Simon A Berger
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Explore the profile of Simon A Berger including associated specialties, affiliations and a list of published articles.
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7
Citations
664
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Recent Articles
1.
Dunthorn M, Otto J, Berger S, Stamatakis A, Mahe F, Romac S, et al.
Mol Biol Evol
. 2014 Jan;
31(4):993-1009.
PMID: 24473288
Nucleotide positions in the hypervariable V4 and V9 regions of the small subunit (SSU)-rDNA locus are normally difficult to align and are usually removed before standard phylogenetic analyses. Yet, with...
2.
Lucking R, Lawrey J, Gillevet P, Sikaroodi M, Dal-Forno M, Berger S
J Mol Evol
. 2013 Dec;
78(2):148-62.
PMID: 24343640
The internal transcribed spacer region (ITS) of the nuclear rDNA cistron represents the barcoding locus for Fungi. Intragenomic variation of this multicopy gene can interfere with accurate phylogenetic reconstruction of...
3.
Sunagawa S, Mende D, Zeller G, Izquierdo-Carrasco F, Berger S, Kultima J, et al.
Nat Methods
. 2013 Oct;
10(12):1196-9.
PMID: 24141494
To quantify known and unknown microorganisms at species-level resolution using shotgun sequencing data, we developed a method that establishes metagenomic operational taxonomic units (mOTUs) based on single-copy phylogenetic marker genes....
4.
Alachiotis N, Berger S, Stamatakis A
BMC Bioinformatics
. 2012 Aug;
13:196.
PMID: 22876807
Background: Aligning short DNA reads to a reference sequence alignment is a prerequisite for detecting their biological origin and analyzing them in a phylogenetic context. With the PaPaRa tool we...
5.
Berger S, Stamatakis A
Bioinformatics
. 2011 Jun;
27(15):2068-75.
PMID: 21636595
Motivation: Likelihood-based methods for placing short read sequences from metagenomic samples into reference phylogenies have been recently introduced. At present, it is unclear how to align those reads with respect...
6.
Berger S, Krompass D, Stamatakis A
Syst Biol
. 2011 Mar;
60(3):291-302.
PMID: 21436105
We present an evolutionary placement algorithm (EPA) and a Web server for the rapid assignment of sequence fragments (short reads) to edges of a given phylogenetic tree under the maximum-likelihood...
7.
Stark M, Berger S, Stamatakis A, von Mering C
BMC Genomics
. 2010 Aug;
11:461.
PMID: 20687950
Background: Shotgun sequencing of environmental DNA is an essential technique for characterizing uncultivated microbes in situ. However, the taxonomic and functional assignment of the obtained sequence fragments remains a pressing...