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Research: Degrees of convergent evolution in rodent adaptations to arid environments
- Domitille Chalopin,
- Carine Rey,
- Jeremy Ganofsky,
- Juliana Blin,
- Pascale Chevret,
- Marion Mouginot,
- Laurent Guéguen,
- Bastien Boussau,
- Sophie Pantalacci,
- and Marie Sémon
Genome Res. March 2026 36: 472-486; Published in Advance January 21, 2026, doi:10.1101/gr.280089.124
...and cell-type composition (abundance). Here, different species may exhibit divergent kidney structures as part of their adaptation to arid environments. We investigated whether tissue composition distinguishes species living in mesic and arid environments by deconvoluting our bulk RNA-seq data with MuSiC...
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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
...Cancer Gene Census (Forbes et al. 2017) and candidate genes suggested by 20/20 (Vogelstein et al. 2013), MutSigCV (Lawrence et al. 2014), TUSON (Davoli et al. 2013), and MuSiC (Kandoth et al. 2013). Of the 465 genes from these combined sources, CI recovered 147 (P-value = 1 × 10−124, hypergeometric test...
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Resource: Maftools: efficient and comprehensive analysis of somatic variants in cancer
- Anand Mayakonda,
- De-Chen Lin,
- Yassen Assenov,
- Christoph Plass,
- and H. Phillip Koeffler
Genome Res. November 2018 28: 1747-1756; Published in Advance October 19, 2018, doi:10.1101/gr.239244.118
...are visualized as forest plots or frequency bar plots (Figs. 4A, 5E,F).Pfam domain summarizationInspired by the Pfam annotation module of MuSiC, we implemented pfamDomains function to identify and group mutations by affected protein domains. However, the approach for grouping mutations is much simpler. MuSiC...
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Research: Exome sequencing of lymphomas from three dog breeds reveals somatic mutation patterns reflecting genetic background
- Ingegerd Elvers,
- Jason Turner-Maier,
- Ross Swofford,
- Michele Koltookian,
- Jeremy Johnson,
- Chip Stewart,
- Cheng-Zhong Zhang,
- Steven E. Schumacher,
- Rameen Beroukhim,
- Mara Rosenberg,
- Rachael Thomas,
- Evan Mauceli,
- Gad Getz,
- Federica Di Palma,
- Jaime F. Modiano,
- Matthew Breen,
- Kerstin Lindblad-Toh,
- and Jessica Alföldi
Genome Res. November 2015 25: 1634-1645; Published in Advance September 16, 2015, doi:10.1101/gr.194449.115
...that the sequencing was deep enough to comprehensively identify mutations and use these for comparison between breeds and tumor types. The nonsilent coding mutations, around 18 per sample (Fig. 1; Supplemental Table S1), were used to identify significantly mutated genes using the Genome MuSiC tool (Dees et al. 2012...
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