by Hassan M. Fathallah-Shaykh, Andrew DeAtkine, Elizabeth Coffee, Elias Khayat, Asim K. Bag, Xiaosi Han, Paula Province Warren, Markus Bredel, John Fiveash, James Markert, Nidhal Bouaynaya, Louis B. Nabors
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by Annette M. McCoy, Samantha K. Beeson, Carl-Johan Rubin, Leif Andersson, Paul Caputo, Sigrid Lykkjen, Alison Moore, Richard J. Piercy, James R. Mickelson, Molly E. McCue
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by Tommy Darrière, Michael Pilsl, Marie-Kerguelen Sarthou, Adrien Chauvier, Titouan Genty, Sylvain Audibert, Christophe Dez, Isabelle Léger-Silvestre, Christophe Normand, Anthony K. Henras, Marta Kwapisz, Olga Calvo, Carlos Fernández-Tornero, Herbert Tschochner, Olivier Gadal
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by Michael Shoujie Sun, Joe Weber, Ariane C. Blattner, Soumya Chaurasia, Christian F. Lehner
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by Arun Durvasula, Sriram Sankararaman
Statistical analyses of genomic data from diverse human populations have demonstrated that archaic hominins, such as Neanderthals and Denisovans, interbred or admixed with the ancestors of present-day humans. Central to these analyses are methods for inferring archaic ancestry along the genomes of present-day individuals (archaic local ancestry). Methods for archaic local ancestry inference rely on the availability of reference genomes from the ancestral archaic populations for accurate inference. Читать дальше...
by David A. Knowles, Gina Bouchard, Sylvia Plevritis
Drug screening studies typically involve assaying the sensitivity of a range of cancer cell lines across an array of anti-cancer therapeutics. Alongside these sensitivity measurements high dimensional molecular characterizations of the cell lines are typically available, including gene expression, copy number variation and genomic mutations. We propose a sparse multitask regression model which learns discriminative latent characteristics... Читать дальше...
by The PLOS Computational Biology Staff
by Le Zhang, Wanyu Bai, Na Yuan, Zhenglin Du
Motivation: Recently, copy number variation (CNV) has gained considerable interest as a type of genomic variation that plays an important role in complex phenotypes and disease susceptibility. Since a number of CNV detection methods have recently been developed, it is necessary to help investigators choose suitable methods for CNV detection depending on their objectives. For this reason, this study compared ten commonly used CNV detection applications... Читать дальше...
by Amber G. F. Griffiths, Ivvet Modinou, Clio Heslop, Charlotte Brand, Aidan Weatherill, Kate Baker, Anna E. Hughes, Jen Lewis, Lee de Mora, Sara Mynott, Katherine E. Roberts, David J. Griffiths
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by Alexander A. Soukas, Ben Zhou
Starvation is among the most ancient of selection pressures, driving evolution of a robust arsenal of starvation survival defenses. In order to survive starvation stress, organisms must be able to curtail anabolic processes during starvation and judiciously activate catabolic pathways. Although the activation of metabolic defenses in response to nutrient deprivation is an obvious component of starvation survival, less appreciated is the importance of the ability... Читать дальше...
by Devin P. Bendixsen, James Collet, Bjørn Østman, Eric J. Hayden
Evolutionary innovations are qualitatively novel traits that emerge through evolution and increase biodiversity. The genetic mechanisms of innovation remain poorly understood. A systems view of innovation requires the analysis of genotype networks—the vast networks of genetic variants that produce the same phenotype. Innovations can occur at the intersection of two different genotype networks. However, the experimental characterization... Читать дальше...