Something from (almost) nothing: the impact of multiple displacement amplification on microbial ecology

[1]  Josh D Neufeld,et al.  Marine methylotrophs revealed by stable-isotope probing, multiple displacement amplification and metagenomics. , 2008, Environmental microbiology.

[2]  Forest Rohwer,et al.  Metagenomic analysis of the microbial community associated with the coral Porites astreoides. , 2007, Environmental microbiology.

[3]  R. J. Mitchell,et al.  Increasing amplification success of forensic DNA samples using multiple displacement amplification , 2007, Forensic science, medicine, and pathology.

[4]  Roger S Lasken,et al.  Single-cell genomic sequencing using Multiple Displacement Amplification. , 2007, Current opinion in microbiology.

[5]  Timothy B. Stockwell,et al.  Nanoliter Reactors Improve Multiple Displacement Amplification of Genomes from Single Cells , 2007, PLoS genetics.

[6]  Garth D Ehrlich,et al.  Insights into the Genome of Large Sulfur Bacteria Revealed by Analysis of Single Filaments , 2007, PLoS biology.

[7]  Michael Wagner,et al.  Raman-FISH: combining stable-isotope Raman spectroscopy and fluorescence in situ hybridization for the single cell analysis of identity and function. , 2007, Environmental microbiology.

[8]  S. Quake,et al.  Dissecting biological “dark matter” with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth , 2007, Proceedings of the National Academy of Sciences.

[9]  Michael Wagner,et al.  Who eats what, where and when? Isotope-labelling experiments are coming of age , 2007, The ISME Journal.

[10]  Jizhong Zhou,et al.  Biphenyl-utilizing bacteria and their functional genes in a pine root zone contaminated with polychlorinated biphenyls (PCBs) , 2007, The ISME Journal.

[11]  R. Stepanauskas,et al.  Matching phylogeny and metabolism in the uncultured marine bacteria, one cell at a time , 2007, Proceedings of the National Academy of Sciences.

[12]  Timothy B. Stockwell,et al.  Mechanism of chimera formation during the Multiple Displacement Amplification reaction , 2007, BMC biotechnology.

[13]  Karsten Zengler,et al.  Targeted Access to the Genomes of Low-Abundance Organisms in Complex Microbial Communities , 2007, Applied and Environmental Microbiology.

[14]  B. Ahring,et al.  Specific single-cell isolation and genomic amplification of uncultured microorganisms , 2007, Applied Microbiology and Biotechnology.

[15]  A. Halpern,et al.  The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific , 2007, PLoS biology.

[16]  Eoin L. Brodie,et al.  Urban aerosols harbor diverse and dynamic bacterial populations , 2007, Proceedings of the National Academy of Sciences.

[17]  Marcy Yann,et al.  ヒト口腔からの微量の培養されないTM7微生物の単一細胞遺伝分析による生物学的「不明な物体」の詳細な分析 , 2007 .

[18]  A. Pérez-García,et al.  Multiple displacement amplification, a powerful tool for molecular genetic analysis of powdery mildew fungi , 2007, Current Genetics.

[19]  D. Foran,et al.  The Utility of Whole Genome Amplification for Typing Compromised Forensic Samples , 2006, Journal of forensic sciences.

[20]  Florent E. Angly,et al.  The Marine Viromes of Four Oceanic Regions , 2006, PLoS biology.

[21]  A. Syvänen,et al.  Multiple Displacement Amplification for Generating an Unlimited Source of DNA for Genotyping in Nonhuman Primate Species , 2006, International Journal of Primatology.

[22]  T. Urich,et al.  Archaea predominate among ammonia-oxidizing prokaryotes in soils , 2006, Nature.

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

[24]  Christopher W. Schadt,et al.  Microarray-Based Analysis of Subnanogram Quantities of Microbial Community DNAs by Using Whole-Community Genome Amplification , 2006, Applied and Environmental Microbiology.

[25]  Daikichi Mukoyama,et al.  Whole-metagenome amplification of a microbial community associated with scleractinian coral by multiple displacement amplification using phi29 polymerase. , 2006, Environmental microbiology.

[26]  G. Church,et al.  Sequencing genomes from single cells by polymerase cloning , 2006, Nature Biotechnology.

[27]  Marina G. Kalyuzhnaya,et al.  Fluorescence In Situ Hybridization-Flow Cytometry-Cell Sorting-Based Method for Separation and Enrichment of Type I and Type II Methanotroph Populations , 2006, Applied and Environmental Microbiology.

[28]  Tsutomu Mikawa,et al.  Improvements of rolling circle amplification (RCA) efficiency and accuracy using Thermus thermophilus SSB mutant protein , 2006, Nucleic acids research.

[29]  L. Van Haute,et al.  Optimization and evaluation of single‐cell whole‐genome multiple displacement amplification , 2006, Human mutation.

[30]  Eoin L. Brodie,et al.  Environmental Whole-Genome Amplification To Access Microbial Populations in Contaminated Sediments , 2006, Applied and Environmental Microbiology.

[31]  Susan E. Brown,et al.  Isothermal Amplification and Molecular Typing of the Obligate Intracellular Pathogen Mycobacterium leprae Isolated from Tissues of Unknown Origins , 2006, Journal of Clinical Microbiology.

[32]  L. Whyte,et al.  Microbial ecology and biodiversity in permafrost , 2006, Extremophiles.

[33]  M. Breitbart,et al.  Using pyrosequencing to shed light on deep mine microbial ecology , 2006, BMC Genomics.

[34]  A. J. Jones,et al.  At Least 1 in 20 16S rRNA Sequence Records Currently Held in Public Repositories Is Estimated To Contain Substantial Anomalies , 2005, Applied and Environmental Microbiology.

[35]  C. Hutchison,et al.  Cell-free cloning using φ29 DNA polymerase , 2005 .

[36]  P. Simonet,et al.  Efficient Procedure for Purification of Obligate Intracellular Wolbachia pipientis and Representative Amplification of Its Genome by Multiple-Displacement Amplification , 2005, Applied and Environmental Microbiology.

[37]  M. Breitbart,et al.  Method for discovering novel DNA viruses in blood using viral particle selection and shotgun sequencing. , 2005, BioTechniques.

[38]  M. Plummer,et al.  Use of whole genome amplification to rescue DNA from plasma samples. , 2005, BioTechniques.

[39]  S. Chanock,et al.  Effects of DNA mass on multiple displacement whole genome amplification and genotyping performance , 2005, BMC biotechnology.

[40]  A. Teske.  The deep subsurface biosphere is alive and well. , 2005, Trends in microbiology.

[41]  D. K. Willis,et al.  Cultivation of Mesophilic Soil Crenarchaeotes in Enrichment Cultures from Plant Roots , 2005, Applied and Environmental Microbiology.

[42]  N. Martin,et al.  Evaluation of multiple displacement amplification in a 5 cM STR genome-wide scan , 2005, Nucleic acids research.

[43]  C. Saiz-Jimenez,et al.  Multiple displacement amplification as a pre-polymerase chain reaction (pre-PCR) to process difficult to amplify samples and low copy number sequences from natural environments. , 2005, Environmental microbiology.

[44]  Li Jin,et al.  Genome amplification of single sperm using multiple displacement amplification , 2005, Nucleic acids research.

[45]  R. Lasken,et al.  Genomic DNA Amplification from a Single Bacterium , 2005, Applied and Environmental Microbiology.

[46]  J. Holbrook,et al.  Exploring whole genome amplification as a DNA recovery tool for molecular genetic studies. , 2005, Journal of biomolecular techniques : JBT.

[47]  S. Foster,et al.  Whole genome amplification from filamentous fungi using Phi29-mediated multiple displacement amplification. , 2005, Fungal genetics and biology : FG & B.

[48]  S. Tringe,et al.  Comparative Metagenomics of Microbial Communities , 2004, Science.

[49]  B. Ahring,et al.  An improved method for single cell isolation of prokaryotes from meso-, thermo- and hyperthermophilic environments using micromanipulation , 2005, Applied Microbiology and Biotechnology.

[50]  M. Rillig,et al.  Application of Phi29 DNA polymerase mediated whole genome amplification on single spores of arbuscular mycorrhizal (AM) fungi. , 2005, FEMS microbiology letters.

[51]  M. Hoy,et al.  Multiple displacement amplification in combination with high-fidelity PCR improves detection of bacteria from single females or eggs of Metaseiulus occidentalis (Nesbitt) (Acari: Phytoseiidae). , 2004, Journal of invertebrate pathology.

[52]  Vladimir Makarov,et al.  Two methods of whole-genome amplification enable accurate genotyping across a 2320-SNP linkage panel. , 2004, Genome research.

[53]  Rameen Beroukhim,et al.  Genome coverage and sequence fidelity of phi29 polymerase-based multiple strand displacement whole genome amplification. , 2004, Nucleic acids research.

[54]  D. Stenger,et al.  Nucleic Acid Amplification Strategies for DNA Microarray-Based Pathogen Detection , 2004, Applied and Environmental Microbiology.

[55]  J. Handelsman,et al.  Census of the Bacterial Community of the Gypsy Moth Larval Midgut by Using Culturing and Culture-Independent Methods , 2004, Applied and Environmental Microbiology.

[56]  Roger S Lasken,et al.  Whole genome amplification: abundant supplies of DNA from precious samples or clinical specimens. , 2003, Trends in biotechnology.

[57]  A. Syvänen,et al.  Quantitative evaluation by minisequencing and microarrays reveals accurate multiplexed SNP genotyping of whole genome amplified DNA. , 2003, Nucleic acids research.

[58]  C. Schleper,et al.  Diversity and abundance of Crenarchaeota in terrestrial habitats studied by 16S RNA surveys and real time PCR. , 2003, Environmental microbiology.

[59]  Roger S Lasken,et al.  Unbiased whole-genome amplification directly from clinical samples. , 2003, Genome research.

[60]  W. Black Iv,et al.  Amplifying whole insect genomes with multiple displacement amplification , 2003, Insect molecular biology.

[61]  Daniel Pinkel,et al.  Whole genome analysis of genetic alterations in small DNA samples using hyperbranched strand displacement amplification and array-CGH. , 2003, Genome research.

[62]  Thomas Huber,et al.  Chimeric 16S rDNA sequences of diverse origin are accumulating in the public databases. , 2003, International journal of systematic and evolutionary microbiology.

[63]  J. Chapman,et al.  Isothermal strand-displacement amplification applications for high-throughput genomics. , 2002, Genomics.

[64]  C. Sensen,et al.  First insight into the genome of an uncultivated crenarchaeote from soil. , 2002, Environmental microbiology.

[65]  C. Fuller,et al.  TempliPhi, phi29 DNA polymerase based rolling circle amplification of templates for DNA sequencing. , 2002, BioTechniques.

[66]  S. Kingsmore,et al.  Comprehensive human genome amplification using multiple displacement amplification , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[67]  E. Mosley‐Thompson,et al.  Isolation of bacteria and 16S rDNAs from Lake Vostok accretion ice. , 2001, Environmental microbiology.

[68]  F. Dean,et al.  Rapid amplification of plasmid and phage DNA using Phi 29 DNA polymerase and multiply-primed rolling circle amplification. , 2001, Genome research.

[69]  V G Cheung,et al.  Whole genome amplification using a degenerate oligonucleotide primer allows hundreds of genotypes to be performed on less than one nanogram of genomic DNA. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[70]  T. Paunio,et al.  Preimplantation diagnosis by whole-genome amplification, PCR amplification, and solid-phase minisequencing of blastomere DNA. , 1996, Clinical chemistry.

[71]  L. Blanco,et al.  Fidelity of phi 29 DNA polymerase. Comparison between protein-primed initiation and DNA polymerization. , 1993, The Journal of biological chemistry.

[72]  R. Hubert,et al.  Whole genome amplification from a single cell: implications for genetic analysis. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[73]  N. Carter,et al.  Degenerate oligonucleotide-primed PCR: general amplification of target DNA by a single degenerate primer. , 1992, Genomics.

[74]  C Garmendia,et al.  Highly efficient DNA synthesis by the phage phi 29 DNA polymerase , 1989 .

[75]  S E Humphries,et al.  Errors in the polymerase chain reaction. , 1988, Nucleic acids research.

[76]  K. Mullis,et al.  Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. , 1988, Science.

[77]  L. Blanco,et al.  Characterization of a 3'----5' exonuclease activity in the phage phi 29-encoded DNA polymerase. , 1985, Nucleic acids research.

[78]  K. Watabe,et al.  A 3' to 5' exonuclease activity is associated with phage 029 DNA polymerase. , 1984, Biochemical and biophysical research communications.

[79]  L. Blanco,et al.  Characterization and purification of a phage phi 29-encoded DNA polymerase required for the initiation of replication. , 1984, Proceedings of the National Academy of Sciences of the United States of America.