Table of Contents

Research

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Active enhancers strengthen insulation by RNA-mediated CTCF binding at chromatin domain boundaries
- Zubairul Islam,
- Bharath Saravanan,
- Kaivalya Walavalkar,
- Umer Farooq,
- Anurag Kumar Singh,
- Sabarinathan Radhakrishnan,
- Jitendra Thakur,
- Awadhesh Pandit,
- Steven Henikoff,
- and Dimple Notani
Genome Res. January 2023 33: 1-17; Published in Advance January 17, 2023, doi:10.1101/gr.276643.122
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Multi-omics analyses demonstrate a critical role for EHMT1 methyltransferase in transcriptional repression during oogenesis
- Hannah Demond,
- Courtney W. Hanna,
- Juan Castillo-Fernandez,
- Fátima Santos,
- Evangelia K. Papachristou,
- Anne Segonds-Pichon,
- Kamal Kishore,
- Simon Andrews,
- Clive S. D'Santos,
- and Gavin Kelsey
Genome Res. January 2023 33: 18-31; Published in Advance January 23, 2023, doi:10.1101/gr.277046.122
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Diversity, duplication, and genomic organization of homeobox genes in Lepidoptera
- Peter O. Mulhair,
- Liam Crowley,
- Douglas H. Boyes,
- Amber Harper,
- Owen T. Lewis,
- Darwin Tree of Life Consortium,
- and Peter W.H. Holland
Genome Res. January 2023 33: 32-44; Published in Advance December 8, 2022, doi:10.1101/gr.277118.122
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Rates and spectra of de novo structural mutations in Chlamydomonas reinhardtii
- Eugenio López-Cortegano,
- Rory J. Craig,
- Jobran Chebib,
- Eniolaye J. Balogun,
- and Peter D. Keightley
Genome Res. January 2023 33: 45-60; Published in Advance December 12, 2022, doi:10.1101/gr.276957.122
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Methods

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An efficient genotyper and star-allele caller for pharmacogenomics
- Ananth Hari,
- Qinghui Zhou,
- Nina Gonzaludo,
- John Harting,
- Stuart A. Scott,
- Xiang Qin,
- Steve Scherer,
- S. Cenk Sahinalp,
- and Ibrahim Numanagić
Genome Res. January 2023 33: 61-70; Published in Advance January 19, 2023, doi:10.1101/gr.277075.122
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A somatic hypermutation–based machine learning model stratifies individuals with Crohn's disease and controls
- Modi Safra,
- Lael Werner,
- Ayelet Peres,
- Pazit Polak,
- Naomi Salamon,
- Michael Schvimer,
- Batia Weiss,
- Iris Barshack,
- Dror S. Shouval,
- and Gur Yaari
Genome Res. January 2023 33: 71-79; Published in Advance December 16, 2022, doi:10.1101/gr.276683.122
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Marker-free characterization of full-length transcriptomes of single live circulating tumor cells
- Sarita Poonia,
- Anurag Goel,
- Smriti Chawla,
- Namrata Bhattacharya,
- Priyadarshini Rai,
- Yi Fang Lee,
- Yoon Sim Yap,
- Jay West,
- Ali Asgar Bhagat,
- Juhi Tayal,
- Anurag Mehta,
- Gaurav Ahuja,
- Angshul Majumdar,
- Naveen Ramalingam,
- and Debarka Sengupta
Genome Res. January 2023 33: 80-95; Published in Advance November 22, 2022, doi:10.1101/gr.276600.122
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Cross-species cell-type assignment from single-cell RNA-seq data by a heterogeneous graph neural network
- Xingyan Liu,
- Qunlun Shen,
- and Shihua Zhang
Genome Res. January 2023 33: 96-111; Published in Advance December 16, 2022, doi:10.1101/gr.276868.122
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Nematode gene annotation by machine-learning-assisted proteotranscriptomics enables proteome-wide evolutionary analysis
- Alejandro Ceron-Noriega,
- Miguel V. Almeida,
- Michal Levin,
- and Falk Butter
Genome Res. January 2023 33: 112-128; Published in Advance January 18, 2023, doi:10.1101/gr.277070.122
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Robust analysis of prokaryotic pangenome gene gain and loss rates with Panstripe
- Gerry Tonkin-Hill,
- Rebecca A. Gladstone,
- Anna K. Pöntinen,
- Sergio Arredondo-Alonso,
- Stephen D. Bentley,
- and Jukka Corander
Genome Res. January 2023 33: 129-140; Published in Advance January 20, 2023, doi:10.1101/gr.277340.122
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Resources

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Dynamic regulation of gonadal transposon control across the lifespan of the naturally short-lived African turquoise killifish
- Bryan B. Teefy,
- Ari Adler,
- Alan Xu,
- Katelyn Hsu,
- Param Priya Singh,
- and Bérénice A. Benayoun
Genome Res. January 2023 33: 141-153; Published in Advance December 28, 2022, doi:10.1101/gr.277301.122
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Genome sequencing of C. elegans balancer strains reveals previously unappreciated complex genomic rearrangements
- Tatiana Maroilley,
- Stephane Flibotte,
- Francesca Jean,
- Victoria Rodrigues Alves Barbosa,
- Andrew Galbraith,
- Afiya Razia Chida,
- Filip Cotra,
- Xiao Li,
- Larisa Oncea,
- Mark Edgley,
- Don Moerman,
- and Maja Tarailo-Graovac
Genome Res. January 2023 33: 154-167; Published in Advance December 5, 2022, doi:10.1101/gr.276988.122

Research

Active enhancers strengthen insulation by RNA-mediated CTCF binding at chromatin domain boundaries

Multi-omics analyses demonstrate a critical role for EHMT1 methyltransferase in transcriptional repression during oogenesis

Diversity, duplication, and genomic organization of homeobox genes in Lepidoptera

Rates and spectra of de novo structural mutations in Chlamydomonas reinhardtii

Methods

An efficient genotyper and star-allele caller for pharmacogenomics

A somatic hypermutation–based machine learning model stratifies individuals with Crohn's disease and controls

Marker-free characterization of full-length transcriptomes of single live circulating tumor cells

Cross-species cell-type assignment from single-cell RNA-seq data by a heterogeneous graph neural network

Nematode gene annotation by machine-learning-assisted proteotranscriptomics enables proteome-wide evolutionary analysis

Robust analysis of prokaryotic pangenome gene gain and loss rates with Panstripe

Resources

Dynamic regulation of gonadal transposon control across the lifespan of the naturally short-lived African turquoise killifish

Genome sequencing of C. elegans balancer strains reveals previously unappreciated complex genomic rearrangements

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