Table of Contents

Research

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The human ribosomal DNA array is composed of highly homogenized tandem clusters
- Yutaro Hori,
- Akira Shimamoto,
- and Takehiko Kobayashi
Genome Res. November 2021 31: 1971-1982; Published in Advance August 18, 2021, doi:10.1101/gr.275838.121
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Embryonic LTR retrotransposons supply promoter modules to somatic tissues
- Kosuke Hashimoto,
- Eeva-Mari Jouhilahti,
- Virpi Töhönen,
- Piero Carninci,
- Juha Kere,
- and Shintaro Katayama
Genome Res. November 2021 31: 1983-1993; Published in Advance October 21, 2021, doi:10.1101/gr.275354.121
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Mutational bias in spermatogonia impacts the anatomy of regulatory sites in the human genome
- Vera B. Kaiser,
- Lana Talmane,
- Yatendra Kumar,
- Fiona Semple,
- Marie MacLennan,
- Deciphering Developmental Disorders Study,
- David R. FitzPatrick,
- Martin S. Taylor,
- and Colin A. Semple
Genome Res. November 2021 31: 1994-2007; Published in Advance August 20, 2021, doi:10.1101/gr.275407.121
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Nuclease deficiencies alter plasma cell-free DNA methylation profiles
- Diana S.C. Han,
- Meng Ni,
- Rebecca W.Y. Chan,
- Danny K.L. Wong,
- Linda T. Hiraki,
- Stefano Volpi,
- Peiyong Jiang,
- Kathy O. Lui,
- K.C. Allen Chan,
- Rossa W.K. Chiu,
- and Y.M. Dennis Lo
Genome Res. November 2021 31: 2008-2021; Published in Advance September 1, 2021, doi:10.1101/gr.275426.121
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RBFOX splicing factors contribute to a broad but selective recapitulation of peripheral tissue splicing patterns in the thymus
- Kathrin Jansen,
- Noriko Shikama-Dorn,
- Moustafa Attar,
- Stefano Maio,
- Maria Lopopolo,
- David Buck,
- Georg A. Holländer,
- and Stephen N. Sansom
Genome Res. November 2021 31: 2022-2034; Published in Advance October 14, 2021, doi:10.1101/gr.275245.121
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Positive selection in noncoding genomic regions of vocal learning birds is associated with genes implicated in vocal learning and speech functions in humans
- James A. Cahill,
- Joel Armstrong,
- Alden Deran,
- Carolyn J. Khoury,
- Benedict Paten,
- David Haussler,
- and Erich D. Jarvis
Genome Res. November 2021 31: 2035-2049; Published in Advance October 19, 2021, doi:10.1101/gr.275989.121
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Genome-wide oscillations in G + C density and sequence conservation
- Zarmik Moqtaderi,
- Susan Brown,
- and Welcome Bender
Genome Res. November 2021 31: 2050-2057; Published in Advance October 14, 2021, doi:10.1101/gr.274332.120
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Cellular abundance shapes function in piRNA-guided genome defense
- Pavol Genzor,
- Parthena Konstantinidou,
- Daniel Stoyko,
- Amirhossein Manzourolajdad,
- Celine Marlin Andrews,
- Alexandra R. Elchert,
- Constantinos Stathopoulos,
- and Astrid D. Haase
Genome Res. November 2021 31: 2058-2068; Published in Advance October 19, 2021, doi:10.1101/gr.275478.121
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Shared evolutionary trajectories of three independent neo-sex chromosomes in Drosophila
- Masafumi Nozawa,
- Yohei Minakuchi,
- Kazuhiro Satomura,
- Shu Kondo,
- Atsushi Toyoda,
- and Koichiro Tamura
Genome Res. November 2021 31: 2069-2079; Published in Advance October 21, 2021, doi:10.1101/gr.275503.121
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Methods

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Effective sequence similarity detection with strobemers
- Kristoffer Sahlin
Genome Res. November 2021 31: 2080-2094; Published in Advance October 19, 2021, doi:10.1101/gr.275648.121
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Cancer-associated dynamics and potential regulators of intronic polyadenylation revealed by IPAFinder using standard RNA-seq data
- Zhaozhao Zhao,
- Qiushi Xu,
- Ran Wei,
- Weixu Wang,
- Dong Ding,
- Yu Yang,
- Jun Yao,
- Liye Zhang,
- Yue-Qing Hu,
- Gang Wei,
- and Ting Ni
Genome Res. November 2021 31: 2095-2106; Published in Advance September 2, 2021, doi:10.1101/gr.271627.120
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Variational inference using approximate likelihood under the coalescent with recombination
- Xinhao Liu,
- Huw A. Ogilvie,
- and Luay Nakhleh
Genome Res. November 2021 31: 2107-2119; Published in Advance August 23, 2021, doi:10.1101/gr.273631.120
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Targeted regulation of transcription in primary cells using CRISPRa and CRISPRi
- Trine I. Jensen,
- Nanna S. Mikkelsen,
- Zongliang Gao,
- Johannes Foßelteder,
- Gabriel Pabst,
- Esben Axelgaard,
- Anders Laustsen,
- Saskia König,
- Andreas Reinisch,
- and Rasmus O. Bak
Genome Res. November 2021 31: 2120-2130; Published in Advance August 18, 2021, doi:10.1101/gr.275607.121
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Efficient computation of Faith's phylogenetic diversity with applications in characterizing microbiomes
- George Armstrong,
- Kalen Cantrell,
- Shi Huang,
- Daniel McDonald,
- Niina Haiminen,
- Anna Paola Carrieri,
- Qiyun Zhu,
- Antonio Gonzalez,
- Imran McGrath,
- Kristen L. Beck,
- Daniel Hakim,
- Aki S. Havulinna,
- Guillaume Méric,
- Teemu Niiranen,
- Leo Lahti,
- Veikko Salomaa,
- Mohit Jain,
- Michael Inouye,
- Austin D. Swafford,
- Ho-Cheol Kim,
- Laxmi Parida,
- Yoshiki Vázquez-Baeza,
- and Rob Knight
Genome Res. November 2021 31: 2131-2137; Published in Advance September 3, 2021, doi:10.1101/gr.275777.121

Resource

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A systematic analysis of Trypanosoma brucei chromatin factors identifies novel protein interaction networks associated with sites of transcription initiation and termination
- Desislava P. Staneva,
- Roberta Carloni,
- Tatsiana Auchynnikava,
- Pin Tong,
- Juri Rappsilber,
- A. Arockia Jeyaprakash,
- Keith R. Matthews,
- and Robin C. Allshire
Genome Res. November 2021 31: 2138-2154; Published in Advance August 18, 2021, doi:10.1101/gr.275368.121
OPEN ACCESS ARTICLE

Research

The human ribosomal DNA array is composed of highly homogenized tandem clusters

Embryonic LTR retrotransposons supply promoter modules to somatic tissues

Mutational bias in spermatogonia impacts the anatomy of regulatory sites in the human genome

Nuclease deficiencies alter plasma cell-free DNA methylation profiles

RBFOX splicing factors contribute to a broad but selective recapitulation of peripheral tissue splicing patterns in the thymus

Positive selection in noncoding genomic regions of vocal learning birds is associated with genes implicated in vocal learning and speech functions in humans

Genome-wide oscillations in G + C density and sequence conservation

Cellular abundance shapes function in piRNA-guided genome defense

Shared evolutionary trajectories of three independent neo-sex chromosomes in Drosophila

Methods

Effective sequence similarity detection with strobemers

Cancer-associated dynamics and potential regulators of intronic polyadenylation revealed by IPAFinder using standard RNA-seq data

Variational inference using approximate likelihood under the coalescent with recombination

Targeted regulation of transcription in primary cells using CRISPRa and CRISPRi

Efficient computation of Faith's phylogenetic diversity with applications in characterizing microbiomes

Resource

A systematic analysis of Trypanosoma brucei chromatin factors identifies novel protein interaction networks associated with sites of transcription initiation and termination

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