| P2093 | author name string | Baiba Vilne | |
| | Irēna Meistere | |
| | Lelde Grantiņa-Ieviņa | |
| | Juris Ķibilds | |
| P2860 | cites work | The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes | Q21284200 |
| | BLAST+: architecture and applications | Q21284368 |
| | Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella | Q24286921 |
| | Metagenomic microbial community profiling using unique clade-specific marker genes | Q24599864 |
| | Comparative analysis of core genome MLST and SNP typing within a European Salmonella serovar Enteritidis outbreak. | Q51783026 |
| | chewBBACA: A complete suite for gene-by-gene schema creation and strain identification. | Q51783712 |
| | Opportunities and obstacles for deep learning in biology and medicine. | Q52331906 |
| | A genomic overview of the population structure of Salmonella. | Q55036075 |
| | Tracking antibiotic resistance gene pollution from different sources using machine-learning classification. | Q55353550 |
| | A pan-genome-based machine learning approach for predicting antimicrobial resistance activities of the Escherichia coli strains. | Q55492324 |
| | Machine learning identifies signatures of host adaptation in the bacterial pathogen Salmonella enterica. | Q55523797 |
| | SKESA: strategic k-mer extension for scrupulous assemblies | Q57026999 |
| | Using machine learning to predict antimicrobial minimum inhibitory concentrations and associated genomic features for nontyphoidal | Q58545265 |
| | Zoonotic Source Attribution of Salmonella enterica Serotype Typhimurium Using Genomic Surveillance Data, United States | Q60922595 |
| | Using average nucleotide identity to improve taxonomic assignments in prokaryotic genomes at the NCBI | Q63256992 |
| | Characterization of Emetic and Diarrheal Strains From a 2016 Foodborne Outbreak Using Whole-Genome Sequencing: Addressing the Microbiological, Epidemiological, and Bioinformatic Challenges | Q64251941 |
| | Mechanistic models versus machine learning, a fight worth fighting for the biological community? | Q88698220 |
| | Use of Whole-Genome Sequencing for Food Safety and Public Health in the United States | Q92717431 |
| | CFSAN SNP Pipeline: an automated method for constructing SNP matrices from next-generation sequence data | Q110949957 |
| | Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies | Q24609520 |
| | QIIME allows analysis of high-throughput community sequencing data | Q24616873 |
| | SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing | Q24629733 |
| | ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences | Q24634141 |
| | Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities | Q24647611 |
| | Velvet: algorithms for de novo short read assembly using de Bruijn graphs | Q24657623 |
| | RNAmmer: consistent and rapid annotation of ribosomal RNA genes | Q24675768 |
| | Mash: fast genome and metagenome distance estimation using MinHash | Q24707164 |
| | The neighbor-joining method: a new method for reconstructing phylogenetic trees | Q25939010 |
| | BEAST: Bayesian evolutionary analysis by sampling trees | Q27860723 |
| | Omics-Based Strategies in Precision Medicine: Toward a Paradigm Shift in Inborn Errors of Metabolism Investigations | Q28068009 |
| | Bioinformatics strategies for taxonomy independent binning and visualization of sequences in shotgun metagenomics | Q28075867 |
| | Microbial bioinformatics for food safety and production | Q28081332 |
| | CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database | Q28584458 |
| | SPANDx: a genomics pipeline for comparative analysis of large haploid whole genome re-sequencing datasets | Q28655611 |
| | Fast filtering for RNA homology search | Q28743147 |
| | SignalP 4.0: discriminating signal peptides from transmembrane regions | Q29547202 |
| | RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees | Q29547265 |
| | Prodigal: prokaryotic gene recognition and translation initiation site identification | Q29547611 |
| | FastTree: computing large minimum evolution trees with profiles instead of a distance matrix | Q29614577 |
| | BLAST: at the core of a powerful and diverse set of sequence analysis tools | Q29615883 |
| | Prokka: rapid prokaryotic genome annotation | Q29616643 |
| | PathogenFinder--distinguishing friend from foe using bacterial whole genome sequence data | Q30690828 |
| | PaPrBaG: A machine learning approach for the detection of novel pathogens from NGS data | Q30833683 |
| | Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data | Q30948004 |
| | Reconstructing 16S rRNA genes in metagenomic data | Q30971304 |
| | VFDB 2016: hierarchical and refined dataset for big data analysis--10 years on | Q31025236 |
| | Gene prediction in metagenomic fragments based on the SVM algorithm. | Q31118752 |
| | A modification of the PHYLIP program: A solution for the redundant cluster problem, and an implementation of an automatic bootstrapping on trees inferred from original data | Q31165360 |
| | VirulentPred: a SVM based prediction method for virulent proteins in bacterial pathogens | Q33316857 |
| | TACOA: taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach | Q33408370 |
| | Improving de novo sequence assembly using machine learning and comparative genomics for overlap correction | Q33524574 |
| | Comprehensive bioinformatics analysis of Mycoplasma pneumoniae genomes to investigate underlying population structure and type-specific determinants | Q33565500 |
| | Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation | Q33622593 |
| | Pan-genome sequence analysis using Panseq: an online tool for the rapid analysis of core and accessory genomic regions | Q33693333 |
| | StrainSeeker: fast identification of bacterial strains from raw sequencing reads using user-provided guide trees | Q33709329 |
| | PanWeb: A web interface for pan-genomic analysis | Q33725008 |
| | Kraken: ultrafast metagenomic sequence classification using exact alignments | Q33742022 |
| | BIGSdb: Scalable analysis of bacterial genome variation at the population level. | Q33767145 |
| | PulseNet International: Vision for the implementation of whole genome sequencing (WGS) for global food-borne disease surveillance | Q33822884 |
| | Bayesian semi-supervised classification of bacterial samples using MLST databases | Q33972144 |
| | IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth | Q34229322 |
| | Reduced set of virulence genes allows high accuracy prediction of bacterial pathogenicity in humans | Q34390820 |
| | Accurate phylogenetic classification of variable-length DNA fragments | Q34593023 |
| | The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes | Q34676711 |
| | MetaGeneAnnotator: detecting species-specific patterns of ribosomal binding site for precise gene prediction in anonymous prokaryotic and phage genomes | Q34862099 |
| | Reconstructing each cell's genome within complex microbial communities-dream or reality? | Q34869203 |
| | MGC: a metagenomic gene caller | Q34882436 |
| | Solving the problem of comparing whole bacterial genomes across different sequencing platforms | Q35222674 |
| | MetaVelvet-SL: an extension of the Velvet assembler to a de novo metagenomic assembler utilizing supervised learning | Q35233831 |
| | Update on RefSeq microbial genomes resources | Q35253461 |
| | PERGA: a paired-end read guided de novo assembler for extending contigs using SVM and look ahead approach | Q35476199 |
| | 16S classifier: a tool for fast and accurate taxonomic classification of 16S rRNA hypervariable regions in metagenomic datasets | Q35554085 |
| | MinION™ nanopore sequencing of environmental metagenomes: a synthetic approach | Q36317841 |
| | A Bayesian taxonomic classification method for 16S rRNA gene sequences with improved species-level accuracy. | Q36367250 |
| | Next-Generation Sequencing and Comparative Analysis of Sequential Outbreaks Caused by Multidrug-Resistant Acinetobacter baumannii at a Large Academic Burn Center | Q36644684 |
| | Antimicrobial Resistance Prediction in PATRIC and RAST. | Q37000598 |
| | ANItools web: a web tool for fast genome comparison within multiple bacterial strains | Q37015389 |
| | Rapid whole-genome sequencing for detection and characterization of microorganisms directly from clinical samples | Q37546541 |
| | Multilocus Sequence Typing for Interpreting Blood Isolates of Staphylococcus epidermidis | Q37644882 |
| | The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). | Q37661996 |
| | A Comparative Analysis of the Lyve-SET Phylogenomics Pipeline for Genomic Epidemiology of Foodborne Pathogens | Q37694453 |
| | Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenic Escherichia coli | Q37713782 |
| | Explaining microbial phenotypes on a genomic scale: GWAS for microbes | Q38102667 |
| | Omics approaches in food safety: fulfilling the promise? | Q38191377 |
| | PhyloPythiaS+: a self-training method for the rapid reconstruction of low-ranking taxonomic bins from metagenomes | Q38342057 |
| | A supervised statistical learning approach for accurate Legionella pneumophila source attribution during outbreaks. | Q38618052 |
| | Whole-Genome Sequencing of Bacterial Pathogens: the Future of Nosocomial Outbreak Analysis | Q38635425 |
| | MetaGene: prokaryotic gene finding from environmental genome shotgun sequences | Q39118049 |
| | Classification of Listeria monocytogenes persistence in retail delicatessen environments using expert elicitation and machine learning. | Q39182193 |
| | The evolution of One Health: a decade of progress and challenges for the future | Q39263984 |
| | Advances in Rapid Identification and Susceptibility Testing of Bacteria in the Clinical Microbiology Laboratory: Implications for Patient Care and Antimicrobial Stewardship Programs | Q39274504 |
| | Roary: rapid large-scale prokaryote pan genome analysis | Q39769468 |
| | Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences | Q39788453 |
| | JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. | Q40312977 |
| | Woods: A fast and accurate functional annotator and classifier of genomic and metagenomic sequences. | Q41088773 |
| | Hierarchical and spatially explicit clustering of DNA sequences with BAPS software | Q41436456 |
| | Metagenome fragment classification using N-mer frequency profiles | Q41947344 |
| | Identification of acquired antimicrobial resistance genes | Q41981445 |
| | Orphelia: predicting genes in metagenomic sequencing reads | Q42021729 |
| | SNVPhyl: a single nucleotide variant phylogenomics pipeline for microbial genomic epidemiology | Q42277652 |
| | Whole genome sequencing (WGS) for food-borne pathogen surveillance and control - taking the pulse. | Q42335711 |
| | Updating benchtop sequencing performance comparison | Q43497116 |
| | OrthoANI: An improved algorithm and software for calculating average nucleotide identity | Q45340509 |
| | Patchy promiscuity: machine learning applied to predict the host specificity of Salmonella enterica and Escherichia coli. | Q45800600 |
| | PATRIC as a unique resource for studying antimicrobial resistance. | Q45945275 |
| | High Throughput Sequencing for Detection of Foodborne Pathogens. | Q46090917 |
| | Gene Prediction in Metagenomic Fragments with Deep Learning | Q46237755 |
| | Surveillance of Foodborne Pathogens: Towards Diagnostic Metagenomics of Fecal Samples. | Q47210600 |
| | Efficiency of PacBio long read correction by 2nd generation Illumina sequencing. | Q47264805 |
| | DeepARG: a deep learning approach for predicting antibiotic resistance genes from metagenomic data | Q47692122 |
| | kSNP3.0: SNP detection and phylogenetic analysis of genomes without genome alignment or reference genome | Q47936283 |
| P275 | copyright license | Creative Commons Attribution 4.0 International | Q20007257 |
| P6216 | copyright status | copyrighted | Q50423863 |
| P921 | main subject | machine learning | Q2539 |
| P304 | page(s) | 1722 | |
| P577 | publication date | 2019-08-06 | |
| P1433 | published in | Frontiers in Microbiology | Q27723481 |
| P1476 | title | Machine Learning Approaches for Epidemiological Investigations of Food-Borne Disease Outbreaks | |
| P478 | volume | 10 | |