Diversity within species: interpreting strains in microbiomes
Studying within-species variation has traditionally been limited to culturable bacterial isolates
and low-resolution microbial community fingerprinting. Metagenomic sequencing and …
and low-resolution microbial community fingerprinting. Metagenomic sequencing and …
glycyrrhizin as a potential treatment for chronic hepatitis C.
Chronic hepatitis C is a slowly progressive liver disease that may evolve into cirrhosis with
its potential complications of liver failure or hepatocellular carcinoma. Current therapy with …
its potential complications of liver failure or hepatocellular carcinoma. Current therapy with …
[HTML][HTML] A faecal microbiota signature with high specificity for pancreatic cancer
…, M Márquez, X Molero, A Orakov, T Van Rossum… - Gut, 2022 - gut.bmj.com
Background Recent evidence suggests a role for the microbiome in pancreatic ductal
adenocarcinoma (PDAC) aetiology and progression. Objective To explore the faecal and salivary …
adenocarcinoma (PDAC) aetiology and progression. Objective To explore the faecal and salivary …
Towards the biogeography of prokaryotic genes
Microbial genes encode the majority of the functional repertoire of life on earth. However,
despite increasing efforts in metagenomic sequencing of various habitats 1 , 2 – 3 , little is …
despite increasing efforts in metagenomic sequencing of various habitats 1 , 2 – 3 , little is …
Pseudomonas Genome Database: facilitating user-friendly, comprehensive comparisons of microbial genomes
GL Winsor, T Van Rossum, R Lo, B Khaira… - Nucleic acids …, 2009 - academic.oup.com
Pseudomonas aeruginosa is a well-studied opportunistic pathogen that is particularly known
for its intrinsic antimicrobial resistance, diverse metabolic capacity, and its ability to cause …
for its intrinsic antimicrobial resistance, diverse metabolic capacity, and its ability to cause …
Reporter‐based screening and selection of enzymes
T van Rossum, SWM Kengen… - The FEBS …, 2013 - Wiley Online Library
The biotech industry is continuously seeking for new or improved biocatalysts. The success
of these efforts is often hampered by the lack of an efficient screening assay. Thus, to be able …
of these efforts is often hampered by the lack of an efficient screening assay. Thus, to be able …
The Burkholderia Genome Database: facilitating flexible queries and comparative analyses
GL Winsor, B Khaira, T Van Rossum, R Lo… - …, 2008 - academic.oup.com
As the genome sequences of multiple strains of a given bacterial species are obtained, more
generalized bacterial genome databases may be complemented by databases that are …
generalized bacterial genome databases may be complemented by databases that are …
[HTML][HTML] Drivers and determinants of strain dynamics following fecal microbiota transplantation
…, R Thielemann, M von Stetten, T Van Rossum… - Nature medicine, 2022 - nature.com
… ) with permissive parameters (-c 10 -t 2 -p 0.001 -d 1000000). Candidate SNVs were retained
if … At multiallelic positions the frequency of each observed allele (A, C, G, T) was normalized …
if … At multiallelic positions the frequency of each observed allele (A, C, G, T) was normalized …
Compensatory frontoparietal activity during working memory: an endophenotype of obsessive-compulsive disorder
…, YD van der Werf, V van der Borden, TB van Rossum… - Biological …, 2014 - Elsevier
Background Subtle deficits in executive functioning are present in patients with obsessive-compulsive
disorder (OCD) and their first-degree relatives, suggesting involvement of the …
disorder (OCD) and their first-degree relatives, suggesting involvement of the …
[HTML][HTML] Evaluation of shotgun metagenomics sequence classification methods using in silico and in vitro simulated communities
Background The field of metagenomics (study of genetic material recovered directly from an
environment) has grown rapidly, with many bioinformatics analysis methods being …
environment) has grown rapidly, with many bioinformatics analysis methods being …