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Results: 118
A new deep branch of eurasian mtDNA macrohaplogroup M reveals additional complexity regarding the settlement of Madagascar.
François-X Ricaut, Harilanto Razafindrazaka, Murray P Cox, Jean-M Dugoujon, Evelyne Guitard, Clement Sambo, Maru Mormina, Marta Mirazon-Lahr, Bertrand Ludes, Eric Crubézy
Jun 16, 2011
The discovery of Halictivirus resolves the Sinaivirus phylogeny.
Diane Bigot, Anne Dalmon, Bronwen Roy, Chunsheng Hou, Michèle Germain, Manon Romary, Shuai Deng, Qingyun Diao, Lucy A Weinert, James M Cook, Elisabeth A Herniou, Philippe Gayral
Jan 26, 2018
By providing pollination services, bees are among the most important insects, both in ecological and economical terms. Combined next-generation and classical sequencing approaches were applied to discover and study new insect...
Mycobacterial genomics and structural bioinformatics
Vaishali P Waman, Sundeep Chaitanya Vedithi, Sherine E Thomas, Bridget P Bannerman, Asma Munir, Marcin J Skwark, Sony Malhotra, Tom L Blundell
Feb 18, 2019
Of the more than 190 distinct species of Mycobacterium genus, many are economically and clinically important pathogens of humans or animals. Among those mycobacteria that infect humans, three species namely Mycobacterium...
Mycobacterium comparative genomics Drug Resistance Mutation structure-guided drug discovery Animals Bacterial Proteins Computational Biology Drug Discovery Drug Resistance Bacterial Genome Bacterial Humans Molecular Sequence Annotation Mycobacterium Mycobacterium abscessus Mycobacterium leprae Mycobacterium tuberculosis Protein Conformation Proteomics Sequence Analysis DNA
Population genetics of mouse lemur vomeronasal receptors
BACKGROUND: A major effort is underway to use population genetic approaches to identify loci involved in adaptation. One issue that has so far received limited attention is whether loci that show a phylogenetic signal of...
Genomic survey of Clostridium difficile reservoirs in the East of England implicates environmental contamination of wastewater treatment plants by clinical lineages.
Danesh Moradigaravand, Theodore Gouliouris, Catherine Ludden, Sandra Reuter, Dorota Jamrozy, Beth Blane, Plamena Naydenova, Kim Judge, Sani H Aliyu, Nazreen F Hadjirin, Mark A Holmes, Estée Török, Nicholas M Brown, Julian Parkhill, Sharon Peacock
May 22, 2018
There is growing evidence that patients with Clostridiumdifficile-associated diarrhoea often acquire their infecting strain before hospital admission. Wastewater is known to be a potential source of surface water that is...
Clostridium difficile One Health genomic epidemiology wastewater treatment plants Bayes Theorem Clostridioides difficile Cross-Sectional Studies DNA Bacterial Diarrhea England Genome Bacterial Genomics Humans Multilocus Sequence Typing Retrospective Studies Sequence Analysis DNA Waste Management Wastewater
Genomic surveillance of Escherichia coli ST131 identifies local expansion and serial replacement of subclones.
Catherine Ludden, Arun Gonzales Decano, Dorota Jamrozy, Derek Pickard, Dearbhaile Morris, Julian Parkhill, Sharon J Peacock, Martin Cormican, Tim Downing
Mar 10, 2020
Escherichia coli sequence type 131 (ST131) is a pandemic clone that is evolving rapidly with increasing levels of antimicrobial resistance. Here, we investigated an outbreak of E. coli ST131 producing extended spectrum...
Structural Implications of Mutations Conferring Rifampin Resistance in Mycobacterium leprae.
Sundeep Chaitanya Vedithi, Sony Malhotra, Madhusmita Das, Sheela Daniel, Nanda Kishore, Anuja George, Shantha Arumugam, Lakshmi Rajan, Mannam Ebenezer, David B Ascher, Eddy Arnold, Tom L Blundell
Sep 27, 2018
The rpoB gene encodes the β subunit of RNA polymerase holoenzyme in Mycobacterium leprae (M. leprae). Missense mutations in the rpoB gene were identified as etiological factors for rifampin resistance in leprosy. In the present...
Adolescent Adult Bacterial Proteins DNA Bacterial DNA-Directed RNA Polymerases Drug Resistance Bacterial Female Humans india Leprostatic Agents Leprosy Male Microbial Sensitivity Tests Middle Aged Mutation Mycobacterium leprae Protein Binding Protein Stability Recurrence Rifampin Sequence Analysis DNA Structure-Activity Relationship Treatment Outcome Young Adult
Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development.
Marilyn B Renfree, Anthony T Papenfuss, Janine E Deakin, James Lindsay, Thomas Heider, Katherine Belov, Willem Rens, Paul D Waters, Elizabeth A Pharo, Geoff Shaw, Emily SW Wong, Christophe M Lefèvre, Kevin R Nicholas, Yoko Kuroki, Matthew J Wakefield, Kyall R Zenger, Chenwei Wang, Malcolm Ferguson-Smith, Frank W Nicholas, Danielle Hickford, Hongshi Yu, Kirsty R Short, Hannah V Siddle, Stephen R Frankenberg, Keng Yih Chew, Brandon R Menzies, Jessica M Stringer, Shunsuke Suzuki, Timothy A Hore, Margaret L Delbridge, Hardip R Patel, Amir Mohammadi, Nanette Y Schneider, Yanqiu Hu, William O'Hara, Shafagh Al Nadaf, Chen Wu, Zhi-Ping Feng, Benjamin G Cocks, Jianghui Wang, Paul Flicek, Stephen MJ Searle, Susan Fairley, Kathryn Beal, Javier Herrero, Dawn M Carone, Yutaka Suzuki, Sumio Sugano, Atsushi Toyoda, Yoshiyuki Sakaki, Shinji Kondo, Yuichiro Nishida, Shoji Tatsumoto, Ion Mandiou, Arthur Hsu, Kaighin A McColl, Benjamin Lansdell, George Weinstock, Elizabeth Kuczek, Annette McGrath, Peter Wilson, Artem Men, Mehlika Hazar-Rethinam, Allison Hall, John Davis, David Wood, Sarah Williams, Yogi Sundaravadanam, Donna M Muzny, Shalini N Jhangiani, Lora R Lewis, Margaret B Morgan, Geoffrey O Okwuonu, San Juana Ruiz, Jireh Santibanez, Lynne Nazareth, Andrew Cree, Gerald Fowler, Christie L Kovar, Huyen H Dinh, Vandita Joshi, Chyn Jing, Fremiet Lara, Rebecca Thornton, Lei Chen, Jixin Deng, Yue Liu, Joshua Y Shen, Xing-Zhi Song, Janette Edson, Carmen Troon, Daniel Thomas, Amber Stephens, Lankesha Yapa, Tanya Levchenko, Richard A Gibbs, Desmond W Cooper, Terence P Speed, Asao Fujiyama, Jennifer AM Graves, Rachel J O'Neill, Andrew J Pask, Susan M Forrest, Kim C Worley
Mar 30, 2012
BACKGROUND: We present the genome sequence of the tammar wallaby, Macropus eugenii, which is a member of the kangaroo family and the first representative of the iconic hopping mammals that symbolize Australia to be sequenced....
Methanol-based fixation is superior to buffered formalin for next-generation sequencing of DNA from clinical cancer samples.
AM Piskorz, D Ennis, G Macintyre, TE Goranova, M Eldridge, N Segui-Gracia, M Valganon, A Hoyle, C Orange, L Moore, M Jimenez-Linan, D Millan, IA McNeish, JD Brenton
Jan 04, 2016
Systematic Surveillance Detects Multiple Silent Introductions and Household Transmission of Methicillin-Resistant Staphylococcus aureus USA300 in the East of England.
Michelle S Toleman, Sandra Reuter, Francesc Coll, Ewan M Harrison, Beth Blane, Nicholas M Brown, M Estée Török, Julian Parkhill, Sharon J Peacock
Apr 29, 2016
MRSA Staphylococcus aureus USA300 molecular epidemiology whole-genome sequencing Adolescent Adult Aged Aged 80 and over Child Child Preschool Disease Transmission Infectious England Epidemiological Monitoring Family Characteristics Family Health Female Genotype Humans Male Methicillin-Resistant Staphylococcus aureus Middle Aged molecular epidemiology Prospective Studies Sequence Analysis DNA Staphylococcal Infections Young Adult
cuRRBS
Daniel E Martin-Herranz, António JM Ribeiro, Felix Krueger, Janet M Thornton, Wolf Reik, Thomas M Stubbs
Jun 17, 2019
DNA methylation is an important epigenetic modification in many species that is critical for development, and implicated in ageing and many complex diseases, such as cancer. Many cost-effective genome-wide analyses of DNA...
Identifying mixed Mycobacterium tuberculosis infections from whole genome sequence data.
Benjamin Sobkowiak, Judith R Glynn, Rein MGJ Houben, Kim Mallard, Jody E Phelan, José Afonso Guerra-Assunção, Louis Banda, Themba Mzembe, Miguel Viveiros, Ruth McNerney, Julian Parkhill, Amelia C Crampin, Taane G Clark
Sep 04, 2019
BACKGROUND: Mixed, polyclonal Mycobacterium tuberculosis infection occurs in natural populations. Developing an effective method for detecting such cases is important in measuring the success of treatment and reconstruction of...
Bioinformatics EPIDEMIOLOGY Genomic analysis Mixed infection Mycobacterium tuberculosis Tuberculosis Adolescent Adult Bayes Theorem DNA Bacterial Female Genome Bacterial Humans Male Middle Aged Mycobacterium tuberculosis Polymorphism Single Nucleotide Sequence Analysis DNA Tuberculosis whole genome sequencing Young Adult
Emerging landscape of oncogenic signatures across human cancers.
Giovanni Ciriello, Martin L Miller, Bülent Arman Aksoy, Yasin Senbabaoglu, Nikolaus Schultz, Chris Sander
Mar 26, 2018
Cancer therapy is challenged by the diversity of molecular implementations of oncogenic processes and by the resulting variation in therapeutic responses. Projects such as The Cancer Genome Atlas (TCGA) provide molecular tumor...
Contrasting patterns of longitudinal population dynamics and antimicrobial resistance mechanisms in two priority bacterial pathogens over 7 years in a single center.
Matthew J Ellington, Eva Heinz, Alexander M Wailan, Matthew J Dorman, Marcus de Goffau, Amy K Cain, Sonal P Henson, Nicholas Gleadall, Christine J Boinett, Gordon Dougan, Nicholas M Brown, Neil Woodford, Julian Parkhill, M Estée Török, Sharon J Peacock, Nicholas R Thomson
Sep 06, 2019
BACKGROUND: Two of the most important pathogens contributing to the global rise in antimicrobial resistance (AMR) are Klebsiella pneumoniae and Enterobacter cloacae. Despite this, most of our knowledge about the changing...
Adenovirus-prime and baculovirus-boost heterologous immunization achieves sterile protection against malaria sporozoite challenge in a murine model.
Kunitaka Yoshida, Mitsuhiro Iyori, Andrew M Blagborough, Ahmed M Salman, Pawan Dulal, Katarzyna A Sala, Daisuke S Yamamoto, Shahid M Khan, Chris J Janse, Sumi Biswas, Tatsuya Yoshii, Yenni Yusuf, Masaharu Tokoro, Adrian VS Hill, Shigeto Yoshida
Jan 31, 2020
With the increasing prevalence of artemisinin-resistant malaria parasites, a highly efficacious and durable vaccine for malaria is urgently required. We have developed an experimental virus-vectored vaccine platform based on an...
Adenoviridae Adenoviridae Infections Animals Antibodies Protozoan Antigens Protozoan Baculoviridae Disease Models Animal Female Immunization Immunization Secondary Malaria Malaria Vaccines Malaria Falciparum Mice Mice Inbred BALB C Plasmodium falciparum Protozoan Proteins Sporozoites Vaccination vaccines DNA
KLF2 mutation is the most frequent somatic change in splenic marginal zone lymphoma and identifies a subset with distinct genotype.
A Clipson, M Wang, L de Leval, M Ashton-Key, A Wotherspoon, G Vassiliou, N Bolli, C Grove, S Moody, L Escudero-Ibarz, G Gundem, K Brugger, X Xue, E Mi, A Bench, M Scott, H Liu, G Follows, EF Robles, JA Martinez-Climent, D Oscier, AJ Watkins, M-Q Du
Dec 16, 2014
Biopsy CARD Signaling Adaptor Proteins DNA-Binding Proteins Exome Frameshift Mutation Gene Rearrangement B-Lymphocyte Heavy Chain genetic variation Genotype Guanylate Cyclase Humans Intracellular Signaling Peptides and Proteins Kruppel-Like Transcription Factors Lymphoma Lymphoma B-Cell Marginal Zone Mutation Mutation Missense Nuclear Proteins Polymerase Chain Reaction Receptor Notch2 Recurrence Sequence Analysis DNA Signal Transduction Splenic Neoplasms Tumor Necrosis Factor alpha-Induced Protein 3
Host Subtraction, Filtering and Assembly Validations for Novel Viral Discovery Using Next Generation Sequencing Data.
Gordon M Daly, Richard M Leggett, William Rowe, Samuel Stubbs, Maxim Wilkinson, Ricardo H Ramirez-Gonzalez, Mario Caccamo, William Bernal, Jonathan L Heeney
Jun 10, 2015
Genome-based characterization of hospital-adapted Enterococcus faecalis lineages.
Kathy E Raven, Sandra Reuter, Theodore Gouliouris, Rosy Reynolds, Julie E Russell, Nicholas M Brown, M Estée Török, Julian Parkhill, Sharon J Peacock
Dec 10, 2015
Infectious Diseases Biodefense Vaccine Related Antimicrobial resistance Prevention Genetics Infection Bacteremia Cross Infection Enterococcus faecalis Genome Bacterial Genotype Gram-Positive Bacterial Infections Hospitals Ireland molecular epidemiology Phylogeography Sequence Analysis DNA United Kingdom Vancomycin-Resistant Enterococci Virulence Factors
Longitudinal genomic surveillance of multidrug-resistant Escherichia coli carriage in a long-term care facility in the United Kingdom.
Hayley J Brodrick, Kathy E Raven, Teemu Kallonen, Dorota Jamrozy, Beth Blane, Nicholas M Brown, Veronique Martin, M Estée Török, Julian Parkhill, Sharon Peacock
Jun 26, 2018
Humans Escherichia coli Escherichia coli Infections beta-Lactamases Escherichia coli Proteins Long-Term Care Sequence Analysis DNA Drug Resistance Multiple Bacterial United Kingdom
Published by: Genome medicine
Whole-genome sequencing reveals transmission of vancomycin-resistant Enterococcus faecium in a healthcare network.
Hayley J Brodrick, Kathy E Raven, Ewan M Harrison, Beth Blane, Sandra Reuter, M Estée Török, Julian Parkhill, Sharon J Peacock
Dec 18, 2015
Genome-based characterization of hospital-adapted Enterococcus faecalis lineages.
Kathy E Raven, Sandra Reuter, Theodore Gouliouris, Rosy Reynolds, Julie E Russell, Nicholas M Brown, M Estée Török, Julian Parkhill, Sharon J Peacock
Mar 19, 2019
Vancomycin-resistant Enterococcus faecalis (VREfs) is an important nosocomial pathogen(1,2). We undertook whole genome sequencing of E. faecalis associated with bloodstream infection in the UK and Ireland over more than a decade...
Bacteremia Cross Infection Enterococcus faecalis Genome Bacterial Genotype Gram-Positive Bacterial Infections Hospitals Ireland molecular epidemiology Phylogeography Sequence Analysis DNA United Kingdom Vancomycin-Resistant Enterococci Virulence Factors
Published by: Nat Microbiol
Changes in duodenal tissue-associated microbiota following hookworm infection and consecutive gluten challenges in humans with coeliac disease
P Giacomin, M Zakrzewski, TP Jenkins, X Su, R Al-Hallaf, J Croese, S de Vries, A Grant, M Mitreva, A Loukas, L Krause, C Cantacessi
Jan 16, 2017
Longitudinal genomic surveillance of multidrug-resistant Escherichia coli carriage in a long-term care facility in the United Kingdom.
Hayley J Brodrick, Kathy E Raven, Teemu Kallonen, Dorota Jamrozy, Beth Blane, Nicholas M Brown, Veronique Martin, M Estée Török, Julian Parkhill, Sharon J Peacock
Jul 25, 2017
BACKGROUND: Residents of long-term care facilities (LTCF) may have high carriage rates of multidrug-resistant pathogens, but are not currently included in surveillance programmes for antimicrobial resistance or...
Emergence and spread of a human-transmissible multidrug-resistant nontuberculous mycobacterium
JM Bryant, DM Grogono, D Rodriguez-Rincon, I Everall, KP Brown, P Moreno, D Verma, E Hill, J Drijkoningen, P Gilligan, CR Esther, PG Noone, O Giddings, SC Bell, R Thomson, CE Wainwright, C Coulter, S Pandey, ME Wood, RE Stockwell, KA Ramsay, LJ Sherrard, TJ Kidd, N Jabbour, GR Johnson, LD Knibbs, L Morawska, PD Sly, A Jones, D Bilton, I Laurenson, M Ruddy, S Bourke, ICJW Bowler, SJ Chapman, A Clayton, M Cullen, O Dempsey, M Denton, M Desai, RJ Drew, F Edenborough, J Evans, J Folb, T Daniels, H Humphrey, B Isalska, S Jensen-Fangel, B Jönsson, AM Jones, TL Katzenstein, T Lillebaek, G MacGregor, S Mayell, M Millar, D Modha, EF Nash, C O'Brien, D O'Brien, C Ohri, CS Pao, D Peckham, F Perrin, A Perry, T Pressler, L Prtak, T Qvist, A Robb, H Rodgers, K Schaffer, N Shafi, J van Ingen, M Walshaw, D Watson, N West, J Whitehouse, CS Haworth, SR Harris, D Ordway, J Parkhill, RA Floto
Dec 06, 2016
Animals Communicable Diseases Emerging Cystic Fibrosis Drug Resistance Multiple Bacterial Genome Bacterial Genomics Humans Incidence Lung Mice Mice SCID Mycobacterium Infections Nontuberculous Nontuberculous mycobacteria Phylogeny Pneumonia Bacterial Polymorphism Single Nucleotide Sequence Analysis DNA
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