High-Throughput Sequencing

[1]  David Hernández,et al.  De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer. , 2008, Genome research.

[2]  A. Larsson,et al.  Open Access , 2019 .

[3]  G. McVean,et al.  De novo assembly and genotyping of variants using colored de Bruijn graphs , 2011, Nature Genetics.

[4]  R. Barrangou,et al.  CRISPR/Cas, the Immune System of Bacteria and Archaea , 2010, Science.

[5]  Narmada Thanki,et al.  CDD: a Conserved Domain Database for the functional annotation of proteins , 2010, Nucleic Acids Res..

[6]  Wei Zhang,et al.  Multi-Virulence-Locus Sequence Typing of Listeria monocytogenes , 2004, Applied and Environmental Microbiology.

[7]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[8]  A. Gnirke,et al.  ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads , 2009, Genome Biology.

[9]  Hilde Kruse,et al.  Food-borne diseases — The challenges of 20 years ago still persist while new ones continue to emerge , 2010, International Journal of Food Microbiology.

[10]  M. Borodovsky,et al.  GeneMark.hmm: new solutions for gene finding. , 1998, Nucleic acids research.

[11]  S. Brunak,et al.  SignalP 4.0: discriminating signal peptides from transmembrane regions , 2011, Nature Methods.

[12]  J. Wain,et al.  High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi , 2008, Nature Genetics.

[13]  Ning Ma,et al.  BLAST+: architecture and applications , 2009, BMC Bioinformatics.

[14]  Chris Mungall,et al.  AmiGO: online access to ontology and annotation data , 2008, Bioinform..

[15]  M. Schatz,et al.  Hybrid error correction and de novo assembly of single-molecule sequencing reads , 2012, Nature Biotechnology.

[16]  James R. Knight,et al.  Genome sequencing in microfabricated high-density picolitre reactors , 2005, Nature.

[17]  F. Mooi,et al.  Multilocus Sequence Typing of Bordetella pertussis Based on Surface Protein Genes , 2002, Journal of Clinical Microbiology.

[18]  Daniel J. Blankenberg,et al.  Galaxy: A Web‐Based Genome Analysis Tool for Experimentalists , 2010, Current protocols in molecular biology.

[19]  Steven J. M. Jones,et al.  De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data , 2009, Genome Biology.

[20]  J. Rothberg,et al.  Prospective Genomic Characterization of the German Enterohemorrhagic Escherichia coli O104:H4 Outbreak by Rapid Next Generation Sequencing Technology , 2011, PloS one.

[21]  Gary Van Domselaar,et al.  Comparative Genomics of Vibrio cholerae from Haiti, Asia, and Africa , 2011, Emerging infectious diseases.

[22]  Steven J. M. Jones,et al.  Abyss: a Parallel Assembler for Short Read Sequence Data Material Supplemental Open Access , 2022 .

[23]  L. Holm,et al.  The Pfam protein families database , 2005, Nucleic Acids Res..

[24]  Susumu Goto,et al.  KEGG: Kyoto Encyclopedia of Genes and Genomes , 2000, Nucleic Acids Res..

[25]  Peter F. Hallin,et al.  RNAmmer: consistent and rapid annotation of ribosomal RNA genes , 2007, Nucleic acids research.

[26]  A. Misra,et al.  SNP genotyping: technologies and biomedical applications. , 2007, Annual review of biomedical engineering.

[27]  Duane Szafron,et al.  BASys: a web server for automated bacterial genome annotation , 2005, Nucleic Acids Res..

[28]  T. Dallman,et al.  Performance comparison of benchtop high-throughput sequencing platforms , 2012, Nature Biotechnology.

[29]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[30]  Satoru Miyano,et al.  Prediction of Transcriptional Terminators in Bacillus subtilis and Related Species , 2005, PLoS Comput. Biol..

[31]  Daniel J. Blankenberg,et al.  Galaxy: a platform for interactive large-scale genome analysis. , 2005, Genome research.

[32]  Christa Lanz,et al.  Comprehensive mutation identification in an evolved bacterial cooperator and its cheating ancestor. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[33]  E. Birney,et al.  Velvet: algorithms for de novo short read assembly using de Bruijn graphs. , 2008, Genome research.

[34]  Peer Bork,et al.  SMART 7: recent updates to the protein domain annotation resource , 2011, Nucleic Acids Res..

[35]  T. Dallman,et al.  Corrigendum: Performance comparison of benchtop high-throughput sequencing platforms , 2012, Nature Biotechnology.

[36]  Mark J. P. Chaisson,et al.  De novo fragment assembly with short mate-paired reads: Does the read length matter? , 2009, Genome research.

[37]  Richard J. Roberts,et al.  COMBREX: a project to accelerate the functional annotation of prokaryotic genomes , 2010, Nucleic Acids Res..

[38]  Mihai Pop,et al.  Comparative Genome Sequencing for Discovery of Novel Polymorphisms in Bacillus anthracis , 2002, Science.

[39]  Martin C. J. Maiden,et al.  BIGSdb: Scalable analysis of bacterial genome variation at the population level , 2010, BMC Bioinformatics.

[40]  Richard Durbin,et al.  Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .

[41]  Anders Krogh,et al.  EasyGene – a prokaryotic gene finder that ranks ORFs by statistical significance , 2003, BMC Bioinformatics.

[42]  Lucian Ilie,et al.  SHRiMP2: Sensitive yet Practical Short Read Mapping , 2011, Bioinform..

[43]  Naryttza N. Diaz,et al.  The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes , 2005, Nucleic acids research.

[44]  Maria Jesus Martin,et al.  The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003 , 2003, Nucleic Acids Res..

[45]  S. Starkenburg,et al.  Bacterial genome annotation. , 2012, Methods in molecular biology.

[46]  Sergey Koren,et al.  Aggressive assembly of pyrosequencing reads with mates , 2008, Bioinform..

[47]  S. Brunak,et al.  Locating proteins in the cell using TargetP, SignalP and related tools , 2007, Nature Protocols.

[48]  Bairong Shen,et al.  A Practical Comparison of De Novo Genome Assembly Software Tools for Next-Generation Sequencing Technologies , 2011, PloS one.

[49]  F. Weill,et al.  CRISPR Typing and Subtyping for Improved Laboratory Surveillance of Salmonella Infections , 2012, PloS one.

[50]  B. Swaminathan,et al.  PulseNet USA: a five-year update. , 2006, Foodborne pathogens and disease.

[51]  James H. Bullard,et al.  Origins of the E. coli strain causing an outbreak of hemolytic-uremic syndrome in Germany. , 2011, The New England journal of medicine.

[52]  G. Olsen,et al.  CRITICA: coding region identification tool invoking comparative analysis. , 1999, Molecular biology and evolution.

[53]  J. Parkhill,et al.  A genomic approach to bacterial taxonomy: an examination and proposed reclassification of species within the genus Neisseria , 2012, Microbiology.

[54]  David R. Riley,et al.  CloVR: A virtual machine for automated and portable sequence analysis from the desktop using cloud computing , 2011, BMC Bioinformatics.

[55]  R. Dixon,et al.  Domain Architectures of σ54-Dependent Transcriptional Activators , 2003 .

[56]  Miriam L. Land,et al.  Trace: Tennessee Research and Creative Exchange Prodigal: Prokaryotic Gene Recognition and Translation Initiation Site Identification Recommended Citation Prodigal: Prokaryotic Gene Recognition and Translation Initiation Site Identification , 2022 .

[57]  M. Achtman,et al.  Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[58]  Juliane C. Dohm,et al.  SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing. , 2007, Genome research.

[59]  M. Schatz,et al.  Algorithms Gage: a Critical Evaluation of Genome Assemblies and Assembly Material Supplemental , 2008 .

[60]  Nigel F. Delaney,et al.  Ultrafast Evolution and Loss of CRISPRs Following a Host Shift in a Novel Wildlife Pathogen, Mycoplasma gallisepticum , 2012, PLoS genetics.

[61]  Mark J. P. Chaisson,et al.  Short read fragment assembly of bacterial genomes. , 2008, Genome research.

[62]  R. Fleischmann,et al.  Modeling Bacterial Evolution with Comparative-Genome-Based Marker Systems: Application to Mycobacterium tuberculosis Evolution and Pathogenesis , 2003, Journal of bacteriology.

[63]  S. Salzberg,et al.  Microbial gene identification using interpolated Markov models. , 1998, Nucleic acids research.

[64]  Paul Keim,et al.  Phylogenetic discovery bias in Bacillus anthracis using single-nucleotide polymorphisms from whole-genome sequencing. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[65]  M. DePristo,et al.  The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. , 2010, Genome research.

[66]  Ole Lund,et al.  Multilocus Sequence Typing of Total-Genome-Sequenced Bacteria , 2012, Journal of Clinical Microbiology.

[67]  James H. Bullard,et al.  The origin of the Haitian cholera outbreak strain. , 2011, The New England journal of medicine.

[68]  Pushkala Jayaraman,et al.  A computational genomics pipeline for prokaryotic sequencing projects , 2010, Bioinform..

[69]  Rick L. Stevens,et al.  The RAST Server: Rapid Annotations using Subsystems Technology , 2008, BMC Genomics.

[70]  Michael Eisenstein,et al.  Oxford Nanopore announcement sets sequencing sector abuzz , 2012, Nature Biotechnology.

[71]  Peter Gerner-Smidt,et al.  Recent developments and future prospects in subtyping of foodborne bacterial pathogens. , 2007, Future microbiology.

[72]  R. Parreñas,et al.  Sequencing and Comparative Analysis of Flagellin Genes fliC, fljB, and flpA from Salmonella , 2004, Journal of Clinical Microbiology.

[73]  P. Fields,et al.  Molecular Determination of H Antigens of Salmonella by Use of a Microsphere-Based Liquid Array , 2010, Journal of Clinical Microbiology.

[74]  A. Nekrutenko,et al.  Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences , 2010, Genome Biology.

[75]  James H. Bullard,et al.  A hybrid approach for the automated finishing of bacterial genomes , 2012, Nature Biotechnology.

[76]  Huanming Yang,et al.  De novo assembly of human genomes with massively parallel short read sequencing. , 2010, Genome research.

[77]  René L. Warren,et al.  Assembling millions of short DNA sequences using SSAKE , 2006, Bioinform..

[78]  M. Wiedmann,et al.  A Whole-Genome Single Nucleotide Polymorphism-Based Approach To Trace and Identify Outbreaks Linked to a Common Salmonella enterica subsp. enterica Serovar Montevideo Pulsed-Field Gel Electrophoresis Type , 2011, Applied and Environmental Microbiology.

[79]  Vincent J. Magrini,et al.  Extending assembly of short DNA sequences to handle error , 2007, Bioinform..

[80]  T. Glenn.  Field guide to next‐generation DNA sequencers , 2011, Molecular ecology resources.

[81]  Julian Parkhill,et al.  Evolution of MRSA During Hospital Transmission and Intercontinental Spread , 2010, Science.

[82]  M. Achtman.  Evolution, population structure, and phylogeography of genetically monomorphic bacterial pathogens. , 2008, Annual review of microbiology.

[83]  Bertil Schmidt,et al.  A fast hybrid short read fragment assembly algorithm , 2009, Bioinform..

[84]  Geeta Shakya,et al.  Population Genetics of Vibrio cholerae from Nepal in 2010: Evidence on the Origin of the Haitian Outbreak , 2011, mBio.

[85]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[86]  A. Gnirke,et al.  High-quality draft assemblies of mammalian genomes from massively parallel sequence data , 2010, Proceedings of the National Academy of Sciences.

[87]  Errol Strain,et al.  Identification of a salmonellosis outbreak by means of molecular sequencing. , 2011, The New England journal of medicine.

[88]  C. Nusbaum,et al.  ALLPATHS: de novo assembly of whole-genome shotgun microreads. , 2008, Genome research.

[89]  Sean R Eddy,et al.  What is a hidden Markov model? , 2004, Nature Biotechnology.

[90]  A. Krogh,et al.  Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. , 2001, Journal of molecular biology.

[91]  C. Médigue,et al.  MaGe: a microbial genome annotation system supported by synteny results , 2006, Nucleic acids research.