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2021
Elucidation of genomic organizations of transgenic soybean plants through de novo genome assembly with short paired-end reads
Molecular Breeding
2021
De novo genome assemblies of butterflies
GigaScience
2021
Taxonomic Composition and Distribution of Alien Suckermouth Armored Catfish (Siluriformes: Loricariidae) in Southern Vietnam
Inland Water Biology
2021
Universal and taxon-specific trends in protein sequences as a function of age
eLife
2021
Comprehensive at-arrival transcriptomic analysis of post-weaned beef cattle uncovers type I interferon and antiviral mechanisms associated with bovine respiratory disease mortality
PLOS ONE
2021
Simplitigs as an efficient and scalable representation of de Bruijn graphs
Genome Biology
2021
Evolutionary history of histamine receptors: Early vertebrate origin and expansion of the H3-H4 subtypes
Molecular Phylogenetics and Evolution
2021
Sequencing facility and DNA source associated patterns of virus-mappable reads in whole-genome sequencing data
Genomics
2020
Enhanced Symbiotic Characteristics in Bacterial Genomes with the Disruption of rRNA Operon
Biology
2020
Long-read sequencing based clinical metagenomics for the detection and confirmation of Pneumocystis jirovecii directly from clinical specimens: A paradigm shift in mycological diagnostics
Medical Mycology
2020
Evaluation of methods for detecting human reads in microbial sequencing datasets
Microbial Genomics
2020
Estimation of the relative abundance of species in artificial mixtures of insects using low-coverage shotgun metagenomics
Metabarcoding and Metagenomics
2020
Mycobacterium bovis: From Genotyping to Genome Sequencing
Microorganisms
2020
Terminating contamination: large-scale search identifies more than 2,000,000 contaminated entries in GenBank
Genome Biology
2020
TreeSAPP: the Tree-based Sensitive and Accurate Phylogenetic Profiler
Bioinformatics
2020
The use of taxon-specific reference databases compromises metagenomic classification
BMC Genomics
2020
BlobToolKit – Interactive Quality Assessment of Genome Assemblies
G3 Genes|Genomes|Genetics
2020
The reuse of public datasets in the life sciences: potential risks and rewards
PeerJ
2020
The what, how and why of archaeological coprolite analysis
Earth-Science Reviews
2020
Prevalence and Implications of Contamination in Public Genomic Resources: A Case Study of 43 Reference Arthropod Assemblies
G3 Genes|Genomes|Genetics
2020
Do I have something in my teeth? The trouble with genetic analyses of diet from archaeological dental calculus
Quaternary International
2020
Organism migration in soils: Should we be so comfortable with diagnosing ancient infectious diseases?
International Journal of Osteoarchaeology
2020
Consistent RNA sequencing contamination in GTEx and other data sets
Nature Communications
2020
The impact of contaminants on the accuracy of genome skimming and the effectiveness of exclusion read filters
Molecular Ecology Resources
2020
Contaminant DNA in bacterial sequencing experiments is a major source of false genetic variability
BMC Biology
2019
PhyloToL: A Taxon/Gene-Rich Phylogenomic Pipeline to Explore Genome Evolution of Diverse Eukaryotes
Molecular Biology and Evolution
2019
Defending Our Public Biological Databases as a Global Critical Infrastructure
Frontiers in Bioengineering and Biotechnology
2019
Plasmid DNA contaminant in molecular reagents
Scientific Reports
2019
ConFindr: rapid detection of intraspecies and cross-species contamination in bacterial whole-genome sequence data
PeerJ
2019
A Bioinformatics Guide to Plant Microbiome Analysis
Frontiers in Plant Science
2019
Human contamination in bacterial genomes has created thousands of spurious proteins
Genome Research
2019
SEPATH: benchmarking the search for pathogens in human tissue whole genome sequence data leads to template pipelines
Genome Biology
2019
Genome-based taxonomic classification
Genome
2019
A Cautionary Report for Pathogen Identification Using Shotgun Metagenomics; A Comparison to Aerobic Culture and Polymerase Chain Reaction for Salmonella enterica Identification
Frontiers in Microbiology
2019
Genetic selection for bovine chromosome 18 haplotypes associated with divergent somatic cell score affects postpartum reproductive and metabolic performance
Journal of Dairy Science
2019
A review of methods and databases for metagenomic classification and assembly
Briefings in Bioinformatics
2018
Horizontally transferred genes in the ctenophore Mnemiopsis leidyi
PeerJ
2018
Investigating Effects of Tulathromycin Metaphylaxis on the Fecal Resistome and Microbiome of Commercial Feedlot Cattle Early in the Feeding Period
Frontiers in Microbiology
2018
Estimation of Recombination Rate and Maternal Linkage Disequilibrium in Half-Sibs
Frontiers in Genetics
2018
Metagenomic analysis of viral diversity in respiratory samples from patients with respiratory tract infections in Kuwait
Journal of Medical Virology
2018
Removing contaminants from databases of draft genomes
PLOS Computational Biology
2018
Culture purification and DNA extraction procedures suitable for next-generation sequencing of euglenids
Journal of Applied Phycology
2018
RefSeq database growth influences the accuracy of k-mer-based lowest common ancestor species identification
Genome Biology
2018
Does apicortin, a characteristic protein of apicomplexan parasites and placozoa, occur in Eumetazoa?
Acta Parasitologica
2018
Genomics-Based Identification of Microorganisms in Human Ocular Body Fluid
Scientific Reports
2018
A software tool ‘CroCo’ detects pervasive cross-species contamination in next generation sequencing data
BMC Biology
2018
Xenosurveillance reflects traditional sampling techniques for the identification of human pathogens: A comparative study in West Africa
PLOS Neglected Tropical Diseases
2018
Consensus assessment of the contamination level of publicly available cyanobacterial genomes
PLOS ONE
2017
Unmapped reads from cattle RNAseq data: A source for missing and misassembled sequences in the reference assemblies and for detection of pathogens in the host
Genomics
2017
PhylOligo: a package to identify contaminant or untargeted organism sequences in genome assemblies
Bioinformatics
2017
Patterns of cross-contamination in a multispecies population genomic project: detection, quantification, impact, and solutions
BMC Biology
2017
Parasite infection of public databases: a data mining approach to identify apicomplexan contaminations in animal genome and transcriptome assemblies
BMC Genomics
2017
Decontaminating eukaryotic genome assemblies with machine learning
BMC Bioinformatics
2017
Novel Substrates as Sources of Ancient DNA: Prospects and Hurdles
Genes
2017
Draft sequencing and assembly of the genome of the world’s largest fish, the whale shark: Rhincodon typus Smith 1828
BMC Genomics
2017
A comprehensive analysis of breast cancer microbiota and host gene expression
PLOS ONE
2016
Use of Metagenomic Shotgun Sequencing Technology To Detect Foodborne Pathogens within the Microbiome of the Beef Production Chain
Applied and Environmental Microbiology
2016
Bovine Genome Database: new tools for gleaning function from theBos taurusgenome
Nucleic Acids Research
2016
Taxonomer: an interactive metagenomics analysis portal for universal pathogen detection and host mRNA expression profiling
Genome Biology
2016
Comparative genomics and transcriptomics of Pichia pastoris
BMC Genomics
2016
Genome sequencing and analysis of the first complete genome ofLactobacillus kunkeeistrain MP2, anApis melliferagut isolate
PeerJ
2016
Identifying contamination with advanced visualization and analysis practices: metagenomic approaches for eukaryotic genome assemblies
PeerJ
2016
Human Contamination in Public Genome Assemblies
PLOS ONE
2016
Outlier SNPs enable food traceability of the southern rock lobster, Jasus edwardsii
Marine Biology
2015
Prokaryotic genes in eukaryotic genome sequences: when to infer horizontal gene transfer and when to suspect an actual microbe
Environmental Microbiology
2015
Here, there, and everywhere
EMBO reports
2015
Composition, taxonomy and functional diversity of the oropharynx microbiome in individuals with schizophrenia and controls
PeerJ
2015
Evolution of satellite DNA sequences in two tribes of Bovidae: A cautionary tale
Genetics and Molecular Biology
2015
Transport of lipopolysaccharide to the Gram-negative bacterial cell surface
FEMS Microbiology Reviews
2015
Two recently sequenced vertebrate genomes are contaminated with apicomplexan species of the Sarcocystidae family
International Journal for Parasitology
2015
Vector sequence contamination of the Plasmodium vivax sequence database in PlasmoDB and In silico correction of 26 parasite sequences
Parasites & Vectors
2015
Beyond research: a primer for considerations on using viral metagenomics in the field and clinic
Frontiers in Microbiology
2015
What’s in your next-generation sequence data? An exploration of unmapped DNA and RNA sequence reads from the bovine reference individual
BMC Genomics
2014
Editors’ Pick: Contamination has always been the issue!
Investigative Genetics
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