811 results on '"Hall, Neil"'
Search Results
2. Standards recommendations for the Earth BioGenome Project
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Lawniczak, Mara KN, Durbin, Richard, Flicek, Paul, Lindblad-Toh, Kerstin, Wei, Xiaofeng, Archibald, John M, Baker, William J, Belov, Katherine, Blaxter, Mark L, Bonet, Tomas Marques, Childers, Anna K, Coddington, Jonathan A, Crandall, Keith A, Crawford, Andrew J, Davey, Robert P, Di Palma, Federica, Fang, Qi, Haerty, Wilfried, Hall, Neil, Hoff, Katharina J, Howe, Kerstin, Jarvis, Erich D, Johnson, Warren E, Johnson, Rebecca N, Kersey, Paul J, Liu, Xin, Lopez, Jose Victor, Myers, Eugene W, Pettersson, Olga Vinnere, Phillippy, Adam M, Poelchau, Monica F, Pruitt, Kim D, Rhie, Arang, Castilla-Rubio, Juan Carlos, Sahu, Sunil Kumar, Salmon, Nicholas A, Soltis, Pamela S, Swarbreck, David, Thibaud-Nissen, Françoise, Wang, Sibo, Wegrzyn, Jill L, Zhang, Guojie, Zhang, He, Lewin, Harris A, and Richards, Stephen
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Human Genome ,Genetics ,Animals ,Base Sequence ,Biodiversity ,Eukaryota ,Genomics ,Humans ,Reference Standards ,Reference Values ,Sequence Analysis ,DNA ,Earth BioGenome Project ,genomics ,ethics ,genome assembly - Abstract
A global international initiative, such as the Earth BioGenome Project (EBP), requires both agreement and coordination on standards to ensure that the collective effort generates rapid progress toward its goals. To this end, the EBP initiated five technical standards committees comprising volunteer members from the global genomics scientific community: Sample Collection and Processing, Sequencing and Assembly, Annotation, Analysis, and IT and Informatics. The current versions of the resulting standards documents are available on the EBP website, with the recognition that opportunities, technologies, and challenges may improve or change in the future, requiring flexibility for the EBP to meet its goals. Here, we describe some highlights from the proposed standards, and areas where additional challenges will need to be met.
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- 2022
3. Why sequence all eukaryotes?
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Blaxter, Mark, Archibald, John M, Childers, Anna K, Coddington, Jonathan A, Crandall, Keith A, Di Palma, Federica, Durbin, Richard, Edwards, Scott V, Graves, Jennifer AM, Hackett, Kevin J, Hall, Neil, Jarvis, Erich D, Johnson, Rebecca N, Karlsson, Elinor K, Kress, W John, Kuraku, Shigehiro, Lawniczak, Mara KN, Lindblad-Toh, Kerstin, Lopez, Jose V, Moran, Nancy A, Robinson, Gene E, Ryder, Oliver A, Shapiro, Beth, Soltis, Pamela S, Warnow, Tandy, Zhang, Guojie, and Lewin, Harris A
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Biotechnology ,Animals ,Base Sequence ,Biodiversity ,Biological Evolution ,Ecology ,Ecosystem ,Eukaryota ,Genome ,Genomics ,Humans ,Phylogeny ,genome ,diversity ,ecology ,evolution ,conservation - Abstract
Life on Earth has evolved from initial simplicity to the astounding complexity we experience today. Bacteria and archaea have largely excelled in metabolic diversification, but eukaryotes additionally display abundant morphological innovation. How have these innovations come about and what constraints are there on the origins of novelty and the continuing maintenance of biodiversity on Earth? The history of life and the code for the working parts of cells and systems are written in the genome. The Earth BioGenome Project has proposed that the genomes of all extant, named eukaryotes-about 2 million species-should be sequenced to high quality to produce a digital library of life on Earth, beginning with strategic phylogenetic, ecological, and high-impact priorities. Here we discuss why we should sequence all eukaryotic species, not just a representative few scattered across the many branches of the tree of life. We suggest that many questions of evolutionary and ecological significance will only be addressable when whole-genome data representing divergences at all of the branchings in the tree of life or all species in natural ecosystems are available. We envisage that a genomic tree of life will foster understanding of the ongoing processes of speciation, adaptation, and organismal dependencies within entire ecosystems. These explorations will resolve long-standing problems in phylogenetics, evolution, ecology, conservation, agriculture, bioindustry, and medicine.
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- 2022
4. Mitochondrial RNA editing in Trypanoplasma borreli: New tools, new revelations
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Gerasimov, Evgeny S., Afonin, Dmitry A., Korzhavina, Oksana A., Lukeš, Julius, Low, Ross, Hall, Neil, Tyler, Kevin, Yurchenko, Vyacheslav, and Zimmer, Sara L.
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- 2022
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5. Comparative genomic analysis of the 'pseudofungus' Hyphochytrium catenoides.
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Leonard, Guy, Labarre, Aurélie, Milner, David S, Monier, Adam, Soanes, Darren, Wideman, Jeremy G, Maguire, Finlay, Stevens, Sam, Sain, Divya, Grau-Bové, Xavier, Sebé-Pedrós, Arnau, Stajich, Jason E, Paszkiewicz, Konrad, Brown, Matthew W, Hall, Neil, Wickstead, Bill, and Richards, Thomas A
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Animals ,Rhinosporidium ,Phylogeny ,Genome ,Molecular Sequence Annotation ,Whole Genome Sequencing ,large DNA virus ,oomycete parasitic traits ,polarized filamentous growth ,secondary plastid endosymbiosis ,Biotechnology ,Infectious Diseases ,Human Genome ,Genetics ,Biochemistry and Cell Biology ,Microbiology ,Immunology - Abstract
Eukaryotic microbes have three primary mechanisms for obtaining nutrients and energy: phagotrophy, photosynthesis and osmotrophy. Traits associated with the latter two functions arose independently multiple times in the eukaryotes. The Fungi successfully coupled osmotrophy with filamentous growth, and similar traits are also manifested in the Pseudofungi (oomycetes and hyphochytriomycetes). Both the Fungi and the Pseudofungi encompass a diversity of plant and animal parasites. Genome-sequencing efforts have focused on host-associated microbes (mutualistic symbionts or parasites), providing limited comparisons with free-living relatives. Here we report the first draft genome sequence of a hyphochytriomycete 'pseudofungus'; Hyphochytrium catenoides Using phylogenomic approaches, we identify genes of recent viral ancestry, with related viral derived genes also present on the genomes of oomycetes, suggesting a complex history of viral coevolution and integration across the Pseudofungi. H. catenoides has a complex life cycle involving diverse filamentous structures and a flagellated zoospore with a single anterior tinselate flagellum. We use genome comparisons, drug sensitivity analysis and high-throughput culture arrays to investigate the ancestry of oomycete/pseudofungal characteristics, demonstrating that many of the genetic features associated with parasitic traits evolved specifically within the oomycete radiation. Comparative genomics also identified differences in the repertoire of genes associated with filamentous growth between the Fungi and the Pseudofungi, including differences in vesicle trafficking systems, cell-wall synthesis pathways and motor protein repertoire, demonstrating that unique cellular systems underpinned the convergent evolution of filamentous osmotrophic growth in these two eukaryotic groups.
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- 2018
6. An investigation into phosphoric iron production in Eastern England
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Hall, Neil Stewart
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669 ,DA Great Britain ,HD Industries. Land use. Labor ,TN Mining engineering. Metallurgy ,TS Manufactures - Abstract
Looking at iron slags from Eastern England, this thesis was designed to assess the possibility of inferring the ore type in use by the chemical composition of the slag. A number of case studies are examined. The first is a group of material from the Foulness Valley, East Yorkshire, which is known to be produced from high phosphorus bog ore. This allows direct comparison between this and other assemblages, based on phosphorus content, to infer if bog or bedded ore was in use. Assemblages from Iron Age East Yorkshire, Roman Caistor St Edmund and the Saxon sites of Quarrington and Flixboroughwere examined to infer on ore exploitation and possible metal production. The background examination provides a definition of phosphoric iron based upon its material properties and the parameters which govern the creation of the alloy. Further discussion of ore exploitation and the reasoning behind why smelting sites are more difficult to locate are covered, while the current direction of research is examined. The body of experimental work is discussed with notable case studies drawn upon to demonstrate where the literature concentrates its focus. This allows for the suggestion of future possibilities based upon the impacts of these works. An experimental smelt was carried out in order to inform on the processes and record observations which helped to dictate the choices made on raw material selection. The experimental material was analysed alongside archaeological slags produced from the same ore, and treated in the same way as the material used in the archaeological case studies. The selection criteria applied to the archaeological assemblages, based on morphology and perceived mass are outlined. A description of the preparation methods for sample examination follows. The physics of electron microscopy are then discussed covering the various effects which govern the generation of the characteristic x-rays which are responsible for the chemical composition data. Each of the case study assemblages are dealt with individually presenting photographs of the pieces before sampling and backscattered electron images of the material. As this is the first scientific analysis conducted upon the Saxon assemblages from Quarrington and Flixborough, the data generated provides critical, new insight into Early Medieval iron production. The data using phase composition and phosphorus content are presented on a site by site basis before being assembled into an overall synthesis which further clarifies the inferences of different ore exploitation. Further comparisons of phosphorus and sulphur content are used to demonstrate the use of the bog ore and Frodingham Ironstone available at Flixborough. The interpretation of the data is then drawn upon for final conclusions and inferences of ore exploitation and the identification of ironstone use at Flixborough which further supports the archaeological and historical evidence for this practice from the 7th century A.D.
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- 2017
7. Single cell ecology
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Richards, Thomas A., Massana, Ramon, Pagliara, Stefano, and Hall, Neil
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- 2019
8. Transcriptional analysis of Rhazya stricta in response to jasmonic acid
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Hajrah, Nahid H., Rabah, Samar O., Alghamdi, Mohammed K., Atef, Ahmed, Edris, Sherif, Alhebshi, Alawiah M., Hassan, Sabah M., Alzahrani, Dhafer A., Bahieldin, Ahmed, Mutwakil, Mohammed H.Z., Alqurashi, Yaser E., Al-Zahrani, Hassan S., Abo-Aba, Salah E.M., Jansen, Robert K., Sabir, Jamal S.M., Hall, Neil, and Kamli, Majid Rasool
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- 2021
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9. Netazepide Inhibits Expression of Pappalysin 2 in Type 1 Gastric Neuroendocrine Tumors
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Lloyd, Katie A., Parsons, Bryony N., Burkitt, Michael D., Moore, Andrew R., Papoutsopoulou, Stamatia, Boyce, Malcolm, Duckworth, Carrie A., Exarchou, Klaire, Howes, Nathan, Rainbow, Lucille, Fang, Yongxiang, Oxvig, Claus, Dodd, Steven, Varro, Andrea, Hall, Neil, and Pritchard, D. Mark
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- 2020
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10. Identification of a non-canonical ciliate nuclear genetic code where UAA and UAG code for different amino acids
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McGowan, Jamie, primary, Kilias, Estelle S., additional, Alacid, Elisabet, additional, Lipscombe, James, additional, Jenkins, Benjamin H., additional, Gharbi, Karim, additional, Kaithakottil, Gemy G., additional, Macaulay, Iain C., additional, McTaggart, Seanna, additional, Warring, Sally D., additional, Richards, Thomas A., additional, Hall, Neil, additional, and Swarbreck, David, additional
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- 2023
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11. A haplotype map of allohexaploid wheat reveals distinct patterns of selection on homoeologous genomes
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Jordan, Katherine W, Wang, Shichen, Lun, Yanni, Gardiner, Laura-Jayne, MacLachlan, Ron, Hucl, Pierre, Wiebe, Krysta, Wong, Debbie, Forrest, Kerrie L, IWGS Consortium, Sharpe, Andrew G, Sidebottom, Christine HD, Hall, Neil, Toomajian, Christopher, Close, Timothy, Dubcovsky, Jorge, Akhunova, Alina, Talbert, Luther, Bansal, Urmil K, Bariana, Harbans S, Hayden, Matthew J, Pozniak, Curtis, Jeddeloh, Jeffrey A, Hall, Anthony, and Akhunov, Eduard
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Biological Sciences ,Genetics ,Human Genome ,Aetiology ,2.1 Biological and endogenous factors ,Generic health relevance ,Chromosome Mapping ,Chromosomes ,Plant ,Exome ,Gene Frequency ,Genome ,Plant ,Genotype ,Haplotypes ,Polymorphism ,Single Nucleotide ,Polyploidy ,Selection ,Genetic ,Triticum ,IWGS Consortium ,Environmental Sciences ,Information and Computing Sciences ,Bioinformatics - Abstract
BackgroundBread wheat is an allopolyploid species with a large, highly repetitive genome. To investigate the impact of selection on variants distributed among homoeologous wheat genomes and to build a foundation for understanding genotype-phenotype relationships, we performed population-scale re-sequencing of a diverse panel of wheat lines.ResultsA sample of 62 diverse lines was re-sequenced using the whole exome capture and genotyping-by-sequencing approaches. We describe the allele frequency, functional significance, and chromosomal distribution of 1.57 million single nucleotide polymorphisms and 161,719 small indels. Our results suggest that duplicated homoeologous genes are under purifying selection. We find contrasting patterns of variation and inter-variant associations among wheat genomes; this, in addition to demographic factors, could be explained by differences in the effect of directional selection on duplicated homoeologs. Only a small fraction of the homoeologous regions harboring selected variants overlapped among the wheat genomes in any given wheat line. These selected regions are enriched for loci associated with agronomic traits detected in genome-wide association studies.ConclusionsEvidence suggests that directional selection in allopolyploids rarely acted on multiple parallel advantageous mutations across homoeologous regions, likely indicating that a fitness benefit could be obtained by a mutation at any one of the homoeologs. Additional advantageous variants in other homoelogs probably either contributed little benefit, or were unavailable in populations subjected to directional selection. We hypothesize that allopolyploidy may have increased the likelihood of beneficial allele recovery by broadening the set of possible selection targets.
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- 2015
12. An accessible, efficient and global approach for the large-scale sequencing of bacterial genomes
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Perez-Sepulveda, Blanca M., Heavens, Darren, Pulford, Caisey V., Predeus, Alexander V., Low, Ross, Webster, Hermione, Dykes, Gregory F., Schudoma, Christian, Rowe, Will, Lipscombe, James, Watkins, Chris, Kumwenda, Benjamin, Shearer, Neil, Costigan, Karl, Baker, Kate S., Feasey, Nicholas A., Hinton, Jay C. D., and Hall, Neil
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- 2021
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13. Subtelomeric assembly of a multi-gene pathway for antimicrobial defense compounds in cereals
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Li, Yan, Leveau, Aymeric, Zhao, Qiang, Feng, Qi, Lu, Hengyun, Miao, Jiashun, Xue, Zheyong, Martin, Azahara C., Wegel, Eva, Wang, Jing, Orme, Anastasia, Rey, Maria-Dolores, Karafiátová, Miroslava, Vrána, Jan, Steuernagel, Burkhard, Joynson, Ryan, Owen, Charlotte, Reed, James, Louveau, Thomas, Stephenson, Michael J., Zhang, Lei, Huang, Xuehui, Huang, Tao, Fan, Danling, Zhou, Congcong, Tian, Qilin, Li, Wenjun, Lu, Yiqi, Chen, Jiaying, Zhao, Yan, Lu, Ying, Zhu, Chuanrang, Liu, Zhenhua, Polturak, Guy, Casson, Rebecca, Hill, Lionel, Moore, Graham, Melton, Rachel, Hall, Neil, Wulff, Brande B. H., Doležel, Jaroslav, Langdon, Tim, Han, Bin, and Osbourn, Anne
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- 2021
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14. Ecological niche adaptation of Salmonella Typhimurium U288 is associated with altered pathogenicity and reduced zoonotic potential
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Kirkwood, Mark, Vohra, Prerna, Bawn, Matt, Thilliez, Gaëtan, Pye, Hannah, Tanner, Jennifer, Chintoan-Uta, Cosmin, Branchu, Priscilla, Petrovska, Liljana, Dallman, Timothy, Hall, Neil, Stevens, Mark P., and Kingsley, Robert A.
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- 2021
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15. Genome Sequence of the Tsetse Fly (Glossina morsitans): Vector of African Trypanosomiasis
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Initiative, International Glossina Genome, Attardo, Geoffrey M, Abila, Patrick P, Auma, Joanna E, Baumann, Aaron A, Benoit, Joshua B, Brelsfoard, Corey L, Ribeiro, José MC, Cotton, James A, Pham, Daphne QD, Darby, Alistair C, Van Den Abbeele, Jan, Denlinger, David L, Field, Linda M, Nyanjom, Steven RG, Gaunt, Michael W, Geiser, Dawn L, Gomulski, Ludvik M, Haines, Lee R, Hansen, Immo A, Jones, Jeffery W, Kibet, Caleb K, Kinyua, Johnson K, Larkin, Denis M, Lehane, Michael J, Rio, Rita VM, Macdonald, Sandy J, Macharia, Rosaline W, Malacrida, Anna R, Marco, Heather G, Marucha, Kevin K, Masiga, Daniel K, Meuti, Megan E, Mireji, Paul O, Obiero, George FO, Koekemoer, Jacobus JO, Okoro, Chinyere K, Omedo, Irene A, Osamor, Victor C, Balyeidhusa, Apollo SP, Peyton, Justin T, Price, David P, Quail, Michael A, Ramphul, Urvashi N, Rawlings, Neil D, Riehle, Michael A, Robertson, Hugh M, Sanders, Mandy J, Scott, Maxwell J, Dashti, Zahra Jalali Sefid, Snyder, Anna K, Srivastava, Tulika P, Stanley, Eleanor J, Swain, Martin T, Hughes, Daniel ST, Tarone, Aaron M, Taylor, Todd D, Telleria, Erich L, Thomas, Gavin H, Walshe, Deirdre P, Wilson, Richard K, Winzerling, Joy J, Acosta-Serrano, Alvaro, Aksoy, Serap, Arensburger, Peter, Aslett, Martin, Bateta, Rosemary, Benkahla, Alia, Berriman, Matthew, Bourtzis, Kostas, Caers, Jelle, Caljon, Guy, Christoffels, Alan, Falchetto, Marco, Friedrich, Markus, Fu, Shuhua, Gäde, Gerd, Githinji, George, Gregory, Richard, Hall, Neil, Harkins, Gordon, Hattori, Masahira, Hertz-Fowler, Christiane, Hide, Winston, Hu, Wanqi, Imanishi, Tadashi, Inoue, Noboru, Jonas, Mario, Kawahara, Yoshihiro, Koffi, Mathurin, Kruger, Adele, Lawson, Daniel, Lehane, Stella, Lehväslaiho, Heikki, Luiz, Thiago, Makgamathe, Mmule, Malele, Imna, Manangwa, Oliver, Manga, Lucien, and Megy, Karyn
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Vector-Borne Diseases ,Genetics ,Prevention ,Infectious Diseases ,Biotechnology ,2.2 Factors relating to the physical environment ,Aetiology ,Infection ,Good Health and Well Being ,Animals ,Blood ,Feeding Behavior ,Female ,Genes ,Insect ,Genome ,Insect ,Insect Proteins ,Insect Vectors ,Microbiota ,Molecular Sequence Annotation ,Molecular Sequence Data ,Reproduction ,Salivary Glands ,Sensation ,Sequence Analysis ,DNA ,Symbiosis ,Trypanosoma ,Trypanosomiasis ,African ,Tsetse Flies ,Wolbachia ,International Glossina Genome Initiative ,General Science & Technology - Abstract
Tsetse flies are the sole vectors of human African trypanosomiasis throughout sub-Saharan Africa. Both sexes of adult tsetse feed exclusively on blood and contribute to disease transmission. Notable differences between tsetse and other disease vectors include obligate microbial symbioses, viviparous reproduction, and lactation. Here, we describe the sequence and annotation of the 366-megabase Glossina morsitans morsitans genome. Analysis of the genome and the 12,308 predicted protein-encoding genes led to multiple discoveries, including chromosomal integrations of bacterial (Wolbachia) genome sequences, a family of lactation-specific proteins, reduced complement of host pathogen recognition proteins, and reduced olfaction/chemosensory associated genes. These genome data provide a foundation for research into trypanosomiasis prevention and yield important insights with broad implications for multiple aspects of tsetse biology.
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- 2014
16. Evolutionary conservation of Trichomonas-mycoplasma symbiosis across the host species barrier
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Bailey, Nicholas P., primary, Shao, Yuxin, additional, Du, Shaodua, additional, Foster, Peter G., additional, Fettweis, Jennifer, additional, Hall, Neil, additional, Wang, Zheng, additional, and Hirt, Robert P., additional
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- 2023
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17. The impact of remote social work field placements on academic performance.
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Hall, Neil
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- 2018
18. Identification of oligo-adenylated small RNAs in the parasite Entamoeba and a potential role for small RNA control
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Zhang, Hanbang, Ehrenkaufer, Gretchen M., Hall, Neil, and Singh, Upinder
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- 2020
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19. Comparative Genomics of Trypanosomatid Parasitic Protozoa
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El-Sayed, Najib M., Myler, Peter J., Blandin, Gaëlle, Berriman, Matthew, Crabtree, Jonathan, Aggarwal, Gautam, Caler, Elisabet, Renauld, Hubert, Worthey, Elizabeth A., Hertz-Fowler, Christiane, Ghedin, Elodie, Peacock, Christopher, Bartholomeu, Daniella C., Haas, Brian J., Tran, Anh-Nhi, Wortman, Jennifer R., Angiuoli, Samuel, Anupama, Atashi, Badger, Jonathan, Bringaud, Frederic, Cadag, Eithon, Carlton, Jane M., Cerqueira, Gustavo C., Creasy, Todd, Delcher, Arthur L., Djikeng, Appolinaire, Embley, T. Martin, Hauser, Christopher, Ivens, Alasdair C., Kummerfeld, Sarah K., Pereira-Leal, Jose B., Nilsson, Daniel, Peterson, Jeremy, Salzberg, Steven L., Shallom, Joshua, Silva, Joana C., Sundaram, Jaideep, Westenberger, Scott, White, Owen, Melville, Sara E., Donelson, John E., Andersson, Björn, Stuart, Kenneth D., and Hall, Neil
- Published
- 2005
20. The Genome of the African Trypanosome Trypanosoma brucei
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Berriman, Matthew, Ghedin, Elodie, Hertz-Fowler, Christiane, Blandin, Gaëlle, Renauld, Hubert, Bartholomeu, Daniella C., Lennard, Nicola J., Caler, Elisabet, Hamlin, Nancy E., Haas, Brian, Böhme, Ulrike, Hannick, Linda, Aslett, Martin A., Shallom, Joshua, Marcello, Lucio, Hou, Lihua, Wickstead, Bill, Arrowsmith, Claire, Atkin, Rebecca J., Barron, Andrew J., Bringaud, Frederic, Brooks, Karen, Carrington, Mark, Cherevach, Inna, Chillingworth, Tracey-Jane, Churcher, Carol, Clark, Louise N., Corton, Craig H., Cronin, Ann, Davies, Rob M., Doggett, Jonathon, Djikeng, Appolinaire, Feldblyum, Tamara, Field, Mark C., Fraser, Audrey, Goodhead, Ian, Hance, Zahra, Harper, David, Harris, Barbara R., Hauser, Heidi, Hostetler, Jessica, Ivens, Al, Jagels, Kay, Johnson, David, Johnson, Justin, Jones, Kristine, Kerhornou, Arnaud X., Koo, Hean, Larke, Natasha, Landfear, Scott, Larkin, Christopher, Leech, Vanessa, Line, Alexandra, Lord, Angela, MacLeod, Annette, Mooney, Paul J., Moule, Sharon, Morgan, Gareth W., Mungall, Karen, Norbertczak, Halina, Ormond, Doug, Pai, Grace, Peacock, Chris S., Peterson, Jeremy, Quail, Michael A., Rabbinowitsch, Ester, Rajandream, Marie-Adele, Reitter, Chris, Salzberg, Steven L., Sanders, Mandy, Schobel, Seth, Sharp, Sarah, Simmonds, Mark, Simpson, Anjana J., Tallon, Luke, Tait, Andrew, Tivey, Adrian R., Van Aken, Susan, Walker, Danielle, Wanless, David, Wang, Shiliang, White, Brian, White, Owen, Whitehead, Sally, Woodward, John, Wortman, Jennifer, Adams, Mark D., Embley, T. Martin, Gull, Keith, Ullu, Elisabetta, Barry, J. David, Fairlamb, Alan H., Opperdoes, Fred, Barrell, Barclay G., Donelson, John E., Hall, Neil, Fraser, Claire M., Melville, Sara E., and El-Sayed, Najib M.
- Published
- 2005
21. Genome Sequence of Theileria parva, a Bovine Pathogen That Transforms Lymphocytes
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Gardner, Malcolm J., Bishop, Richard, Shah, Trushar, de Villiers, Etienne P., Carlton, Jane M., Hall, Neil, Ren, Qinghu, Paulsen, Ian T., Pain, Arnab, Berriman, Matthew, Sato, Shigeharu, Ralph, Stuart A., Mann, David J., Xiong, Zikai, Shallom, Shamira J., Weidman, Janice, Jiang, Lingxia, Lynn, Jeffery, Weaver, Bruce, Shoaibi, Azadeh, Domingo, Alexander R., Wasawo, Delia, Crabtree, Jonathan, Wortman, Jennifer R., Haas, Brian, Angiuoli, Samuel V., Creasy, Todd H., Lu, Charles, Suh, Bernard, Silva, Joana C., Utterback, Teresa R., Feldblyum, Tamara V., Pertea, Mihaela, Allen, Jonathan, Nierman, William C., Salzberg, Steven L., White, Owen R., Fitzhugh, Henry A., Morzaria, Subhash, Venter, J. Craig, Fraser, Claire M., and Nene, Vishvanath
- Published
- 2005
22. An Ancestral Oomycete Locus Contains Late Blight Avirulence Gene Avr3a, Encoding a Protein That Is Recognized in the Host Cytoplasm
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Armstrong, Miles R., Whisson, Stephen C., Pritchard, Leighton, Venter, Eduard, Avrova, Anna O., Rehmany, Anne P., Böhme, Ulrike, Brooks, Karen, Cherevach, Inna, Hamlin, Nancy, White, Brian, Fraser, Audrey, Lord, Angela, Quail, Michael A., Churcher, Carol, Hall, Neil, Berriman, Matthew, Huang, Sanwen, Kamoun, Sophien, Beynon, Jim L., and Cook, R. James
- Published
- 2005
23. A Comprehensive Survey of the Plasmodium Life Cycle by Genomic, Transcriptomic, and Proteomic Analyses
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Hall, Neil, Karras, Marianna, Raine, J. Dale, Carlton, Jane M., Berriman, Matthew, Florens, Laurence, Janssen, Christoph S., Pain, Arnab, Christophides, Georges K., James, Keith, Rutherford, Kim, Harris, Barbara, Harris, David, Churcher, Carol, Quail, Michael A., Ormond, Doug, Doggett, Jon, Trueman, Holly E., Mendoza, Jacqui, Bidwell, Shelby L., Rajandream, Marie-Adele, Carucci, Daniel J., Yates, John R., Kafatos, Fotis C., Janse, Chris J., Barrell, Bart, Waters, Andrew P., and Sinden, Robert E.
- Published
- 2005
24. An Evaluation of Computer Based Activities in an Early Intervention Program. A Report to the Early Special Education Program.
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Wollongong Univ., New South Wales (Australia). Dept. of Education., Elliott, Alison, and Hall, Neil
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This study investigated ways of using computer-based learning activities to complement curriculum practices in preschool programs with an early intervention component through the use of computer-based learning activities. Particular attention was given to supporting the development of young children's early mathematical skills. The study took place in a preschool center in the Illawarra region of New South Wales that served at-risk children and families in crisis. The focus of the study was on teaching methodologies and learner experiences that were likely to develop the skills necessary for successful integration into formal schooling. Participants were 11 students (6 in the experimental group and 5 in the control group) who had difficulty in using language fluently and effectively in a range of situations; were unable to persevere with tasks and activities; lacked purposefulness, imagination, and variety in play; lacked initiative; and lacked normal social skills and emotional maturity. Children in the experimental group took part in 7-12 sessions at a computer over a 6-8 week period. Total computer time ranged from 140 to 240 minutes. Paired control group subjects had access to nonmathematical computer-based activities. Findings indicated that experimental group subjects gained dramatically and significantly in mathematical skills and understanding. Appendices include the pretest and posttest, descriptions of software used in the study, and criteria for evaluating early childhood software. (RH)
- Published
- 1990
25. BioFAIR Final Report
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Technopolis Group, Soranzo, Nicola, Knox, Catherine, Norman, Hannah, Andrews, Robert, Beck, Tim, Micklem, Gos, Orengo, Christine, Sansone, Susanna Assunta, Hall, Neil, and Goble, Carole
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Digital Research Infrastructure ,training ,life sciences ,productivity ,interviews ,Community of Practice ,capacity building ,bioscience ,metadata ,Research Data Management ,Data Stewardship ,curation ,bioinformatics ,artificial intelligence ,ELIXIR ,UKRI ,BioFAIR ,BioCommons ,open science ,survey ,e-infrastructure ,reproducibility ,FAIR - Abstract
In order to identify and address the Research Data Management needs of UK bioscience researchers, in 2020 UK Research and Innovation (UKRI) Biotechnology and Biological Science Research Council (BBSRC), UKRI Medical Research Council (MRC) and Wellcome Trust funded a 9-month study to gather evidence about the adoption of the Findable, Accessible, Interoperable, Reusable (FAIR) principles, and evaluate the feasibility and impact of the creation of a new UK Institute (tentatively called "BioFAIR") delivering a FAIR Data and Method BioCommons. This is the final report of this feasibility study and has followed the standard business case process in use by UKRI and BEIS. It has been carried out by Technopolis Group in collaboration with ELIXIR-UK (the UK Node of ELIXIR) and has involved a wide-ranging programme of desk research, stakeholder consultations (online researcher surveys and institutional interviews) and a series of deliberative discussions with groups of UKRI funders, the ELIXIR-UK All Hands workshop and the ELIXIR-UK Scientific and Industry Advisory Board. The report is underpinned by a series of analytical presentations and reports, including the results of the online survey, international comparisons and cost-benefit analysis.
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- 2023
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26. Editor's introduction: 'To boldly go...' charting rough territory in field education
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Fox, Mim, Hall, Neil, and Short, Monica
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- 2018
27. Mutagenesis of nitrate reductase in Aspergillus nidulans
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Hall, Neil
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572 ,Biosphere ,Nitrogen ,Nitrate assimilation - Published
- 1997
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28. The influence of Schopenhauer and Wagner upon the early thought of Nietzsche
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Hall, Neil S.
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100 ,Philosophy - Published
- 1994
29. DNA extraction and amplicon production strategies deeply inf luence the outcome of gut mycobiome studies
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Frau, Alessandra, Kenny, John G., Lenzi, Luca, Campbell, Barry J., Ijaz, Umer Z., Duckworth, Carrie A., Burkitt, Michael D., Hall, Neil, Anson, Jim, Darby, Alistair C., and Probert, Christopher S. J.
- Published
- 2019
- Full Text
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30. Analysis of the recombination landscape of hexaploid bread wheat reveals genes controlling recombination and gene conversion frequency
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Gardiner, Laura-Jayne, Wingen, Luzie U., Bailey, Paul, Joynson, Ryan, Brabbs, Thomas, Wright, Jonathan, Higgins, James D., Hall, Neil, Griffiths, Simon, Clavijo, Bernardo J., and Hall, Anthony
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- 2019
- Full Text
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31. Cardinality constraints on qualitatively uncertain data
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Hall, Neil, Koehler, Henning, Link, Sebastian, Prade, Henri, and Zhou, Xiaofang
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- 2015
- Full Text
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32. Human Factors Considerations for the Application of Augmented Reality in an Operational Railway Environment
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Hall, Neil, Lowe, Christopher, and Hirsch, Robin
- Published
- 2015
- Full Text
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33. Euglena International Network (EIN): Driving euglenoid biotechnology for the benefit of a challenged world
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Ebenezer, ThankGod Echezona, primary, Low, Ross S., additional, O'Neill, Ellis Charles, additional, Huang, Ishuo, additional, DeSimone, Antonio, additional, Farrow, Scott C., additional, Field, Robert A., additional, Ginger, Michael L., additional, Guerrero, Sergio Adrián, additional, Hammond, Michael, additional, Hampl, Vladimír, additional, Horst, Geoff, additional, Ishikawa, Takahiro, additional, Karnkowska, Anna, additional, Linton, Eric W., additional, Myler, Peter, additional, Nakazawa, Masami, additional, Cardol, Pierre, additional, Sánchez-Thomas, Rosina, additional, Saville, Barry J., additional, Shah, Mahfuzur R., additional, Simpson, Alastair G. B., additional, Sur, Aakash, additional, Suzuki, Kengo, additional, Tyler, Kevin M., additional, Zimba, Paul V., additional, Hall, Neil, additional, and Field, Mark C., additional
- Published
- 2022
- Full Text
- View/download PDF
34. UKRI-BBSRC Review of technology development in the biosciences
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Errington, Rachel, Collinson, Lucy, Faulds, Karen, Hall, Neil, Chue Hong, Neil P, Hoogenboom, Bart, Kaler, Jasmeet, Kemsley, Kate, de Mel, Geeth, and Woolfson, Dek
- Abstract
Breakthrough technologies often create a big impact, highlighting the critical dependence of world-class transformative research and innovation on newtechnologies becoming available.In 2021, the Biotechnology and Biological Sciences Research Council (BBSRC) initiated a review of technology development in recognition of its crucial importance in the biosciences. The development of transformative technologies is integral in enabling future discoveries as it allows researchers to push the boundaries of bioscience discovery, stimulate innovation and enable better understanding of biological processes and organisms. Support for this area offers significant opportunities to work across disciplines and sectors, to improve on existing technologies and create new ones across the variety of science relevant to BBSRC’s mission.The review found strong evidence for the pervasiveness of technology development across BBSRC’s portfolio, but also identified a range of challenges impacting the bioscience community. An expert task and finish group was convened to help guide and advise BBSRC during the review process. In considering the evidence gathered from our community, 7 key recommendations that aim to support the continued expansion of technology development within the biosciences have been developed:1. To enable support of the different types and stages of technology development, BBSRC should establish a comprehensive support framework, leading to an increase in investment 2. BBSRC should consider innovation in its peer review processes and fully embed technology development as a recognised and valuable component3. BBSRC should prioritise short and long-term actions to support different training needs and career stages, with an emphasis on interdisciplinary and innovator skill sets 4. BBSRC should work with the research technical professional community to highlight their talent and promote their central role in technology development in the biosciences5. BBSRC should promote the value of diversity and team working in the biosciences and foster an open, dynamic, and inclusive system of technology development in the UK 6. BBSRC should consider mechanisms to bring together the technology development communities and facilitate interdisciplinary engagement7. BBSRC should consider opportunities to support the underpinning infrastructure required for technology development
- Published
- 2022
35. Regulation of Sexual Development of Plasmodium by Translational Repression
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Mair, Gunnar R., Garver, Lindsey S., Hall, Neil, Dirks, Roeland W., Khan, Shahid M., Dimopoulos, George, Janse, Chris J., and Waters, Andrew P.
- Published
- 2006
36. Genome of the Host-Cell Transforming Parasite Theileria annulata Compared with T. parva
- Author
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Pain, Arnab, Renauld, Hubert, Berriman, Matthew, Murphy, Lee, Yeats, Corin A., Weir, William, Kerhornou, Arnaud, Aslett, Martin, Bishop, Richard, Bouchier, Christiane, Cochet, Madeleine, Cronin, Ann, de Villiers, Etienne P., Fraser, Audrey, Fosker, Nigel, Gardner, Malcolm, Goble, Arlette, Griffiths-Jones, Sam, Harris, David E., Katzer, Frank, Larke, Natasha, Lord, Angela, Maser, Pascal, McKellar, Sue, Mooney, Paul, Morton, Fraser, Nene, Vishvanath, O'Neil, Susan, Price, Claire, Quail, Michael A., Rabbinowitsch, Ester, Rawlings, Neil D., Rutter, Simon, Saunders, David, Seeger, Kathy, Shah, Trushar, Squares, Robert, Squares, Steven, Tivey, Adrian, Walker, Alan R., Woodward, John, Langsley, Gordon, Rajandream, Marie-Adele, McKeever, Declan, Shiels, Brian, Tait, Andrew, Barrell, Bart, and Hall, Neil
- Published
- 2005
37. Single-cell genomics reveals population structures from in vitro evolutionary studies of Salmonella
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Bawn, Matt, primary, Hernandez, Johana, additional, Trampari, Eleftheria, additional, Thilliez, Gaetan, additional, Quince, Christopher, additional, Webber, Mark A., additional, Kingsley, Robert A., additional, Hall, Neil, additional, and Macaulay, Iain C., additional
- Published
- 2022
- Full Text
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38. Flaviviruses hijack the host microbiota to facilitate their transmission
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Gul, Lejla, primary, Korcsmaros, Tamas, additional, and Hall, Neil, additional
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- 2022
- Full Text
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39. A modified sequence capture approach allowing standard and methylation analyses of the same enriched genomic DNA sample
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Olohan, Lisa, Gardiner, Laura-Jayne, Lucaci, Anita, Steuernagel, Burkhard, Wulff, Brande, Kenny, John, Hall, Neil, and Hall, Anthony
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- 2018
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40. The industrial melanism mutation in British peppered moths is a transposable element
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Hof, Arjen E. vant, Campagne, Pascal, Rigden, Daniel J., Yung, Carl J., Lingley, Jessica, Quail, Michael A., Hall, Neil, Darby, Alistair C., and Saccheri, Ilik J.
- Subjects
Mutation -- Research ,Moths -- Genetic aspects -- Environmental aspects ,Biological research ,Environmental issues ,Science and technology ,Zoology and wildlife conservation - Abstract
Author(s): Arjen E. vant Hof [1]; Pascal Campagne [1]; Daniel J. Rigden [1]; Carl J. Yung [1]; Jessica Lingley [1]; Michael A. Quail [2]; Neil Hall [1]; Alistair C. Darby [...]
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- 2016
- Full Text
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41. The Earth BioGenome Project 2020: Starting the clock
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Lewin, Harris A., Richards, Stephen, Aiden, Erez, Allende, Miguel L., Archibald, John M., Bálint, Miklós M., Barker, Katharine M., Baumgartnerk, Bridget, Belov, Katherine, Bertorelle, Giorgio, Blaxter, Mark, Cai, Jing, Caperello, Nicolette, Carlson, Keith, Castilla-Rubio, Juan Carlos, Chaw, Shu-Miaw, Chen, Lei, Childers, Anna K., Coddington, Jonathan A., Conde, Dalia A., Corominas, Montserrat, Crandall, Keith A., Crawford, Andrew J., Di Palma, Federica, Durbin, Richard, Ebenezer, ThankGod E., Edwards, Scott, Fedrigo, Olivier, Flicek, Paul, Formenti, Giulio, Gibbs, Richard A., Gilbert, M. Thomas P., Goldstein, Melissa M., Marshall Graves, Jennifer A., Greely, Henry, Grigoriev, Igor, Hackett, Kevin J., Hall, Neil, Haussler, David, Helgen, Kristofer M., Hogg, Carolyn J., Isobe, Sachiko, Jakobsen, Kjetill Sigurd, Janke, Axel, Jarvis, Erich D., Johnson, Warren E., Jones, Steven J.M., Karlsson, Elinor K., Kersey, Paul J., Kim, Jin-Hyoung, Kress, W. John, Kuraku, Shigehiro, Lawniczak, Mara K.N., Leebens-Mack, James H., Li, Xueyan, Lindblad-Toh, Kerstin, Liu, Xin, Lopez, Jose V., Marques-Bonet, Tomas, Mazard, Sofhie, Mazet, Jonna, Mazzoni, Camila J., Myers, Eugene W., O'Neill, Rachel J., Paez, Sadye, Park, Hyun, Robinson, Gene, Roquet, Cristina, Ryder, Oliver, Sabir, Jamal S.M., Shaffer, Howard Bradley, Shank, Timothy M., Sherkow, Jacob S., Soltis, Pamela, Tang, Boping, Tedersoo, Leho, Uliano-Silva, Marcela, Wang, Kun, Wei, Xiaofeng, Wetzer, Regina, Wilson, Julia L., Xu, Xun, Yang, Huanming, Yoder, Anne, Zhang, Guojie, Lewin, Harris A., Richards, Stephen, Aiden, Erez, Allende, Miguel L., Archibald, John M., Bálint, Miklós M., Barker, Katharine M., Baumgartnerk, Bridget, Belov, Katherine, Bertorelle, Giorgio, Blaxter, Mark, Cai, Jing, Caperello, Nicolette, Carlson, Keith, Castilla-Rubio, Juan Carlos, Chaw, Shu-Miaw, Chen, Lei, Childers, Anna K., Coddington, Jonathan A., Conde, Dalia A., Corominas, Montserrat, Crandall, Keith A., Crawford, Andrew J., Di Palma, Federica, Durbin, Richard, Ebenezer, ThankGod E., Edwards, Scott, Fedrigo, Olivier, Flicek, Paul, Formenti, Giulio, Gibbs, Richard A., Gilbert, M. Thomas P., Goldstein, Melissa M., Marshall Graves, Jennifer A., Greely, Henry, Grigoriev, Igor, Hackett, Kevin J., Hall, Neil, Haussler, David, Helgen, Kristofer M., Hogg, Carolyn J., Isobe, Sachiko, Jakobsen, Kjetill Sigurd, Janke, Axel, Jarvis, Erich D., Johnson, Warren E., Jones, Steven J.M., Karlsson, Elinor K., Kersey, Paul J., Kim, Jin-Hyoung, Kress, W. John, Kuraku, Shigehiro, Lawniczak, Mara K.N., Leebens-Mack, James H., Li, Xueyan, Lindblad-Toh, Kerstin, Liu, Xin, Lopez, Jose V., Marques-Bonet, Tomas, Mazard, Sofhie, Mazet, Jonna, Mazzoni, Camila J., Myers, Eugene W., O'Neill, Rachel J., Paez, Sadye, Park, Hyun, Robinson, Gene, Roquet, Cristina, Ryder, Oliver, Sabir, Jamal S.M., Shaffer, Howard Bradley, Shank, Timothy M., Sherkow, Jacob S., Soltis, Pamela, Tang, Boping, Tedersoo, Leho, Uliano-Silva, Marcela, Wang, Kun, Wei, Xiaofeng, Wetzer, Regina, Wilson, Julia L., Xu, Xun, Yang, Huanming, Yoder, Anne, and Zhang, Guojie
- Published
- 2022
42. Standards recommendations for the Earth BioGenome Project
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Lawniczak, Mara K.N., Durbin, Richard, Flicek, Paul, Lindblad-Toh, Kerstin, Wei, Xiaofeng, Archibald, John M., Baker, William J, Belov, Katherine, Blaxter, Mark, Marques-Bonet, Tomas, Childers, Anna K., Coddington, Jonathan A., Crandall, Keith A., Crawford, Andrew J., Davey, Robert P., Di Palma, Federica, Fang, Qi, Haerty, Wilfried, Hall, Neil, Hoff, Katharina, Howe, Kerstin, Jarvis, Erich D., Johnson, Warren E., Johnson, Rebecca, Kersey, Paul J., Liu, Xin, Lopez, Jose V., Myers, Eugene W., Vinnere Pettersson, Olga, Phillippy, Adam M., Poelchau, Monica, Pruitt, Kim D., Rhie, Arang, Castilla-Rubio, Juan Carlos, Sahu, Sunil Kumar, Salmon, Nicholas A., Soltis, Pamela, Swarbreck, David, Thibaud-Nissen, Francoise, Wang, Sibo, Wegrzyn, Jill, Zhang, Guojie, Zhang, He, Lewin, Harris A., Richards, Stephen, Lawniczak, Mara K.N., Durbin, Richard, Flicek, Paul, Lindblad-Toh, Kerstin, Wei, Xiaofeng, Archibald, John M., Baker, William J, Belov, Katherine, Blaxter, Mark, Marques-Bonet, Tomas, Childers, Anna K., Coddington, Jonathan A., Crandall, Keith A., Crawford, Andrew J., Davey, Robert P., Di Palma, Federica, Fang, Qi, Haerty, Wilfried, Hall, Neil, Hoff, Katharina, Howe, Kerstin, Jarvis, Erich D., Johnson, Warren E., Johnson, Rebecca, Kersey, Paul J., Liu, Xin, Lopez, Jose V., Myers, Eugene W., Vinnere Pettersson, Olga, Phillippy, Adam M., Poelchau, Monica, Pruitt, Kim D., Rhie, Arang, Castilla-Rubio, Juan Carlos, Sahu, Sunil Kumar, Salmon, Nicholas A., Soltis, Pamela, Swarbreck, David, Thibaud-Nissen, Francoise, Wang, Sibo, Wegrzyn, Jill, Zhang, Guojie, Zhang, He, Lewin, Harris A., and Richards, Stephen
- Abstract
A global international initiative, such as the Earth BioGenome Project (EBP), requires both agreement and coordination on standards to ensure that the collective effort generates rapid progress toward its goals. To this end, the EBP initiated five technical standards committees comprising volunteer members from the global genomics scientific community: Sample Collection and Processing, Sequencing and Assembly, Annotation, Analysis, and IT and Informatics. The current versions of the resulting standards documents are available on the EBP website, with the recognition that opportunities, technologies, and challenges may improve or change in the future, requiring flexibility for the EBP to meet its goals. Here, we describe some highlights from the proposed standards, and areas where additional challenges will need to be met.
- Published
- 2022
43. Standards recommendations for the Earth BioGenome Project
- Author
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Lawniczak, Mara K. N., Durbin, Richard, Flicek, Paul, Lindblad-Toh, Kerstin, Wei, Xiaofeng, Archibald, John M., Baker, William J., Belov, Katherine, Blaxter, Mark L., Bonet, Tomas Marques, Childers, Anna K., Coddington, Jonathan A., Crandall, Keith A., Crawford, Andrew J., Davey, Robert P., Di Palma, Federica, Fang, Qi, Haerty, Wilfried, Hall, Neil, Hoff, Katharina J., Howe, Kerstin, Jarvis, Erich D., Johnson, Warren E., Johnson, Rebecca N., Kersey, Paul J., Liu, Xin, Lopez, Jose Victor, Myers, Eugene W., Vinnere Pettersson, Olga, Phillippy, Adam M., Poelchau, Monica F., Pruitt, Kim D., Rhie, Arang, Castilla-Rubio, Juan Carlos, Sahu, Sunil Kumar, Salmon, Nicholas A., Soltis, Pamela S., Swarbreck, David, Thibaud-Nissen, Francoise, Wang, Sibo, Wegrzyn, Jill L., Zhang, Guojie, Zhang, He, Lewin, Harris A., Richards, Stephen, Lawniczak, Mara K. N., Durbin, Richard, Flicek, Paul, Lindblad-Toh, Kerstin, Wei, Xiaofeng, Archibald, John M., Baker, William J., Belov, Katherine, Blaxter, Mark L., Bonet, Tomas Marques, Childers, Anna K., Coddington, Jonathan A., Crandall, Keith A., Crawford, Andrew J., Davey, Robert P., Di Palma, Federica, Fang, Qi, Haerty, Wilfried, Hall, Neil, Hoff, Katharina J., Howe, Kerstin, Jarvis, Erich D., Johnson, Warren E., Johnson, Rebecca N., Kersey, Paul J., Liu, Xin, Lopez, Jose Victor, Myers, Eugene W., Vinnere Pettersson, Olga, Phillippy, Adam M., Poelchau, Monica F., Pruitt, Kim D., Rhie, Arang, Castilla-Rubio, Juan Carlos, Sahu, Sunil Kumar, Salmon, Nicholas A., Soltis, Pamela S., Swarbreck, David, Thibaud-Nissen, Francoise, Wang, Sibo, Wegrzyn, Jill L., Zhang, Guojie, Zhang, He, Lewin, Harris A., and Richards, Stephen
- Abstract
A global international initiative, such as the Earth BioGenome Project (EBP), requires both agreement and coordination on standards to ensure that the collective effort generates rapid progress toward its goals. To this end, the EBP initiated five technical standards committees comprising volunteer members from the global genomics scientific community: Sample Collection and Processing, Sequencing and Assembly, Annotation, Analysis, and IT and Informatics. The current versions of the resulting standards documents are available on the EBP website, with the recognition that opportunities, technologies, and challenges may improve or change in the future, requiring flexibility for the EBP to meet its goals. Here, we describe some highlights from the proposed standards, and areas where additional challenges will need to be met.
- Published
- 2022
- Full Text
- View/download PDF
44. Standards recommendations for the Earth BioGenome Project
- Author
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National Library of Medicine (US), National Institutes of Health (US), Swedish Research Council, National Museum of Natural History Smithsonian Institution, Howard Hughes Medical Institute, Wellcome, European Molecular Biology Laboratory, National Science Foundation (US), Department of Agriculture (US), Agricultural Research Service (US), Lawniczak, Mara K. N., Durbin, Richard, Flicek, Paul, Lindblad-Toh, Kerstin, Wei, Xiaofeng, Archibald, John M., Baker, William J., Belov, Katherine, Blaxter, Mark, Marqués-Bonet, Tomàs, Childers, Anna K., Coddington, Jonathan A., Crandall, Keith A., Crawford, Andrew J., Davey, Robert P., Di Palma, Federica, Fang, Qi, Haerty, Wilfried, Hall, Neil, Hoff, Katharina J., Howe, Kerstin, Jarvis, Erich D., Johnson, Warren E., Johnson, Rebecca N., Kersey, Paul J., Liu, Xin, López, José Víctor, Myers, Eugene W., Vinnere Pettersson, Olga, Phillippy, Adam M., Poelchau, Monica F., Pruitt, kim D., Rhie, Arang, Castilla-Rubio, Juan Carlos, Kumar Sahu, Sunil, Salmon, Nicholas A., Soltis, Pamela S., Swarbreck, David, Thibaud-Nissen, Francoise, Wang, Sibo, Wegrzyn, Jill L., Zhang, Guojie, Zhang, He, Lewin, Harris A., Richards, Stephen, National Library of Medicine (US), National Institutes of Health (US), Swedish Research Council, National Museum of Natural History Smithsonian Institution, Howard Hughes Medical Institute, Wellcome, European Molecular Biology Laboratory, National Science Foundation (US), Department of Agriculture (US), Agricultural Research Service (US), Lawniczak, Mara K. N., Durbin, Richard, Flicek, Paul, Lindblad-Toh, Kerstin, Wei, Xiaofeng, Archibald, John M., Baker, William J., Belov, Katherine, Blaxter, Mark, Marqués-Bonet, Tomàs, Childers, Anna K., Coddington, Jonathan A., Crandall, Keith A., Crawford, Andrew J., Davey, Robert P., Di Palma, Federica, Fang, Qi, Haerty, Wilfried, Hall, Neil, Hoff, Katharina J., Howe, Kerstin, Jarvis, Erich D., Johnson, Warren E., Johnson, Rebecca N., Kersey, Paul J., Liu, Xin, López, José Víctor, Myers, Eugene W., Vinnere Pettersson, Olga, Phillippy, Adam M., Poelchau, Monica F., Pruitt, kim D., Rhie, Arang, Castilla-Rubio, Juan Carlos, Kumar Sahu, Sunil, Salmon, Nicholas A., Soltis, Pamela S., Swarbreck, David, Thibaud-Nissen, Francoise, Wang, Sibo, Wegrzyn, Jill L., Zhang, Guojie, Zhang, He, Lewin, Harris A., and Richards, Stephen
- Abstract
A global international initiative, such as the Earth BioGenome Project (EBP), requires both agreement and coordination on standards to ensure that the collective effort generates rapid progress toward its goals. To this end, the EBP initiated five technical standards committees comprising volunteer members from the global genomics scientific community: Sample Collection and Processing, Sequencing and Assembly, Annotation, Analysis, and IT and Informatics. The current versions of the resulting standards documents are available on the EBP website, with the recognition that opportunities, technologies, and challenges may improve or change in the future, requiring flexibility for the EBP to meet its goals. Here, we describe some highlights from the proposed standards, and areas where additional challenges will need to be met.
- Published
- 2022
45. The Earth BioGenome Project 2020:Starting the clock
- Author
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Lewin, Harris A., Richards, Stephen, Aiden, Erez Lieberman, Allende, Miguel L., Archibald, John M., Bálint, Miklós, Barker, Katharine B., Baumgartner, Bridget, Belov, Katherine, Bertorelle, Giorgio, Blaxter, Mark L., Cai, Jing, Caperello, Nicolette D., Carlson, Keith, Castilla-Rubio, Juan Carlos, Chaw, Shu Miaw, Chen, Lei, Childers, Anna K., Coddington, Jonathan A., Conde, Dalia A., Corominas, Montserrat, Crandall, Keith A., Crawford, Andrew J., DiPalma, Federica, Durbin, Richard, Ebenezer, ThankGod E., Edwards, Scott V., Fedrigo, Olivier, Flicek, Paul, Formenti, Giulio, Gibbs, Richard A., Gilbert, M. Thomas P., Goldstein, Melissa M., Graves, Jennifer Marshall, Greely, Henry T., Grigoriev, Igor V., Hackett, Kevin J., Hall, Neil, Haussler, David, Helgen, Kristofer M., Hogg, Carolyn J., Isobe, Sachiko, Jakobsen, Kjetill Sigurd, Janke, Axel, Jarvis, Erich D., Johnson, Warren E., Jones, Steven J. M., Karlsson, Elinor K., Kersey, Paul J., Kim, Jin Hyoung, Kress, W. John, Kuraku, Shigehiro, Lawniczak, Mara K. N., Leebens-Mack, James H., Li, Xueyan, Lindblad-Toh, Kerstin, Liu, Xin, Lopez, Jose V., Marques-Bonet, Tomas, Mazard, Sophie, Mazet, Jonna A. K., Mazzoni, Camila J., Myers, Eugene W., O’Neill, Rachel J., Paez, Sadye, Park, Hyun, Robinson, Gene E., Roquet, Cristina, Ryder, Oliver A., Sabir, Jamal S. M., Shaffer, H. Bradley, Shank, Timothy M., Sherkow, Jacob S., Soltis, Pamela S., Tang, Boping, Tedersoo, Leho, Uliano-Silva, Marcela, Wang, Kun, Wei, Xiaofeng, Wetzer, Regina, Wilson, Julia L., Xu, Xun, Yang, Huanming, Yoder, Anne D., Zhang, Guojie, Lewin, Harris A., Richards, Stephen, Aiden, Erez Lieberman, Allende, Miguel L., Archibald, John M., Bálint, Miklós, Barker, Katharine B., Baumgartner, Bridget, Belov, Katherine, Bertorelle, Giorgio, Blaxter, Mark L., Cai, Jing, Caperello, Nicolette D., Carlson, Keith, Castilla-Rubio, Juan Carlos, Chaw, Shu Miaw, Chen, Lei, Childers, Anna K., Coddington, Jonathan A., Conde, Dalia A., Corominas, Montserrat, Crandall, Keith A., Crawford, Andrew J., DiPalma, Federica, Durbin, Richard, Ebenezer, ThankGod E., Edwards, Scott V., Fedrigo, Olivier, Flicek, Paul, Formenti, Giulio, Gibbs, Richard A., Gilbert, M. Thomas P., Goldstein, Melissa M., Graves, Jennifer Marshall, Greely, Henry T., Grigoriev, Igor V., Hackett, Kevin J., Hall, Neil, Haussler, David, Helgen, Kristofer M., Hogg, Carolyn J., Isobe, Sachiko, Jakobsen, Kjetill Sigurd, Janke, Axel, Jarvis, Erich D., Johnson, Warren E., Jones, Steven J. M., Karlsson, Elinor K., Kersey, Paul J., Kim, Jin Hyoung, Kress, W. John, Kuraku, Shigehiro, Lawniczak, Mara K. N., Leebens-Mack, James H., Li, Xueyan, Lindblad-Toh, Kerstin, Liu, Xin, Lopez, Jose V., Marques-Bonet, Tomas, Mazard, Sophie, Mazet, Jonna A. K., Mazzoni, Camila J., Myers, Eugene W., O’Neill, Rachel J., Paez, Sadye, Park, Hyun, Robinson, Gene E., Roquet, Cristina, Ryder, Oliver A., Sabir, Jamal S. M., Shaffer, H. Bradley, Shank, Timothy M., Sherkow, Jacob S., Soltis, Pamela S., Tang, Boping, Tedersoo, Leho, Uliano-Silva, Marcela, Wang, Kun, Wei, Xiaofeng, Wetzer, Regina, Wilson, Julia L., Xu, Xun, Yang, Huanming, Yoder, Anne D., and Zhang, Guojie
- Published
- 2022
46. Sequence locally, think globally:The Darwin tree of life project
- Author
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Barnes, Ian, Berriman, Matthew, Broad, Gavin, Durbin, Richard, Flicek, Paul, Gaya, Ester, Hall, Neil, Hart, Michelle, Holland, Peter, Hollingsworth, Pete, Howe, Kevin, Kersey, Paul, Lawniczak, Mara K N, Lewis, Owen, Mieszkowska, Nova, Richards, Thomas, Twyford, Alexander D, and Wilson, Willie
- Abstract
The goals of the Earth Biogenome Project-to sequence the genomes of all eukaryotic life on earth-are as daunting as they are ambitious. The Darwin Tree of Life Project was founded to demonstrate the credibility of these goals and to deliver at-scale genome sequences of unprecedented quality for a biogeographic region: the archipelago of islands that constitute Britain and Ireland. The Darwin Tree of Life Project is a collaboration between biodiversity organizations (museums, botanical gardens, and biodiversity institutes) and genomics institutes. Together, we have built a workflow that collects specimens from the field, robustly identifies them, performs sequencing, generates high-quality, curated assemblies, and releases these openly for the global community to use to build future science and conservation efforts.
- Published
- 2022
47. The Earth BioGenome Project 2020: Starting the clock
- Author
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Lewin, Harris A., primary, Richards, Stephen, additional, Lieberman Aiden, Erez, additional, Allende, Miguel L., additional, Archibald, John M., additional, Bálint, Miklós, additional, Barker, Katharine B., additional, Baumgartner, Bridget, additional, Belov, Katherine, additional, Bertorelle, Giorgio, additional, Blaxter, Mark L., additional, Cai, Jing, additional, Caperello, Nicolette D., additional, Carlson, Keith, additional, Castilla-Rubio, Juan Carlos, additional, Chaw, Shu-Miaw, additional, Chen, Lei, additional, Childers, Anna K., additional, Coddington, Jonathan A., additional, Conde, Dalia A., additional, Corominas, Montserrat, additional, Crandall, Keith A., additional, Crawford, Andrew J., additional, DiPalma, Federica, additional, Durbin, Richard, additional, Ebenezer, ThankGod E., additional, Edwards, Scott V., additional, Fedrigo, Olivier, additional, Flicek, Paul, additional, Formenti, Giulio, additional, Gibbs, Richard A., additional, Gilbert, M. Thomas P., additional, Goldstein, Melissa M., additional, Graves, Jennifer Marshall, additional, Greely, Henry T., additional, Grigoriev, Igor V., additional, Hackett, Kevin J., additional, Hall, Neil, additional, Haussler, David, additional, Helgen, Kristofer M., additional, Hogg, Carolyn J., additional, Isobe, Sachiko, additional, Jakobsen, Kjetill Sigurd, additional, Janke, Axel, additional, Jarvis, Erich D., additional, Johnson, Warren E., additional, Jones, Steven J. M., additional, Karlsson, Elinor K., additional, Kersey, Paul J., additional, Kim, Jin-Hyoung, additional, Kress, W. John, additional, Kuraku, Shigehiro, additional, Lawniczak, Mara K. N., additional, Leebens-Mack, James H., additional, Li, Xueyan, additional, Lindblad-Toh, Kerstin, additional, Liu, Xin, additional, Lopez, Jose V., additional, Marques-Bonet, Tomas, additional, Mazard, Sophie, additional, Mazet, Jonna A. K., additional, Mazzoni, Camila J., additional, Myers, Eugene W., additional, O’Neill, Rachel J., additional, Paez, Sadye, additional, Park, Hyun, additional, Robinson, Gene E., additional, Roquet, Cristina, additional, Ryder, Oliver A., additional, Sabir, Jamal S. M., additional, Shaffer, H. Bradley, additional, Shank, Timothy M., additional, Sherkow, Jacob S., additional, Soltis, Pamela S., additional, Tang, Boping, additional, Tedersoo, Leho, additional, Uliano-Silva, Marcela, additional, Wang, Kun, additional, Wei, Xiaofeng, additional, Wetzer, Regina, additional, Wilson, Julia L., additional, Xu, Xun, additional, Yang, Huanming, additional, Yoder, Anne D., additional, and Zhang, Guojie, additional
- Published
- 2022
- Full Text
- View/download PDF
48. Horizontal gene transfer facilitated the evolution of plant parasitic mechanisms in the oomycetes
- Author
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Richards, Thomas A., Soanes, Darren M., Jones, Meredith D. M., Vasieva, Olga, Leonard, Guy, Paszkiewicz, Konrad, Foster, Peter G., Hall, Neil, and Talbot, Nicholas J.
- Published
- 2011
49. Evolutionary genomics of Entamoeba
- Author
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Weedall, Gareth D. and Hall, Neil
- Published
- 2011
- Full Text
- View/download PDF
50. A Bioinformatics Approach to Identifying Potential Biomarkers for Cryptosporidium parvum: A Coccidian Parasite Associated with Fetal Diarrhea
- Author
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Sabir, Mumdooh J., primary, Low, Ross, additional, Hall, Neil, additional, Kamli, Majid Rasool, additional, and Malik, Md. Zubbair, additional
- Published
- 2021
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