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Method: Bayesian inference of sample-specific coexpression networks
- Enakshi Saha,
- Viola Fanfani,
- Panagiotis Mandros,
- Marouen Ben Guebila,
- Jonas Fischer,
- Katherine H. Shutta,
- Dawn L. DeMeo,
- Camila M. Lopes-Ramos,
- and John Quackenbush
Genome Res. September 2024 34: 1397-1410; Published in Advance August 12, 2024, doi:10.1101/gr.279117.124
...whether genetically perturbed samples showed stronger perturbations in the edges connected to the knocked-out TF. For each growth medium and each TF, we selected only the edges with the highest weights and tested whether these edges in the wild-type were significantly different compared to the perturbed...
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Method: Optimized sample selection for cost-efficient long-read population sequencing
- T. Rhyker Ranallo-Benavidez,
- Zachary Lemmon,
- Sebastian Soyk,
- Sergey Aganezov,
- William J. Salerno,
- Rajiv C. McCoy,
- Zachary B. Lippman,
- Michael C. Schatz,
- and Fritz J. Sedlazeck
Genome Res. May 2021 31: 910-918; Published in Advance April 2, 2021, doi:10.1101/gr.264879.120
..., and 3024 s from the 3000 Rice Genomes Project and show the rankings it computes are more representative than alternative naive strategies. When selecting an optimal subset of 100 samples in these cohorts, SVCollector identifies individuals from every subpopulation, whereas naive methods yield an unbalanced...
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Research: Evolutionarily new genes in humans with disease phenotypes reveal functional enrichment patterns shaped by adaptive innovation and sexual selection
- Jian-Hai Chen,
- Patrick Landback,
- Deanna Arsala,
- Alexander Guzzetta,
- Shengqian Xia,
- Jared Atlas,
- Dylan Sosa,
- Yong E. Zhang,
- Jingqiu Cheng,
- Bairong Shen,
- and Manyuan Long
Genome Res. March 2025 35: 379-392; Published in Advance February 14, 2025, doi:10.1101/gr.279498.124
...million years). Despite this stable pace, we observe distinct patterns in phenotypic enrichment, pleiotropy, and selective pressures across gene ages. Young genes show significant enrichment in diseases related to the male reproductive system, indicating strong sexual selection. Young genes also exhibit...
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Method: Inferring the mode and strength of ongoing selection
- Gustavo V. Barroso and
- Kirk E. Lohmueller
Genome Res. April 2023 33: 632-643; Published in Advance April 13, 2023, doi:10.1101/gr.276386.121
...number of ancient samples is not always available from the relevant population. Finally, a different approach to find signatures of ongoing selection is to look for allele frequency changes with the age of present-day individuals (Mostafavi et al. 2017) or transmission distortions in family trios (Meyer...
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Research: Meta-analysis of human and mouse ALS astrocytes reveals multi-omic signatures of inflammatory reactive states
- Oliver J. Ziff,
- Benjamin E. Clarke,
- Doaa M. Taha,
- Hamish Crerar,
- Nicholas M. Luscombe,
- and Rickie Patani
Genome Res. January 2022 32: 71-84; Published in Advance December 28, 2021, doi:10.1101/gr.275939.121
....Amyotrophic lateral sclerosis (ALS) is characterized by the selective degeneration of motor neurons and the presence of TARDBP pathology in >97% of cases (Neumann et al. 2006; Rohan et al. 2014; Al-Chalabi et al. 2017). Mutations in approximately 30 genes are causative for ALS, including C9orf72, SOD1, FUS, TARDBP...
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Method: A general calculus of fitness landscapes finds genes under selection in cancers
- Teng-Kuei Hsu,
- Jennifer Asmussen,
- Amanda Koire,
- Byung-Kwon Choi,
- Mayur A. Gadhikar,
- Eunna Huh,
- Chih-Hsu Lin,
- Daniel M. Konecki,
- Young Won Kim,
- Curtis R. Pickering,
- Marek Kimmel,
- Lawrence A. Donehower,
- Mitchell J. Frederick,
- Jeffrey N. Myers,
- Panagiotis Katsonis,
- and Olivier Lichtarge
Genome Res. May 2022 32: 916-929; Published in Advance March 17, 2022, doi:10.1101/gr.275811.121
...as we reduced the number of test population exomes by down-sampling. First, we defined a target set of 58 genes, as those identified by CI using all 7916 test exomes and also reported as cancer associated by at least four of five reference sources (see Supplemental Table S4; Davoli et al. 2013; Kandoth...
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Research: Evolution and genomic signatures of spontaneous somatic mutation in Drosophila intestinal stem cells
- Nick Riddiford,
- Katarzyna Siudeja,
- Marius van den Beek,
- Benjamin Boumard,
- and Allison J. Bardin
Genome Res. August 2021 31: 1419-1432; Published in Advance June 24, 2021, doi:10.1101/gr.268441.120
.... This results in a de novo TE signature. (G) A schematic showing genomic regions before (top) and after (bottom) the integration of a fragment of a viral in the context of a complex rearrangement detected in sample P31. Although our sequencing data support this configuration, it is possible that alternative...
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Research: Crossover-active regions of the wheat genome are distinguished by DMC1, the chromosome axis, H3K27me3, and signatures of adaptation
- Andrew J. Tock,
- Daniel M. Holland,
- Wei Jiang,
- Kim Osman,
- Eugenio Sanchez-Moran,
- James D. Higgins,
- Keith J. Edwards,
- Cristobal Uauy,
- F. Chris H. Franklin,
- and Ian R. Henderson
Genome Res. September 2021 31: 1614-1628; Published in Advance August 23, 2021, doi:10.1101/gr.273672.120
...to adaptive traits, we investigated connections between DMC1, ASY1, historical crossovers, nucleotide diversity, and signatures of selection. We estimated historical recombination using per-gene RM divided by gene width. RM is the minimum number of crossovers in the history of a sample, based on the four...
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Method: Identifying loci under positive selection in complex population histories
- Alba Refoyo-Martínez,
- Rute R. da Fonseca,
- Katrín Halldórsdóttir,
- Einar Árnason,
- Thomas Mailund,
- and Fernando Racimo
Genome Res. September 2019 29: 1506-1520; Published in Advance July 30, 2019, doi:10.1101/gr.246777.118
...to detect positive selection along sequenced s, however, use simplified representations of past histories as models of genetic drift. Here, we present the first method that can detect signatures of strong local adaptation across the using arbitrarily complex admixture graphs, which are typically used...
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Research: Immune signatures correlate with L1 retrotransposition in gastrointestinal cancers
- Hyunchul Jung,
- Jung Kyoon Choi,
- and Eunjung Alice Lee
Genome Res. August 2018 28: 1136-1146; Published in Advance July 3, 2018, doi:10.1101/gr.231837.117
...diverse immune-stimulatory cell types.Characterization of cancer subgroups with differential immune activityBased on the 49 L1-associated immune pathways in 112 cancer samples, we identified two distinct cancer subgroups with different immune signatures for stomach/esophageal cancer (SE; SE-High and SE...
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