Identification of new protein coding sequences and signal peptidase cleavage sites of Helicobacter pylori strain 26695 by proteogenomics.

[1]  Johannes Griss,et al.  The Proteomics Identifications (PRIDE) database and associated tools: status in 2013 , 2012, Nucleic Acids Res..

[2]  S. Kalkhof,et al.  Quantitative proteomics reveals altered expression of extracellular matrix related proteins of human primary dermal fibroblasts in response to sulfated hyaluronan and collagen applied as artificial extracellular matrix , 2012, Journal of Materials Science: Materials in Medicine.

[3]  Karl Mechtler,et al.  Analysis of protein mixtures from whole-cell extracts by single-run nanoLC-MS/MS using ultralong gradients , 2012, Nature Protocols.

[4]  Gian Franco Gensini,et al.  Management of Helicobacter pylori infection—the Maastricht IV/ Florence Consensus Report , 2012, Gut.

[5]  Sherry L. Niessen,et al.  Type I Signal Peptidase and Protein Secretion in Staphylococcus aureus , 2012, Journal of bacteriology.

[6]  T. Parish,et al.  Inhibition of the Sole Type I Signal Peptidase of Mycobacterium tuberculosis Is Bactericidal under Replicating and Nonreplicating Conditions , 2012, Journal of bacteriology.

[7]  T. Hibi,et al.  FecA1, a bacterial iron transporter, determines the survival of Helicobacter pylori in the stomach. , 2012, Free radical biology & medicine.

[8]  Y. Yamaoka,et al.  Molecular epidemiology, population genetics, and pathogenic role of Helicobacter pylori. , 2012, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.

[9]  Peter Williams,et al.  IMG: the integrated microbial genomes database and comparative analysis system , 2011, Nucleic Acids Res..

[10]  Andrew M. Smith,et al.  The UCSC Archaeal Genome Browser: 2012 update , 2011, Nucleic Acids Res..

[11]  P. Stadler,et al.  Genome-wide transcriptome analysis of the plant pathogen Xanthomonas identifies sRNAs with putative virulence functions , 2011, Nucleic acids research.

[12]  C. Dutta,et al.  In silico quest for putative drug targets in Helicobacter pylori HPAG1: molecular modeling of candidate enzymes from lipopolysaccharide biosynthesis pathway , 2012, Journal of Molecular Modeling.

[13]  J. C. Tran,et al.  Intact proteome fractionation strategies compatible with mass spectrometry , 2011, Expert review of proteomics.

[14]  J. Armengaud,et al.  Comparative Proteogenomics of Twelve Roseobacter Exoproteomes Reveals Different Adaptive Strategies Among These Marine Bacteria* , 2011, Molecular & Cellular Proteomics.

[15]  Martin Kircher,et al.  Deep proteome and transcriptome mapping of a human cancer cell line , 2011, Molecular systems biology.

[16]  M. Mann,et al.  System-wide Perturbation Analysis with Nearly Complete Coverage of the Yeast Proteome by Single-shot Ultra HPLC Runs on a Bench Top Orbitrap* , 2011, Molecular & Cellular Proteomics.

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

[18]  Liam J McGuffin,et al.  Proteogenomics and in silico structural and functional annotation of the barley powdery mildew Blumeria graminis f. sp. hordei. , 2011, Methods.

[19]  M. Sarwal,et al.  Functional proteogenomics--embracing complexity. , 2011, Seminars in immunology.

[20]  P. Graumann,et al.  Helicobacter pyloriPossesses Four Coiled-Coil-Rich Proteins That Form Extended Filamentous Structures and Control Cell Shape and Motility , 2011, Journal of bacteriology.

[21]  Michaela Scigelova,et al.  Fourier Transform Mass Spectrometry , 2011, Molecular & Cellular Proteomics.

[22]  Nick Goldman,et al.  RNAcode: robust discrimination of coding and noncoding regions in comparative sequence data. , 2011, RNA.

[23]  Lennart Martens,et al.  SearchGUI: An open‐source graphical user interface for simultaneous OMSSA and X!Tandem searches , 2011, Proteomics.

[24]  M. Bergen,et al.  Cell fractionation - an important tool for compartment proteomics , 2011 .

[25]  Sven Nahnsen,et al.  Mass spectrometry at the interface of proteomics and genomics. , 2011, Molecular bioSystems.

[26]  M. Tomita,et al.  OryzaPG-DB: Rice Proteome Database based on Shotgun Proteogenomics , 2011, BMC Plant Biology.

[27]  N. Malys,et al.  Translation initiation: variations in the mechanism can be anticipated , 2011, Cellular and Molecular Life Sciences.

[28]  Hwee Tong Tan,et al.  Subcellular fractionation methods and strategies for proteomics , 2010, Proteomics.

[29]  T. Hirayama,et al.  Helicobacter pylori CagA inhibits endocytosis of cytotoxin VacA in host cells , 2010, Disease Models & Mechanisms.

[30]  Manolis Kellis,et al.  Optimization of parameters for coverage of low molecular weight proteins , 2010, Analytical and bioanalytical chemistry.

[31]  R. Sommer,et al.  Proteogenomics of Pristionchus pacificus reveals distinct proteome structure of nematode models. , 2010, Genome research.

[32]  E. Lahner,et al.  Helicobacter pylori immunoproteomics in gastric cancer and gastritis of the carcinoma phenotype , 2010, Expert review of proteomics.

[33]  Masaru Tomita,et al.  One-dimensional capillary liquid chromatographic separation coupled with tandem mass spectrometry unveils the Escherichia coli proteome on a microarray scale. , 2010, Analytical chemistry.

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

[35]  J. Coon,et al.  Value of using multiple proteases for large-scale mass spectrometry-based proteomics. , 2010, Journal of proteome research.

[36]  D. Vergara,et al.  Biomolecular pathogenesis of borderline ovarian tumors: focusing target discovery through proteogenomics. , 2010, Current cancer drug targets.

[37]  Lennart Martens,et al.  The Proteomics Identifications database: 2010 update , 2009, Nucleic Acids Res..

[38]  Sabine S. Lange,et al.  Helicobacter pylori proteomics by 2‐DE/MS, 1‐DE‐LC/MS and functional data mining , 2010, Proteomics.

[39]  Wu-chun Feng,et al.  Missing genes in the annotation of prokaryotic genomes , 2010, BMC Bioinformatics.

[40]  Carrie D. Nicora,et al.  Proteomic Detection of Non-Annotated Protein-Coding Genes in Pseudomonas fluorescens Pf0-1 , 2009, PloS one.

[41]  J. Vogel,et al.  Deep sequencing analysis of the Methanosarcina mazei Gö1 transcriptome in response to nitrogen availability , 2009, Proceedings of the National Academy of Sciences.

[42]  B. Roschitzki,et al.  Community proteogenomics reveals insights into the physiology of phyllosphere bacteria , 2009, Proceedings of the National Academy of Sciences.

[43]  James K. Hane,et al.  Deep proteogenomics; high throughput gene validation by multidimensional liquid chromatography and mass spectrometry of proteins from the fungal wheat pathogen Stagonospora nodorum , 2009, BMC Bioinformatics.

[44]  Laurie J. Heyer,et al.  Evaluation of Three Automated Genome Annotations for Halorhabdus utahensis , 2009, PloS one.

[45]  K. Sandra,et al.  Highly efficient peptide separations in proteomics. Part 2: bi- and multidimensional liquid-based separation techniques. , 2009, Journal of chromatography. B, Analytical technologies in the biomedical and life sciences.

[46]  F. Denoeud,et al.  Annotating genomes with massive-scale RNA sequencing , 2008, Genome Biology.

[47]  T. D. Schneider,et al.  Small membrane proteins found by comparative genomics and ribosome binding site models , 2008, Molecular microbiology.

[48]  Tim R. Mercer,et al.  Differentiating Protein-Coding and Noncoding RNA: Challenges and Ambiguities , 2008, PLoS Comput. Biol..

[49]  W. Qu,et al.  The changes of proteomes components of Helicobacter pylori in response to acid stress without urea , 2008, The Journal of Microbiology.

[50]  B. Williams,et al.  Mapping and quantifying mammalian transcriptomes by RNA-Seq , 2008, Nature Methods.

[51]  X. Mao,et al.  Proteomic Insights into Helicobacter pylori Coccoid Forms Under Oxidative Stress , 2008, Current Microbiology.

[52]  K. Sandra,et al.  Highly efficient peptide separations in proteomics Part 1. Unidimensional high performance liquid chromatography. , 2008, Journal of chromatography. B, Analytical technologies in the biomedical and life sciences.

[53]  J. C. Tran,et al.  Gel-eluted liquid fraction entrapment electrophoresis: an electrophoretic method for broad molecular weight range proteome separation. , 2008, Analytical chemistry.

[54]  Richard D. Smith,et al.  Proteogenomics: needs and roles to be filled by proteomics in genome annotation. , 2008, Briefings in functional genomics & proteomics.

[55]  William Stafford Noble,et al.  Posterior error probabilities and false discovery rates: two sides of the same coin. , 2008, Journal of proteome research.

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

[57]  Steven Salzberg,et al.  Identifying bacterial genes and endosymbiont DNA with Glimmer , 2007, Bioinform..

[58]  E. Kuipers,et al.  Pathogenesis of Helicobacter pylori Infection , 2006, Clinical Microbiology Reviews.

[59]  F. Mégraud,et al.  Identification of Markers for Helicobacter pylori Strains Isolated from Children with Peptic Ulcer Disease by Suppressive Subtractive Hybridization , 2006, Infection and Immunity.

[60]  Katherine S. Pollard,et al.  The UCSC Archaeal Genome Browser , 2005, Nucleic Acids Res..

[61]  Ming-Shiang Wu,et al.  Proteomic analysis of proteins expressed by Helicobacter pylori under oxidative stress , 2005, Proteomics.

[62]  Mark Borodovsky,et al.  GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses , 2005, Nucleic Acids Res..

[63]  Iain Beattie,et al.  Ultra-performance liquid chromatography coupled to quadrupole-orthogonal time-of-flight mass spectrometry. , 2004, Rapid communications in mass spectrometry : RCM.

[64]  Jacob D. Jaffe,et al.  The complete genome and proteome of Mycoplasma mobile. , 2004, Genome research.

[65]  Dieter Jahn,et al.  PrediSi: prediction of signal peptides and their cleavage positions , 2004, Nucleic Acids Res..

[66]  G. Crooks,et al.  WebLogo: a sequence logo generator. , 2004, Genome research.

[67]  D. Haussler,et al.  Aligning multiple genomic sequences with the threaded blockset aligner. , 2004, Genome research.

[68]  A. Labigne,et al.  A revised annotation and comparative analysis of Helicobacter pylori genomes. , 2003, Nucleic acids research.

[69]  Mark Borodovsky,et al.  Prokaryotic Gene Prediction Using GeneMark and GeneMark.hmm , 2003, Current protocols in bioinformatics.

[70]  W. Pearson,et al.  Current Protocols in Bioinformatics , 2002 .

[71]  C. Gualerzi,et al.  Leaderless mRNAs in bacteria: surprises in ribosomal recruitment and translational control , 2002, Molecular microbiology.

[72]  S. Andrews,et al.  Iron acquisition and virulence in Helicobacter pylori: a major role for FeoB, a high‐affinity ferrous iron transporter , 2000, Molecular microbiology.

[73]  M. Paetzel,et al.  The structure and mechanism of bacterial type I signal peptidases. A novel antibiotic target. , 2000, Pharmacology & therapeutics.

[74]  A Danchin,et al.  Detecting and analyzing DNA sequencing errors: toward a higher quality of the Bacillus subtilis genome sequence. , 1999, Genome research.

[75]  S. Armand,et al.  Regulation of the transcription of genes encoding different virulence factors in Helicobacter pylori by free iron. , 1999, FEMS microbiology letters.

[76]  Benjamin L. King,et al.  Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori , 1999, Nature.

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

[78]  Mark Borodovsky,et al.  The complete genome sequence of the gastric pathogen Helicobacter pylori , 1997, Nature.

[79]  K. Mullis,et al.  Specific enzymatic amplification of DNA in vitro: the polymerase chain reaction. , 1986, Cold Spring Harbor symposia on quantitative biology.

[80]  R. Doolittle,et al.  A simple method for displaying the hydropathic character of a protein. , 1982, Journal of molecular biology.

[81]  R. Staden.  A strategy of DNA sequencing employing computer programs. , 1979, Nucleic acids research.

[82]  F. Sanger,et al.  Nucleotide sequence of bacteriophage φX174 DNA , 1977, Nature.