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1. Full Text A complete bacterial genome assembled de novo using only nanopore sequencing data
by Loman, Nicholas J and Quick, Joshua and Simpson, Jared T
Nature methods, ISSN 1548-7091, 07/2015, Volume 12, Issue 8, pp. 733 - 735
Biochemistry & Molecular Biology | Life Sciences & Biomedicine | Biochemical Research Methods | Science & Technology | Computational Biology - methods | Genome, Bacterial | Reproducibility of Results | Algorithms | Nanotechnology - methods | Software | Escherichia coli K12 - genetics | High-Throughput Nucleotide Sequencing - methods | Nanopores | Sequence Analysis, DNA - methods | Contig Mapping - methods | Escherichia coli | Innovations | Genetic aspects | Nucleotides | Properties | Chromosomes | Identification and classification | Nanotechnology | Scientific method | E coli | Genomics | Deoxyribonucleic acid--DNA | Index Medicus
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2. Full Text Binning metagenomic contigs by coverage and composition
by Alneberg, J and Bjarnason, B.S and Bruijn, de, I and Schirmer, M and Quick, J and Ijaz, U.Z and Lahti, L.M and Loman, N.J and Andersson, A.F and Quince, C
Nature methods, ISSN 1548-7091, 2014, Volume 11, Issue 11, pp. 1144 - 1146
sequences | genomes | Biochemistry & Molecular Biology | Life Sciences & Biomedicine | Biochemical Research Methods | Science & Technology | Bifidobacterium - genetics | Humans | Metagenomics - methods | Gastrointestinal Tract - microbiology | Shiga-Toxigenic Escherichia coli - genetics | Feces - microbiology | Genome, Bacterial - genetics | Metagenome - genetics | Algorithms | Microbiota - genetics | Software | Escherichia coli K12 - genetics | Sequence Analysis, DNA - methods | Contig Mapping - methods | Genomics | Innovations | Genetic research | Nucleotide sequencing | Research | DNA sequencing | Computational biology | Microbiology | Biotechnology | Index Medicus
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3. Full Text Repeatability and Contingency in the Evolution of a Key Innovation in Phage Lambda
by Justin R. Meyer and Devin T. Dobias and Joshua S. Weitz and Jeffrey E. Barrick and Ryan T. Quick and Richard E. Lenski
Science (American Association for the Advancement of Science), ISSN 0036-8075, 1/2012, Volume 335, Issue 6067, pp. 428 - 432
Bacteriophages | Microbial genetics | Receptors | Ecological genetics | RESEARCH ARTICLES | Evolution | Bacteria | Viruses | Evolutionary genetics | Infections | Genetic mutation | Science & Technology - Other Topics | Multidisciplinary Sciences | Science & Technology | Fundamental and applied biological sciences. Psychology | Biological and medical sciences | Genetics | Microbiology | Virology | Viral Tail Proteins - genetics | Genome, Viral | Genome, Bacterial | Porins - genetics | Receptors, Virus - metabolism | Porins - metabolism | Selection, Genetic | Bacteriophage lambda - physiology | Receptors, Virus - genetics | Viral Tail Proteins - chemistry | Escherichia coli - virology | Bacterial Outer Membrane Proteins - metabolism | Escherichia coli - genetics | Alleles | Escherichia coli - metabolism | Polymorphism, Single Nucleotide | Bacteriophage lambda - genetics | Mutation | Viral Tail Proteins - metabolism | Bacterial Outer Membrane Proteins - genetics | Evolution, Molecular | Evolutionary biology | Ecology | Contingency | Index Medicus
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4. Full Text Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella
by Quick, Joshua and Ashton, Philip and Calus, Szymon and Chatt, Carole and Gossain, Savita and Hawker, Jeremy and Nair, Satheesh and Neal, Keith and Nye, Kathy and Peters, Tansy and De Pinna, Elizabeth and Robinson, Esther and Struthers, Keith and Webber, Mark and Catto, Andrew and Dallman, Timothy J and Hawkey, Peter and Loman, Nicholas J
Genome Biology, ISSN 1474-7596, 05/2015, Volume 16, Issue 1, pp. 114 - 114
Genetics & Heredity | Life Sciences & Biomedicine | Biotechnology & Applied Microbiology | Science & Technology | Salmonella Infections - epidemiology | Salmonella enteritidis - isolation & purification | Disease Outbreaks | Cross Infection - microbiology | Humans | Salmonella Infections - microbiology | Hospitalization | Salmonella enteritidis - classification | Salmonella enteritidis - genetics | Sequence Analysis, DNA - methods | Cross Infection - epidemiology | Salmonella | Food contamination & poisoning | Laboratories | Phages | Outbreaks | Genomes | Phylogeny | Patients | Epidemiology | Disease control | Tuberculosis | Hospitals | Surveillance | Phylogenetics | Bioinformatics | Public health | DNA sequencing | Index Medicus | Research
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5. Full Text Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples
by Quick, Joshua and Grubaugh, Nathan D and Pullan, Steven T and Claro, Ingra M and Smith, Andrew D and Gangavarapu, Karthik and Oliveira, Glenn and Robles-Sikisaka, Refugio and Rogers, Thomas F and Beutler, Nathan A and Burton, Dennis R and Lewis-Ximenez, Lia Laura and De Jesus, Jaqueline Goes and Giovanetti, Marta and Hill, Sarah C and Black, Allison and Bedford, Trevor and Carroll, Miles W and Nunes, Marcio and Alcantara, Luiz Carlos and Sabino, Ester C and Baylis, Sally A and Faria, Nuno R and Loose, Matthew and Simpson, Jared T and Pybus, Oliver G and Andersen, Kristian G and Loman, Nicholas J
Nature protocols, ISSN 1754-2189, 06/2017, Volume 12, Issue 6, pp. 1261 - 1266
Biochemistry & Molecular Biology | Life Sciences & Biomedicine | Biochemical Research Methods | Science & Technology | RNA Viruses - genetics | Genome, Viral | Multiplex Polymerase Chain Reaction - methods | Molecular Epidemiology - methods | Sequence Analysis, DNA - methods | DNA Viruses - genetics | Polymerase chain reaction | Nucleotide sequencing | Observations | Methods | DNA sequencing | Index Medicus
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6. Full Text A reference bacterial genome dataset generated on the MinION™ portable single-molecule nanopore sequencer
by Quick, Joshua and Quinlan, Aaron R and Loman, Nicholas J
Gigascience, ISSN 2047-217X, 10/2014, Volume 3, Issue 1, pp. 22 - 22
Nanopore sequencing | Genomics | Science & Technology - Other Topics | Biology | Multidisciplinary Sciences | Life Sciences & Biomedicine - Other Topics | Life Sciences & Biomedicine | Science & Technology
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7. A culture-independent sequence-based metagenomics approach to the investigation of an outbreak of shiga-toxigenic Escherichia coli O104:H4
by Loman, Nicholas J and Constantinidou, Chrystala and Christner, Martin and Chan, Jacqueline Z.-M and Quick, Joshua and Weir, Jacqueline C and Quince, Christopher and Smith, Geoffrey P and Betley, Jason R and Aepfelbacher, Martin and Pallen, Mark J
JAMA : the journal of the American Medical Association, ISSN 0098-7484, 04/2013, Volume 309, Issue 14, pp. 1502 - 1510
Medicine, General & Internal | Life Sciences & Biomedicine | General & Internal Medicine | Science & Technology | Computational Biology - methods | Escherichia coli Infections - diagnosis | Humans | Metagenomics - methods | Diarrhea | Escherichia coli Infections - microbiology | Shiga-Toxigenic Escherichia coli - genetics | Shiga-Toxigenic Escherichia coli - isolation & purification | Feces - microbiology | Shiga Toxin - genetics | Time Factors | Disease Outbreaks | Sensitivity and Specificity | DNA, Bacterial - analysis | Retrospective Studies | Sequence Analysis, DNA - methods | Epidemics | Pathogens | E coli | Genomics | Index Medicus | Abridged Index Medicus
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8. Full Text Genomic epidemiology reveals multiple introductions of Zika virus into the United States
by Grubaugh, Nathan D and Ladner, Jason T and Kraemer, Moritz U. G and Dudas, Gytis and Tan, Amanda L and Gangavarapu, Karthik and Wiley, Michael R and White, Stephen and Thézé, Julien and Magnani, Diogo M and Prieto, Karla and Reyes, Daniel and Bingham, Andrea M and Paul, Lauren M and Robles-Sikisaka, Refugio and Oliveira, Glenn and Pronty, Darryl and Barcellona, Carolyn M and Metsky, Hayden C and Baniecki, Mary Lynn and Barnes, Kayla G and Chak, Bridget and Freije, Catherine A and Gladden-Young, Adrianne and Gnirke, Andreas and Luo, Cynthia and MacInnis, Bronwyn and Matranga, Christian B and Park, Daniel J and Qu, James and Schaffner, Stephen F and Tomkins-Tinch, Christopher and West, Kendra L and Winnicki, Sarah M and Wohl, Shirlee and Yozwiak, Nathan L and Quick, Joshua and Fauver, Joseph R and Khan, Kamran and Brent, Shannon E and Reiner, Robert C and Lichtenberger, Paola N and Ricciardi, Michael J and Bailey, Varian K and Watkins, David I and Cone, Marshall R and Kopp, Edgar W and Hogan, Kelly N and Cannons, Andrew C and Jean, Reynald and Monaghan, Andrew J and Garry, Robert F and Loman, Nicholas J and Faria, Nuno R and Porcelli, Mario C and Vasquez, Chalmers and Nagle, Elyse R and Cummings, Derek A. T and Stanek, Danielle and Rambaut, Andrew and Sanchez-Lockhart, Mariano and Sabeti, Pardis C and Gillis, Leah D and Michael, Scott F and Bedford, Trevor and Pybus, Oliver G and Isern, Sharon and Palacios, Gustavo and Andersen, Kristian G
Nature (London), ISSN 0028-0836, 06/2017, Volume 546, Issue 7658, pp. 401 - 405
Science & Technology - Other Topics | Multidisciplinary Sciences | Science & Technology | Florida - epidemiology | Zika Virus - genetics | Caribbean Region - epidemiology | Genome, Viral - genetics | Humans | Disease Outbreaks - statistics & numerical data | Zika Virus - isolation & purification | Mosquito Vectors - virology | Incidence | Zika Virus Infection - transmission | Zika Virus Infection - virology | Aedes - virology | Animals | Zika Virus Infection - epidemiology | Molecular Epidemiology | Female | Gene expression | Health aspects | Vector-borne diseases | Epidemics | Traffic | Viruses | Outbreaks | Infections | Zika virus | Genomes | Aquatic insects | Epidemiology | Tropical diseases | Gene sequencing | Datasets | Mosquitoes | Disease transmission | West Nile virus | Phylogenetics | Public health | Index Medicus | Life Sciences
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9. Full Text Extensive modulation of the fecal metagenome in children with Crohn's disease during exclusive enteral nutrition
by Quince, Christopher and Ijaz, Umer Zeeshan and Loman, Nick and Eren, A Murat and Saulnier, Delphine and Russell, Julie and Haig, Sarah J and Calus, Szymon T and Quick, Joshua and Barclay, Andrew and Bertz, Martin and Blaut, Michael and Hansen, Richard and Mcgrogan, Paraic and Russell, Richard K and Edwards, Christine A and Gerasimidis, Konstantinos
The American journal of gastroenterology, ISSN 0002-9270, 12/2015, Volume 110, Issue 12, pp. 1718 - 1729
Gastroenterology & Hepatology | Life Sciences & Biomedicine | Science & Technology | Crohn Disease - genetics | Humans | Leukocyte L1 Antigen Complex - metabolism | Metagenomics - methods | Crohn Disease - metabolism | Linear Models | Male | Enteral Nutrition | Feces - chemistry | Sequence Analysis, RNA | Microbiota - genetics | Crohn Disease - blood | Adolescent | Crohn Disease - microbiology | Female | RNA, Ribosomal, 16S | Child | Metagenome | Index Medicus | Pediatrics
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10. Full Text Eighteenth-century genomes show that mixed infections were common at time of peak tuberculosis in Europe
by Kay, Gemma L and Sergeant, Martin J and Zhou, Zhemin and Chan, Jacqueline Z.-M and Millard, Andrew and Quick, Joshua and Szikossy, Ildikó and Pap, Ildikó and Spigelman, Mark and Loman, Nicholas J and Achtman, Mark and Donoghue, Helen D and Pallen, Mark J
Nature communications, ISSN 2041-1723, 04/2015, Volume 6, Issue 1, pp. 6717 - 6717
Science & Technology - Other Topics | Multidisciplinary Sciences | Science & Technology | Tuberculosis - epidemiology | Metagenomics | Humans | Middle Aged | Hungary - epidemiology | Europe - epidemiology | Tuberculosis - history | Genotype | Male | Tuberculosis - microbiology | History, 18th Century | Phylogeny | Young Adult | Genome, Bacterial - genetics | Coinfection - microbiology | Molecular Epidemiology | Bayes Theorem | Adult | DNA, Bacterial - analysis | Female | Mycobacterium tuberculosis - genetics | Index Medicus
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