Search
Results: 358
Metagenomic analyses and genetic diversity of Tomato leaf curl Arusha virus affecting tomato plants in Kenya.
Edith Khamonya Avedi, Adedapo Olutola Adediji, Dora Chao Kilalo, Florence Mmogi Olubayo, Isaac Macharia, Elijah Miinda Ateka, Eunice Magoma Machuka, Josiah Musembi Mutuku
Jan 07, 2021
Phylogeographical analysis of the dominant multidrug-resistant H58 clade of Salmonella Typhi identifies inter- and intracontinental transmission events.
Vanessa K Wong, Stephen Baker, Derek J Pickard, Julian Parkhill, Andrew J Page, Nicholas A Feasey, Robert A Kingsley, Nicholas R Thomson, Jacqueline A Keane, François-Xavier Weill, David J Edwards, Jane Hawkey, Simon R Harris, Alison E Mather, Amy K Cain, James Hadfield, Peter J Hart, Nga Tran Vu Thieu, Elizabeth J Klemm, Dafni A Glinos, Robert F Breiman, Conall H Watson, Samuel Kariuki, Melita A Gordon, Robert S Heyderman, Chinyere Okoro, Jan Jacobs, Octavie Lunguya, W John Edmunds, Chisomo Msefula, Jose A Chabalgoity, Mike Kama, Kylie Jenkins, Shanta Dutta, Florian Marks, Josefina Campos, Corinne Thompson, Stephen Obaro, Calman A MacLennan, Christiane Dolecek, Karen H Keddy, Anthony M Smith, Christopher M Parry, Abhilasha Karkey, E Kim Mulholland, James I Campbell, Sabina Dongol, Buddha Basnyat, Muriel Dufour, Don Bandaranayake, Take Toleafoa Naseri, Shalini Pravin Singh, Mochammad Hatta, Paul Newton, Robert S Onsare, Lupeoletalalei Isaia, David Dance, Viengmon Davong, Guy Thwaites, Lalith Wijedoru, John A Crump, Elizabeth de Pinna, Satheesh Nair, Eric J Nilles, Duy Pham Thanh, Paul Turner, Sona Soeng, Mary Valcanis, Joan Powling, Karolina Dimovski, Geoff Hogg, Jeremy Farrar, Kathryn E Holt, Gordon Dougan
Jan 08, 2020
The emergence of multidrug-resistant (MDR) typhoid is a major global health threat affecting many countries where the disease is endemic. Here whole-genome sequence analysis of 1,832 Salmonella enterica serovar Typhi (S. Typhi)...
Flexible and scalable diagnostic filtering of genomic variants using G2P with Ensembl VEP.
Anja Thormann, Mihail Halachev, William McLaren, David J Moore, Victoria Svinti, Archie Campbell, Shona M Kerr, Marc Tischkowitz, Sarah E Hunt, Malcolm G Dunlop, Matthew E Hurles, Caroline F Wright, Helen V Firth, Fiona Cunningham, David R FitzPatrick
Feb 07, 2020
We aimed to develop an efficient, flexible and scalable approach to diagnostic genome-wide sequence analysis of genetically heterogeneous clinical presentations. Here we present G2P ( www.ebi.ac.uk/gene2phenotype ) as an online...
Fratricide activity of MafB protein of N. meningitidis strain B16B6.
Jesús Arenas, Vincent de Maat, Laura Catón, Massis Krekorian, Juan Cruz Herrero, Flavio Ferrara, Jan Tommassen
May 11, 2020
BACKGROUND: Neisseria meningitidis is an inhabitant of the mucosal surfaces of the human nasopharynx. We recently demonstrated that the secreted meningococcal Two-partner secretion protein A (TpsA) is involved in interbacterial...
Frequency of rare recessive mutations in unexplained late onset cerebellar ataxia.
MJ Keogh, H Steele, K Douroudis, A Pyle, J Duff, R Hussain, T Smertenko, H Griffin, M Santibanez-Koref, R Horvath, PF Chinnery
Mar 07, 2019
Sporadic late onset cerebellar ataxia is a well-described clinical presentation with a broad differential diagnosis that adult neurologists should be familiar with. However, despite extensive clinical investigations, an acquired...
Wave 2 strains of atypical Vibrio cholerae El Tor caused the 2009-2011 cholera outbreak in Papua New Guinea.
Andrew R Greenhill, Ankur Mutreja, Dieter Bulach, Matthew J Belousoff, Marinjho H Jonduo, Deirdre A Collins, Monalisa P Kas, Johanna Wapling, Torsten Seemann, Alice Lafana, Gordon Dougan, Mark V Brown, Paul F Horwood
Mar 11, 2019
Vibrio cholerae is the causative agent of cholera, a globally important human disease for at least 200 years. In 2009-2011, the first recorded cholera outbreak in Papua New Guinea (PNG) occurred. We conducted genetic and...
Rapid sequencing of MRSA direct from clinical plates in a routine microbiology laboratory.
Beth Blane, Kathy E Raven, Danielle Leek, Nicholas Brown, Julian Parkhill, Sharon J Peacock
Apr 12, 2019
BACKGROUND: Routine sequencing of MRSA could bring about significant improvements to outbreak detection and investigation. Sequencing is commonly performed using DNA extracted from a pure culture, but overcoming the delay...
The use of panel testing in familial breast and ovarian cancer.
Advances in sequencing technology have led to the introduction of panel testing in hereditary breast and ovarian cancer. While direct-to-consumer testing services have become widely available, the clinical validity of many of...
Breast Cancer gene panel genetic testing and hereditary cancer ovarian cancer AMP-Activated Protein Kinase Kinases Antigens CD Cadherins DNA-Binding Proteins Epithelial Cell Adhesion Molecule Female Genes BRCA1 Genes BRCA2 Genetic Predisposition to Disease Genetic Testing Hereditary Breast and Ovarian Cancer Syndrome High-Throughput Nucleotide Sequencing Humans Li-Fraumeni Syndrome Lynch Syndrome II MutL Protein Homolog 1 MutS Homolog 2 Protein PTEN Phosphohydrolase Peutz-Jeghers Syndrome Protein Serine-Threonine Kinases Sequence Analysis DNA Tumor Suppressor Protein p53
Functional Alleles of Chicken BG Genes, Members of the Butyrophilin Gene Family, in Peripheral T Cells.
B-G B7 family Adaptive Immunity innate immunity Membrane Protein Alleles Alternative Splicing Amino Acid Sequence Animals Butyrophilins Chickens Cloning Molecular Exons Gene Expression Haplotypes Introns Models Molecular Multigene Family Phylogeny Protein Conformation Sequence Analysis DNA Structure-Activity Relationship T-Lymphocytes
Sharing of carbapenemase-encoding plasmids between Enterobacteriaceae in UK sewage uncovered by MinION sequencing
C Ludden, S Reuter, K Judge, T Gouliouris, B Blane, F Coll, P Naydenova, M Hunt, A Tracey, K Hopkins, N Brown, N Woodford, J Parkhill, S Peacock
Jul 13, 2017
False gene and chromosome losses in genome assemblies caused by GC content variation and repeats.
Juwan Kim, Chul Lee, Byung June Ko, Dong Ahn Yoo, Sohyoung Won, Adam M Phillippy, Olivier Fedrigo, Guojie Zhang, Kerstin Howe, Jonathan Wood, Richard Durbin, Giulio Formenti, Samara Brown, Lindsey Cantin, Claudio V Mello, Seoae Cho, Arang Rhie, Heebal Kim, Erich D Jarvis
Sep 28, 2022
BACKGROUND: Many short-read genome assemblies have been found to be incomplete and contain mis-assemblies. The Vertebrate Genomes Project has been producing new reference genome assemblies with an emphasis on being as complete...
New perspectives on Neanderthal dispersal and turnover from Stajnia Cave (Poland).
Andrea Picin, Mateja Hajdinjak, Wioletta Nowaczewska, Stefano Benazzi, Mikołaj Urbanowski, Adrian Marciszak, Helen Fewlass, Marjolein D Bosch, Paweł Socha, Krzysztof Stefaniak, Marcin Żarski, Andrzej Wiśniewski, Jean-Jacques Hublin, Adam Nadachowski, Sahra Talamo
Mar 08, 2022
The Micoquian is the broadest and longest enduring cultural facies of the Late Middle Palaeolithic that spread across the periglacial and boreal environments of Europe between Eastern France, Poland, and Northern Caucasus. Here...
A Comprehensive Functional Analysis of NTRK1 Missense Mutations Causing Hereditary Sensory and Autonomic Neuropathy Type IV (HSAN IV).
Samiha S Shaikh, Ya-Chun Chen, Sally-Anne Halsall, Michael S Nahorski, Kiyoyuki Omoto, Gareth T Young, Anne Phelan, Christopher Geoffrey Woods
Nov 28, 2016
CIPA NGF TRKA neuropathy Pain Alleles Cell Line Computational Biology DNA Mutational Analysis Gene Order Genetic Association Studies Genetic Loci Genetic Predisposition to Disease Genotype Glycosylation Hereditary Sensory and Autonomic Neuropathies Humans Molecular Imaging Mutation Missense Neurites Phospholipase C gamma Phosphorylation Protein Binding Protein Interaction Domains and Motifs Receptor trkA Recombinant Fusion Proteins Sequence Analysis DNA Signal Transduction
Construction and analysis of tag single nucleotide polymorphism maps for six human-mouse orthologous candidate genes in type 1 diabetes.
Lisa M Maier, Deborah J Smyth, Adrian Vella, Felicity Payne, Jason D Cooper, Rebecca Pask, Christopher Lowe, John Hulme, Luc J Smink, Heather Fraser, Carolyn Moule, Kara M Hunter, Giselle Chamberlain, Neil Walker, Sarah Nutland, Dag E Undlien, Kjersti S Rønningen, Cristian Guja, Constantin Ionescu-Tîrgoviste, David A Savage, David P Strachan, Laurence B Peterson, John A Todd, Linda S Wicker, Rebecca C Twells
Jun 14, 2011
Detecting microRNA binding and siRNA off-target effects from expression data.
Sylamer is a method for detecting microRNA target and small interfering RNA off-target signals in 3' untranslated regions from a ranked gene list, sorted from upregulated to downregulated, after a microRNA perturbation or RNA...
Exploration of signals of positive selection derived from genotype-based human genome scans using re-sequencing data.
Min Hu, Qasim Ayub, José Afonso Guerra-Assunção, Quan Long, Zemin Ning, Ni Huang, Irene Gallego Romero, Lira Mamanova, Pelin Akan, Xin Liu, Alison J Coffey, Daniel J Turner, Harold Swerdlow, John Burton, Michael A Quail, Donald F Conrad, Anton J Enright, Chris Tyler-Smith, Yali Xue
Jan 23, 2018
We have investigated whether regions of the genome showing signs of positive selection in scans based on haplotype structure also show evidence of positive selection when sequence-based tests are applied, whether the target of...
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
Extensive sequence duplication in Arabidopsis revealed by pseudo-heterozygosity.
Benjamin Jaegle, Rahul Pisupati, Luz Mayela Soto-Jiménez, Robin Burns, Fernando A Rabanal, Magnus Nordborg
Mar 09, 2023
BACKGROUND: It is apparent that genomes harbor much structural variation that is largely undetected for technical reasons. Such variation can cause artifacts when short-read sequencing data are mapped to a reference genome....
Isothermal DNA amplification using the T4 replisome
Yolanda Schaerli, Viktor Stein, Michelle M Spiering, Stephen J Benkovic, Chris Abell, Florian Hollfelder
Jan 06, 2021
In vitro reconstitution of the bacteriophage T4 replication machinery provides a novel system for fast and processive isothermal DNA amplification. We have characterized this system in two formats: (i) in circular nicking...
Divergence of regulatory networks governed by the orthologous transcription factors FLC and PEP1 in Brassicaceae species.
Julieta L Mateos, Vicky Tilmes, Pedro Madrigal, Edouard Severing, René Richter, Colin WM Rijkenberg, Paweł Krajewski, George Coupland
Jun 19, 2020
Genome-wide landscapes of transcription factor (TF) binding sites (BSs) diverge during evolution, conferring species-specific transcriptional patterns. The rate of divergence varies in different metazoan lineages but has not...
Arabidopsis Arabis alpina binding-site evolution flowering vernalization Arabidopsis Proteins Binding Sites Brassicaceae Environment Flowers Gene Expression Regulation Plant Gene Regulatory Networks Gene-Environment Interaction genetic variation MADS Domain Proteins Nucleotide Motifs Plant Proteins Protein Binding Sequence Analysis DNA Transcription Factors
Seeding and Establishment of Legionella pneumophila in Hospitals
Sophia David, Baharak Afshar, Massimo Mentasti, Christophe Ginevra, Isabelle Podglajen, Simon R Harris, Victoria J Chalker, Sophie Jarraud, Timothy G Harrison, Julian Parkhill
Sep 06, 2019
BACKGROUND: Legionnaires' disease is an important cause of hospital-acquired pneumonia and is caused by infection with the bacterium Legionella. Because current typing methods often fail to resolve the infection source in...
Legionella pneumophila Legionnaires’ disease bacterial genomics whole-genome sequencing Nosocomial infections Computational Biology Cross Infection Genomics Genotype Hospitals Humans Legionella pneumophila Legionnaires' Disease molecular epidemiology Molecular Typing Phylogeny Sequence Analysis DNA Water Microbiology
Staphylococcus caeli sp. nov., isolated from air sampling in an industrial rabbit holding.
Strain 82T, a Gram-stain-positive, coagulase-negative staphylococcus was isolated from an air sample obtained from an industrial rabbit holding in Italy. It is phylogenetically closely related to the coagulase-negative species...
Inferring Transmission Bottleneck Size from Viral Sequence Data Using a Novel Haplotype Reconstruction Method.
|
|< |
< |
1 |