Piercing the dark matter: bioinformatics of long-range sequencing and mapping
Several new genomics technologies have become available that offer long-read sequencing
or long-range mapping with higher throughput and higher resolution analysis than ever …
or long-range mapping with higher throughput and higher resolution analysis than ever …
Genome-based prediction of bacterial antibiotic resistance
Clinical microbiology has long relied on growing bacteria in culture to determine
antimicrobial susceptibility profiles, but the use of whole-genome sequencing for antibiotic …
antimicrobial susceptibility profiles, but the use of whole-genome sequencing for antibiotic …
ARCS: scaffolding genome drafts with linked reads
Motivation Sequencing of human genomes is now routine, and assembly of shotgun reads is
increasingly feasible. However, assemblies often fail to inform about chromosome-scale …
increasingly feasible. However, assemblies often fail to inform about chromosome-scale …
Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genomes assembled from metagenomes
Metagenomic samples are snapshots of complex ecosystems at work. They comprise
hundreds of known and unknown species, contain multiple strain variants and vary greatly …
hundreds of known and unknown species, contain multiple strain variants and vary greatly …
Tigmint: correcting assembly errors using linked reads from large molecules
Background Genome sequencing yields the sequence of many short snippets of DNA
(reads) from a genome. Genome assembly attempts to reconstruct the original genome from …
(reads) from a genome. Genome assembly attempts to reconstruct the original genome from …
Longitudinal linked-read sequencing reveals ecological and evolutionary responses of a human gut microbiome during antibiotic treatment
Gut microbial communities can respond to antibiotic perturbations by rapidly altering their
taxonomic and functional composition. However, little is known about the strain-level …
taxonomic and functional composition. However, little is known about the strain-level …
ARKS: chromosome-scale scaffolding of human genome drafts with linked read kmers
Background The long-range sequencing information captured by linked reads, such as
those available from 10× Genomics (10xG), helps resolve genome sequence repeats, and …
those available from 10× Genomics (10xG), helps resolve genome sequence repeats, and …
Advances in decoding axolotl limb regeneration
BJ Haas, JL Whited - Trends in Genetics, 2017 - cell.com
Humans and other mammals are limited in their natural abilities to regenerate lost body
parts. By contrast, many salamanders are highly regenerative and can spontaneously …
parts. By contrast, many salamanders are highly regenerative and can spontaneously …
A comprehensive review of scaffolding methods in genome assembly
J Luo, Y Wei, M Lyu, Z Wu, X Liu, H Luo… - Briefings in …, 2021 - academic.oup.com
In the field of genome assembly, scaffolding methods make it possible to obtain a more
complete and contiguous reference genome, which is the cornerstone of genomic research …
complete and contiguous reference genome, which is the cornerstone of genomic research …
Biological computation and computational biology: survey, challenges, and discussion
Biological computation involves the design and development of computational techniques
inspired by natural biota. On the other hand, computational biology involves the …
inspired by natural biota. On the other hand, computational biology involves the …