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Results: 551
Reassessment of weak parent-of-origin expression bias shows it rarely exists outside of known imprinted regions.
Carol A Edwards, William MD Watkinson, Stephanie B Telerman, Lisa C Hulsmann, Russell S Hamilton, Anne C Ferguson-Smith
Apr 12, 2023
Genomic Subtypes of Non-invasive Bladder Cancer with Distinct Metabolic Profile and Female Gender Bias in KDM6A Mutation Frequency.
Carolyn D Hurst, Olivia Alder, Fiona M Platt, Alastair Droop, Lucy F Stead, Julie E Burns, George J Burghel, Sunjay Jain, Leszek J Klimczak, Helen Lindsay, Jo-An Roulson, Claire F Taylor, Helene Thygesen, Angus J Cameron, Anne J Ridley, Helen R Mott, Dmitry A Gordenin, Margaret A Knowles
Feb 08, 2018
Bladder cancer incurs a higher lifetime treatment cost than other cancers due to frequent recurrence of non-invasive disease. Improved prognostic biomarkers and localized therapy are needed for this large patient group. We...
KDM6A RHOB bladder cancer Gender Genomics mTORC1 metabolism recurrence-free survival subtypes Carcinoma Transitional Cell Cell Line Tumor Female Gene Expression Profiling Gene Expression Regulation Neoplastic Gene Frequency Genomics HEK293 Cells Histone Demethylases Humans Male Metabolome Metabolomics Mutation Nuclear Proteins Sex Factors Urinary Bladder Neoplasms
SecretSanta
MOTIVATION: The secretome denotes the collection of secreted proteins exported outside of the cell. The functional roles of secreted proteins include the maintenance and remodelling of the extracellular matrix as well as...
Genomic analysis of European bovine Staphylococcus aureus from clinical versus subclinical mastitis.
Jurriaan Hoekstra, Aldert L Zomer, Victor PMG Rutten, Lindert Benedictus, Arjan Stegeman, Mirlin P Spaninks, Torben W Bennedsgaard, Andrew Biggs, Sarne De Vliegher, Demetrio Herrera Mateo, Reglindis Huber-Schlenstedt, Jørgen Katholm, Péter Kovács, Volker Krömker, Guillaume Lequeux, Paolo Moroni, Luís Pinho, Sebastian Smulski, Karlien Supré, Jantijn M Swinkels, Mark A Holmes, Theo JGM Lam, Gerrit Koop
Jan 08, 2021
Intramammary infections (IMI) with Staphylococcus aureus are a common cause of bovine mastitis and can result in both clinical (CM) or subclinical mastitis (SCM). Although bacterial isolates of S. aureus differ in their...
Animals Anti-Bacterial Agents Bacterial Typing Techniques Cattle Clonal Evolution Drug Resistance Bacterial Europe Female Genes Bacterial genetic variation Genome-Wide Association Study Genomics Genotype Mastitis Bovine Multilocus Sequence Typing Phylogeny Staphylococcus aureus Virulence Virulence Factors
A hidden gene in astroviruses encodes a viroporin.
Predicting the Occurrence of Variants in RAG1 and RAG2
Dylan Lawless, Hana Lango Allen, James Thaventhiran, Flavia Hodel, Rashida Anwar, Jacques Fellay, Jolan E. Walter, Sinisa Savic
Aug 05, 2020
Abstract: While widespread genome sequencing ushers in a new era of preventive medicine, the tools for predictive genomics are still lacking. Time and resource limitations mean that human diseases remain uncharacterized because...
FlyBase
Aoife Larkin, Steven J Marygold, Giulia Antonazzo, Helen Attrill, Gilberto Dos Santos, Phani V Garapati, Joshua L Goodman, L Sian Gramates, Gillian Millburn, Victor B Strelets, Christopher J Tabone, Jim Thurmond, FlyBase Consortium
Oct 20, 2020
FlyBase (flybase.org) is an essential online database for researchers using Drosophila melanogaster as a model organism, facilitating access to a diverse array of information that includes genetic, molecular, genomic and reagent...
Attitudes of Costa Rican individuals towards donation of personal genetic data for research
Gabriela Chavarria-Soley, Fernanda Francis-Cartin, Fabiola Jimenez-Gonzalez, Alejandro Ávila-Aguirre, Maria Jose Castro-Gomez, Lauren Robarts, Anna Middleton, Henriette Raventós
Feb 26, 2021
Aim: We explore attitudes from the public in Costa Rica regarding willingness to donate DNA data for research. Materials & methods: A total of 224 Costa Rican individuals answered the anonymous online survey ‘Your DNA, Your...
Comparative Genomics
Duncan T Odom
Jan 31, 2020
Using a common analysis pipeline to compare data from three major lineages of complex eukaryotes reveals that transcription seems to evolve at a common rate.
Ontology-based prediction of cancer driver genes.
Sara Althubaiti, Andreas Karwath, Ashraf Dallol, Adeeb Noor, Shadi Salem Alkhayyat, Rolina Alwassia, Katsuhiko Mineta, Takashi Gojobori, Andrew D Beggs, Paul N Schofield, Georgios V Gkoutos, Robert Hoehndorf
Nov 27, 2019
Identifying and distinguishing cancer driver genes among thousands of candidate mutations remains a major challenge. Accurate identification of driver genes and driver mutations is critical for advancing cancer research and...
Agricultural intensification and the evolution of host specialism in the enteric pathogen Campylobacter jejuni.
Evangelos Mourkas, Aidan J Taylor, Guillaume Méric, Sion C Bayliss, Ben Pascoe, Leonardos Mageiros, Jessica K Calland, Matthew D Hitchings, Anne Ridley, Ana Vidal, Ken J Forbes, Norval JC Strachan, Craig T Parker, Julian Parkhill, Keith A Jolley, Alison J Cody, Martin CJ Maiden, David J Kelly, Samuel K Sheppard
Jun 19, 2020
Modern agriculture has dramatically changed the distribution of animal species on Earth. Changes to host ecology have a major impact on the microbiota, potentially increasing the risk of zoonotic pathogens being transmitted to...
Campylobacter Adaptation evolution Genomics Recombination Adaptation Physiological agriculture Animals Biofilms Campylobacter jejuni Cattle Diet evolution Molecular Gene Transfer Horizontal Genomics homologous recombination Host Specificity Hydrophobic and Hydrophilic Interactions Mutagenesis Phenotype Recombination Genetic specialization
Comparative genomics of Czech vaccine strains of Bordetella pertussis.
Ana Dienstbier, Derek Pouchnik, Mark Wildung, Fabian Amman, Ivo L Hofacker, Julian Parkhill, Jana Holubova, Peter Sebo, Branislav Vecerek
Sep 10, 2019
Bordetella pertussis is a strictly human pathogen causing the respiratory infectious disease called whooping cough or pertussis. B. pertussis adaptation to acellular pertussis vaccine pressure has been repeatedly highlighted...
Understanding polygenic models, their development and the potential application of polygenic scores in healthcare.
The use of genomic information to better understand and prevent common complex diseases has been an ongoing goal of genetic research. Over the past few years, research in this area has proliferated with several proposed methods...
CHiCAGO
Jonathan Cairns, Paula Freire-Pritchett, Steven W Wingett, Csilla Várnai, Andrew Dimond, Vincent Plagnol, Daniel Zerbino, Stefan Schoenfelder, Biola-Maria Javierre, Cameron Osborne, Peter Fraser, Mikhail Spivakov
Jul 15, 2019
Capture Hi-C (CHi-C) is a method for profiling chromosomal interactions involving targeted regions of interest, such as gene promoters, globally and at high resolution. Signal detection in CHi-C data involves a number of...
Genetic and environmental risk factors for atherosclerosis regulate transcription of phosphatase and actin regulating gene PHACTR1.
Michael E Reschen, Da Lin, Anil Chalisey, Elizabeth J Soilleux, Christopher A O'Callaghan
Dec 17, 2018
BACKGROUND AND AIMS: Coronary artery disease (CAD) risk is associated with non-coding genetic variants at the phosphatase and actin regulating protein 1(PHACTR1) gene locus. The PHACTR1 gene encodes an actin-binding protein with...
Atherosclerosis Expression quantitative trait locus (eQTL) Functional genomics genetic disease Genetic polymorphism Genomics Low-density lipoprotein (LDL) Myocardial Infarction Oxidized low density lipoprotein (oxLDL) PHACTR1 Adult Aged Alleles Atherosclerosis Coronary Artery Disease Coronary Vessels Endothelial Cells Gene Expression Regulation Gene-Environment Interaction Genotype Humans Inflammation Lipopolysaccharides MACROPHAGES Microfilament Proteins Middle Aged Muscle Smooth Vascular Polymorphism Single Nucleotide Tumor Necrosis Factor-alpha Young Adult
Single-cell RNA-seq reveals hidden transcriptional variation in malaria parasites.
Adam J Reid, Arthur M Talman, Hayley M Bennett, Ana R Gomes, Mandy J Sanders, Christopher JR Illingworth, Oliver Billker, Matthew Berriman, Mara Kn Lawniczak
Oct 10, 2018
Single-cell RNA-sequencing is revolutionising our understanding of seemingly homogeneous cell populations but has not yet been widely applied to single-celled organisms. Transcriptional variation in unicellular malaria parasites...
Copy number signatures and mutational processes in ovarian carcinoma.
Geoff Macintyre, Teodora E Goranova, Dilrini De Silva, Darren Ennis, Anna M Piskorz, Matthew Eldridge, Daoud Sie, Liz-Anne Lewsley, Aishah Hanif, Cheryl Wilson, Suzanne Dowson, Rosalind M Glasspool, Michelle Lockley, Elly Brockbank, Ana Montes, Axel Walther, Sudha Sundar, Richard Edmondson, Geoff D Hall, Andrew Clamp, Charlie Gourley, Marcia Hall, Christina Fotopoulou, Hani Gabra, James Paul, Anna Supernat, David Millan, Aoisha Hoyle, Gareth Bryson, Craig Nourse, Laura Mincarelli, Luis Navarro Sanchez, Bauke Ylstra, Mercedes Jimenez-Linan, Luiza Moore, Oliver Hofmann, Florian Markowetz, Iain A McNeish, James D Brenton
Sep 11, 2018
Genome-wide meta-analysis of macronutrient intake of 91,114 European ancestry participants from the cohorts for heart and aging research in genomic epidemiology consortium.
Jordi Merino, Hassan S Dashti, Sherly X Li, Chloé Sarnowski, Anne E Justice, Misa Graff, Constantina Papoutsakis, Caren E Smith, George V Dedoussis, Rozenn N Lemaitre, Mary K Wojczynski, Satu Männistö, Julius S Ngwa, Minjung Kho, Tarunveer S Ahluwalia, Natalia Pervjakova, Denise K Houston, Claude Bouchard, Tao Huang, Marju Orho-Melander, Alexis C Frazier-Wood, Dennis O Mook-Kanamori, Louis Pérusse, Craig E Pennell, Paul S de Vries, Trudy Voortman, Olivia Li, Stavroula Kanoni, Lynda M Rose, Terho Lehtimäki, Jing Hua Zhao, Mary F Feitosa, Jian'an Luan, Nicola M McKeown, Jennifer A Smith, Torben Hansen, Niina Eklund, Mike A Nalls, Tuomo Rankinen, Jinyan Huang, Dena G Hernandez, Christina-Alexandra Schulz, Ani Manichaikul, Ruifang Li-Gao, Marie-Claude Vohl, Carol A Wang, Frank JA van Rooij, Jean Shin, Ioanna P Kalafati, Felix Day, Paul M Ridker, Mika Kähönen, David S Siscovick, Claudia Langenberg, Wei Zhao, Arne Astrup, Paul Knekt, Melissa Garcia, DC Rao, Qibin Qi, Luigi Ferrucci, Ulrika Ericson, John Blangero, Albert Hofman, Zdenka Pausova, Vera Mikkilä, Nick J Wareham, Sharon LR Kardia, Oluf Pedersen, Antti Jula, Joanne E Curran, M Carola Zillikens, Jorma S Viikari, Nita G Forouhi, José M Ordovás, John C Lieske, Harri Rissanen, André G Uitterlinden, Olli T Raitakari, Jessica C Kiefte-de Jong, Josée Dupuis, Jerome I Rotter, Kari E North, Robert A Scott, Michael A Province, Markus Perola, L Adrienne Cupples, Stephen T Turner, Thorkild IA Sørensen, Veikko Salomaa, Yongmei Liu, Yun J Sung, Lu Qi, Stefania Bandinelli, Stephen S Rich, Renée de Mutsert, Angelo Tremblay, Wendy H Oddy, Oscar H Franco, Tomas Paus, Jose C Florez, Panos Deloukas, Leo-Pekka Lyytikäinen, Daniel I Chasman, Audrey Y Chu, Toshiko Tanaka
Sep 19, 2018
Macronutrient intake, the proportion of calories consumed from carbohydrate, fat, and protein, is an important risk factor for metabolic diseases with significant familial aggregation. Previous studies have identified two...
Aged aging Alpha-Ketoglutarate-Dependent Dioxygenase FTO Cohort Studies Energy Intake Female Fibroblast Growth Factors Genetic Loci Genetic Predisposition to Disease Genome-Wide Association Study Genomics Genotype Heart Diseases Humans Male Membrane Proteins Middle Aged nutrients obesity Polymorphism Single Nucleotide Receptors Retinoic Acid White People
Genomic Risk Prediction of Coronary Artery Disease in 480,000 Adults
Michael Inouye, Gad Abraham, Christopher P Nelson, Angela M Wood, Michael J Sweeting, Frank Dudbridge, Florence Y Lai, Stephen Kaptoge, Marta Brozynska, Tingting Wang, Shu Ye, Thomas R Webb, Martin K Rutter, Ioanna Tzoulaki, Riyaz S Patel, Ruth JF Loos, Bernard Keavney, Harry Hemingway, John Thompson, Hugh Watkins, Panos Deloukas, Emanuele Di Angelantonio, Adam S Butterworth, John Danesh, Nilesh J Samani, UK Biobank CardioMetabolic Consortium CHD working group
Nov 22, 2018
BACKGROUND: Coronary artery disease (CAD) has substantial heritability and a polygenic architecture. However, the potential of genomic risk scores to help predict CAD outcomes has not been evaluated comprehensively, because...
Coronary Artery Disease genomic risk prediction Primary Prevention Coronary Artery Disease Female Genome-Wide Association Study Genomics Humans Male Mass Screening Middle Aged Multifactorial Inheritance Predictive Value of Tests Primary Prevention Research Design Risk Assessment Risk Factors United Kingdom
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...
Genomic surveillance of Escherichia coli in municipal wastewater treatment plants as an indicator of clinically relevant pathogens and their resistance genes.
Kathy E Raven, Catherine Ludden, Theodore Gouliouris, Beth Blane, Plamena Naydenova, Nicholas M Brown, Julian Parkhill, Sharon J Peacock
Apr 15, 2019
We examined whether genomic surveillance of Escherichia coli in wastewater could capture the dominant E. coli lineages associated with bloodstream infection and livestock in the East of England, together with the...
Escherichia coli Genomic Surveillance resistance Wastewater Animals Cross-Sectional Studies England Environmental Monitoring Escherichia coli Escherichia coli Infections Escherichia coli Proteins Genes Bacterial Genomics Hospitals Humans Interspersed Repetitive Sequences Livestock Multilocus Sequence Typing Phylogeny Public Health Wastewater Water Purification beta-Lactamases
modMine
Sergio Contrino, Richard N Smith, Daniela Butano, Adrian Carr, Fengyuan Hu, Rachel Lyne, Kim Rutherford, Alex Kalderimis, Julie Sullivan, Seth Carbon, Ellen T Kephart, Paul Lloyd, EO Stinson, Nicole L Washington, Marc D Perry, Peter Ruzanov, Zheng Zha, Suzanna E Lewis, Lincoln D Stein, Gos Micklem
Aug 01, 2018
In an effort to comprehensively characterize the functional elements within the genomes of the important model organisms Drosophila melanogaster and Caenorhabditis elegans, the NHGRI model organism Encyclopaedia of DNA Elements...
The African Genome Variation Project shapes medical genetics in Africa.
Deepti Gurdasani, Tommy Carstensen, Fasil Tekola-Ayele, Luca Pagani, Ioanna Tachmazidou, Konstantinos Hatzikotoulas, Savita Karthikeyan, Louise Iles, Martin O Pollard, Ananyo Choudhury, Graham RS Ritchie, Yali Xue, Jennifer Asimit, Rebecca N Nsubuga, Elizabeth H Young, Cristina Pomilla, Katja Kivinen, Kirk Rockett, Anatoli Kamali, Ayo P Doumatey, Gershim Asiki, Janet Seeley, Fatoumatta Sisay-Joof, Muminatou Jallow, Stephen Tollman, Ephrem Mekonnen, Rosemary Ekong, Tamiru Oljira, Neil Bradman, Kalifa Bojang, Michele Ramsay, Adebowale Adeyemo, Endashaw Bekele, Ayesha Motala, Shane A Norris, Fraser Pirie, Pontiano Kaleebu, Dominic Kwiatkowski, Chris Tyler-Smith, Charles Rotimi, Eleftheria Zeggini, Manjinder S Sandhu
Aug 15, 2018
Given the importance of Africa to studies of human origins and disease susceptibility, detailed characterization of African genetic diversity is needed. The African Genome Variation Project provides a resource with which to...
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