Comparative genomics on gene and single nucleotide level

[1]  F. Crick,et al.  Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid , 1953, Nature.

[2]  R. Franklin,et al.  Molecular Configuration in Sodium Thymonucleate , 1953, Nature.

[3]  L. Pauling,et al.  Molecules as documents of evolutionary history. , 1965, Journal of theoretical biology.

[4]  W. Fitch Distinguishing homologous from analogous proteins. , 1970, Systematic zoology.

[5]  W. Gilbert,et al.  A new method for sequencing DNA. , 1977, Proceedings of the National Academy of Sciences of the United States of America.

[6]  H. S. Heaps,et al.  Information retrieval, computational and theoretical aspects , 1978 .

[7]  M S Waterman,et al.  Identification of common molecular subsequences. , 1981, Journal of molecular biology.

[8]  T. Macke,et al.  A phylogenetic definition of the major eubacterial taxa. , 1985, Systematic and applied microbiology.

[9]  N. Saitou,et al.  The neighbor-joining method: a new method for reconstructing phylogenetic trees. , 1987, Molecular biology and evolution.

[10]  C. Woese,et al.  Bacterial evolution , 1987, Microbiological reviews.

[11]  P. Nyrén,et al.  Enzymatic method for continuous monitoring of DNA polymerase activity. , 1987, Analytical biochemistry.

[12]  O. Kandler,et al.  International Committee on Systematic Bacteriology: announcement of the report of the ad hoc Committee on Reconciliation of Approaches to Bacterial Systematics. , 1987, Zentralblatt fur Bakteriologie, Mikrobiologie, und Hygiene. Series A, Medical microbiology, infectious diseases, virology, parasitology.

[13]  F. Sanger,et al.  A Rapid Method for Determining Sequences in DNA by Primed Synthesis with DNA Polymerase , 1989 .

[14]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[15]  S. Henikoff,et al.  Amino acid substitution matrices from protein blocks. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[16]  F. Studier,et al.  DNA sequencing by primer walking with strings of contiguous hexamers. , 1992, Science.

[17]  J. T. Crawford,et al.  Strain identification of Mycobacterium tuberculosis by DNA fingerprinting: recommendations for a standardized methodology , 1993, Journal of clinical microbiology.

[18]  Isidore Rigoutsos,et al.  FLASH: a fast look-up algorithm for string homology , 1993, Proceedings of IEEE Conference on Computer Vision and Pattern Recognition.

[19]  F. Crick,et al.  Molecular structure of nucleic acids , 2004, JAMA.

[20]  D. J. Wheeler,et al.  A Block-sorting Lossless Data Compression Algorithm , 1994 .

[21]  J. Roach,et al.  Pairwise end sequencing: a unified approach to genomic mapping and sequencing. , 1995, Genomics.

[22]  M. Ronaghi,et al.  Real-time DNA sequencing using detection of pyrophosphate release. , 1996, Analytical biochemistry.

[23]  N. W. Davis,et al.  The complete genome sequence of Escherichia coli K-12. , 1997, Science.

[24]  D. Lipman,et al.  A genomic perspective on protein families. , 1997, Science.

[25]  P. Green,et al.  Consed: a graphical tool for sequence finishing. , 1998, Genome research.

[26]  X. Huang,et al.  CAP3: A DNA sequence assembly program. , 1999, Genome research.

[27]  S. Dongen Graph clustering by flow simulation , 2000 .

[28]  Giovanni Manzini,et al.  Opportunistic data structures with applications , 2000, Proceedings 41st Annual Symposium on Foundations of Computer Science.

[29]  B. Snel,et al.  STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene. , 2000, Nucleic acids research.

[30]  Eugene W. Myers,et al.  A whole-genome assembly of Drosophila. , 2000, Science.

[31]  Torbjørn Rognes,et al.  Six-fold speed-up of Smith-Waterman sequence database searches using parallel processing on common microprocessors , 2000, Bioinform..

[32]  W. Fitch Homology a personal view on some of the problems. , 2000, Trends in genetics : TIG.

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

[34]  中尾 光輝,et al.  KEGG(Kyoto Encyclopedia of Genes and Genomes)〔和文〕 (特集 ゲノム医学の現在と未来--基礎と臨床) -- (データベース) , 2000 .

[35]  S Rozen,et al.  Primer3 on the WWW for general users and for biologist programmers. , 2000, Methods in molecular biology.

[36]  N. W. Davis,et al.  Genome sequence of enterohaemorrhagic Escherichia coli O157:H7 , 2001, Nature.

[37]  J. Ohnishi,et al.  A novel methodology employing Corynebacterium glutamicum genome information to generate a new L-lysine-producing mutant , 2001, Applied Microbiology and Biotechnology.

[38]  J. V. Moran,et al.  Initial sequencing and analysis of the human genome. , 2001, Nature.

[39]  J. Hoheisel,et al.  Strategy to sequence the genome of Corynebacterium glutamicum ATCC 13032: use of a cosmid and a bacterial artificial chromosome library. , 2002, Journal of biotechnology.

[40]  E. Branscomb,et al.  On the High Value of Low Standards , 2002, Journal of bacteriology.

[41]  Enno Ohlebusch,et al.  Efficient multiple genome alignment , 2002, ISMB.

[42]  I. Jolliffe Principal Component Analysis , 2002 .

[43]  S. Salzberg,et al.  The Value of Complete Microbial Genome Sequencing (You Get What You Pay For) , 2002, Journal of bacteriology.

[44]  N. Moran,et al.  50 Million Years of Genomic Stasis in Endosymbiotic Bacteria , 2002, Science.

[45]  N. Moran,et al.  From Gene Trees to Organismal Phylogeny in Prokaryotes:The Case of the γ-Proteobacteria , 2003, PLoS biology.

[46]  R. Giegerich,et al.  GenDB--an open source genome annotation system for prokaryote genomes. , 2003, Nucleic acids research.

[47]  A. Pühler,et al.  Genome-wide analysis of the L-methionine biosynthetic pathway in Corynebacterium glutamicum by targeted gene deletion and homologous complementation. , 2003, Journal of biotechnology.

[48]  S. Salzberg,et al.  Versatile and open software for comparing large genomes , 2004, Genome Biology.

[49]  Chuong B. Do,et al.  Access the most recent version at doi: 10.1101/gr.926603 References , 2003 .

[50]  M. Maiden,et al.  Multi-locus sequence typing: a tool for global epidemiology. , 2003, Trends in microbiology.

[51]  D. P. Wall,et al.  Detecting putative orthologs , 2003, Bioinform..

[52]  Ikuo Uchiyama,et al.  MBGD: microbial genome database for comparative analysis , 2003, Nucleic Acids Res..

[53]  C. Stoeckert,et al.  OrthoMCL: identification of ortholog groups for eukaryotic genomes. , 2003, Genome research.

[54]  Christian von Mering,et al.  STRING: a database of predicted functional associations between proteins , 2003, Nucleic Acids Res..

[55]  F. Blattner,et al.  Mauve: multiple alignment of conserved genomic sequence with rearrangements. , 2004, Genome research.

[56]  Michael Brudno,et al.  The CHAOS/DIALIGN WWW server for multiple alignment of genomic sequences , 2004, Nucleic Acids Res..

[57]  Gitanjali Yadav,et al.  NRPS-PKS: a knowledge-based resource for analysis of NRPS/PKS megasynthases , 2004, Nucleic Acids Res..

[58]  Enrique Merino,et al.  GeConT: gene context analysis , 2004, Bioinform..

[59]  Lior Pachter,et al.  VISTA: computational tools for comparative genomics , 2004, Nucleic Acids Res..

[60]  Caroline Allix,et al.  Utility of fast mycobacterial interspersed repetitive unit-variable number tandem repeat genotyping in clinical mycobacteriological analysis. , 2004, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

[61]  R. Rappuoli,et al.  Genome-derived vaccines , 2004, Expert review of vaccines.

[62]  M. Melkonian,et al.  Are combined analyses better than single gene phylogenies? A case study using SSU rDNA and rbcL sequence comparisons in the Zygnematophyceae (Streptophyta). , 2003, Molecular biology and evolution.

[63]  A. Goffeau,et al.  Complete sequence and comparative genome analysis of the dairy bacterium Streptococcus thermophilus , 2004, Nature Biotechnology.

[64]  M. P. Cummings PHYLIP (Phylogeny Inference Package) , 2004 .

[65]  K. Holsinger The neutral theory of molecular evolution , 2004 .

[66]  S. Schuster,et al.  Comparative analysis of four Campylobacterales , 2004, Nature Reviews Microbiology.

[67]  Robert C. Edgar,et al.  MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.

[68]  A. Galazka,et al.  Resurgence of diphtheria , 1995, European Journal of Epidemiology.

[69]  Oscar P. Kuipers,et al.  Projector 2: contig mapping for efficient gap-closure of prokaryotic genome sequence assemblies , 2005, Nucleic Acids Res..

[70]  S. Lee,et al.  Metabolic Engineering of Escherichia coli for Enhanced Production of Succinic Acid, Based on Genome Comparison and In Silico Gene Knockout Simulation , 2005, Applied and Environmental Microbiology.

[71]  Jaideep P. Sundaram,et al.  Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome". , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[72]  Erik L. L. Sonnhammer,et al.  Inparanoid: a comprehensive database of eukaryotic orthologs , 2004, Nucleic Acids Res..

[73]  Kim R. Rasmussen,et al.  Efficient q-Gram Filters for Finding All-Matches Over a Given Length , 2005 .

[74]  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.

[75]  Sang Yup Lee,et al.  Systems biotechnology for strain improvement. , 2005, Trends in biotechnology.

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

[77]  Gaston H. Gonnet,et al.  OMA, A Comprehensive, Automated Project for the Identification of Orthologs from Complete Genome Data: Introduction and First Achievements , 2005, Comparative Genomics.

[78]  Daniela Bartels,et al.  BACCardI-a tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison , 2005, Bioinform..

[79]  H. Tettelin,et al.  The microbial pan-genome. , 2005, Current opinion in genetics & development.

[80]  H. Tettelin,et al.  Identification of a Universal Group B Streptococcus Vaccine by Multiple Genome Screen , 2005, Science.

[81]  B. Snel,et al.  Toward Automatic Reconstruction of a Highly Resolved Tree of Life , 2006, Science.

[82]  Mark J. Pallen,et al.  xBASE, a collection of online databases for bacterial comparative genomics , 2005, Nucleic Acids Res..

[83]  M. Stanhope,et al.  Evolution of the core and pan-genome of Streptococcus: positive selection, recombination, and genome composition , 2007, Genome Biology.

[84]  C. Buchrieser,et al.  How to become a uropathogen: Comparative genomic analysis of extraintestinal pathogenic Escherichia coli strains , 2006, Proceedings of the National Academy of Sciences.

[85]  Katherine H. Huang,et al.  Comparative genomics of the lactic acid bacteria , 2006, Proceedings of the National Academy of Sciences.

[86]  Weiguo Liu,et al.  Bio-sequence database scanning on a GPU , 2006, Proceedings 20th IEEE International Parallel & Distributed Processing Symposium.

[87]  Stijn van Dongen,et al.  miRBase: microRNA sequences, targets and gene nomenclature , 2005, Nucleic Acids Res..

[88]  Jun Yao,et al.  SAGE and related approaches for cancer target identification. , 2006, Drug discovery today.

[89]  M. Inui,et al.  Comparative analysis of the Corynebacterium glutamicum group and complete genome sequence of strain R. , 2007, Microbiology.

[90]  Daniel H. Huson,et al.  OSLay: optimal syntenic layout of unfinished assemblies , 2007, Bioinform..

[91]  Bastien Chevreux MIRA: An Automated Genome and EST Assembler , 2007 .

[92]  R. Rappuoli,et al.  The pan-genome: towards a knowledge-based discovery of novel targets for vaccines and antibacterials. , 2007, Drug discovery today.

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

[94]  Gerard Talavera,et al.  Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. , 2007, Systematic biology.

[95]  Chris Mungall,et al.  A Chado case study: an ontology-based modular schema for representing genome-associated biological information , 2007, ISMB/ECCB.

[96]  Robert S. Harris,et al.  Improved pairwise alignment of genomic dna , 2007 .

[97]  Ikuo Uchiyama,et al.  MBGD: a platform for microbial comparative genomics based on the automated construction of orthologous groups , 2006, Nucleic Acids Res..

[98]  Michael Farrar,et al.  Sequence analysis Striped Smith – Waterman speeds database searches six times over other SIMD implementations , 2007 .

[99]  Lucian Ilie,et al.  Multiple spaced seeds for homology search , 2007, Bioinform..

[100]  A. Mortazavi,et al.  Genome-Wide Mapping of in Vivo Protein-DNA Interactions , 2007, Science.

[101]  P. Bork,et al.  Quantification of insect genome divergence. , 2007, Trends in genetics : TIG.

[102]  Ziheng Yang PAML 4: phylogenetic analysis by maximum likelihood. , 2007, Molecular biology and evolution.

[103]  Amitabh Varshney,et al.  High-throughput sequence alignment using Graphics Processing Units , 2007, BMC Bioinformatics.

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

[105]  Alexander Goesmann,et al.  EDGAR: A software framework for the comparative analysis of prokaryotic genomes , 2009, BMC Bioinformatics.

[106]  M. Freeling,et al.  How to usefully compare homologous plant genes and chromosomes as DNA sequences. , 2008, The Plant journal : for cell and molecular biology.

[107]  Jens Stoye,et al.  MeltDB: a software platform for the analysis and integration of metabolomics experiment data , 2008, Bioinform..

[108]  Christophe Dessimoz,et al.  SWPS3 – fast multi-threaded vectorized Smith-Waterman for IBM Cell/B.E. and ×86/SSE2 , 2008, BMC Research Notes.

[109]  David R. Riley,et al.  Comparative genomics: the bacterial pan-genome. , 2008, Current opinion in microbiology.

[110]  A. Goesmann,et al.  Whole-genome comparison of disease and carriage strains provides insights into virulence evolution in Neisseria meningitidis , 2008, Proceedings of the National Academy of Sciences.

[111]  Ruiqiang Li,et al.  SOAP: short oligonucleotide alignment program , 2008, Bioinform..

[112]  Nancy F. Hansen,et al.  Accurate Whole Human Genome Sequencing using Reversible Terminator Chemistry , 2008, Nature.

[113]  Jiaqi Tang,et al.  Identification and Experimental Verification of Protective Antigens Against Streptococcus suis Serotype 2 Based on Genome Sequence Analysis , 2008, Current Microbiology.

[114]  Giorgio Valle,et al.  CUDA compatible GPU cards as efficient hardware accelerators for Smith-Waterman sequence alignment , 2008, BMC Bioinformatics.

[115]  J. Poulain,et al.  High quality draft sequences for prokaryotic genomes using a mix of new sequencing technologies , 2008, BMC Genomics.

[116]  Mark J. Pallen,et al.  xBASE2: a comprehensive resource for comparative bacterial genomics , 2007, Nucleic Acids Res..

[117]  Cole Trapnell,et al.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.

[118]  Andreas Tauch,et al.  EMMA 2 – A MAGE-compliant system for the collaborative analysis and integration of microarray data , 2009, BMC Bioinformatics.

[119]  E. Sontheimer,et al.  Origins and Mechanisms of miRNAs and siRNAs , 2009, Cell.

[120]  C. Fields,et al.  Biogeography of the Sulfolobus islandicus pan-genome , 2009, Proceedings of the National Academy of Sciences.

[121]  Andrew R. Francis,et al.  The epidemiological fitness cost of drug resistance in Mycobacterium tuberculosis , 2009, Proceedings of the National Academy of Sciences.

[122]  H. Tettelin The bacterial pan-genome and reverse vaccinology. , 2009, Genome dynamics.

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

[124]  A. Goesmann,et al.  Complete genome sequence and lifestyle of black-pigmented Corynebacterium aurimucosum ATCC 700975 (formerly C. nigricans CN-1) isolated from a vaginal swab of a woman with spontaneous abortion , 2010, BMC Genomics.

[125]  J. Kitzman,et al.  Personalized Copy-Number and Segmental Duplication Maps using Next-Generation Sequencing , 2009, Nature Genetics.

[126]  Michael Brudno,et al.  SHRiMP: Accurate Mapping of Short Color-space Reads , 2009, PLoS Comput. Biol..

[127]  Brian D. Ondov,et al.  Structure and Complexity of a Bacterial Transcriptome , 2009, Journal of bacteriology.

[128]  Aaron E. Darling,et al.  Reordering contigs of draft genomes using the Mauve Aligner , 2009, Bioinform..

[129]  Christophe Dessimoz,et al.  Phylogenetic and Functional Assessment of Orthologs Inference Projects and Methods , 2009, PLoS Comput. Biol..

[130]  M. Gerstein,et al.  RNA-Seq: a revolutionary tool for transcriptomics , 2009, Nature Reviews Genetics.

[131]  Thomas M. Keane,et al.  ABACAS: algorithm-based automatic contiguation of assembled sequences , 2009, Bioinform..

[132]  S. Turner,et al.  Real-Time DNA Sequencing from Single Polymerase Molecules , 2009, Science.

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

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

[135]  Giorgio Valle,et al.  PASS: a program to align short sequences , 2009, Bioinform..

[136]  Siu-Ming Yiu,et al.  SOAP2: an improved ultrafast tool for short read alignment , 2009, Bioinform..

[137]  Paolo Ferragina,et al.  Indexing compressed text , 2005, JACM.

[138]  Lisa J. Murray,et al.  Genomic Diversity among Drug Sensitive and Multidrug Resistant Isolates of Mycobacterium tuberculosis with Identical DNA Fingerprints , 2009, PloS one.

[139]  Yongchao Liu,et al.  CUDASW++: optimizing Smith-Waterman sequence database searches for CUDA-enabled graphics processing units , 2009, BMC Research Notes.

[140]  Yongxiang Zhang,et al.  Pan-genome sequence analysis using Panseq: an online tool for the rapid analysis of core and accessory genomic regions , 2010, BMC Bioinformatics.

[141]  Erin Beck,et al.  The comprehensive microbial resource , 2000, Nucleic Acids Res..

[142]  Roger D. Chamberlain,et al.  Accelerating HMMER on GPUs by implementing hybrid data and task parallelism , 2010, BCB '10.

[143]  Kristin Reiche,et al.  The primary transcriptome of the major human pathogen Helicobacter pylori , 2010, Nature.

[144]  T. H. Smits,et al.  Complete genome sequence of the fire blight pathogen Erwinia amylovora CFBP 1430 and comparison to other Erwinia spp. , 2010, Molecular plant-microbe interactions : MPMI.

[145]  Faraz Hach,et al.  mrsFAST: a cache-oblivious algorithm for short-read mapping , 2010, Nature Methods.

[146]  D. Ussery,et al.  Comparison of 61 Sequenced Escherichia coli Genomes , 2010, Microbial Ecology.

[147]  Jens Stoye,et al.  BIOINFORMATICS APPLICATIONS NOTE , 2009 .

[148]  Ikuo Uchiyama,et al.  MBGD update 2010: toward a comprehensive resource for exploring microbial genome diversity , 2009, Nucleic Acids Res..

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

[150]  Stefan Götz,et al.  SIMAP—a comprehensive database of pre-calculated protein sequence similarities, domains, annotations and clusters , 2009, Nucleic Acids Res..

[151]  S. Salzberg,et al.  Probing the pan-genome of Listeria monocytogenes: new insights into intraspecific niche expansion and genomic diversification , 2010, BMC Genomics.

[152]  S. Jonjić,et al.  Modulation of natural killer cell activity by viruses. , 2010, Current opinion in microbiology.

[153]  E. Lyons,et al.  Comparative genomics with maize and other grasses: from genes to genomes! , 2011 .

[154]  T. H. Smits,et al.  Genome of a European Fresh-Vegetable Food Safety Outbreak Strain of Salmonella enterica subsp. enterica Serovar Weltevreden , 2011, Journal of bacteriology.

[155]  E. Eichler,et al.  Limitations of next-generation genome sequence assembly , 2011, Nature Methods.

[156]  J. Brosius,et al.  The rocks and shallows of deep RNA sequencing: Examples in the Vibrio cholerae RNome. , 2011, RNA.

[157]  M. Iacono,et al.  The genomics of Acinetobacter baumannii: Insights into genome plasticity, antimicrobial resistance and pathogenicity , 2011, IUBMB life.

[158]  T. H. Smits,et al.  Genome Sequence of an Erwinia amylovora Strain with Pathogenicity Restricted to Rubus Plants , 2010, Journal of bacteriology.

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

[160]  Kelvin H. Lee,et al.  The genomic sequence of the Chinese hamster ovary (CHO)-K1 cell line , 2011, Nature Biotechnology.

[161]  Burkhard Linke,et al.  Conveyor: a workflow engine for bioinformatics analyses , 2011, Bioinform..

[162]  W. D. de Vos,et al.  Comparative genomics of Lactobacillus , 2011, Microbial biotechnology.

[163]  M. Chase,et al.  Use of whole genome sequencing to estimate the mutation rate of Mycobacterium tuberculosis during latent infection , 2011, Nature Genetics.

[164]  T. H. Smits,et al.  Metabolic Versatility and Antibacterial Metabolite Biosynthesis Are Distinguishing Genomic Features of the Fire Blight Antagonist Pantoea vagans C9-1 , 2011, PloS one.

[165]  J. Stoye,et al.  Sequencing of high G+C microbial genomes using the ultrafast pyrosequencing technology. , 2011, Journal of biotechnology.

[166]  Robert Grossman,et al.  PeakRanger: A cloud-enabled peak caller for ChIP-seq data , 2011, BMC Bioinformatics.

[167]  Damian Szklarczyk,et al.  The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored , 2010, Nucleic Acids Res..

[168]  Jens Stoye,et al.  Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming , 2011, Bioinform..

[169]  Sean R. Eddy,et al.  Accelerated Profile HMM Searches , 2011, PLoS Comput. Biol..

[170]  H. Klenk,et al.  Relationship of Bacillus amyloliquefaciens clades associated with strains DSM 7T and FZB42T: a proposal for Bacillus amyloliquefaciens subsp. amyloliquefaciens subsp. nov. and Bacillus amyloliquefaciens subsp. plantarum subsp. nov. based on complete genome sequence comparisons. , 2011, International journal of systematic and evolutionary microbiology.

[171]  J. Blom,et al.  Erwinia amylovora Novel Plasmid pEI70: Complete Sequence, Biogeography, and Role in Aggressiveness in the Fire Blight Phytopathogen , 2011, PloS one.

[172]  J. Blom,et al.  Complete genome sequence, lifestyle, and multi-drug resistance of the human pathogen Corynebacterium resistens DSM 45100 isolated from blood samples of a leukemia patient , 2012, BMC Genomics.

[173]  A. Goesmann,et al.  RAPYD--rapid annotation platform for yeast data. , 2011, Journal of biotechnology.

[174]  Juliane C. Dohm,et al.  Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome Analyzer systems , 2011, Genome Biology.

[175]  Gaston H. Gonnet,et al.  OMA 2011: orthology inference among 1000 complete genomes , 2010, Nucleic Acids Res..

[176]  Complete Genome Sequence of Clinical Isolate Pantoea ananatis LMG 5342 , 2012, Journal of bacteriology.

[177]  A. Goesmann,et al.  Comparative analysis of the Hrp pathogenicity island of Rubus- and Spiraeoideae-infecting Erwinia amylovora strains identifies the IT region as a remnant of an integrative conjugative element. , 2012, Gene.

[178]  Siu-Ming Yiu,et al.  SOAP3: ultra-fast GPU-based parallel alignment tool for short reads , 2012, Bioinform..

[179]  J. Blom,et al.  The Complete Genome of Bacillus amyloliquefaciens subsp. plantarum CAU B946 Contains a Gene Cluster for Nonribosomal Synthesis of Iturin A , 2012, Journal of bacteriology.

[180]  T. H. Smits,et al.  Comparative genomic analysis of Salmonella enterica subsp. enterica serovar Weltevreden foodborne strains with other serovars. , 2012, International journal of food microbiology.

[181]  J. Blom,et al.  Pangenomic Study of Corynebacterium diphtheriae That Provides Insights into the Genomic Diversity of Pathogenic Isolates from Cases of Classical Diphtheria, Endocarditis, and Pneumonia , 2012, Journal of bacteriology.

[182]  Jae-Yoon Jung,et al.  Roundup 2.0: enabling comparative genomics for over 1800 genomes , 2012, Bioinform..

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

[184]  A. Goesmann,et al.  Insights into the completely annotated genome of Lactobacillus buchneri CD034, a strain isolated from stable grass silage. , 2012, Journal of biotechnology.

[185]  Jonathan Crabtree,et al.  Using Sybil for interactive comparative genomics of microbes on the web , 2011, Bioinform..

[186]  Damian Szklarczyk,et al.  eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges , 2011, Nucleic Acids Res..

[187]  J. Blom,et al.  Complete genome sequence of Saccharothrix espanaensis DSM 44229T and comparison to the other completely sequenced Pseudonocardiaceae , 2012, BMC Genomics.

[188]  J. Blom,et al.  Sequence of Two Plasmids from Clostridium perfringens Chicken Necrotic Enteritis Isolates and Comparison with C. perfringens Conjugative Plasmids , 2012, PloS one.

[189]  I-Min A. Chen,et al.  The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata , 2011, Nucleic Acids Res..

[190]  J. Baumbach,et al.  PIPS: Pathogenicity Island Prediction Software , 2012, PloS one.

[191]  Yongchao Liu,et al.  CUSHAW: a CUDA compatible short read aligner to large genomes based on the Burrows-Wheeler transform , 2012, Bioinform..

[192]  Oliver Jahns ChIP-basierter Screen und Untersuchungen zu Protein-DNA-Interaktionen ausgewählter Regulatoren der Flavonoidbiosynthese in Arabidopsis thaliana , 2012 .

[193]  J. Kalinowski,et al.  Corynebacterium glutamicum promoters: a practical approach , 2013, Microbial biotechnology.