Results 81 to 90 of about 709,139 (287)

Modelling stem cell differentiation related processes—A practical overview for biologists

FEBS Letters, EarlyView.
Stem cell differentiation is complex and difficult to control experimentally. This review introduces suitable computational modelling approaches that can support stem cell research, from mechanistic ODE and abstract models to multiscale and deep learning methods.
Ricco Zeegelaar, Xinqi Yan, Lucas F. Jansen Klomp, Stefano Schivo, Janine N. Post   +4 more
wiley   +1 more source

Comparing Variant Call Files for Performance Benchmarking of Next-Generation Sequencing Variant Calling Pipelines [PDF]

, 2015
ABSTRACT Summary To evaluate and compare the performance of variant calling methods and their confidence scores, comparisons between a test call set and a “gold standard” need to be carried out ...
Cleary, John G., Braithwaite, Ross, Gaastra, Kurt, Hilbush, Brian S, Inglis, Stuart, Irvine, Sean A, Jackson, Alan, Littin, Richard, Rathod, Mehul, Ware, David, Zook, Justin M., Trigg, Len, De La Vega, Francisco M.   +12 more
openaire   +1 more source

Reconstructing enzyme evolution by protein engineering

FEBS Letters, EarlyView.
Natural enzyme evolution can be retraced by protein engineering methods such as directed evolution, rational design, and ancestral sequence reconstruction. These approaches reveal how enzymes emerged from ligand‐binding scaffolds, developed varying substrate preferences, formed oligomeric complexes, adapted to environmental changes, and evolved novel ...
Lukas Drexler, Markus R. Busch, Reinhard Sterner   +2 more
wiley   +1 more source

Somatic variant calling benchmarking

, 2017
The increased number of sequenced cancer genomes since the completion of the human genome project, and the importance of correctly identifying somatic mutations, which can influence treatment or prognosis, is driving forward the development of novel somatic variant calling tools (somatic callers).
Mijalković, Sanja, Domazet, Milan, Makragic, Aleksandar   +2 more
openaire   +1 more source

Conserved binding mode but diverse interfaces of MreC‐PBP2 interactions

FEBS Letters, EarlyView.
The crystal structure of abMreC reveals a conserved two β‐barrel architecture and provides structural insights into its role within the bacterial elongasome. The abMreC–abPBP2 complex model identifies the molecular basis of MreC‐mediated PBP2 recognition, contributing to the regulation of peptidoglycan synthesis.
Hyunseok Jang, Hyo Been Jin, Chang Min Kim, So Yeon Lee, Hyun Ho Park   +4 more
wiley   +1 more source

Improving bioinformatic pipelines for exome variant calling [PDF]

Genome Medicine, 2012
Exome sequencing analysis is a cost-effective approach for identifying variants in coding regions. However, recognizing the relevant single nucleotide variants, small insertions and deletions remains a challenge for many researchers and diagnostic laboratories typically do not have access to the bioinformatic analysis pipelines necessary for clinical ...
openaire   +2 more sources

Local read haplotagging enables accurate long-read small variant calling

Nature Communications
Long-read sequencing technology has enabled variant detection in difficult-to-map regions of the genome and enabled rapid genetic diagnosis in clinical settings. Rapidly evolving third-generation sequencing platforms like Pacific Biosciences (PacBio) and
Alexey Kolesnikov, Daniel Cook, Maria Nattestad, Lucas Brambrink, Brandy McNulty, John Gorzynski, Sneha Goenka, Euan A. Ashley, Miten Jain, Karen H. Miga, Benedict Paten, Pi-Chuan Chang, Andrew Carroll, Kishwar Shafin   +13 more
doaj   +1 more source

Microbiome‐blood–brain barrier interactions in aging — mechanisms and therapeutic potential

FEBS Letters, EarlyView.
Aging reshapes the gut microbiome (↓SCFA‐producing commensals; ↑pro‐inflammatory outputs), shifting circulating metabolites (↓SCFAs; ↑LPS, ↑TMAO, ↑PAA) that act at the BBB to increase nonspecific transcytosis, alter transport, and promote astrocyte reactivity, heightening brain vulnerability.
Daniel Cuervo‐Zanatta, Hari Baskar Balasubramanian, Amir Pasokh, Marietta Zille   +3 more
wiley   +1 more source

A synthetic-diploid benchmark for accurate variant-calling evaluation [PDF]

Nature Methods, 2017
Constructed from the consensus of multiple variant callers based on short-read data, existing benchmark datasets for evaluating variant calling accuracy are biased toward easy regions accessible by known algorithms. We derived a new benchmark dataset from the de novo PacBio assemblies of two human ...
Heng Li, Jonathan M. Bloom, Yossi Farjoun, Mark Fleharty, Laura Gauthier, Benjamin Neale, Daniel MacArthur   +6 more
openaire   +3 more sources

Structure‐forward targeting of claudins with synthetic binders

FEBS Letters, EarlyView.
Claudins form the paracellular barriers between epithelial and endothelial tissues at tight junctions and are targets for molecular binders with the goal of modulating barrier permeability. Claudin‐binding molecules are relevant in drug delivery or in altering claudin interactions with disease‐causing proteins.
Alex J. Vecchio
wiley   +1 more source