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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
...and so fail to fully capture population heterogeneity. Bayesian optimized networks obtained by assimilating omic data (BONOBO) is a scalable Bayesian model for deriving individual sample-specific coexpression matrices that recognizes variations in molecular interactions across individuals. For each...
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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
...may result in misleading inference if there have been substantial fluctuations in selective pressures during the history of the population under study. Although progress has been recently made in inferring temporal trajectories of selection using ancient DNA samples (Mathieson 2020), a sufficient...
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Research: Mapping genome variation of SARS-CoV-2 worldwide highlights the impact of COVID-19 super-spreaders
- Alberto Gómez-Carballa,
- Xabier Bello,
- Jacobo Pardo-Seco,
- Federico Martinón-Torres,
- and Antonio Salas
Genome Res. October 2020 30: 1434-1448; Published in Advance September 2, 2020, doi:10.1101/gr.266221.120
...haplotypes in the database (as a proxy for the life-span period of a SARS-CoV-2 ) worldwide and in various countries (by way of example, we only included those data sets having high sample sizes).SARS-CoV-2 weighted mean substitution rate, as inferred from the ML tree, is 5.42 × 10−4 substitutions per site...
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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
...dramatic population declines perhaps due to the extreme loss of wolf habitat with Late Pleistocene glaciations in the Tibetan Plateau. These findings suggest the recent worldwide history of wolves is complex and needs to be assessed with a fuller sample of s from throughout the historic range...
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Method: A probabilistic method for testing and estimating selection differences between populations
- Yungang He,
- Minxian Wang,
- Xin Huang,
- Ran Li,
- Hongyang Xu,
- Shuhua Xu,
- and Li Jin
Genome Res. December 2015 25: 1903-1909; Published in Advance October 13, 2015, doi:10.1101/gr.192336.115
.... Our approach supplies estimates and their confidence intervals for differences in selection coefficients. To demonstrate the capability of our approach, we conducted statistical hypothesis testing on a whole- data set including samples of Han Chinese and Tibetan populations. The results regarding...
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Research: Genome-wide signals of positive selection in human evolution
- David Enard,
- Philipp W. Messer,
- and Dmitri A. Petrov
Genome Res. June 2014 24: 885-895; Published in Advance March 11, 2014, doi:10.1101/gr.164822.113
...#2;3; European, P = 23 10#2;4). Even inAfrica,where the signal of positive selection is consistently weaker in both the near-vs-far and the functional-vs-nonfunctional tests, the probability of both observed decreasing by chance is <1%. In European and Asian populations, the same probability is <0.1%. Taken...
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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
...Consortium 2015) and a SNP capture data set (Human Origins) (Patterson et al. 2012) from different populations sampled around the world (Fig. 4) and obtained the top candidate regions from the scan (P-value < 10−7). Many of these have been identified in previous world-wide positive selection scans, and some...
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Research: Adaptive selection of an incretin gene in Eurasian populations
- Chia Lin Chang,
- James J. Cai,
- Chiening Lo,
- Jorge Amigo,
- Jae-Il Park,
- and Sheau Yu Teddy Hsu
Genome Res. January 2011 21: 21-32; Published in Advance October 26, 2010, doi:10.1101/gr.110593.110
...Adaptive selection of an incretin gene in Eurasian populations Chia Lin Chang 1 , James J. Cai 2 , 3 , Chiening Lo 4 , Jorge Amigo 5 , Jae-Il Park 6 and Sheau Yu Teddy Hsu 7 , 8 1 Department of Obstetrics...
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LETTER: The portability of tagSNPs across populations: A worldwide survey
- Anna González-Neira,
- Xiayi Ke,
- Oscar Lao,
- Francesc Calafell,
- Arcadi Navarro,
- David Comas,
- Howard Cann,
- Suzannah Bumpstead,
- Jilur Ghori,
- Sarah Hunt,
- Panos Deloukas,
- Ian Dunham,
- Lon R. Cardon,
- and Jaume Bertranpetit
Genome Res. March 2006 16: 323-330; Published in Advance February 8, 2006, doi:10.1101/gr.4138406
...cases, samples from only two or three populations are studied (usually European, Asian, and African), even though previous worldwide surveys of small genomic regions have shown that haplotype composition, LD structure, and LD decay with physical distance are heterogeneous across populations ( Pritchard...
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Research: Signatures of positive selection apparent in a small sample of human exomes
- Jacob A. Tennessen,
- Jennifer Madeoy,
- and Joshua M. Akey
Genome Res. October 2010 20: 1327-1334; Published in Advance August 6, 2010, doi:10.1101/gr.106161.110
...or temporally complex modes of selection may not leave a clear signal. One well-documented example of positive selection in humans, LCT (Bersaglieri et al. 2004), is excluded as a selection candidate by ourmethods. The unknown specific ancestry of our European samples might include populations where LCT...

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