Results 101 to 110 of about 709,139 (287)

Evaluating variant calling best practices

, 2020
: Analyzing human DNA sequence data allows researchers to identify variants associated with disease, reconstruct the demographic histories of human populations, and further understand the structure and function of the genome.

core  

Benchmarking reveals superiority of deep learning variant callers on bacterial nanopore sequence data

eLife
Variant calling is fundamental in bacterial genomics, underpinning the identification of disease transmission clusters, the construction of phylogenetic trees, and antimicrobial resistance detection.
Michael B Hall, Ryan R Wick, Louise M Judd, An N Nguyen, Eike J Steinig, Ouli Xie, Mark Davies, Torsten Seemann, Timothy P Stinear, Lachlan Coin   +9 more
doaj   +1 more source

From junk to function — How weak selection in eukaryotes builds new parts and drives genomic complexity

FEBS Letters, EarlyView.
How do genomes gain new functional parts? In eukaryotes, which tend to evolve under weak selection, much of the genome is junk. Palazzo and Qiu borrow the logic of Markov chains to show how non‐functional DNA becomes functional through the appearance of intermediate states, which arise due to epistasis, buffering, and biochemical messiness, allowing ...
Alexander F. Palazzo, Yi Qiu
wiley   +1 more source

The Shewanella oneidensis Fic enzyme SoFic targets the switch‐I region of EF‐Tu for AMPylation

FEBS Letters, EarlyView.
Fic enzymes mediate diverse post‐translational modifications across all domains of life, including AMPylation. Prokaryotic EF‐Tu can be AMPylated and deAMPylated by the conserved Fic enzyme SoFic. Structural and biochemical approaches were used to characterize the effect of AMPylation on EF‐Tu, SoFic's enzymatic activities, and the enzyme‐target ...
Svenja Runge, Vivian Pogenberg, Alexander Baumgart, Bente Siebels, Hartmut Schlüter, Michael Hecht‐Bucher, Aymelt Itzen   +6 more
wiley   +1 more source

Benchmarking variant calling tools for NGS data

, 2017
Next-generation sequencing (NGS) has revolutionized the application of personalized medicine. Already, sequencing results influence diagnosis, prognosis and even therapy. However, for the application of NGS in clinical routine, it is most essential to deal with valid results.
Sandmann, Sarah, Graaf, Aniek De, Karimi, Mohsen, Reijden, Bert Van Der, Hellström-Lindberg, Eva, Jansen, Joop, Dugas, Martin   +6 more
openaire   +1 more source

Identification and validation of loss of function variants in clinical contexts

Molecular Genetics & Genomic Medicine, 2014
The choice of an appropriate variant calling pipeline for exome sequencing data is becoming increasingly more important in translational medicine projects and clinical contexts. Within GOSgene, which facilitates genetic analysis as part of a joint effort
Francesco Lescai, Elena Marasco, Chiara Bacchelli, Philip Stanier, Vilma Mantovani, Philip Beales   +5 more
doaj   +1 more source

IntroMap: a signal analysis based method for the detection of genomic introgressions

BMC Genetics, 2017
Background Breeding programs often rely on marker-assisted tests or variant calling of next generation sequence (NGS) data to identify regions of genomic introgression arising from the hybridization of two plant species. In this paper we present IntroMap,
Daniel J. Shea, Motoki Shimizu, Namiko Nishida, Eigo Fukai, Takashi Abe, Ryo Fujimoto, Keiichi Okazaki   +6 more
doaj   +1 more source

Chiral separation of chloroalkanes with the chromatographic column onboard Martian rovers

FEBS Letters, EarlyView.
Computer image of the Rosalind Franklin Rover of ESA's ExoMars mission. ExoMars is scheduled to land on planet Mars in Oxia Planum in 2029. This area represents an interesting spot to look for biosignatures. Investigations of ExoMars include measurement on molecular chirality. We show that chiral chloroalkanes, that have been identified on Mars, can be
Asma Merzougui, Agnes Banreti, Armelle L. Ernst, Guillaume Leseigneur, Uwe J. Meierhenrich   +4 more
wiley   +1 more source

Quantitative Analysis of Pseudogene-Associated Errors During Germline Variant Calling. [PDF]

Int J Mol Sci
A pseudogene is a non-functional copy of a protein-coding gene. Processed pseudogenes, which are created by the reverse transcription of mRNA and subsequent integration of the resulting cDNA into the genome, being a major pseudogene class, represent a ...
Podvalnyi A, Kopernik A, Sayganova M, Woroncow M, Zobkova G, Smirnova A, Esibov A, Deviatkin A, Volchkov P, Albert E.   +9 more
europepmc   +2 more sources

RNA‐related functions of BRCA2 in transcription, replication, and genome stability

FEBS Letters, EarlyView.
Beyond its role in homologous recombination, BRCA2 regulates R‐loop homeostasis, DNA–RNA hybrid resolution, RNA polymerase II dynamics, and transcriptional activation. Disruption of any of these functions can contribute to genome instability, inflammatory signaling, and tumorigenesis. BRCA2 is a central tumor suppressor protein best known for its roles
Lucia Alvaro‐Aranda, Sreerama Chaitanya Sridhara, Aura Carreira   +2 more
wiley   +1 more source