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Research: Integrating genetic variation with deep learning provides context for variants impacting transcription factor binding during embryogenesis
- Olga M. Sigalova,
- Mattia Forneris,
- Frosina Stojanovska,
- Bingqing Zhao,
- Rebecca R. Viales,
- Adam Rabinowitz,
- Fayrouz Hammal,
- Benoît Ballester,
- Judith B. Zaugg,
- and Eileen E.M. Furlong
Genome Res. May 2025 35: 1138-1153; Published in Advance April 15, 2025, doi:10.1101/gr.279652.124
...European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, D-69117 Heidelberg, Germany; 3Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Faculty of Biosciences, D-69117 Heidelberg, Germany; 4Aix Marseille Univ, INSERM, TAGC, 13009 Marseille, France...
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Research: Major impacts of widespread structural variation on sorghum
- Zhihai Zhang,
- Joao Paulo Gomes Viana,
- Bosen Zhang,
- Kimberly K.O. Walden,
- Hans Müller Paul,
- Stephen P. Moose,
- Geoffrey P. Morris,
- Chris Daum,
- Kerrie W. Barry,
- Nadia Shakoor,
- and Matthew E. Hudson
Genome Res. February 2024 34: 286-299; Published in Advance March 13, 2024, doi:10.1101/gr.278396.123
...Department of Soil and Crop Science, Colorado State University, Fort Collins, Colorado 80523, USA; 5United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA; 6Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA...
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Resource: Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines
- Wen Huang,
- Andreas Massouras,
- Yutaka Inoue,
- Jason Peiffer,
- Miquel Ràmia,
- Aaron M. Tarone,
- Lavanya Turlapati,
- Thomas Zichner,
- Dianhui Zhu,
- Richard F. Lyman,
- Michael M. Magwire,
- Kerstin Blankenburg,
- Mary Anna Carbone,
- Kyle Chang,
- Lisa L. Ellis,
- Sonia Fernandez,
- Yi Han,
- Gareth Highnam,
- Carl E. Hjelmen,
- John R. Jack,
- Mehwish Javaid,
- Joy Jayaseelan,
- Divya Kalra,
- Sandy Lee,
- Lora Lewis,
- Mala Munidasa,
- Fiona Ongeri,
- Shohba Patel,
- Lora Perales,
- Agapito Perez,
- LingLing Pu,
- Stephanie M. Rollmann,
- Robert Ruth,
- Nehad Saada,
- Crystal Warner,
- Aneisa Williams,
- Yuan-Qing Wu,
- Akihiko Yamamoto,
- Yiqing Zhang,
- Yiming Zhu,
- Robert R.H. Anholt,
- Jan O. Korbel,
- David Mittelman,
- Donna M. Muzny,
- Richard A. Gibbs,
- Antonio Barbadilla,
- J. Spencer Johnston,
- Eric A. Stone,
- Stephen Richards,
- Bart Deplancke,
- and Trudy F.C. Mackay
Genome Res. July 2014 24: 1193-1208; Published in Advance April 8, 2014, doi:10.1101/gr.171546.113
..., and genome-wide analyses of quantitative traits identify novel candidate genes. The DGRP lines, sequence data, genotypes, quality scores, phenotypes, and analysis and visualization tools are publicly available. Footnotes ↵ 10 Joint first authors ↵ 11 Senior authors ↵ 16...
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Resource: Impact of genomic structural variation in Drosophila melanogaster based on population-scale sequencing
- Thomas Zichner,
- David A. Garfield,
- Tobias Rausch,
- Adrian M. Stütz,
- Enrico Cannavó,
- Martina Braun,
- Eileen E.M. Furlong,
- and Jan O. Korbel
Genome Res. March 2013 23: 568-579; Published in Advance December 6, 2012, doi:10.1101/gr.142646.112
...the construction of a more comprehensive, accurate SV map (Cridland and Thornton 2010). The DGRP project has recently generated deep-sequence coverage (median coverage = 183) data for a panel of isogenic fly lines. These lines were inbred over 20 generations, yielding a set of isogenic strains distributed across...
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Resource: Genetic dissection of a model complex trait using the Drosophila Synthetic Population Resource
- Elizabeth G. King,
- Chris M. Merkes,
- Casey L. McNeil,
- Steven R. Hoofer,
- Saunak Sen,
- Karl W. Broman,
- Anthony D. Long,
- and Stuart J. Macdonald
Genome Res. August 2012 22: 1558-1566; Published in Advance April 10, 2012, doi:10.1101/gr.134031.111
...of the total segregating variation. As a genetic reference panel freely available to the community (FlyRILs.org) the DSPR allows multiple traits to be assayed Fine mapping QTL in the DSPR Genome Research 1563 www..org in multiple environments, facilitating analyses of pleiotropy, genotype...
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Research: High resolution genomes of multiple Xiphophorus species provide new insights into microevolution, hybrid incompatibility, and epistasis
- Yuan Lu,
- Edward Rice,
- Kang Du,
- Susanne Kneitz,
- Magali Naville,
- Corentin Dechaud,
- Jean-Nicolas Volff,
- Mikki Boswell,
- William Boswell,
- LaDeana Hillier,
- Chad Tomlinson,
- Kremitzki Milin,
- Ronald B. Walter,
- Manfred Schartl,
- and Wesley C. Warren
Genome Res. April 2023 33: 557-571; Published in Advance May 5, 2023, doi:10.1101/gr.277434.122
..., we ran smoove call on each individual sample, then smoove merge to combine all sets of calls from each individual into a merged call set followed by smoove genotype to perform joint genotyping of each sample over the merged call set, and, finally, smoove paste to concatenate the results into a single...
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Perspective: Genetic architecture of quantitative traits in mice, flies, and humans
- Jonathan Flint and
- Trudy F.C. Mackay
Genome Res. May 2009 19: 723-733; doi:10.1101/gr.086660.108
...the joint posterior distribution of all unknowns, including the main and epistatic effects, given the observed data (Yi et al. 2007). Using this approach, Yi and colleagues detected Figure 1. Effect sizes (expressed as odds ratios) in human -wide association studies. Data are from http...

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