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1. Full Text A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers
by Quail, Michael A and Smith, Miriam and Coupland, Paul and Otto, Thomas D and Harris, Simon R and Connor, Thomas R and Bertoni, Anna and Swerdlow, Harold P and Gu, Yong
BMC Genomics, ISSN 1471-2164, 07/2012, Volume 13, Issue 1, pp. 341 - 341
Background: Next generation sequencing (NGS) technology has revolutionized genomic and genetic research. The pace of change in this area is rapid with three... 
GC-rich | Next-generation sequencing | Pacific biosciences | Bias | PGM | SMRT | Ion torrent | AT-rich | Illumina | MiSeq | Genome coverage | AMPLIFICATION-FREE | GENOME SEQUENCE | ALIGNMENT | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | GENETICS & HEREDITY | SEQ | Staphylococcus aureus - genetics | Gene Library | Nucleotide Motifs - genetics | Bordetella pertussis - genetics | Databases, Genetic | Genome, Bacterial - genetics | Sequence Analysis, DNA - instrumentation | Base Sequence | Plasmodium falciparum - genetics | Polymorphism, Single Nucleotide - genetics | Genome, Protozoan - genetics | Base Composition - genetics | Sequence Analysis, DNA - methods | Usage | DNA sequencers | Nucleotide sequencing | Comparative analysis | Methods | DNA sequencing | Plasmodium falciparum | Malaria | Genomics | Hostages | Genomes | Instrument industry | Silicon wafers | Real time | Price quotations
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2. Full Text Leukemia-Associated Somatic Mutations Drive Distinct Patterns of Age-Related Clonal Hemopoiesis
by McKerrell, Thomas and Park, Naomi and Moreno, Thaidy and Grove, Carolyn S and Ponstingl, Hannes and Stephens, Jonathan and Crawley, Charles and Craig, Jenny and Scott, Mike A and Hodkinson, Clare and Baxter, Joanna and Rad, Roland and Forsyth, Duncan R and Quail, Michael A and Zeggini, Eleftheria and Ouwehand, Willem and Varela, Ignacio and Vassiliou, George S and Understanding Soc Scientific Grp
Cell Reports, ISSN 2211-1247, 03/2015, Volume 10, Issue 8, pp. 1239 - 1245
Clonal hemopoiesis driven by leukemia-associated gene mutations can occur without evidence of a blood disorder. To investigate this phenomenon, we interrogated... 
TWINS | SEQUENCE | STEM-CELL NICHE | ACUTE MYELOID-LEUKEMIA | IDENTIFICATION | DISEASE EVOLUTION | CANCER | MYELODYSPLASTIC SYNDROMES | MOSAICISM | CELL BIOLOGY
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3. Full Text A large genome center's improvements to the Illumina sequencing system
by Swerdlow, Harold and Durbin, Richard and Scally, Aylwyn and Smith, Frances and Turner, Daniel J and Quail, Michael A and Stephens, Philip J and Kozarewa, Iwanka
Nature Methods, ISSN 1548-7091, 12/2008, Volume 5, Issue 12, pp. 1005 - 1010
The Wellcome Trust Sanger Institute is one of the world's largest genome centers, and a substantial amount of our sequencing is performed with... 
DNA | BIOCHEMICAL RESEARCH METHODS | Academies and Institutes | Genomics - instrumentation | Sequence Analysis, DNA - instrumentation | Polymerase Chain Reaction - instrumentation | Equipment Design | Chromosome Mapping - instrumentation | Polymerase chain reaction | Usage | Genomic libraries | DNA sequencers | Management | Parallel processing | Data analysis | Research centers | Genomics | Research methodology
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4. Full Text Whole-genome sequencing for analysis of an outbreak of meticillin-resistant Staphylococcus aureus : a descriptive study
by Harris, Simon R, PhD and Cartwright, Edward JP, MBBS and Török, M Estée, FRCP and Holden, Matthew TG, PhD and Brown, Nicholas M, MD and Ogilvy-Stuart, Amanda L, FRCP and Ellington, Matthew J, DPhil and Quail, Michael A, PhD and Bentley, Stephen D, PhD and Parkhill, Julian, Prof and Peacock, Sharon J, Prof
Lancet Infectious Diseases, The, ISSN 1473-3099, 2013, Volume 13, Issue 2, pp. 130 - 136
Summary Background The emergence of meticillin-resistant Staphylococcus aureus (MRSA) that can persist in the community and replace existing hospital-adapted... 
Infectious Disease | STRAINS | INFECTIOUS DISEASES | INFECTIONS | DISEASE | MRSA | Leukocidins - genetics | Carrier State - epidemiology | Humans | Carrier State - microbiology | Infant | Sequence Analysis, DNA | Staphylococcal Infections - transmission | Genome, Bacterial - genetics | Point Mutation | Staphylococcal Infections - epidemiology | Intensive Care Units, Neonatal | Disease Outbreaks | Exotoxins - genetics | Bacterial Toxins - genetics | Retrospective Studies | Staphylococcal Infections - microbiology | Methicillin-Resistant Staphylococcus aureus - isolation & purification | Methicillin-Resistant Staphylococcus aureus - genetics | Infant, Newborn | Carrier State - transmission | Staphylococcus aureus | Staphylococcus aureus infections
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5. Full Text Rapid Pneumococcal Evolution in Response to Clinical Interventions
by Nicholas J. Croucher and Simon R. Harris and Christophe Fraser and Michael A. Quail and John Burton and Mark van der Linden and Lesley McGee and Anne von Gottberg and Jae Hoon Song and Kwan Soo Ko and Bruno Pichon and Stephen Baker and Christopher M. Parry and Lotte M. Lambertsen and Dea Shahinas and Dylan R. Pillai and Timothy J. Mitchell and Gordon Dougan and Alexander Tomasz and Keith P. Klugman and Julian Parkhill and William P. Hanage and Stephen D. Bentley
Science, ISSN 0036-8075, 1/2011, Volume 331, Issue 6016, pp. 430 - 434
Epidemiological studies of the naturally transformable bacterial pathogen Streptococcus pneumoniae have previously been confounded by high rates of... 
Capsules | Antibiotics | Macrolides | RESEARCH ARTICLES | Vaccination | Genes | Genetic loci | Genomes | Ice | Phylogeny | Epidemiology | UNITED-STATES | TRANSFORMATION | INTERCONTINENTAL SPREAD | MULTIDISCIPLINARY SCIENCES | DISEASE | SEQUENCE | ANTIBIOTIC-RESISTANCE | RESISTANT STREPTOCOCCUS-PNEUMONIAE | EMERGENCE | 23F CLONE | SEROTYPE 19A | Adaptation, Physiological | Pneumococcal Infections - drug therapy | Genome, Bacterial | Streptococcus pneumoniae - classification | Streptococcus pneumoniae - drug effects | Antigenic Variation | Streptococcus Phages - genetics | Humans | Phylogeography | Selection, Genetic | DNA Transposable Elements | Prophages - genetics | Streptococcus pneumoniae - immunology | Molecular Epidemiology | Recombination, Genetic | Drug Resistance, Multiple, Bacterial | Streptococcus pneumoniae - genetics | Pneumococcal Vaccines - immunology | Pneumococcal Infections - microbiology | Anti-Bacterial Agents - pharmacology | Polymorphism, Single Nucleotide | Serotyping | Evolution, Molecular | Microbial genetics | Genetic aspects | Research | Identification and classification | Streptococcus pneumoniae | Evolutionary biology | Microbiology | Drug resistance | Streptococcus infections
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6. Full Text Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes
by Sanders, Mandy J and Kozarewa, Iwanka and Quail, Michael A and Berriman, Matthew and Ning, Zemin and Turner, Daniel J
Nature Methods, ISSN 1548-7091, 04/2009, Volume 6, Issue 4, pp. 291 - 295
Amplification artifacts introduced during library preparation for the Illumina Genome Analyzer increase the likelihood that an appreciable proportion of these... 
DIAGNOSIS | FRAGMENTS | PCR BIAS | DNA | CONSTRUCTION | BIOCHEMICAL RESEARCH METHODS | PARASITE PLASMODIUM-FALCIPARUM | YEAST ARTIFICIAL CHROMOSOMES | IDENTIFICATION | SINGLE NUCLEOTIDE | Gene Library | Base Composition | Base Sequence | Chromosome Mapping - methods | Molecular Sequence Data | Polymorphism, Single Nucleotide - genetics | Sequence Analysis, DNA - methods | Nucleic Acid Amplification Techniques | Polymerase chain reaction | Plasmodium falciparum | Gene amplification | Usage | Malaria | Genetic aspects | Research | Nucleotide sequencing | Methods | Microbiology | Bioinformatics | Research methodology | Genomics | Deoxyribonucleic acid--DNA
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7. Full Text Evolution of MRSA during Hospital Transmission and Intercontinental Spread
by Simon R. Hams and Edward J. Feil and Matthew T. G. Holden and Michael A. Quail and Emma K. Nickerson and Narisara Chantratita and Susana Gardete and Ana Tavares and Nick Day and Jodi A. Lindsay and Jonathan D. Edgeworth and Herminia de Lencastre and Julian Parkhill and Sharon J. Peacock and Stephen D. Bentley
Science, ISSN 0036-8075, 1/2010, Volume 327, Issue 5964, pp. 469 - 474
Current methods for differentiating isolates of predominant lineages of pathogenic bacteria often do not provide sufficient resolution to define precise... 
Pathogens | Disease transmission | Carrier proteins | Phylogenetics | Data transmission | Evolution | Reports | Genomes | Sequencing | Genetic mutation | Staphylococcus aureus | TRIMETHOPRIM | MULTIDISCIPLINARY SCIENCES | MUTATION | RESISTANT STAPHYLOCOCCUS-AUREUS | IDENTIFICATION | STRAIN | CLONES | United States - epidemiology | Humans | Methicillin-Resistant Staphylococcus aureus - classification | Molecular Sequence Data | Phylogeny | Cross Infection - transmission | Likelihood Functions | South America - epidemiology | Time Factors | Bacterial Typing Techniques | Staphylococcal Infections - microbiology | Genomics - methods | Methicillin-Resistant Staphylococcus aureus - genetics | Cross Infection - epidemiology | Genome, Bacterial | Europe - epidemiology | Sequence Analysis, DNA | Staphylococcal Infections - transmission | Asia - epidemiology | Staphylococcal Infections - epidemiology | Molecular Epidemiology | Cross Infection - microbiology | Polymorphism, Single Nucleotide | Methicillin-Resistant Staphylococcus aureus - isolation & purification | Evolution, Molecular | Analysis | Genomics | Bacteria, Pathogenic | Genetic aspects | Research | Epidemiology | Staphylococcus infections | Nosocomial infections | Microbiology
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8. Full Text The industrial melanism mutation in British peppered moths is a transposable element
by Hof, Arjen E. Van't and Campagne, Pascal and Rigden, Daniel J and Yung, Carl J and Lingley, Jessica and Quail, Michael A and Hall, Neil and Darby, Alistair C and Saccheri, Ilik J
Nature, ISSN 0028-0836, 06/2016, Volume 534, Issue 7605, pp. 102 - 105
Discovering the mutational events that fuel adaptation to environmental change remains an important challenge for evolutionary biology. The classroom example... 
APC/C | LINKAGE DISEQUILIBRIUM | EVOLUTIONARY GENETICS | GENOMICS | SPOT | MULTIDISCIPLINARY SCIENCES | ADAPTATION | SEQUENCE | BISTON-BETULARIA | SELECTION | Cell Cycle - genetics | Moths - cytology | Genes, Insect - genetics | Male | Selection, Genetic - genetics | Moths - genetics | Haplotypes - genetics | Wings, Animal - growth & development | Pigmentation - genetics | Adaptation, Physiological - genetics | DNA Transposable Elements - genetics | Moths - physiology | Melanosis - genetics | Introns - genetics | Melanosis - veterinary | Pigmentation - physiology | Color | United Kingdom | Mutation - genetics | Mutagenesis, Insertional - genetics | Wings, Animal - physiology | Biological Evolution | Phenotype | Animals | Alleles | Moths | Genetic aspects | Melanism (Evolutionary adaptation) | Biological research | Environmental aspects | Research | Mutation (Biology) | Biology, Experimental | Haplotypes | Genes | Cell division | Butterflies & moths | Amino acids | Mutation | Artificial chromosomes | Evolution & development | Adaptation
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9. Full Text The patterns and dynamics of genomic instability in metastatic pancreatic cancer
by Stebbings, Lucy A and Iacobuzio-Donahue, Christine and Futreal, P. Andrew and Latimer, Calli and McLaren, Stuart and Butler, Adam P and Campbell, Peter J and Morsberger, Laura A and Pleasance, Erin D and Swerdlow, Harold and Mudie, Laura J and Yachida, Shinichi and Varela, Ignacio and Nik-Zainal, Serena A and McBride, David J and Stratton, Michael R and Lin, Meng-Lay and Jia, Mingming and Burton, John and Leroy, Catherine and Teague, Jon W and Griffin, Constance A and Quail, Michael A and Stephens, Philip J and Menzies, Andrew
Nature, ISSN 0028-0836, 10/2010, Volume 467, Issue 7319, pp. 1109 - 1113
Pancreatic cancer is an aggressive malignancy with a five-year mortality of 97-98%, usually due to widespread metastatic disease. Previous studies indicate... 
CELLS | EVOLUTION | MULTIDISCIPLINARY SCIENCES | RESOLUTION | GENETIC-HETEROGENEITY | COPY NUMBER ANALYSIS | MUTATIONS | LEUKEMIA | HUMAN BREAST-CANCER | REARRANGEMENTS | TUMORS | Lung Neoplasms - genetics | Cell Cycle - genetics | Adenocarcinoma - pathology | Liver Neoplasms - genetics | Humans | Pancreatic Neoplasms - pathology | Mutagenesis - genetics | Pancreatic Neoplasms - genetics | Organ Specificity | Clone Cells - metabolism | Disease Progression | Neoplasm Metastasis - genetics | Telomere - pathology | Clone Cells - pathology | Lung Neoplasms - secondary | DNA Mutational Analysis | Neoplasm Metastasis - pathology | Adenocarcinoma - genetics | Liver Neoplasms - secondary | Genes, Neoplasm - genetics | Cell Lineage - genetics | Genomic Instability - genetics | Evolution, Molecular | Telomere - genetics | Genetic aspects | Metastasis | Research | Pancreatic cancer | Patient outcomes | Cancer | Genomics | Deoxyribonucleic acid--DNA
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