Next-generation sequencing: big data meets high performance computing
B Schmidt, A Hildebrandt - Drug discovery today, 2017 - Elsevier
Highlights•Analysis of massive NGS datasets poses difficult computational challenges.•Big
data algorithms are often adapted for NGS analysis.•HPC becomes pivotal as NGS …
data algorithms are often adapted for NGS analysis.•HPC becomes pivotal as NGS …
Mash: fast genome and metagenome distance estimation using MinHash
Mash extends the MinHash dimensionality-reduction technique to include a pairwise
mutation distance and P value significance test, enabling the efficient clustering and search …
mutation distance and P value significance test, enabling the efficient clustering and search …
Fecal microbial transplant effect on clinical outcomes and fecal microbiome in active Crohn's disease
DL Suskind, MJ Brittnacher, G Wahbeh… - Inflammatory bowel …, 2015 - academic.oup.com
Background Crohn's disease (CD) is a chronic idiopathic inflammatory intestinal disorder
associated with fecal dysbiosis. Fecal microbial transplant (FMT) is a potential therapeutic …
associated with fecal dysbiosis. Fecal microbial transplant (FMT) is a potential therapeutic …
Impact of fire on active layer and permafrost microbial communities and metagenomes in an upland Alaskan boreal forest
Permafrost soils are large reservoirs of potentially labile carbon (C). Understanding the
dynamics of C release from these soils requires us to account for the impact of wildfires …
dynamics of C release from these soils requires us to account for the impact of wildfires …
[图书][B] Genome-scale algorithm design
High-throughput sequencing has revolutionised the field of biological sequence analysis. Its
application has enabled researchers to address important biological questions, often for the …
application has enabled researchers to address important biological questions, often for the …
The ocean sampling day consortium
A Kopf, M Bicak, R Kottmann, J Schnetzer, I Kostadinov… - Gigascience, 2015 - Springer
Abstract Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial
Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine …
Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine …
Environmental characteristics of Agulhas rings affect interocean plankton transport
Agulhas rings provide the principal route for ocean waters to circulate from the Indo-Pacific
to the Atlantic basin. Their influence on global ocean circulation is well known, but their role …
to the Atlantic basin. Their influence on global ocean circulation is well known, but their role …
Comparison of microbiome samples: methods and computational challenges
The study of microbial communities crucially relies on the comparison of metagenomic next-
generation sequencing data sets, for which several methods have been designed in recent …
generation sequencing data sets, for which several methods have been designed in recent …
Multiple comparative metagenomics using multiset k-mer counting
Background Large scale metagenomic projects aim to extract biodiversity knowledge
between different environmental conditions. Current methods for comparing microbial …
between different environmental conditions. Current methods for comparing microbial …
Small Searchable κ-Spectra via Subset Rank Queries on the Spectral Burrows-Wheeler Transform
The κ-spectrum of a string is the set of all distinct substrings of length κ occurring in the
string. This is a lossy but computationally convenient representation of the information in the …
string. This is a lossy but computationally convenient representation of the information in the …