K
Konrad Scheffler
Researcher at Illumina
Publications - 55
Citations - 6860
Konrad Scheffler is an academic researcher from Illumina. The author has contributed to research in topics: Selection (genetic algorithm) & Phylogenetic tree. The author has an hindex of 27, co-authored 53 publications receiving 5192 citations. Previous affiliations of Konrad Scheffler include University of Cape Town & University of California, San Diego.
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Journal ArticleDOI
Detecting individual sites subject to episodic diversifying selection.
Ben Murrell,Ben Murrell,Joel O. Wertheim,Sasha Moola,Thomas Weighill,Konrad Scheffler,Konrad Scheffler,Sergei L. Kosakovsky Pond +7 more
TL;DR: It is found that episodic selection is widespread and it is concluded that the number of sites experiencing positive selection may have been vastly underestimated.
Journal ArticleDOI
FUBAR : A Fast, Unconstrained Bayesian AppRoximation for inferring selection
Ben Murrell,Sasha Moola,Sasha Moola,Amandla Mabona,Amandla Mabona,Thomas Weighill,Daniel J. Sheward,Sergei L. Kosakovsky Pond,Konrad Scheffler,Konrad Scheffler +9 more
TL;DR: This work presents an approximate hierarchical Bayesian method using a Markov chain Monte Carlo (MCMC) routine that ensures robustness against model misspecification by averaging over a large number of predefined site classes, and leaves the distribution of selection parameters essentially unconstrained.
Journal ArticleDOI
Strelka2: fast and accurate calling of germline and somatic variants.
Sangtae Kim,Konrad Scheffler,Aaron L. Halpern,Mitchell A. Bekritsky,Eunho Noh,Morten Källberg,Xiaoyu Chen,Yeonbin Kim,Doruk Beyter,Doruk Beyter,Peter Krusche,Christopher T. Saunders +11 more
TL;DR: Strelka2 introduces a novel mixture-model-based estimation of insertion/deletion error parameters from each sample, an efficient tiered haplotype-modeling strategy, and a normal sample contamination model to improve liquid tumor analysis.
Journal ArticleDOI
Less is More: an Adaptive Branch-Site Random Effects Model for Efficient Detection of Episodic Diversifying Selection
M. D. Smith,Joel O. Wertheim,Steven Weaver,Ben Murrell,Konrad Scheffler,Sergei L. Kosakovsky Pond +5 more
TL;DR: Adaptive branch-site random effects likelihood (aBSREL), whose key innovation is variable parametric complexity chosen with an information theoretic criterion, delivers statistical performance matching or exceeding best-in-class existing approaches, while running an order of magnitude faster.
Journal ArticleDOI
RELAX: Detecting Relaxed Selection in a Phylogenetic Framework
Joel O. Wertheim,Ben Murrell,M. D. Smith,Sergei L. Kosakovsky Pond,Konrad Scheffler,Konrad Scheffler +5 more
TL;DR: This work presents a general hypothesis testing framework (RELAX) for detecting relaxed selection in a codon-based phylogenetic framework and demonstrates the power of RELAX in a variety of biological scenarios where relaxation of selection has been hypothesized or demonstrated previously.