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Corrigendum: Corrigendum: Diversifying the genomic data science research community
- The Genomic Data Science Community Network
Genome Res. October 2022 32: 1965_2; doi:10.1101/gr.277322.122
...The Genomic Data Science Community Network Genome Research 32: 1231–1241 (2022)The authors would like to provide alternative (alt) text descriptions of the main figures for the visually or print impaired. A pointer to the alt text has been added at the end of the Acknowledgments section...
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Research: Genomic regulatory landscape underlying the antiviral response of Atlantic salmon
- Shahmir Naseer,
- Thomas C Clark,
- Bertrand Collet,
- Pooran Dewari,
- Damir Baranasic,
- Daniel J Macqueen,
- Pierre Boudinot,
- and Samuel A.M. Martin
Genome Res. October 22, 2025 gr.280579.125; Published in Advance October 22, 2025, doi:10.1101/gr.280579.125
...provides novel insights into the genomic regulatory landscape underlying antiviral 33 immunity in a farmed fish with a complex . 34 Introduction 35 The innate immune response to viral infection, which is mainly based on the type I interferon 36 (type I IFN) pathway is crucial to both disease progression...
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Research: The genomic consequences and persistence of sociality in spiders
- Jilong Ma,
- Jesper Bechsgaard,
- Anne Aagaard,
- Palle Villesen,
- Trine Bilde,
- and Mikkel Heide Schierup
Genome Res. March 2025 35: 499-511; Published in Advance February 20, 2025, doi:10.1101/gr.279503.124
..., sociality is accompanied by a transition from outcrossing to inbreeding. In concert, these traits reduce effective population size, potentially rendering transitions to sociality “evolutionarily dead-ends.” We addressed this hypothesis in a comparative genomic study in spiders, in which sociality has...
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Research: The genomic basis of evolutionary differentiation among honey bees
- Bertrand Fouks,
- Philipp Brand,
- Hung N. Nguyen,
- Jacob Herman,
- Francisco Camara,
- Daniel Ence,
- Darren E. Hagen,
- Katharina J. Hoff,
- Stefanie Nachweide,
- Lars Romoth,
- Kimberly K.O. Walden,
- Roderic Guigo,
- Mario Stanke,
- Giuseppe Narzisi,
- Mark Yandell,
- Hugh M. Robertson,
- Nikolaus Koeniger,
- Panuwan Chantawannakul,
- Michael C. Schatz,
- Kim C. Worley,
- Gene E. Robinson,
- Christine G. Elsik,
- and Olav Rueppell
Genome Res. July 2021 31: 1203-1215; Published in Advance May 4, 2021, doi:10.1101/gr.272310.120
...University, New York, New York 10065, USA; 5MU Institute for Data Science and Informatics, University of Missouri, Columbia, Missouri 65211, USA; 6Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08036 Barcelona, Spain; 7School of Forest Resources and Conservation...
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Research: Competition for DNA binding between paralogous transcription factors determines their genomic occupancy and regulatory functions
- Yuning Zhang,
- Tiffany D. Ho,
- Nicolas E. Buchler,
- and Raluca Gordân
Genome Res. July 2021 31: 1216-1229; Published in Advance May 11, 2021, doi:10.1101/gr.275145.120
...Yuning Zhang1,2, Tiffany D. Ho1,3, Nicolas E. Buchler4 and Raluca Gordân1,3,5 1Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA; 2Program in Computational Biology and Bioinformatics, Duke University, Durham, North Carolina 27708, USA; 3Department...
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Method: Fast and flexible bacterial genomic epidemiology with PopPUNK
- John A. Lees,
- Simon R. Harris,
- Gerry Tonkin-Hill,
- Rebecca A. Gladstone,
- Stephanie W. Lo,
- Jeffrey N. Weiser,
- Jukka Corander,
- Stephen D. Bentley,
- and Nicholas J. Croucher
Genome Res. February 2019 29: 304-316; Published in Advance January 24, 2019, doi:10.1101/gr.241455.118
...and Microbes, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom; 3Department of Biostatistics, University of Oslo, 0372 Oslo, Norway; 4Helsinki Institute of Information Technology, Department of Mathematics and Statistics, University of Helsinki, 00014 Helsinki, Finland; 5...
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Research: Worldwide patterns of genomic variation and admixture in gray wolves
- Zhenxin Fan,
- Pedro Silva,
- Ilan Gronau,
- Shuoguo Wang,
- Aitor Serres Armero,
- Rena M. Schweizer,
- Oscar Ramirez,
- John Pollinger,
- Marco Galaverni,
- Diego Ortega Del-Vecchyo,
- Lianming Du,
- Wenping Zhang,
- Zhihe Zhang,
- Jinchuan Xing,
- Carles Vilà,
- Tomas Marques-Bonet,
- Raquel Godinho,
- Bisong Yue,
- and Robert K. Wayne
Genome Res. February 2016 26: 163-173; Published in Advance December 17, 2015, doi:10.1101/gr.197517.115
...et al. 2007; vonHoldt et al. 2011). Genome-wide approaches using SNP genotyping arrays have confirmed these environmentally related genetic partitions and demonstrated extensive admixture with coyotes and, to a more limited extent, with domestic dogs (Pilot et al. 2010, 2014; vonHoldt et al. 2010...
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Research: Transcriptome-wide systematic search does not detect A-to-I RNA editing in cis-antisense RNA duplexes
- Zohar Rosenwasser,
- Roni Cohen-Fultheim,
- Ofir Shliefer,
- Erez Y. Levanon,
- and Eli Eisenberg
Genome Res. March 12, 2026 gr.280820.125; Published in Advance March 12, 2026, doi:10.1101/gr.280820.125
...sites. Nat Commun 5: 4726. Porath HT, Knisbacher BA, Eisenberg E, Levanon EY. 2017. Massive A-to-I RNA editing is common across the Metazoa and correlates with dsRNA abundance. Genome Biol 18: 185. Ramaswami G, Li JB. 2014. RADAR: A rigorously annotated database of A-to-I RNA editing. Nucleic Acids Res...
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Research: Gene flow, ancient polymorphism, and ecological adaptation shape the genomic landscape of divergence among Darwin's finches
- Fan Han,
- Sangeet Lamichhaney,
- B. Rosemary Grant,
- Peter R. Grant,
- Leif Andersson,
- and Matthew T. Webster
Genome Res. June 2017 27: 1004-1015; Published in Advance April 25, 2017, doi:10.1101/gr.212522.116
...Gene flow, ancient polymorphism, and ecological adaptation shape the genomic landscape of divergence among Darwin’s finches Fan Han,1 Sangeet Lamichhaney,1 B. Rosemary Grant,2 Peter R. Grant,2 Leif Andersson,1,3,4 and Matthew T. Webster1 1Department of Medical Biochemistry and Microbiology, Science...
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Method: Early feature extraction drives model performance in high-resolution chromatin accessibility prediction
- Aayush Grover,
- Till Muser,
- Liine Kasak,
- Lin Zhang,
- Ekaterina Krymova,
- and Valentina Boeva
Genome Res. March 2026 36: 619-629; Published in Advance January 12, 2026, doi:10.1101/gr.281042.125
....211733). These cell lines consist of healthy and cancer cells, thereby creating a diverse data set.To further diversify our validation data sets, we used ATAC-seq data of two COAD and two KIRP tumors from The Cancer Genome Atlas (TCGA) (Corces et al. 2018). These data sets have been made available...
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