St Andrews Bioinformatics Unit

Publications

Publications listed below are in most recent publication order for all researchers within the St Andrews Bioinformatics community

100 (of 142 /dk/atira/pure/researchoutput/status/published available) for St Andrews Bioinformatics Unit (source: University of St Andrews PURE)
Please click title of any item for full details

The role of multidimensional poverty in antibiotic misuse Dominique LaShari Green, Katherine Lisa Keenan, Sarah Insia Huque, Martha F Mushi, Catherine Kansiime, Benon Asiimwe, John Kiiru, Stephen Mshana, Stella Neema, Joseph R Mwanga, Mike Kesby, Andy Lynch, Hannah Worthington, Emmanuel Olawale Olamijuwon, Mary Abed Al Ahad, Annette Aduda, John Mwaniki Njeru, Blandina T Mmbaga, Joel Bazira, Alison Fiona Sandeman, John Stelling, Stephen Henry Gillespie, Gibson Kibiki, Wilber Sabiiti, Derek James Sloan, Matthew Holden, V Anne Smith, Arun Decano, Antonio Maldonado-Barragan, David Aanensen, Nyanda E Ntinginya, Alison Elliott,
The Lancet Global Health 2023 vol. 11 pp. e59-e68
Characterisation of arabinogalactan endo β 1,4 galactanases from Globodera rostochiensis, Globodera pallida and Rotylenchulus reniformis Sophie Mantelin, Sebastian Eves-van den Akker, John Jones
Physiological and Molecular Plant Pathology 2023 vol. 123
Molecular characterizations of the coagulase-negative staphylococci species causing urinary tract infection in Tanzania Shukrani Phillip, Martha F. Mushi, Arun Decano, Jeremiah Seni, Blandina T. Mmbaga, Happiness Kumburu, Eveline T. Konje, Joseph R. Mwanga, Benson R. Kidenya, Betrand Msemwa, Stephen Henry Gillespie, Antonio Maldonado-Barragan, Alison Fiona Sandeman, Wilber Sabiiti, Matthew Holden, Stephen Mshana
Pathogens 2023 vol. 12
Amphioxus muscle transcriptomes reveal vertebrate-like myoblast fusion genes and a highly conserved role of insulin signalling in the metabolism of muscle David Ellard Keith Ferrier
BMC Genomics 2022 vol. 23
ARHGEF39, a gene implicated in developmental language disorder, activates RHOA and is involved in cell de-adhesion and neural progenitor cell proliferation Midas Anijs, Paolo Devanna, Sonja Vernes
Frontiers in Molecular Neuroscience 2022 vol. 15
Cyclic nucleotide signaling in phage defense and counter-defense Januka S. Athukoralage, Malcolm White
Annual Review of Virology 2022 vol. 9 pp. 451-468
The indirect genetic effect interaction coefficient ψ Nathan William Bailey, Camille Desjonqueres
Journal of Heredity 2022 vol. 113 pp. 79–90
Bringing bioinformatics to schools with the 4273pi project Stevie Bain, Heleen Plaisier, Felicity Anderson, Nicola Cook, Kathryn Crouch, Thomas Robert Meagher, Michael Gordon Ritchie, Edward Wallace, Daniel Barker
PLoS Computational Biology 2022 vol. 18
Genetic variance in fitness indicates rapid contemporary adaptive evolution in wild animals Timothée Bonnet, Michael Blair Morrissey, Pierre de Villemereuil, Susan C. Alberts, Peter Arcese, Liam D. Bailey, Stan Boutin, Patricia Brekke, Lauren J. N. Brent, Glauco Camenisch, Anne Charmantier, Tim H. Clutton-Brock, Andrew Cockburn, David W. Coltman, Alexandre Courtiol, Eve Davidian, Simon R. Evans, John G. Ewen, Marco Festa-Bianchet, Christophe de Franceschi, Lars Gustafsson, Oliver P. Höner, Thomas M. Houslay, Lukas F. Keller, Marta Manser, Andrew G. McAdam, Emily McLean, Pirmin Nietlisbach, Helen L. Osmond, Josephine M. Pemberton, Erik Postma, Jane M. Reid, Alexis Rutschmann, Anna W. Santure, Ben C. Sheldon, Jon Slate, Céline Teplitsky, Marcel E. Visser, Bettina Wachter, Loeske E. B. Kruuk
Science 2022 vol. 376 pp. 1012-1016
Nucleotide usage biases distort inferences of the species tree Rui Borges, Bastien Boussau, Gergely J Szöllősi, Carolin Kosiol
Genome Biology and Evolution 2022 vol. 14
The architecture of clonal expansions in morphologically normal tissue from cancerous and non-cancerous prostates Claudia Buhigas, Anne Y. Warren, Wing-Kit Leung, Hayley Whitaker, Hayley J. Luxton, Steve Hawkins, Jonathan Kay, Adam Butler, Yaobo Xu, Dan Woodcock, Sue Merson, Fiona M. Frame, Atef Sahli, Federico Abascal, Iñigo Martincorena, G. Steven Bova, Christopher S. Foster, Peter Campbell, Norman Maitland, David E. Neal, Charlie E. Massie, Andy Lynch, Rosalind A. Eeles, Colin S. Cooper, David C. Wedge, Univ Anglia
Molecular Cancer 2022 vol. 21
Rare germline variants are associated with rapid biochemical recurrence after radical prostate cancer treatment Daniel Burns, Ezequiel Anokiana, Edward J Saunders, Robert G Bristow, Michael Fraser, Jüri Reimand, Thorsten Schlomm, Guido Sauter, Benedikt Brors, Jan Korbeli, Joachim Weischenfeldt, Sebastian M Waszak, Niall M Corcoran, Chol-Hee Jung, Bernard J Pope, Chris M Hovens, Géraldine Cancel-Tassin, Olivier Cussenot, Massimo Loda, Chris Sander, Vanessa M Hayes, Karina Dalsgaard Sorensen, Yong-Jie Lu, Freddie C Hamdy, Christopher S Foster, Vincent Gnanapragasam, Adam Butler, Andy Lynch, Charlie E Massie, Dan J Woodcock, Colin S Cooper, David C Wedge, Daniel S Brewer, Zsofia Kote-Jarai, Rosalind Eeles
European Urology 2022 vol. 82 pp. 201-211
Density-dependent dispersal promotes female-biased sex allocation in viscous populations Andy Gardner
Biology Letters 2022 vol. 18
KIAA0319 influences cilia length, cell migration and mechanical cell-substrate interaction Nils Michael Kronenberg, Angela Martinelli, Andrew Clive Riches, Malte Christian Gather, Silvia Paracchini
Scientific Reports 2022 vol. 12
Contradictory phylogenetic signals in the laurasiatheria anomaly zone Liliya Doronina, Graham M. Hughes, Diana Moreno-Santillan, Colleen Lawless, Tadhg Lonergan, Louise Ryan, David Jebb, Bogdan M. Kirilenko, Jennifer M. Korstian, Liliana M. Dávalos, Sonja Vernes, Eugene W. Myers, Emma C. Teeling, Michael Hiller, Lars S. Jermiin, Jürgen Schmitz, Mark S. Springer, David A. Ray
Genes 2022 vol. 13
Discovery of 42 genome-wide significant loci associated with dyslexia Catherine Doust, Pierre Fontanillas, Else Eising, Scott D Gordon, Zhengjun Wang, Gökberk Alagöz, Barbara Moltz, Beate St Pourcain, Clyde Francks, Riccardo E Marioni, Jingjing Zhao, Silvia Paracchini, Joel B Talcott, Anthony P Monaco, John F Stein, Jeffrey R Gruen, Richard K Olson, Erik G Willcutt, John C DeFries, Bruce F Pennington, Shelley D Smith, Margaret J Wright, Nicholas G Martin, Adam Auton, Timothy C Bates, Simon E Fisher, Michelle Luciano
Nature Genetics 2022 vol. Online First
Auditory cortex asymmetries relate to vocabulary knowledge because of shared polygenic influences Mark A. Eckert, Kenneth I. Vaden, Jr. , Silvia Paracchini
2022
Genome-wide analyses of individual differences in quantitatively assessed reading- and language-related skills in up to 34,000 people Else Elsing, Nazine Mirza-Schreiber, Eveline L. De Zeeuw, Carol A. Wang, Dongnhu T. Truong, Andrea G. Allegrini, Chin Yang Shapland, Gu Zhu, Karen G. Wigg, Margot Gerritse, Barbara Molz, Gökberk Alagöz, Alessandro Gialluisi, Kaili Rimfeld, Marjolein van Donkelaar, Zhijie Liao, Philip R. Jansen, Till F. M. Andlauer, Timothy C. Bates, Manon Bernard, Kirsten Blokland, Milene Bonte, Anders D. Børglum, Thomas Bourgeron, Daniel Brandeis, Fabiola Ceroni, Valeria Csépe, Philip S. Dale, Peter F. de Jong, John C. DeFries, Jean-François Démonet, Ditte Demontis, Yu Feng, Scott D. Gordon, Sharon L. Guger, Marianna E. Hayiou-Thomas, Juan A. Hernández-Cabrera, Jouke-Jan Hottenga, Charles Hulme, Juha Kere, Elizabeth N. Kerr, Tanner Koomar, Karin Landerl, Gabriel Leonard, Maureen W. Lovett, Heikki Lyytinen, Nicholas G. Martin, Angela Martinelli, Urs Maurer, Jacob Michaelson, Kristina Moll, Anthony P. Monaco, Angela T. Morgan, Markus M. Noethen, Zdenka Pausova, Craig E. Pennell, Bruce F. Pennington, Kaitlyn M. Price, Veera M. Rajagopal, Franck Ramus, Louis Richer, Nuala H. Simpson, Shelley Smith, Margaret J. Snowling, John Stein, Lisa J. Strug, Joel B. Talcott, Henning Tiemeier, Marc M.P. van der Schroeff, Ellen Verhoef, Kate E. Watkins, Margaret Wilkinson, Margaret J. Wright, Cathy L. Barr, Dorret I. Boomsma, Manuel Carreiras, Marie-Christine J. Franken, Jeffrey R. Gruen, Michelle Luciano, Bertram Müller-Myhsok, Dianne F. Newbury, Richard . Olson, Silvia Paracchini, Tomas Paus, Robert Plomin, Sheena Reilly, Gerd Schulte-Körne, Bruce Tomblin, Elsje van Bergen, Andrew J.O. Whitehouse, Erik G. Willcutt, Beate St Pourcain, Clyde Francks, Simon E. Fisher
Proceedings of the National Academy of Sciences of the United States of America 2022 vol. 119
The era of reference genomes in conservation genomics Giulio Formenti, Kathrin Theissinger, Carlos Fernandes, Iliana Bista, Aureliano Bombarely, Christoph Bleidorn, Claudio Ciofi, Angelica Crottini, José A. Godoy, Jacob Höglund, Joanna Malukiewicz, Alice Mouton, Rebekah A. Oomen, Sadye Paez, Per J. Palsbøll, Christophe Pampoulie, María J. Ruiz-López, Hannes Svardal, Constantina Theofanopoulou, Jan de Vries, Ann-Marie Waldvogel, Guojie Zhang, Camila J. Mazzoni, Erich D. Jarvis, Miklós Bálint, Fedor Čiampor, Jacob Hoglund, Per Palsbøll, María José Ruiz-López, Goujie Zhang, Erich Jarvis, Sargis A. Aghayan, Tyler S. Alioto, Isabel Almudi, Nadir Alvarez, Paulo C. Alves, Isabel R. Amorim, Agostinho Antunes, Paula Arribas, Petr Baldrian, Paul R. Berg, Giorgio Bertorelle, Astrid Böhne, Andrea Bonisoli-Alquati, Ljudevit L. Boštjančić, Bastien Boussau, Catherine M. Breton, Elena Buzan, Paula F. Campos, Sonja Vernes,
Trends in Ecology & Evolution 2022 vol. 37 pp. 197-202
Causation, not collinearity Sam Froman Walmsley, Michael Blair Morrissey
Evolution Letters 2022 vol. 6 pp. 234-244
Mapping HPV 16 sub-lineages in anal cancer and implications for disease outcomes Sara Arroyo-Mühr, Raluca Grigorescu, Matthew Holden, Kate Cuschieri
Diagnostics 2022 vol. 12
Identification of plasma proteins associated with oesophageal cancer chemotherapeutic treatment outcomes using SWATH-MS Giorgos Minas, Silvia Anna Synowsky, Margaret R. Dunne, Hasnain Ahmed, Rhiannon McShane, Anshul Bhardwaj, Noel E. Donlon, Cliona Lorton, Jacintha O'Sullivan, John V. Reynolds, Peter David Caie, Sally Lorna Shirran, Andy Lynch, Alan J. Stewart, Swati Arya
Journal of Proteomics 2022 vol. 266
Paternal genome elimination promotes altruism in viscous populations Andy Gardner
Evolution 2022 vol. 76 pp. 2191-2198
Cyclic nucleotide-induced helical structure activates a TIR immune effector Gaelle Hogrel, Abbie Guild, Shirley Graham, Hannah Rickman, Sabine Gruschow, Quentin Bertrand, Laura Spagnolo, Malcolm White
Nature 2022 vol. 608 pp. 808–812
Bayesian Networks as a novel tool to enhance interpretability and predictive power of ecological models Richard Stafford, Iain McCombe Matthews, V Anne Smith
Ecological Informatics 2022 vol. 68
Microbiomes of urine and the prostate are linked to human prostate cancer risk groups Rachel Hurst, Emma Meader, Abraham Gihawi, Ghanasyam Rallapalli, Jeremy Clark, Gemma L. Kay, Martyn Webb, Kate Manley, Helen Curley, Helen Walker, Ravi Kumar, Katarzyna Schmidt, Lisa Crossman, Rosalind A. Eeles, David C. Wedge, Andy Lynch, Charlie E. Massie, Marcelino Yazbek-Hanna, Mark Rochester, Robert D. Mills, Richard F. Mithen, Maria H. Traka, Richard Y. Ball, Justin O'Grady, Daniel S. Brewer, John Wain, Colin S. Cooper
European Urology Oncology 2022 vol. 5 pp. 412-419
Population viscosity promotes altruism under density-dependent dispersal Jasmeen Kaur Kanwal, Andy Gardner
Proceedings of the Royal Society of London Series B: Biological Sciences 2022 vol. 289
Treatment of missing data in Bayesian network structure learning Katherine Lisa Keenan, V Anne Smith
BMC Medical Research Methodology 2022 vol. 22
Salmonella exhibit altered cellular localization in the presence of HLA-B27 and codistribute with endo-reticular membrane Janos Kriston-Vizi, Izabela Lenart, Takao Iwawaki, Keith Gould, Darren Nesbeth, Simon John Powis, Antony N. Antoniou
Journal of Immunology Research 2022 vol. 2022 pp. 1-9
Tumour-associated antigenic peptides are present in the HLA class I ligandome of cancer cell line derived extracellular vesicles Pankaj Kumar, Caitlin Margaret Boyne, Ayesha Qureshi, Peter Jacob Thorpe, Silvia Anna Synowsky, Sally Lorna Shirran, Simon John Powis
Immunology 2022 vol. 166 pp. 249-264
Genomic surveillance of Salmonella spp. in the Philippines during 2013-2014 Marietta L Lagrada, Silvia Argimón, Janice B Borlasa, Jaywardeen P Abad, June M Gayeta, Melissa L Masim, Agnettah M Olorosa, Victoria Cohen, Benjamin Jeffrey, Khalil Abudahab, Sonia B Sia, Charmian M Hufano, John Stelling, Matthew Holden, David M Aanensen, Celia C Carlos
Transactions of the Royal Society of Tropical Medicine and Hygiene 2022 vol. 116 pp. 1202-1213
Emergence of methicillin resistance predates the clinical use of antibiotics Jesper Larsen, Claire L Raisen, Xiaoliang Ba, Nicholas J Sadgrove, Guillermo F Padilla-González, Monique S J Simmonds, Igor Loncaric, Heidrun Kerschner, Petra Apfalter, Rainer Hartl, Ariane Deplano, Stien Vandendriessche, Barbora Černá Bolfíková, Pavel Hulva, Maiken C Arendrup, Rasmus K Hare, Céline Barnadas, Marc Stegger, Raphael N Sieber, Robert L Skov, Andreas Petersen, Øystein Angen, Sophie L Rasmussen, Carmen Espinosa-Gongora, Frank M Aarestrup, Laura J Lindholm, Suvi M Nykäsenoja, Frederic Laurent, Karsten Becker, Birgit Walther, Corinna Kehrenberg, Christiane Cuny, Franziska Layer, Guido Werner, Wolfgang Witte, Ivonne Stamm, Paolo Moroni, Hannah J Jørgensen, Hermínia de Lencastre, Emilia Cercenado, Fernando García-Garrote, Stefan Börjesson, Sara Hæggman, Vincent Perreten, Christopher J Teale, Andrew S Waller, Bruno Pichon, Martin D Curran, Matthew J Ellington, John J Welch, Sharon J Peacock, David J Seilly, Fiona J E Morgan, Julian Parkhill, Nazreen F Hadjirin, Jodi A Lindsay, Matthew Holden, Giles F Edwards, Geoffrey Foster, Gavin K Paterson, Xavier Didelot, Mark A Holmes, Ewan M Harrison, Anders R Larsen
Nature 2022 vol. 602 pp. 135-141
PCR duplicate proportion estimation and consequences for DNA copy number calculations Andy Lynch, Mike Smith, Matthew Eldridge, Simon Tavaré
2022 vol. 398 pp. 259-279
Degree correlations in graphs with clique clustering Peter Stephen Mann, V Anne Smith, John B. O. Mitchell, Simon Andrew Dobson
Physical Review. E, Statistical, nonlinear, and soft matter physics 2022 vol. 105
N-strain epidemic model using bond percolation Peter Stephen Mann, V Anne Smith, John B. O. Mitchell, Simon Andrew Dobson
Physical Review. E, Statistical, nonlinear, and soft matter physics 2022 vol. 106
Presence of optrA-mediated linezolid resistance in multiple lineages and plasmids of Enterococcus faecalis revealed by long read sequencing Martin Patrick McHugh, Kerry Andrea Pettigrew, Geoff Toner, Elham Khatamzas, Noha el Sakka, Anne Marie Karcher, Joanna Walker, Robert Weir, Danièle Meunier, Katie L. Hopkins, Neil Woodford, Kate E. Templeton, Stephen Henry Gillespie, Matthew Holden
Microbiology 2022 vol. 168
Ancestral sex-role plasticity facilitates the evolution of same-sex sexual behavior Nobuaki Mizumoto, Thomas Bourguignon, Nathan William Bailey
Proceedings of the National Academy of Sciences 2022 vol. 119
Analytical results for directional and quadratic selection gradients for log-linear models of fitness functions Michael Blair Morrissey, Ian Britton James Goudie
Evolution 2022 vol. 76
Non-prescribed antibiotic dispensing practices for symptoms of urinary tract infection in community pharmacies and accredited drug dispensing outlets in Tanzania Pendo M. Ndaki, Martha F. Mushi, Joseph R. Mwanga, Eveline T. Konje, Stella Mugassa, Msilikale W. Manyiri, Stanley M. Mwita, Nyanda E. Ntinginya, Blandina T. Mmbaga, Katherine Lisa Keenan, Wilber Sabiiti, Mike Kesby, Manuel Fernando Benitez Paez, Alison Fiona Sandeman, Matthew Holden, Stephen E. Mshana
BMC Primary Care 2022 vol. 23
Insights into the genetics of the Zhonghua 11 Resistance to Meloidogyne graminicola and its molecular determinism in rice Hue Thi Nguyen, Sophie Mantelin, Cuong Viet Ha, Mathias Lorieux, John Jones, Chung Duc Mai, Stéphane Bellafiore
Frontiers in Plant Science 2022 vol. 13
Genomic epidemiology of SARS-CoV-2 in a university outbreak setting and implications for public health planning Sema Nickbakhsh, Joseph Hughes, Nicolaos Christofidis, Emily Griffiths, Sharif Shaaban, Jessica Enright, Katherine Smollett, Kyriaki Nomikou, Natasha Palmalux, Lily Tong, Stephen Carmichael, Vattipally B. Sreenu, Richard Orton, Emily J. Goldstein, Rachael M. Tomb, Kate Templeton, Rory N. Gunson, Ana da Silva Filipe, Catriona Milosevic, Emma Thomson, David L. Robertson, Matthew Holden, Christopher J. R. Illingworth, Alison Smith-Palmer, Martin Patrick McHugh
Scientific Reports 2022 vol. 12
Biogeography in the deep Aubrie Onoufriou, Oscar Eduardo Gaggiotti, Natacha Aguilar de Soto, Morgan L. McCarthy, Phillip A. Morin, Massimiliano Rosso, Merel Dalebout, Nicholas Davison, Robin W. Baird, C. Scott Baker, Simon Berrow, Andrew Brownlow, Daniel Burns, Florence Caurant, Rochelle Constantine, Fabien Demaret, Sascha Dreyer, Martina Ðuras, John Durban, Alexandros Frantzis, Gabrielle Genty, Ana Galov, Sabine S. Hansen, Andrew C. Kitchener, Vidal Martin, Antonio A. Mignucci-Giannoni, Valeria Montano, Aurelie Moulins, Carlos Olavarría, M. Michael Poole, Cristel Reyes Suárez, Emer Rogan, Conor Ryan, Agustina Schiavi, Paola Tepsich, Jorge Urban, Kristi West, Morten Tange Olsen, Emma Louise Carroll
Global Ecology and Conservation 2022 vol. 40
De novo assembly of Plasmodium knowlesi genomes from clinical samples explain the counterintuitive intrachromosomal organization of variant SICAvar and kir multiple gene family members Peter Jacob Thorpe, Ernest D. Benavente, Susanna Campino, Muh Fauzi, Robert W. Moon, Taane G. Clark, Janet Cox-Singh
Frontiers in Genetics 2022 vol. 13
Molecular modelling of the HCMV IL-10 protein isoforms and analysis of their interaction with the human IL-10 receptor Simone Queiroz Pantaleão, Lívia de Moraes Bomediano Camillo, Tainan Cerqueira Neves, Isabela de Godoy Menezes, Lucas Matheus Stangherlin, Helena Beatriz de Carvalho Ruthner Batista, Emma Poole, Michael Martin Nevels, Eric Alisson Philot, Ana Ligia Scott, Maria Cristina Carlan da Silva
PLoS ONE 2022 vol. 17
A genome-wide association study of Chinese and English language abilities in Hong Kong Chinese children Silvia Paracchini
2022
Identification of loci involved in childhood visual acuity and associations with cognitive skill and educational attainment Silvia Paracchini, Judith Schmitz,
2022
Non-right handedness is associated with language and reading impairments Silvia Paracchini
2022
The genetics of dyslexia Silvia Paracchini
2022
Handedness in twins Lena Sophie Pfeifer, Judith Schmitz, Marietta Papadatou-Pastou, Jutta Peterburs, Silvia Paracchini, Sebastian Ocklenburg
BMC Psychology 2022 vol. 10
Hypothesis-driven genome-wide association studies provide novel insights into genetics of reading disabilities Kaitlyn M. Price, Karen G. Wigg, Else Eising, Yu Feng, Kirsten Blokland, Margaret Wilkinson, Elizabeth N. Kerr, Sharon L. Guger, Simon E. Fisher, Maureen W. Lovett, Lisa J. Strug, Cathy L. Barr, Silvia Paracchini
Translational Psychiatry 2022 vol. 12
Life Sciences New Talent collection Malcolm White, Steve Brown
Royal Society Open Science 2022 vol. 9
A synthesis of senescence predictions for indeterminate growth, and support from multiple tests in wild lake trout Craig F Purchase, Anna C Rooke, Michael J Gaudry, Jason R Treberg, Lizy Mittell, Michael Blair Morrissey, Michael D Rennie
Proceedings. Biological sciences 2022 vol. 289
Deciphering signatures of natural selection via deep learning Xinghu Qin, Charleston Chiang, Oscar Eduardo Gaggiotti
Briefings in Bioinformatics 2022 vol. 23
Information-based summary statistics for spatial genetic structure inference Xinghu Qin, Oscar Eduardo Gaggiotti
Molecular Ecology Resources 2022 vol. 22 pp. 2183-2195
KLFDAPC Xinghu Qin, Charleston W K Chiang, Oscar Eduardo Gaggiotti
Briefings in Bioinformatics 2022 vol. 23
The persistence and evolutionary consequences of vestigial behaviours Jack Gregory Rayner, Nathan William Bailey
Biological Reviews of the Cambridge Philosophical Society 2022 vol. 97 pp. 1389-1407
Quantitative multidimensional phenotypes improve genetic analysis of laterality traits Judith Schmitz, Mo Zheng, Kelvin F. H. Lui, Catherine McBride, Connie S.-H. Ho, Silvia Paracchini
Translational Psychiatry 2022 vol. 12
Structure and mechanism of the type I-G CRISPR effector Shirley Graham, Ramasubramanian Sundaramoorthy, Malcolm White
Nucleic Acids Research 2022 vol. 50 pp. 11214-11228
The genome and lifestage-specific transcriptomes of a plant-parasitic nematode and its host reveal susceptibility genes involved in trans-kingdom synthesis of vitamin B5 Shahid Siddique, Zoran S. Radakovic, Clarissa Hiltl, Clement Pellegrin, Thomas J. Baum, Helen Beasley, Andrew F. Bent, Oliver Chitambo, Divykriti Chopra, Etienne G. J. Danchin, Eric Grenier, Samer S. Habash, M. Shamim Hasan, Johannes Helder, Tarek Hewezi, Julia Holbein, Martijn Holterman, Sławomir Janakowski, Georgios D. Koutsovoulos, Olaf P. Kranse, Jose L. Lozano-Torres, Tom R. Maier, Rick E. Masonbrink, Badou Mendy, Esther Riemer, Mirosław Sobczak, Unnati Sonawala, Mark G. Sterken, Peter Jacob Thorpe, Joris J. M. van Steenbrugge, Nageena Zahid, Florian Grundler, Sebastian Eves-van den Akker
Nature Communications 2022 vol. 13
World Society for Virology first international conference Maria Söderlund-Venermo, Anupam Varma, Deyin Guo, Douglas P. Gladue, Emma L. Poole, Flor H. Pujol, Hanu Pappu, Jesús L. Romalde, Laura Kramer, Mariana Baz, Marietjie Venter, Matthew D. Moore, Michael Martin Nevels, Sayeh Ezzikouri, Vikram N. Vakharia, William C. Wilson, Yashpal S. Malik, Zhengli Shi, Ahmed S. Abdel-Moneim
Virology 2022 vol. 566 pp. 114-121
Evolutionary diversification of the canonical Wnt signaling effector TCF/LEF in chordates Nuria Torres, Marika Salonna, Stefan Hoppler, David Ellard Keith Ferrier
Development, Growth & Differentiation 2022 vol. 64 pp. 120-137
Statistical challenges in mutational signature analyses of cancer sequencing data Victor Velasco Pardo, Michail Papathomas, Andy Lynch
2022 pp. 241-258
The pale spear-nosed bat Sonja Vernes, Paolo Devanna, Stephen Hoerpel, Ine Alvarez van Tussenbroek, Uwe Firzlaff, Peter Hagoort, Michael Hiller, Nienke Hoeksema, Graham M. Hughes, Ksenia Lavrichenko, Janine Mengede, Ariadna Morales, Maximilian Wiesmann
Annals of the New York Academy of Sciences 2022 vol. 1517 pp. 125-142
Light-induced asymmetries in embryonic retinal gene expression are mediated by the vascular system and extracellular matrix Elisabetta Versace, Paola Sgadò, Julia George, Jasmine L. Loveland, Joseph Ward, Peter Jacob Thorpe, Lars Juhl Jensen, Karen Anne Spencer, Silvia Paracchini, Giorgio Vallortigara
Scientific Reports 2022 vol. 12
A Bayesian network structure learning approach to identify genes associated with stress in spleens of chickens Emiliano Ariel Videla Rodriguez, John B. O. Mitchell, V Anne Smith
Scientific Reports 2022 vol. 12
Practical application of a Bayesian network approach to poultry epigenetics and stress Emiliano Ariel Videla Rodriguez, Fábio Pértille, Carlos Guerrero-Bosagna, John B. O. Mitchell, Per Jensen, V Anne Smith
BMC Bioinformatics 2022 vol. 23
SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway Brian J. Willett, Joe Grove, Oscar A. MacLean, Craig Wilkie, Giuditta De Lorenzo, Wilhelm Furnon, Diego Cantoni, Sam Scott, Nicola Logan, Shirin Ashraf, Maria Manali, Agnieszka Szemiel, Vanessa Cowton, Elen Vink, William T. Harvey, Chris Davis, Patawee Asamaphan, Katherine Smollett, Lily Tong, Richard Orton, Joseph Hughes, Poppy Holland, Vanessa Silva, David J. Pascall, Kathryn Puxty, Ana da Silva Filipe, Gonzalo Yebra, Sharif Shaaban, Matthew Holden, Rute Maria Pinto, Rory Gunson, Kate Templeton, Pablo R. Murcia, Arvind H. Patel, Paul Klenerman, Susanna Dunachie, John Haughney, David L. Robertson, Massimo Palmarini, Surajit Ray, Emma C. Thomson
Nature Microbiology 2022 vol. First Online
The genus Serratia revisited by genomics David J. Williams, Patrick A. D. Grimont, Adrián Cazares, Francine Grimont, Elisabeth Ageron, Kerry Andrea Pettigrew, Daniel Cazares, Elisabeth Njamkepo, François-Xavier Weill, Eva Heinz, Matthew Holden, Nicholas R. Thomson, Sarah J. Coulthurst
Nature Communications 2022 vol. 13
Divergence and introgression among the virilis group of Drosophila Venera Tyukmaeva, Anneli Hoikkala, Michael Gordon Ritchie
Evolution Letters 2022 vol. 6 pp. 537-551
Improved understanding of the role of gene and genome duplications in chordate evolution with new genome and transcriptome sequences David Ellard Keith Ferrier
Frontiers in Ecology and Evolution 2021 vol. 9
Protocol for an interdisciplinary cross-sectional study investigating the social, biological and community-level drivers of antimicrobial resistance (AMR) Benon Asiimwe, John Kiiru, Stephen Mshana, Stella Neema, Katherine Lisa Keenan, Mike Kesby, Joseph R. Mwanga, Derek James Sloan, Blandina T. Mmbaga, V Anne Smith, Stephen Henry Gillespie, Andy Lynch, Alison Fiona Sandeman, John Stelling, Alison Elliott, David M. Aanensen, Gibson E. Kibiki, Wilber Sabiiti, Matthew Holden,
BMJ Open 2021 vol. 11
Cyclic oligoadenylate signaling and regulation by ring nucleases during type III CRISPR defense Januka Sahan Athukoralage, Malcolm White
RNA 2021 vol. 27 pp. 855-867
A neglected conceptual problem regarding phenotypic plasticity’s role in adaptive evolution Nathan William Bailey, Camille Desjonqueres, Jack Gregory Rayner, Xiao Zhang
Evolution Letters 2021 vol. 5 pp. 444-457
The distinction between repeatability and correlation in studies of animal behaviour Miguel Borges Da Costa Guint Barbosa, Michael Blair Morrissey
Animal Behaviour 2021 vol. 175 pp. 201-217
Complete genome for Actinobacillus pleuropneumoniae serovar 8 reference strain 405 Janine T. Bossé, Yanwen Li, Liza Miriam Cohen, Marc Stegger, Øystein Angen, Sonia Lacouture, Marcelo Gottschalk, Liancheng Lei, Miriam Koene, Peter Kuhnert, Aloka B. Bandara, Thomas J. Inzana, Matthew Holden, David Harris, Olusegun Oshota, Duncan J. Maskell, Alexander W. Tucker, Brendan W. Wren, Andrew N. Rycroft, Paul R. Langford,
Microbial Genomics 2021 vol. 7
Rationally designed mariner vectors for functional genomic analysis of Actinobacillus pleuropneumoniae and other Pasteurellaceae species by transposon-directed insertion-site sequencing (TraDIS) Janine T. Bossé, Yanwen Li, Leon G. Leanse, Liqing Zhou, Roy R. Chaudhuri, Sarah E. Peters, Jinhong Wang, Gareth A. Maglennon, Matthew Holden, Duncan J. Maskell, Alexander W. Tucker, Brendan W. Wren, Andrew N. Rycroft, Paul R. Langford, Alexander W. (. Dan) Tucker, Lucy A. Weinert, Jinhong (. Tracy) Wang, Shi-Lu Luan, Jessica Beddow, Jon Cuccui, Vanessa S. Terra, on behalf of the BRaDP1T consortium
Animal Diseases 2021 vol. 1
What is the role of HLA-I on cancer derived extracellular vesicles? Defining the challenges in characterisation and potential uses of this ligandome Caitlin Margaret Boyne, Simon John Powis, Pankaj Kumar
International Journal of Molecular Sciences 2021 vol. 22
Speciation in the deep Emma Louise Carroll, Michael R. McGowen, Morgan L. McCarthy, Felix G. Marx, Natacha Aguilar, Merel L. Dalebout, Sascha Dreyer, Oscar Eduardo Gaggiotti, Sabine S. Hansen, Anton van Helden, Aubrie Onoufriou, Robin W. Baird, C. Scott Baker, Simon Berrow, Danielle Cholewiak, Rochelle Constantine, Nicholas J. Davison, Catarina Eira, R. Ewan Fordyce, John Gatesy, G. J. Greg Hofmeyr, Vidal Martín, James G. Mead, Antonio A. Mignucci-Giannoni, Phillip A. Morin, Cristel Reyes, Emer Rogan, Massimiliano Rosso, Mark S. Springer, Debbie Steel, Morten Tange Olsen
Proceedings of the Royal Society B: Biological Sciences 2021 vol. 288
Genomic surveillance of Acinetobacter baumannii in the Philippines, 2013-2014 J Chilam, S Argimon, MT Limas, ML Masim, JM Gayeta, ML Lagrada, AM Olorosa, V Cohen, LT Hernandez, B Jeffrey, K Abudahab, CM Hufano, SB Sia, Matthew Holden, J Stelling, DM Aanensen, CC Carlos,
Western Pacific Surveillance and Response Journal 2021 vol. 12
Gill transcriptomic responses to toxin-producing alga Prymnesium parvum in rainbow trout Morag Clinton, Elżbieta Król, Dagoberto Sepúlveda, Nikolaj R. Andersen, Andrew Stuart Brierley, David Ellard Keith Ferrier, Per Juel Hansen, Niels Lorenzen, Samuel A. M. Martin
Frontiers in Immunology 2021 vol. 12
Impacts of jellyfish on marine cage aquaculture Morag Clinton, David Ellard Keith Ferrier, Samuel A M Martin, Andrew Stuart Brierley
ICES Journal of Marine Science 2021 vol. 78 pp. 1557–1573
Sampling the fish gill microbiome Morag Clinton, Samuel A. M. Martin, Andrew Stuart Brierley, David Ellard Keith Ferrier
BMC Microbiology 2021 vol. 21
Genome expression dynamics reveal the parasitism regulatory landscape of the root-knot nematode Meloidogyne incognita and a promoter motif associated with effector genes Martine Da Rocha, Caroline Bournaud, Julie Dazenière, Peter Jacob Thorpe, Marc Bailly-Bechet, Clément Pellegrin, Arthur Péré, Priscila Grynberg, Laetitia Perfus-Barbeoch, Sebastian Eves-van den Akker, Etienne G. J. Danchin
Genes 2021 vol. 12
Re-identification of individuals from images using spot constellations Ignacy T. De¸bicki, Lizy Mittell, Bjarni K. Kristjánsson, Camille A. Leblanc, Michael Blair Morrissey, Kasim Terzic
Royal Society Open Science 2021 vol. 8
Pan-resistome characterization of uropathogenic Escherichia coli and Klebsiella pneumoniae strains circulating in Uganda and Kenya, isolated from 2017-2018 Arun Decano, Kerry Andrea Pettigrew, Wilber Sabiiti, Derek James Sloan, Stella Neema, Joel Bazira, John Kiiru, Helen Atieno Onyango, Benon Asiimwe, Matthew Holden
Antibiotics 2021 vol. 10
A genome-wide investigation of adaptive signatures in protein-coding genes related to tool behaviour in New Caledonian and Hawaiian crows Nicolas Dussex, Verena E. Kutschera, Gavin R. Hunt, Russell D. Gray, Kim Rutherford, Hideaki Abe, Robert C. Fleischer, Michael Gordon Ritchie, Christian Rutz, Jochen B.Wolf, Neil J. Gemmell
Molecular Ecology 2021 vol. 30 pp. 973-986
Genome-wide association analyses of individual differences in quantitatively assessed reading- and language-related skills in up to 34,000 people Else Eising, Nazanin Mirza-Schreiber, Eveline L. de Zeeuw, Carol A. Wang, Dongnhu T. Truong, Andrea G. Allegrini, Chin Yang Shapland, Gu Zhu, Karen G. Wigg, Margot Gerritse, Barbara Molz, Gökberk Alagöz, Alessandro Gialluisi, Kaili Rimfeld, Marjolein van Donkelaar, Zhijie Liao, Philip R. Jansen, Till F. M. Andlauer, Timothy C. Bates, Manon Bernard, Kirsten Blokland, Anders D. Børglum, Thomas Bourgeron, Daniel Brandeis, Fabiola Ceroni, Philip S. Dale, Karin Landerl, Heikki Lyytinen, Peter F. de Jong, John C. DeFries, Ditte Demontis, Yu Feng, Scott D. Gordon, Sharon L. Guger, Marianna E. Hayiou-Thomas, Juan A. Hernández-Cabrera, Jouke-Jan Hottenga, Charles Hulme, Elizabeth N. Kerr, Tanner Koomar, Maureen W. Lovett, Nicholas G. Martin, Angela Martinelli, Urs Maurer, Jacob J. Michaelson, Kristina Moll, Anthony P. Monaco, Angela T. Morgan, Markus M. Nöthen, Zdenka Pausova, Craig E. Pennell, Bruce F Pennington, Kaitlyn M. Price, Veera M. Rajagopal, Frank Ramus, Louis Richer, Nuala H. Simpson, Shelley Smith, Margaret J. Snowling, John Stein, Lisa J. Strug, Joel B. Talcott, Henning Tiemeier, Marc M.P. van de Schroeff, Ellen Verhoef, Kate E. Watkins, Margaret Wilkinson, Margaret J. Wright, Cathy L. Barr, Dorret I. Boomsma, Manuel Carreiras, Marie-Christine J. Franken, Jeffrey R. Gruen, Michelle Luciano, Bertram Müller-Myhsok, Dianne F. Newbury, Richard K. Olson, Silvia Paracchini, Tomas Paus, Robert Plomin, Gerd Schulte-Körne, Sheena Reilly, J. Bruce Tomblin, Elsje van Bergen, Andrew J.O. Whitehouse, Erik G. Willcutt, Beate St Pourcain, Clyde Francks, Simon E. Fisher
2021
Insights into dyslexia genetics research from the last two decades Florina Erbeli, Marianne Rice, Silvia Paracchini
Brain Sciences 2021 vol. 12
DrosoPhyla Cédric Finet, Victoria A Kassner, Antonio B Carvalho, Henry Chung, Jonathan P Day, Stephanie Day, Emily K Delaney, Francine C De Ré, Héloïse D Dufour, Eduardo Dupim, Hiroyuki F Izumitani, Thaísa B Gautério, Jessa Justen, Toru Katoh, Artyom Kopp, Shigeyuki Koshikawa, Ben Longdon, Elgion L Loreto, Maria D S Nunes, Komal K B Raja, Mark Rebeiz, Michael Gordon Ritchie, Gayane Saakyan, Tanya Sneddon, Machiko Teramoto, Venera Tyukmaeva, Thyago Vanderlinde, Emily E Wey, Thomas Werner, Thomas M Williams, Lizandra J Robe, Masanori J Toda, Ferdinand Marlétaz
Genome Biology and Evolution 2021 vol. 13
Genomic analysis of global Staphylococcus argenteus strains reveals distinct lineages with differing virulence and antibiotic resistance gene content Cosmika Goswami, Stephen Fox, Matthew Holden, Alistair Leanord, Thomas J Evans
Frontiers in Microbiology 2021 vol. 12
PHYTO-THREATS Sarah Green, David E. L. Cooke, Mike Dunn, Louise Barwell, Bethan Purse, Daniel S. Chapman, Gregory Valatin, Alexandra Schlenzig, Jane Barbrook, Tim Pettitt, Colin Price, Ana Pérez-Sierra, Debra Frederickson-Matika, Leighton Pritchard, Peter Jacob Thorpe, Peter J. A. Cock, Eva Randall, Beatrix Keillor, Mariella Marzano
Forests 2021 vol. 12
The role of multidimensional poverty in antibiotic misuse Dominique LaShari Green, Katherine Lisa Keenan, Sarah Insia Huque, Mike Kesby, Martha F. Mushi, Catherine Kansiime, Benon Asiimwe, John Kiiru, Stephen Mshana, Stella Neema, Joseph R. Mwanga, Andy Lynch, Hannah Worthington, Emmanuel Olawale Olamijuwon, Mary Abed Al Ahad, Annette Aduda, Blandina T. Mmbaga, Joel Bazira, Alison Fiona Sandeman, John Stelling, Stephen Henry Gillespie, Gibson Kibiki, Wilber Sabiti, Derek James Sloan, Matthew Holden, Hatua Consortium
2021
Specificity and sensitivity of an RNA targeting type III CRISPR complex coupled with a NucC endonuclease effector Sabine Gruschow, Catherine S Adamson, Malcolm White
Nucleic Acids Research 2021 vol. 49 pp. 13122-13134
Sex-biased demography modulates male harm across the genome Andy Gardner
Proceedings of the Royal Society of London Series B: Biological Sciences 2021 vol. 288
Neuroanatomy of the grey seal brain Nienke Hoeksema, Laura Verga, Janine Mengede, Corné van Roessel, Stella Villanueva, Anna Salazar-Casals, Ana Rubio-Garcia, Branislava Ćurčić-Blake, Sonja Vernes, Andrea Ravignani
Philosophical Transactions of the Royal Society B: Biological Sciences 2021 vol. 376
Animal personality adds complexity to the processes of divergence between sympatric morphs of Arctic charr Quentin J.-B. Horta-Lacueva, David Benhaïm, Michael Blair Morrissey, Sigurður S. Snorrason, Kalina H. Kapralova
Animal Behaviour 2021 vol. 175 pp. 57-73
Multivariate analysis of morphology, behaviour, growth and developmental timing in hybrids brings new insights into the divergence of sympatric Arctic charr morphs Quentin J.-B. Horta-Lacueva, Sigurður S. Snorrason, Michael Blair Morrissey, Camille A.-L. Leblanc, Kalina H. Kapralova
BMC Ecology and Evolution 2021 vol. 21
Genomic surveillance of Neisseria gonorrhoeae in the Philippines, 2013-2014 Manuel C Jamoralin, Silvia Argimón, Marietta L Lagrada, Alfred S Villamin, Melissa L Masim, June M Gayeta, Karis D Boehme, Agnettah M Olorosa, Sonia B Sia, Charmian M Hufano, Victoria Cohen, Lara T Hernandez, Benjamin Jeffrey, Khalil Abudahab, John Stelling, Matthew Holden, David M Aanensenb, Celia C Carlosa
Western Pacific Surveillance and Response Journal 2021 vol. 12 pp. 17-25
Toward genetic modification of plant-parasitic nematodes Olaf Kranse, Helen Beasley, Sally Adams, Andre Pires-daSilva, Christopher Bell, Catherine J Lilley, Peter E Urwin, David Bird, Eric Miska, Geert Smant, Godelieve Gheysen, John Jones, Mark Viney, Pierre Abad, Thomas R Maier, Thomas J Baum, Shahid Siddique, Valerie Williamson, Alper Akay, Sebastian Eves-van den Akker
G3: Genes, Genomes, Genetics 2021 vol. 11
Hearing sensitivity and amplitude coding in bats are differentially shaped by echolocation calls and social calls Ella Z Lattenkamp, Martina Nagy, Markus Drexl, Sonja Vernes, Lutz Wiegrebe, Mirjam Knörnschild
Proceedings of the Royal Society B: Biological Sciences 2021 vol. 288

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