Results 1 to 10 of about 233,149 (149)
The SoftWipe tool and benchmark for assessing coding standards adherence of scientific software
Scientific Reports, 2021 Scientific software from all areas of scientific research is pivotal to obtaining novel insights. Yet the coding standards adherence of scientific software is rarely assessed, even though it might lead to incorrect scientific results in the worst case ...
Adrian Zapletal +3 more
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Root Digger: a root placement program for phylogenetic trees
BMC Bioinformatics, 2021 Background In phylogenetic analysis, it is common to infer unrooted trees. However, knowing the root location is desirable for downstream analyses and interpretation.
Ben Bettisworth, Alexandros Stamatakis
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CellPhy: accurate and fast probabilistic inference of single-cell phylogenies from scDNA-seq data
Genome Biology, 2022 We introduce CellPhy, a maximum likelihood framework for inferring phylogenetic trees from somatic single-cell single-nucleotide variants. CellPhy leverages a finite-site Markov genotype model with 16 diploid states and considers amplification error and ...
Alexey Kozlov +3 more
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Phylogeography by diffusion on a sphere: whole world phylogeography [PDF]
PeerJ, 2016 Background Techniques for reconstructing geographical history along a phylogeny can answer many questions of interest about the geographical origins of species. Bayesian models based on the assumption that taxa move through a diffusion process have found
Remco Bouckaert
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Spatial heterogeneity analysis of the human virome with Taylor’s power law
Computational and Structural Biotechnology Journal, 2021 Spatial heterogeneity is a fundamental characteristic of organisms from viruses to humans. Measuring heterogeneity is challenging, especially for naked-eye invisible viruses, but of obvious importance.
Zhanshan (Sam) Ma
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Age-related late-onset disease heritability patterns and implications for genome-wide association studies [PDF]
PeerJ, 2019 Genome-wide association studies (GWASs) and other computational biology techniques are gradually discovering the causal gene variants that contribute to late-onset human diseases.
Roman Teo Oliynyk
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BMC Evolutionary Biology, 2017 Background The impact of predator-prey interactions on the evolution of many marine invertebrates is poorly understood. Since barriers to genetic exchange are less obvious in the marine realm than in terrestrial or freshwater systems, non-allopatric ...
Jessica A. Goodheart +4 more
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Nature Communications, 2019 Ecological speciation can proceed rapidly, but the origin of genetic variation facilitating it has remained elusive. Here, the authors show that secondary contact and introgression between deeply diverged lineages of stickleback fish facilitated rapid ...
David A. Marques +4 more
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The evolution of emergent computation. [PDF]
Proceedings of the National Academy of Sciences, 1995 A simple evolutionary process can discover sophisticated methods for emergent information processing in decentralized spatially extended systems. The mechanisms underlying the resulting emergent computation are explicated by a technique for analyzing particle-based logic embedded in pattern-forming systems.
Crutchfield, James P., Mitchell, Melanie
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Immunosuppressive niche engineering at the onset of human colorectal cancer
Nature Communications, 2022 Integration of mathematical modeling, ecological analyses of patient biopsies, and neoantigen heterogeneity suggests recruitment of immunosuppressive cells is key to initializing transformation from adenoma to carcinoma in human colorectal cancer.
Chandler D. Gatenbee +17 more
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