Defending Our Public Biological Databases as a Global Critical Infrastructure

Cyberbiosecurity: From Naive Trust to Risk Awareness

(2018) Jean Peccoud et al.   TRENDS IN BIOTECHNOLOGY

Removing contaminants from databases of draft genomes

(2018) Jennifer Lu et al.   PLoS Computational Biology

Realizing the potential of blockchain technologies in genomics

(2018) Halil Ibrahim Ozercan et al.   GENOME RESEARCH

Consensus assessment of the contamination level of publicly available cyanobacterial genomes

(2018) Luc Cornet et al.   PLoS One

Detection of bacterial contaminants and hybrid sequences in the genome of the kelp Saccharina japonica using Taxoblast

(2017) Simon M. Dittami et al.   PeerJ

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

(2016) Markus Lux et al.   BMC BIOINFORMATICS

Phylogeny-aware identification and correction of taxonomically mislabeled sequences

(2016) Alexey M. Kozlov et al.   NUCLEIC ACIDS RESEARCH

Human Contamination in Public Genome Assemblies

(2016) Kirill Kryukov et al.   PLoS One

Meeting report: GenBank microbial genomic taxonomy workshop (12–13 May, 2015)

(2016) Scott Federhen et al.   Standards in Genomic Sciences

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Private genome analysis through homomorphic encryption

(2015) Miran Kim et al.   BMC Medical Informatics and Decision Making

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

Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning

(2015) Babak Alipanahi et al.   NATURE BIOTECHNOLOGY

Predicting effects of noncoding variants with deep learning–based sequence model

(2015) Jian Zhou et al.   NATURE METHODS

GenomePeek—an online tool for prokaryotic genome and metagenome analysis

(2015) Katelyn McNair et al.   PeerJ

Strategies to Avoid Wrongly Labelled Genomes Using as Example the Detected Wrong Taxonomic Affiliation for Aeromonas Genomes in the GenBank Database

(2015) Roxana Beaz-Hidalgo et al.   PLoS One

Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes

(2014) M. Kim et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Benchmarking of Methods for Genomic Taxonomy

(2014) M. V. Larsen et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Type material in the NCBI Taxonomy Database

(2014) Scott Federhen   NUCLEIC ACIDS RESEARCH

Bioinformatic Genome Comparisons for Taxonomic and Phylogenetic Assignments Using Aeromonas as a Test Case

(2014) Sophie M. Colston et al.   mBio

Microbial Contamination in Next Generation Sequencing: Implications for Sequence-Based Analysis of Clinical Samples

(2014) Michael J. Strong et al.   PLoS Pathogens

Proof by synthesis of Tobacco mosaic virus

(2014) Bret Cooper   GENOME BIOLOGY

Unexpected cross-species contamination in genome sequencing projects

(2014) Samier Merchant et al.   PeerJ

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Monitoring DNA Contamination in Handled vs. Directly Excavated Ancient Human Skeletal Remains

(2013) Elena Pilli et al.   PLoS One

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

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

Prokaryotic taxonomy in the sequencing era - the polyphasic approach revisited

(2011) Peter Kämpfer et al.   ENVIRONMENTAL MICROBIOLOGY

Abundant Human DNA Contamination Identified in Non-Primate Genome Databases

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

Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough

(2011) Hervé Philippe et al.   PLOS BIOLOGY

Classifier evaluation and attribute selection against active adversaries

(2010) Murat Kantarcıoğlu et al.   DATA MINING AND KNOWLEDGE DISCOVERY

Shifting the genomic gold standard for the prokaryotic species definition

(2009) Michael Richter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Re-Assembly of the Genome of Francisella tularensis Subsp. holarctica OSU18

(2008) Daniela Puiu et al.   PLoS One