12 Result(s)

Article

Author Correction: An evaluation of the accuracy and speed of metagenome analysis tools

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Stinus Lindgreen, Karen L. Adair, Paul P. Gardner in Scientific Reports (2020)

Article

Above and belowground community strategies respond to different global change drivers

Environmental changes alter the diversity and structure of communities. By shifting the range of species traits that will be successful under new conditions, environmental drivers can also dramatically impact ...

Karen L. Adair, Stinus Lindgreen, Anthony M. Poole, Laura M. Young… in Scientific Reports (2019)

Article

Major sulfonate transporter Soa1 in Saccharomyces cerevisiae and considerable substrate diversity in its fungal family

Sulfate is a well-established sulfur source for fungi; however, in soils sulfonates and sulfate esters, especially choline sulfate, are often much more prominent. Here we show that Saccharomyces cerevisiae YIL166...

Sylvester Holt, Harish Kankipati, Stijn De Graeve… in Nature Communications (2017)

Article

AdapterRemoval v2: rapid adapter trimming, identification, and read merging

As high-throughput sequencing platforms produce longer and longer reads, sequences generated from short inserts, such as those obtained from fossil and degraded material, are increasingly expected to contain a...

Mikkel Schubert, Stinus Lindgreen, Ludovic Orlando in BMC Research Notes (2016)

Article

An evaluation of the accuracy and speed of metagenome analysis tools

Metagenome studies are becoming increasingly widespread, yielding important insights into microbial communities covering diverse environments from terrestrial and aquatic ecosystems to human skin and gut. With...

Stinus Lindgreen, Karen L. Adair, Paul P. Gardner in Scientific Reports (2016)

Article

SNPest: a probabilistic graphical model for estimating genotypes

As the use of next-generation sequencing technologies is becoming more widespread, the need for robust software to help with the analysis is growing as well. A key challenge when analyzing sequencing data is t...

Stinus Lindgreen, Anders Krogh, Jakob Skou Pedersen in BMC Research Notes (2014)

Article

Adaptable probabilistic map** of short reads using position specific scoring matrices

Modern DNA sequencing methods produce vast amounts of data that often requires map** to a reference genome. Most existing programs use the number of mismatches between the read and the genome as a measure of...

Peter Kerpedjiev, Jes Frellsen, Stinus Lindgreen, Anders Krogh in BMC Bioinformatics (2014)

Article

AdapterRemoval: easy cleaning of next-generation sequencing reads

With the advent of next-generation sequencing there is an increased demand for tools to pre-process and handle the vast amounts of data generated. One recurring problem is adapter contamination in the reads, i...

Stinus Lindgreen in BMC Research Notes (2012)

Article

Improving ancient DNA read map** against modern reference genomes

Next-Generation Sequencing has revolutionized our approach to ancient DNA (aDNA) research, by providing complete genomic sequences of ancient individuals and extinct species. However, the recovery of genetic m...

Mikkel Schubert, Aurelien Ginolhac, Stinus Lindgreen, John F Thompson… in BMC Genomics (2012)

Article

Ancient human genome sequence of an extinct Palaeo-Eskimo

We report here the genome sequence of an ancient human. Obtained from ∼4,000-year-old permafrost-preserved hair, the genome represents a male individual from the first known culture to settle in Greenland. Seq...

Morten Rasmussen, Yingrui Li, Stinus Lindgreen, Jakob Skou Pedersen… in Nature (2010)

Article

Multiple alignment and structure prediction of non-coding RNA sequences

Stinus Lindgreen, Paul P Gardner, Anders Krogh in BMC Bioinformatics (2007)