Approaches to analyse dynamic microbial communities such as those seen in cystic fibrosis lung

[1]  Nello Cristianini,et al.  Support vector machines , 2009, Encyclopedia of Algorithms.

[2]  E. Mardis.  Next-generation DNA sequencing methods. , 2008, Annual review of genomics and human genetics.

[3]  D. Spandidos,et al.  Molecular diagnostic tools in mycobacteriology. , 2008, Journal of microbiological methods.

[4]  Andreas Christmann,et al.  Support vector machines , 2008, Data Mining and Knowledge Discovery Handbook.

[5]  P. Berche,et al.  Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for Identification of Nonfermenting Gram-Negative Bacilli Isolated from Cystic Fibrosis Patients , 2008, Journal of Clinical Microbiology.

[6]  Caleb Webber,et al.  SCANPS: a web server for iterative protein sequence database searching by dynamic programing, with display in a hierarchical SCOP browser , 2008, Nucleic Acids Res..

[7]  R. Widen,et al.  Comparison of DNA Pyrosequencing with Alternative Methods for Identification of Mycobacteria , 2008, Journal of Clinical Microbiology.

[8]  P. Demirev,et al.  Mass spectrometry for rapid characterization of microorganisms. , 1993, Annual review of analytical chemistry.

[9]  K. Hjort,et al.  Rapid lab-on-a-chip profiling of human gut bacteria. , 2008, Journal of microbiological methods.

[10]  S. Schuster.  Next-generation sequencing transforms today's biology , 2008, Nature Methods.

[11]  N. Pace,et al.  Molecular identification of bacteria in bronchoalveolar lavage fluid from children with cystic fibrosis , 2007, Proceedings of the National Academy of Sciences.

[12]  K. Patrick,et al.  454 Life Sciences: Illuminating the future of genome sequencing and personalized medicine , 2007, The Yale journal of biology and medicine.

[13]  Jay D. Evans,et al.  A Metagenomic Survey of Microbes in Honey Bee Colony Collapse Disorder , 2007, Science.

[14]  Ruth Ann Luna,et al.  DNA Pyrosequencing-Based Bacterial Pathogen Identification in a Pediatric Hospital Setting , 2007, Journal of Clinical Microbiology.

[15]  K. Mathee,et al.  Microbial Metagenome Profiling Using Amplicon Length Heterogeneity‐Polymerase Chain Reaction Proves More Effective Than Elemental Analysis in Discriminating Soil Specimens * , 2006, Journal of forensic sciences.

[16]  K. Mathee,et al.  An assessment of the hypervariable domains of the 16S rRNA genes for their value in determining microbial community diversity: the paradox of traditional ecological indices. , 2006, FEMS microbiology ecology.

[17]  Susan M. Huse,et al.  Microbial diversity in the deep sea and the underexplored “rare biosphere” , 2006, Proceedings of the National Academy of Sciences.

[18]  I. Vliegen,et al.  Rapid identification of bacteria by real-time amplification and sequencing of the 16S rRNA gene. , 2006, Journal of microbiological methods.

[19]  J. Mcgowan.  Resistance in nonfermenting gram-negative bacteria: multidrug resistance to the maximum. , 2006, The American journal of medicine.

[20]  S. Rüsch-Gerdes,et al.  Evaluation of the GenoType Mycobacterium Assay for Identification of Mycobacterial Species from Cultures , 2006, Journal of Clinical Microbiology.

[21]  G. Narasimhan,et al.  An eco-informatics tool for microbial community studies: supervised classification of Amplicon Length Heterogeneity (ALH) profiles of 16S rRNA. , 2006, Journal of microbiological methods.

[22]  R. Zbinden,et al.  16S rRNA Gene Sequencing versus the API 20 NE System and the VITEK 2 ID-GNB Card for Identification of Nonfermenting Gram-Negative Bacteria in the Clinical Laboratory , 2006, Journal of Clinical Microbiology.

[23]  Eoin L. Brodie,et al.  Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB , 2006, Applied and Environmental Microbiology.

[24]  M. Doud.  The role of amplicon length heterogeneity-polymerase chain reaction in microbial community profiling and presumptive testing of bioagents , 2006 .

[25]  S. Hober,et al.  Pyrosequencing: history, biochemistry and future. , 2006, Clinica chimica acta; international journal of clinical chemistry.

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

[27]  S. Grossman,et al.  Pathophysiology of cystic fibrosis: implications for critical care nurses. , 2005, Critical care nurse.

[28]  P. Berche,et al.  Age-Related Prevalence and Distribution of Nontuberculous Mycobacterial Species among Patients with Cystic Fibrosis , 2005, Journal of Clinical Microbiology.

[29]  Xiuwen Liu,et al.  Face detection using spectral histograms and SVMs , 2005, IEEE Transactions on Systems, Man, and Cybernetics, Part B (Cybernetics).

[30]  G. Procop,et al.  Pyrosequencing as a tool for the identification of common isolates of Mycobacterium sp. , 2005, Diagnostic microbiology and infectious disease.

[31]  K. Field,et al.  Microbial community dynamics based on 16S rRNA gene profiles in a Pacific Northwest estuary and its tributaries. , 2005, FEMS microbiology ecology.

[32]  P. Vandamme,et al.  PCR-Based Assay for Differentiation of Pseudomonas aeruginosa from Other Pseudomonas Species Recovered from Cystic Fibrosis Patients , 2004, Journal of Clinical Microbiology.

[33]  O. White,et al.  Environmental Genome Shotgun Sequencing of the Sargasso Sea , 2004, Science.

[34]  Bernhard Schölkopf,et al.  Kernel Methods in Computational Biology , 2005 .

[35]  C. Hart,et al.  Bacterial Diversity in Cases of Lung Infection in Cystic Fibrosis Patients: 16S Ribosomal DNA (rDNA) Length Heterogeneity PCR and 16S rDNA Terminal Restriction Fragment Length Polymorphism Profiling , 2003, Journal of Clinical Microbiology.

[36]  Eric R. Ziegel,et al.  The Elements of Statistical Learning , 2003, Technometrics.

[37]  C. Litchfield,et al.  A comparison of DNA profiling techniques for monitoring nutrient impact on microbial community composition during bioremediation of petroleum-contaminated soils. , 2003, Journal of microbiological methods.

[38]  Yoonkyung Lee,et al.  Classification of Multiple Cancer Types by Multicategory Support Vector Machines Using Gene Expression Data , 2003, Bioinform..

[39]  J. Miller,et al.  Evaluation of the Vitek 2 ID-GNB Assay for Identification of Members of the Family Enterobacteriaceae and Other Nonenteric Gram-Negative Bacilli and Comparison with the Vitek GNI+ Card , 2003, Journal of Clinical Microbiology.

[40]  K. Walsh,et al.  Using ecological diversity measures with bacterial communities. , 2003, FEMS microbiology ecology.

[41]  E. Paul,et al.  Terminal Restriction Fragment Length Polymorphism Data Analysis for Quantitative Comparison of Microbial Communities , 2003, Applied and Environmental Microbiology.

[42]  Gaolin Zheng,et al.  Neural Network Classifiers and Gene Selection Methods for Microarray Data on Human Lung Adenocarcinoma , 2003 .

[43]  Thomas P. Curtis,et al.  Estimating prokaryotic diversity and its limits , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[44]  Lawrence O. Ticknor,et al.  Empirical and Theoretical Bacterial Diversity in Four Arizona Soils , 2002, Applied and Environmental Microbiology.

[45]  Gerald B. Pier,et al.  Lung Infections Associated with Cystic Fibrosis , 2002, Clinical Microbiology Reviews.

[46]  J. Jonasson,et al.  Classification, identification and subtyping of bacteria based on pyrosequencing and signature matching of 16S rDNA fragments , 2002, APMIS : acta pathologica, microbiologica, et immunologica Scandinavica.

[47]  K. Carroll,et al.  Identification of Mycobacterium spp. by Using a Commercial 16S Ribosomal DNA Sequencing Kit and Additional Sequencing Libraries , 2002, Journal of Clinical Microbiology.

[48]  Jean-Philippe Vert,et al.  Support Vector Machine Prediction of Signal Peptide Cleavage Site Using a New Class of Kernels for Strings , 2001, Pacific Symposium on Biocomputing.

[49]  John Quackenbush,et al.  Genesis: cluster analysis of microarray data , 2002, Bioinform..

[50]  David Haussler,et al.  Classifying G-protein coupled receptors with support vector machines , 2002, Bioinform..

[51]  S. Whittier.  Update on the microbiology of crystic fibrosis: traditional and emergin pathogens , 2001 .

[52]  J. Jonasson,et al.  Rapid molecular identification and subtyping of Helicobacter pylori by pyrosequencing of the 16S rDNA variable V1 and V3 regions. , 2001, FEMS microbiology letters.

[53]  Lawrence O. Ticknor,et al.  Phylogenetic Specificity and Reproducibility and New Method for Analysis of Terminal Restriction Fragment Profiles of 16S rRNA Genes from Bacterial Communities , 2001, Applied and Environmental Microbiology.

[54]  James R. Cole,et al.  rrndb: the Ribosomal RNA Operon Copy Number Database , 2001, Nucleic Acids Res..

[55]  R. Griffiths,et al.  Rapid Method for Coextraction of DNA and RNA from Natural Environments for Analysis of Ribosomal DNA- and rRNA-Based Microbial Community Composition , 2000, Applied and Environmental Microbiology.

[56]  P. Beringer,et al.  Unusual respiratory bacterial flora in cystic fibrosis: microbiologic and clinical features , 2000, Current opinion in pulmonary medicine.

[57]  Nello Cristianini,et al.  Support vector machine classification and validation of cancer tissue samples using microarray expression data , 2000, Bioinform..

[58]  C. Kuske,et al.  Assessment of Microbial Diversity in Four Southwestern United States Soils by 16S rRNA Gene Terminal Restriction Fragment Analysis , 2000, Applied and Environmental Microbiology.

[59]  M. Schutter,et al.  Use of Length Heterogeneity PCR and Fatty Acid Methyl Ester Profiles To Characterize Microbial Communities in Soil , 2000, Applied and Environmental Microbiology.

[60]  D Haussler,et al.  Knowledge-based analysis of microarray gene expression data by using support vector machines. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[61]  A. Hiraishi,et al.  Terminal restriction pattern analysis of 16S rRNA genes for the characterization of bacterial communities of activated sludge. , 2000, Journal of bioscience and bioengineering.

[62]  A. van Belkum,et al.  Comparison of conventional and molecular methods for the detection of bacterial pathogens in sputum samples from cystic fibrosis patients. , 2000, FEMS immunology and medical microbiology.

[63]  P. Wigley,et al.  Genotypic and phenotypic relationships in Burkholderia cepacia isolated from cystic fibrosis patients and the environment , 1999, Journal of applied microbiology.

[64]  K. Kunzelmann.  The cystic fibrosis transmembrane conductance regulator and its function in epithelial transport. , 1999, Reviews of physiology, biochemistry and pharmacology.

[65]  James R. Cole,et al.  A new version of the RDP (Ribosomal Database Project) , 1999, Nucleic Acids Res..

[66]  S. Giovannoni,et al.  Kinetic Bias in Estimates of Coastal Picoplankton Community Structure Obtained by Measurements of Small-Subunit rRNA Gene PCR Amplicon Length Heterogeneity , 1998, Applied and Environmental Microbiology.

[67]  M. Ronaghi,et al.  A Sequencing Method Based on Real-Time Pyrophosphate , 1998, Science.

[68]  J. C. BurgesChristopher.  A Tutorial on Support Vector Machines for Pattern Recognition , 1998 .

[69]  S. Giovannoni,et al.  Bacterial diversity among small-subunit rRNA gene clones and cellular isolates from the same seawater sample , 1997, Applied and environmental microbiology.

[70]  Y Van de Peer,et al.  A quantitative map of nucleotide substitution rates in bacterial rRNA. , 1996, Nucleic acids research.

[71]  Huan Liu,et al.  Book review: Machine Learning, Neural and Statistical Classification Edited by D. Michie, D.J. Spiegelhalter and C.C. Taylor (Ellis Horwood Limited, 1994) , 1996, SGAR.

[72]  David J. Spiegelhalter,et al.  Machine Learning, Neural and Statistical Classification , 2009 .

[73]  J. Sninsky,et al.  Recent advances in the polymerase chain reaction , 1991, Science.

[74]  D. M. Ward,et al.  16S rRNA sequences reveal uncultured inhabitants of a well-studied thermal community. , 1990, FEMS microbiology reviews.

[75]  D. M. Ward,et al.  16S rRNA sequences reveal numerous uncultured microorganisms in a natural community , 1990, Nature.

[76]  R. Colwell,et al.  Survival strategies of bacteria in the natural environment. , 1987, Microbiological reviews.

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

[78]  F. Sanger,et al.  DNA sequencing with chain-terminating inhibitors. , 1977, Proceedings of the National Academy of Sciences of the United States of America.

[79]  E. A. Morgan,et al.  Genetics of bacterial ribosomes. , 1977, Annual review of genetics.

[80]  M. Nomura,et al.  Reconstitution of 50S Ribosomal Subunits from Dissociated Molecular Components , 1970, Nature.