Microbiome bioinformatics

A large number of microorganisms, including bacteria, archaea, fungi and other eukaryotes are present in our bodies and in our environment. Although usually invisible, their presence or absence is essential for our health.

Recent progress in sequencing technology have enabled large scale sequencing of mixtures of the DNA from all the organisms present in a sample simultaneously. We are developing computational tools to analyse this kind of data in order to identify and classify the species present and their abundances. Microbiome analysis is now making an impact in many areas, including marine biology, medical sciences, forensic science and agriculture.

Principal investigator

Torbjørn Rognes

Research groups involved

Rognes group

Recent publications 

Rognes T, Flouri T, Nichols B, Quince C, Mahé F (2016)
VSEARCH: a versatile open source tool for metagenomics
PeerJ, 4, e2584
DOI 10.7717/peerj.2584

Kopylova E, Navas-Molina JA, Mercier C, Xu ZZ, Mahé F, He Y, Zhou HW, Rognes T, Caporaso JG, Knight R (2016)
Open-Source Sequence Clustering Methods Improve the State Of the Art
mSystems, 1 (1)
DOI 10.1128/mSystems.00003-15

Mahé F, Rognes T, Quince C, de Vargas C, Dunthorn M (2015)
Swarm v2: highly-scalable and high-resolution amplicon clustering
PeerJ, 3, e1420
DOI 10.7717/peerj.1420

Mahé F, Rognes T, Quince C, de Vargas C, Dunthorn M (2014)
Swarm: robust and fast clustering method for amplicon-based studies
PeerJ, 2, e593
DOI 10.7717/peerj.593

Collaborations

Frédéric Mahé (CIRAD, France)

Lars Snipen, Knut Rudi (NMBU, Ås)

Håvard Kauserud (IBV)

Johannes E. R. Hov (OUS)
 

Published Apr. 30, 2019 6:18 PM - Last modified Apr. 30, 2019 8:30 PM