3 results in DNA replication defects and altered origin dynamics in C. elegans

Distinctive regulatory architectures of germline-active and somatic genes in C. elegans

Global regulatory features of alternative splicing across tissues and within the nervous system of C. elegans

Sequencing identifies multiple early introductions of SARS-CoV-2 to the New York City region

Methods

Ultrafast and scalable variant annotation and prioritization with big functional genomics data

Identifying chromosomal subpopulations based on their recombination histories advances the study of the genetic basis of phenotypic traits

Cross-species analysis of enhancer logic using deep learning

Predicting unrecognized enhancer-mediated genome topology by an ensemble machine learning model

Pooled protein tagging, cellular imaging, and in situ sequencing for monitoring drug action in real time

Corrigendum

Corrigendum: Transcriptome evidence reveals enhanced autophagy-lysosomal function in centenarians

Reviewer Index

Reviewer Index, Volume 30, 2020

This Issue

Preprint Server

Current Issue

In This Issue

Table of Contents

Research

Complex mosaic structural variations in human fetal brains

Widespread intron retention impairs protein homeostasis in C9orf72 ALS brains

Sequence analysis in Bos taurus reveals pervasiveness of X–Y arms races in mammalian lineages

Tissue-specific patterns of regulatory changes underlying gene expression differences among Ficedula flycatchers and their naturally occurring F1 hybrids

Loss of histone H3.3 results in DNA replication defects and altered origin dynamics in C. elegans

Distinctive regulatory architectures of germline-active and somatic genes in C. elegans

Global regulatory features of alternative splicing across tissues and within the nervous system of C. elegans

Sequencing identifies multiple early introductions of SARS-CoV-2 to the New York City region

Methods

Ultrafast and scalable variant annotation and prioritization with big functional genomics data

Identifying chromosomal subpopulations based on their recombination histories advances the study of the genetic basis of phenotypic traits

Cross-species analysis of enhancer logic using deep learning

Predicting unrecognized enhancer-mediated genome topology by an ensemble machine learning model

Pooled protein tagging, cellular imaging, and in situ sequencing for monitoring drug action in real time

Corrigendum

Corrigendum: Transcriptome evidence reveals enhanced autophagy-lysosomal function in centenarians

Reviewer Index

Reviewer Index, Volume 30, 2020

This Issue

Preprint Server

Current Issue

In This Issue

Tissue-specific patterns of regulatory changes underlying gene expression differences among Ficedula flycatchers and their naturally occurring F₁ hybrids