Consensus assessment of the contamination level of publicly available cyanobacterial genomes

Phylogenomics Places Orphan Protistan Lineages in a Novel Eukaryotic Super-Group

(2018) Matthew W Brown et al.   Genome Biology and Evolution

Characterization of the first cultured representative of a Bacteroidetes clade specialized on the scavenging of cyanobacteria

(2017) Wajdi Ben Hania et al.   ENVIRONMENTAL MICROBIOLOGY

A Metagenomic Approach to Cyanobacterial Genomics

(2017) Danillo O. Alvarenga et al.   Frontiers in Microbiology

Nutrient recycling facilitates long-term stability of marine microbial phototroph–heterotroph interactions

(2017) Joseph A. Christie-Oleza et al.   Nature Microbiology

Probabilistic inference of lateral gene transfer events

(2016) Mehmood Alam Khan et al.   BMC BIOINFORMATICS

acdc – Automated Contamination Detection and Confidence estimation for single-cell genome data

(2016) Markus Lux et al.   BMC BIOINFORMATICS

A polyphasic approach for the taxonomy of cyanobacteria: principles and applications

(2016) Jiří Komárek   EUROPEAN JOURNAL OF PHYCOLOGY

Phylogenomic networks reveal limited phylogenetic range of lateral gene transfer by transduction

(2016) Ovidiu Popa et al.   ISME Journal

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

ProDeGe: a computational protocol for fully automated decontamination of genomes

(2015) Kristin Tennessen et al.   ISME Journal

Cyanobacterial reuse of extracellular organic carbon in microbial mats

(2015) Rhona K Stuart et al.   ISME Journal

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities

(2015) Dongwan D. Kang et al.   PeerJ

VizBin - an application for reference-independent visualization and human-augmented binning of metagenomic data

(2015) Cedric C Laczny et al.   Microbiome

Intra-genomic 16S rRNA gene heterogeneity in cyanobacterial genomes.

(2015) Niclas Engene et al.   Fottea

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Binning metagenomic contigs by coverage and composition

(2014) Johannes Alneberg et al.   NATURE METHODS

Separating endogenous ancient DNA from modern day contamination in a Siberian Neandertal

(2014) Pontus Skoglund et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The plastid ancestor originated among one of the major cyanobacterial lineages

(2014) Jesús A. G. Ochoa de Alda et al.   Nature Communications

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

Unexpected cross-species contamination in genome sequencing projects

(2014) Samier Merchant et al.   PeerJ

GroopM: an automated tool for the recovery of population genomes from related metagenomes

(2014) Michael Imelfort et al.   PeerJ

MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm

(2014) Yu-Wei Wu et al.   Microbiome

From Green to Red: Horizontal Gene Transfer of the Phycoerythrin Gene Cluster between Planktothrix Strains

(2013) Ave Tooming-Klunderud et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Interactions between specific phytoplankton and bacteria affect lake bacterial community succession

(2013) Sara F. Paver et al.   ENVIRONMENTAL MICROBIOLOGY

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

The genome portal of the Department of Energy Joint Genome Institute: 2014 updates

(2013) Henrik Nordberg et al.   NUCLEIC ACIDS RESEARCH

SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes

(2012) Elmar Pruesse et al.   BIOINFORMATICS

Domain enhanced lookup time accelerated BLAST

(2012) Grzegorz M Boratyn et al.   Biology Direct

Origin of land plants revisited in the light of sequence contamination and missing data

(2012) Simon Laurin-Lemay et al.   CURRENT BIOLOGY

Transcription Analysis and Small Non-Protein Coding RNAs Associated with Bacterial Ribosomal Protein Operons

(2012) G.A. Khayrullina et al.   CURRENT MEDICINAL CHEMISTRY

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer among prokaryotes

(2011) O. Popa et al.   GENOME RESEARCH

Large-Scale Phylogenomic Analyses Indicate a Deep Origin of Primary Plastids within Cyanobacteria

(2011) Alexis Criscuolo et al.   MOLECULAR BIOLOGY AND EVOLUTION

Abundant Human DNA Contamination Identified in Non-Primate Genome Databases

(2011) Mark S. Longo et al.   PLoS One

Heterotrophic bacterial diversity in aquatic microbial mat communities from Antarctica

(2011) Karolien Peeters et al.   POLAR BIOLOGY

Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough

(2011) Hervé Philippe et al.   PLOS BIOLOGY

Multigene Phylogeny of the Green Lineage Reveals the Origin and Diversification of Land Plants

(2010) Cédric Finet et al.   CURRENT BIOLOGY

Molecular mechanisms underlying roseobacter–phytoplankton symbioses

(2010) Haifeng Geng et al.   CURRENT OPINION IN BIOTECHNOLOGY

Occurrence of phosphate acquisition genes inProchlorococcuscells from different ocean regions

(2009) Adam C. Martiny et al.   ENVIRONMENTAL MICROBIOLOGY

Pathway Evolution by Horizontal Transfer and Positive Selection Is Accommodated by Relaxed Negative Selection upon Upstream Pathway Genes in Purple Bacterial Carotenoid Biosynthesis

(2009) J. L. Klassen   JOURNAL OF BACTERIOLOGY

Facilitation of Robust Growth of Prochlorococcus Colonies and Dilute Liquid Cultures by "Helper" Heterotrophic Bacteria

(2008) J. J. Morris et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Evidence for positive selection acting on microcystin synthetase adenylation domains in three cyanobacterial genera

(2008) Ave Tooming-Klunderud et al.   BMC EVOLUTIONARY BIOLOGY

Genome evolution in cyanobacteria: The stable core and the variable shell

(2008) T. Shi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA