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1. The Gene Ontology knowledgebase in 2023

Author

Aleksander, Suzi A, Balhoff, James, Carbon, Seth, Cherry, J Michael, Drabkin, Harold J, Ebert, Dustin, Feuermann, Marc, Gaudet, Pascale, Harris, Nomi L, Hill, David P, Lee, Raymond, Mi, Huaiyu, Moxon, Sierra, Mungall, Christopher J, Muruganugan, Anushya, Mushayahama, Tremayne, Sternberg, Paul W, Thomas, Paul D, Van Auken, Kimberly, Ramsey, Jolene, Siegele, Deborah A, Chisholm, Rex L, Fey, Petra, Aspromonte, Maria Cristina, Nugnes, Maria Victoria, Quaglia, Federica, Tosatto, Silvio, Giglio, Michelle, Nadendla, Suvarna, Antonazzo, Giulia, Attrill, Helen, dos Santos, Gil, Marygold, Steven, Strelets, Victor, Tabone, Christopher J, Thurmond, Jim, Zhou, Pinglei, Ahmed, Saadullah H, Asanitthong, Praoparn, Buitrago, Diana Luna, Erdol, Meltem N, Gage, Matthew C, Kadhum, Mohamed Ali, Li, Kan Yan Chloe, Long, Miao, Michalak, Aleksandra, Pesala, Angeline, Pritazahra, Armalya, Saverimuttu, Shirin CC, Su, Renzhi, Thurlow, Kate E, Lovering, Ruth C, Logie, Colin, Oliferenko, Snezhana, Blake, Judith, Christie, Karen, Corbani, Lori, Dolan, Mary E, Ni, Li, Sitnikov, Dmitry, Smith, Cynthia, Cuzick, Alayne, Seager, James, Cooper, Laurel, Elser, Justin, Jaiswal, Pankaj, Gupta, Parul, Naithani, Sushma, Lera-Ramirez, Manuel, Rutherford, Kim, Wood, Valerie, De Pons, Jeffrey L, Dwinell, Melinda R, Hayman, G Thomas, Kaldunski, Mary L, Kwitek, Anne E, Laulederkind, Stanley JF, Tutaj, Marek A, Vedi, Mahima, Wang, Shur-Jen, D’Eustachio, Peter, Aimo, Lucila, Axelsen, Kristian, Bridge, Alan, Hyka-Nouspikel, Nevila, Morgat, Anne, Engel, Stacia R, Karra, Kalpana, Miyasato, Stuart R, Nash, Robert S, Skrzypek, Marek S, Weng, Shuai, Wong, Edith D, Bakker, Erika, and Berardini, Tanya Z

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, 1.1 Normal biological development and functioning, Underpinning research, Gene Ontology, Proteins, Molecular Sequence Annotation, Databases, Genetic, Computational Biology, gene annotation, gene function, knowledgebase, knowledge graphs, Gene Ontology Consortium, Developmental Biology, Biochemistry and cell biology
Abstract

The Gene Ontology (GO) knowledgebase (http://geneontology.org) is a comprehensive resource concerning the functions of genes and gene products (proteins and noncoding RNAs). GO annotations cover genes from organisms across the tree of life as well as viruses, though most gene function knowledge currently derives from experiments carried out in a relatively small number of model organisms. Here, we provide an updated overview of the GO knowledgebase, as well as the efforts of the broad, international consortium of scientists that develops, maintains, and updates the GO knowledgebase. The GO knowledgebase consists of three components: (1) the GO-a computational knowledge structure describing the functional characteristics of genes; (2) GO annotations-evidence-supported statements asserting that a specific gene product has a particular functional characteristic; and (3) GO Causal Activity Models (GO-CAMs)-mechanistic models of molecular "pathways" (GO biological processes) created by linking multiple GO annotations using defined relations. Each of these components is continually expanded, revised, and updated in response to newly published discoveries and receives extensive QA checks, reviews, and user feedback. For each of these components, we provide a description of the current contents, recent developments to keep the knowledgebase up to date with new discoveries, and guidance on how users can best make use of the data that we provide. We conclude with future directions for the project.

Published
2023

3. Author Correction: Dense sampling of bird diversity increases power of comparative genomics

Author

Feng, Shaohong, Stiller, Josefin, Deng, Yuan, Armstrong, Joel, Fang, Qi, Reeve, Andrew Hart, Xie, Duo, Chen, Guangji, Guo, Chunxue, Faircloth, Brant C, Petersen, Bent, Wang, Zongji, Zhou, Qi, Diekhans, Mark, Chen, Wanjun, Andreu-Sánchez, Sergio, Margaryan, Ashot, Howard, Jason Travis, Parent, Carole, Pacheco, George, Sinding, Mikkel-Holger S, Puetz, Lara, Cavill, Emily, Ribeiro, Ângela M, Eckhart, Leopold, Fjeldså, Jon, Hosner, Peter A, Brumfield, Robb T, Christidis, Les, Bertelsen, Mads F, Sicheritz-Ponten, Thomas, Tietze, Dieter Thomas, Robertson, Bruce C, Song, Gang, Borgia, Gerald, Claramunt, Santiago, Lovette, Irby J, Cowen, Saul J, Njoroge, Peter, Dumbacher, John Philip, Ryder, Oliver A, Fuchs, Jérôme, Bunce, Michael, Burt, David W, Cracraft, Joel, Meng, Guanliang, Hackett, Shannon J, Ryan, Peter G, Jønsson, Knud Andreas, Jamieson, Ian G, da Fonseca, Rute R, Braun, Edward L, Houde, Peter, Mirarab, Siavash, Suh, Alexander, Hansson, Bengt, Ponnikas, Suvi, Sigeman, Hanna, Stervander, Martin, Frandsen, Paul B, van der Zwan, Henriette, van der Sluis, Rencia, Visser, Carina, Balakrishnan, Christopher N, Clark, Andrew G, Fitzpatrick, John W, Bowman, Reed, Chen, Nancy, Cloutier, Alison, Sackton, Timothy B, Edwards, Scott V, Foote, Dustin J, Shakya, Subir B, Sheldon, Frederick H, Vignal, Alain, Soares, André ER, Shapiro, Beth, González-Solís, Jacob, Ferrer-Obiol, Joan, Rozas, Julio, Riutort, Marta, Tigano, Anna, Friesen, Vicki, Dalén, Love, Urrutia, Araxi O, Székely, Tamás, Liu, Yang, Campana, Michael G, Corvelo, André, Fleischer, Robert C, Rutherford, Kim M, Gemmell, Neil J, Dussex, Nicolas, Mouritsen, Henrik, Thiele, Nadine, Delmore, Kira, Liedvogel, Miriam, Franke, Andre, Hoeppner, Marc P, and Krone, Oliver

Subjects
General Science & Technology
Abstract

In Supplementary Table 1 of this Article, 23 samples (B10K-DU-029-32, B10K-DU-029-33, B10K-DU-029-36 to B10K-DU-029-44, B10K-DU- 029-46, B10K-DU-029-47, B10K-DU-029-49 to B10K-DU-029-53, B10K-DU- 029-75 to B10K-DU-029-77, B10K-DU-029-80, and B10K-DU-030-03; styled in boldface in the revised table) were assigned to the incorrect institution. Supplementary Table 1 has been amended to reflect the correct source institution for these samples, and associated data (tissue, museum ID/source specimen ID, site, state/province, latitude, longitude, date collected and sex) have been updated accordingly. The original table is provided as Supplementary Information to this Amendment, and the original Article has been corrected online.

Published
2021

5. The Gene Ontology resource: enriching a GOld mine

Author

Carbon, Seth, Douglass, Eric, Good, Benjamin M, Unni, Deepak R, Harris, Nomi L, Mungall, Christopher J, Basu, Siddartha, Chisholm, Rex L, Dodson, Robert J, Hartline, Eric, Fey, Petra, Thomas, Paul D, Albou, Laurent-Philippe, Ebert, Dustin, Kesling, Michael J, Mi, Huaiyu, Muruganujan, Anushya, Huang, Xiaosong, Mushayahama, Tremayne, LaBonte, Sandra A, Siegele, Deborah A, Antonazzo, Giulia, Attrill, Helen, Brown, Nick H, Garapati, Phani, Marygold, Steven J, Trovisco, Vitor, dos Santos, Gil, Falls, Kathleen, Tabone, Christopher, Zhou, Pinglei, Goodman, Joshua L, Strelets, Victor B, Thurmond, Jim, Garmiri, Penelope, Ishtiaq, Rizwan, Rodríguez-López, Milagros, Acencio, Marcio L, Kuiper, Martin, Lægreid, Astrid, Logie, Colin, Lovering, Ruth C, Kramarz, Barbara, Saverimuttu, Shirin CC, Pinheiro, Sandra M, Gunn, Heather, Su, Renzhi, Thurlow, Katherine E, Chibucos, Marcus, Giglio, Michelle, Nadendla, Suvarna, Munro, James, Jackson, Rebecca, Duesbury, Margaret J, Del-Toro, Noemi, Meldal, Birgit HM, Paneerselvam, Kalpana, Perfetto, Livia, Porras, Pablo, Orchard, Sandra, Shrivastava, Anjali, Chang, Hsin-Yu, Finn, Robert Daniel, Mitchell, Alexander Lawson, Rawlings, Neil David, Richardson, Lorna, Sangrador-Vegas, Amaia, Blake, Judith A, Christie, Karen R, Dolan, Mary E, Drabkin, Harold J, Hill, David P, Ni, Li, Sitnikov, Dmitry M, Harris, Midori A, Oliver, Stephen G, Rutherford, Kim, Wood, Valerie, Hayles, Jaqueline, Bähler, Jürg, Bolton, Elizabeth R, De Pons, Jeffery L, Dwinell, Melinda R, Hayman, G Thomas, Kaldunski, Mary L, Kwitek, Anne E, Laulederkind, Stanley JF, Plasterer, Cody, Tutaj, Marek A, Vedi, Mahima, Wang, Shur-Jen, D’Eustachio, Peter, Matthews, Lisa, Balhoff, James P, Aleksander, Suzi A, Alexander, Michael J, Cherry, J Michael, Engel, Stacia R, Gondwe, Felix, and Karra, Kalpana

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Networking and Information Technology R&D (NITRD), Genetics, 1.5 Resources and infrastructure (underpinning), 2.6 Resources and infrastructure (aetiology), Animals, Arabidopsis, Caenorhabditis elegans, Dictyostelium, Drosophila melanogaster, Escherichia coli, Gene Ontology, Humans, Internet, Mice, Molecular Sequence Annotation, Rats, Saccharomyces cerevisiae, Schizosaccharomyces, User-Computer Interface, Zebrafish, Gene Ontology Consortium, Environmental Sciences, Information and Computing Sciences, Developmental Biology, Biological sciences, Chemical sciences, Environmental sciences
Abstract

The Gene Ontology Consortium (GOC) provides the most comprehensive resource currently available for computable knowledge regarding the functions of genes and gene products. Here, we report the advances of the consortium over the past two years. The new GO-CAM annotation framework was notably improved, and we formalized the model with a computational schema to check and validate the rapidly increasing repository of 2838 GO-CAMs. In addition, we describe the impacts of several collaborations to refine GO and report a 10% increase in the number of GO annotations, a 25% increase in annotated gene products, and over 9,400 new scientific articles annotated. As the project matures, we continue our efforts to review older annotations in light of newer findings, and, to maintain consistency with other ontologies. As a result, 20 000 annotations derived from experimental data were reviewed, corresponding to 2.5% of experimental GO annotations. The website (http://geneontology.org) was redesigned for quick access to documentation, downloads and tools. To maintain an accurate resource and support traceability and reproducibility, we have made available a historical archive covering the past 15 years of GO data with a consistent format and file structure for both the ontology and annotations.

Published
2021

6. Dense sampling of bird diversity increases power of comparative genomics

Author

Feng, Shaohong, Stiller, Josefin, Deng, Yuan, Armstrong, Joel, Fang, Qi, Reeve, Andrew Hart, Xie, Duo, Chen, Guangji, Guo, Chunxue, Faircloth, Brant C, Petersen, Bent, Wang, Zongji, Zhou, Qi, Diekhans, Mark, Chen, Wanjun, Andreu-Sánchez, Sergio, Margaryan, Ashot, Howard, Jason Travis, Parent, Carole, Pacheco, George, Sinding, Mikkel-Holger S, Puetz, Lara, Cavill, Emily, Ribeiro, Ângela M, Eckhart, Leopold, Fjeldså, Jon, Hosner, Peter A, Brumfield, Robb T, Christidis, Les, Bertelsen, Mads F, Sicheritz-Ponten, Thomas, Tietze, Dieter Thomas, Robertson, Bruce C, Song, Gang, Borgia, Gerald, Claramunt, Santiago, Lovette, Irby J, Cowen, Saul J, Njoroge, Peter, Dumbacher, John Philip, Ryder, Oliver A, Fuchs, Jérôme, Bunce, Michael, Burt, David W, Cracraft, Joel, Meng, Guanliang, Hackett, Shannon J, Ryan, Peter G, Jønsson, Knud Andreas, Jamieson, Ian G, da Fonseca, Rute R, Braun, Edward L, Houde, Peter, Mirarab, Siavash, Suh, Alexander, Hansson, Bengt, Ponnikas, Suvi, Sigeman, Hanna, Stervander, Martin, Frandsen, Paul B, van der Zwan, Henriette, van der Sluis, Rencia, Visser, Carina, Balakrishnan, Christopher N, Clark, Andrew G, Fitzpatrick, John W, Bowman, Reed, Chen, Nancy, Cloutier, Alison, Sackton, Timothy B, Edwards, Scott V, Foote, Dustin J, Shakya, Subir B, Sheldon, Frederick H, Vignal, Alain, Soares, André ER, Shapiro, Beth, González-Solís, Jacob, Ferrer-Obiol, Joan, Rozas, Julio, Riutort, Marta, Tigano, Anna, Friesen, Vicki, Dalén, Love, Urrutia, Araxi O, Székely, Tamás, Liu, Yang, Campana, Michael G, Corvelo, André, Fleischer, Robert C, Rutherford, Kim M, Gemmell, Neil J, Dussex, Nicolas, Mouritsen, Henrik, Thiele, Nadine, Delmore, Kira, Liedvogel, Miriam, Franke, Andre, Hoeppner, Marc P, and Krone, Oliver

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Evolutionary Biology, Genetics, Human Genome, Biotechnology, Generic health relevance, Life on Land, Animals, Birds, Chickens, Conservation of Natural Resources, Datasets as Topic, Finches, Genome, Genomics, Humans, Phylogeny, Selection, Genetic, Synteny, General Science & Technology
Abstract

Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity1-4. Sparse taxon sampling has previously been proposed to confound phylogenetic inference5, and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families-including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species.

Published
2020

7. Term Matrix: a novel Gene Ontology annotation quality control system based on ontology term co-annotation patterns.

Author

Wood, Valerie, Carbon, Seth, Harris, Midori A, Lock, Antonia, Engel, Stacia R, Hill, David P, Van Auken, Kimberly, Attrill, Helen, Feuermann, Marc, Gaudet, Pascale, Lovering, Ruth C, Poux, Sylvain, Rutherford, Kim M, and Mungall, Christopher J

Subjects
annotation, biocuration, gene ontology, quality control, Biochemistry and Cell Biology, Microbiology, Immunology
Abstract

Biological processes are accomplished by the coordinated action of gene products. Gene products often participate in multiple processes, and can therefore be annotated to multiple Gene Ontology (GO) terms. Nevertheless, processes that are functionally, temporally and/or spatially distant may have few gene products in common, and co-annotation to unrelated processes probably reflects errors in literature curation, ontology structure or automated annotation pipelines. We have developed an annotation quality control workflow that uses rules based on mutually exclusive processes to detect annotation errors, based on and validated by case studies including the three we present here: fission yeast protein-coding gene annotations over time; annotations for cohesin complex subunits in human and model species; and annotations using a selected set of GO biological process terms in human and five model species. For each case study, we reviewed available GO annotations, identified pairs of biological processes which are unlikely to be correctly co-annotated to the same gene products (e.g. amino acid metabolism and cytokinesis), and traced erroneous annotations to their sources. To date we have generated 107 quality control rules, and corrected 289 manual annotations in eukaryotes and over 52 700 automatically propagated annotations across all taxa.

Published
2020

8. RNAcentral: a hub of information for non-coding RNA sequences

Author

Sweeney, Blake A, Petrov, Anton I, Burkov, Boris, Finn, Robert D, Bateman, Alex, Szymanski, Maciej, Karlowski, Wojciech M, Gorodkin, Jan, Seemann, Stefan E, Cannone, Jamie J, Gutell, Robin R, Fey, Petra, Basu, Siddhartha, Kay, Simon, Cochrane, Guy, Billis, Kostantinos, Emmert, David, Marygold, Steven J, Huntley, Rachael P, Lovering, Ruth C, Frankish, Adam, Chan, Patricia P, Lowe, Todd M, Bruford, Elspeth, Seal, Ruth, Vandesompele, Jo, Volders, Pieter-Jan, Paraskevopoulou, Maria, Ma, Lina, Zhang, Zhang, Griffiths-Jones, Sam, Bujnicki, Janusz M, Boccaletto, Pietro, Blake, Judith A, Bult, Carol J, Chen, Runsheng, Zhao, Yi, Wood, Valerie, Rutherford, Kim, Rivas, Elena, Cole, James, Laulederkind, Stanley JF, Shimoyama, Mary, Gillespie, Marc E, Orlic-Milacic, Marija, Kalvari, Ioanna, Nawrocki, Eric, Engel, Stacia R, Cherry, J Michael, Team, SILVA, Berardini, Tanya Z, Hatzigeorgiou, Artemis, Karagkouni, Dimitra, Howe, Kevin, Davis, Paul, Dinger, Marcel, He, Shunmin, Yoshihama, Maki, Kenmochi, Naoya, Stadler, Peter F, and Williams, Kelly P

Subjects
Biological Sciences, Environmental Sciences, Chemical Sciences, The RNAcentral Consortium, Information and Computing Sciences, Developmental Biology, Biological sciences, Chemical sciences, Environmental sciences
Published
2019

9. Adipose transcriptome analysis provides novel insights into molecular regulation of prolonged fasting in northern elephant seal pups

Author

Martinez, Bridget, Khudyakov, Jane, Rutherford, Kim, Crocker, Daniel E, Gemmell, Neil, and Ortiz, Rudy M

Subjects
Biotechnology, Nutrition, Genetics, Underpinning research, 2.1 Biological and endogenous factors, Aetiology, 1.1 Normal biological development and functioning, Metabolic and endocrine, Adipose Tissue, Adiposity, Animals, Carbohydrate Metabolism, Energy Metabolism, Fasting, Gene Expression Profiling, Lipid Metabolism, Proteome, Seals, Earless, Transcriptome, Weaning, adipose, de novo assembly, extracellular matrix, fasting, transcriptome, Medical Physiology, Biochemistry & Molecular Biology
Abstract

The physiological and cellular adaptations to extreme fasting in northern elephant seals ( Mirounga angustirostris, NES) are remarkable and may help to elucidate endocrine mechanisms that regulate lipid metabolism and energy homeostasis in mammals. Recent studies have highlighted the importance of thyroid hormones in the maintenance of a lipid-based metabolism during prolonged fasting in weaned NES pups. To identify additional molecular regulators of fasting, we used a transcriptomics approach to examine changes in global gene expression profiles before and after 6-8 wk of fasting in weaned NES pups. We produced a de novo assembly and identified 98 unique protein-coding genes that were differentially expressed between early and late fasting. Most of the downregulated genes were associated with lipid, carbohydrate, and protein metabolism. A number of downregulated genes were also associated with maintenance of the extracellular matrix, consistent with tissue remodeling during weight loss and the multifunctional nature of blubber tissue, which plays both metabolic and structural roles in marine mammals. Using this data set, we predict potential mechanisms by which NES pups sustain metabolism and regulate adipose stores throughout the fast, and provide a valuable resource for additional studies of extreme metabolic adaptations in mammals.

Published
2018

11. Revised fission yeast gene and allele nomenclature guidelines for machine readability

Author

Lera-Ramírez, Manuel, primary, Bähler, Jürg, additional, Mata, Juan, additional, Rutherford, Kim, additional, Hoffman, Charles S, additional, Lambert, Sarah, additional, Oliferenko, Snezhana, additional, Martin, Sophie G, additional, Gould, Kathleen L, additional, Du, Li-Lin, additional, Sabatinos, Sarah A, additional, Forsburg, Susan L, additional, Nielsen, Olaf, additional, Nurse, Paul, additional, and Wood, Valerie, additional

Published
2023
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13. A Comprehensive Survey of the Plasmodium Life Cycle by Genomic, Transcriptomic, and Proteomic Analyses

Author

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

14. Genomic Plasticity of the Causative Agent of Melioidosis, Burkholderia pseudomallei

Author

Titball, Richard W., Peacock, Sharon J., Cerdeño-Tárraga, Ana M., Atkins, Timothy, Crossman, Lisa C., Pitt, Tyrone, Churcher, Carol, Mungall, Karen, Bentley, Stephen D., Sebaihia, Mohammed, Thomson, Nicholas R., Bason, Nathalie, Beacham, Ifor R., Brooks, Karen, Brown, Katherine A., Brown, Nat F., Challis, Greg L., Cherevach, Inna, Chillingworth, Tracy, Cronin, Ann, Crossett, Ben, Davis, Paul, DeShazer, David, Feltwell, Theresa, Fraser, Audrey, Hance, Zahra, Hauser, Heidi, Holroyd, Simon, Jagels, Kay, Keith, Karen E., Maddison, Mark, Moule, Sharon, Price, Claire, Quail, Michael A., Rabbinowitsch, Ester, Rutherford, Kim, Sanders, Mandy, Simmonds, Mark, Songsivilai, Sirirurg, Stevens, Kim, Tumapa, Sarinna, Vesaratchavest, Monkgol, Whitehead, Sally, Yeats, Corin, Barrell, Bart G., Parkhill, Julian, and Greenberg, E. Peter

Published
2004

15. Complete Genomes of Two Clinical Staphylococcus aureus Strains: Evidence for the Rapid Evolution of Virulence and Drug Resistance

Author

Feil, Edward J., Lindsay, Jodi A., Peacock, Sharon J., Enright, Mark C., Foster, Tim J., Moore, Catrin E., Hurst, Laurence, Atkin, Rebecca, Barron, Andrew, Bason, Nathalie, Bentley, Stephen D., Chillingworth, Carol, Chillingworth, Tracey, Churcher, Carol, Clark, Louise, Corton, Craig, Cronin, Ann, Doggett, Jon, Dowd, Linda, Feltwell, Theresa, Hance, Zahra, Harris, Barbara, Hauser, Heidi, Holroyd, Simon, Jagels, Kay, James, Keith D., Lennard, Nicola, Line, Alexandra, Mayes, Rebecca, Moule, Sharon, Mungall, Karen, Ormond, Douglas, Quail, Michael A., Rabbinowitsch, Ester, Rutherford, Kim, Sanders, Mandy, Sharp, Sarah, Simmonds, Mark, Stevens, Kim, Whitehead, Sally, Barrell, Bart G., Spratt, Brian G., Parkhill, Julian, and Mekalanos, John J.

Published
2004

17. The Gene Ontology knowledgebase in 2023

Author

Gene Ontology Consortium, Aleksander, Suzi A, Balhoff, James, Carbon, Seth, Cherry, J Michael, Drabkin, Harold J, Ebert, Dustin, Feuermann, Marc, Gaudet, Pascale, Harris, Nomi L, Hill, David P, Lee, Raymond, Mi, Huaiyu, Moxon, Sierra, Mungall, Christopher J, Muruganugan, Anushya, Mushayahama, Tremayne, Sternberg, Paul W, Thomas, Paul D, Van Auken, Kimberly, Ramsey, Jolene, Siegele, Deborah A, Chisholm, Rex L, Fey, Petra, Aspromonte, Maria Cristina, Nugnes, Maria Victoria, Quaglia, Federica, Tosatto, Silvio, Giglio, Michelle, Nadendla, Suvarna, Antonazzo, Giulia, Attrill, Helen, Dos Santos, Gil, Marygold, Steven, Strelets, Victor, Tabone, Christopher J, Thurmond, Jim, Zhou, Pinglei, Ahmed, Saadullah H, Asanitthong, Praoparn, Luna Buitrago, Diana, Erdol, Meltem N, Gage, Matthew C, Ali Kadhum, Mohamed, Li, Kan Yan Chloe, Long, Miao, Michalak, Aleksandra, Pesala, Angeline, Pritazahra, Armalya, Saverimuttu, Shirin CC, Su, Renzhi, Thurlow, Kate E, Lovering, Ruth C, Logie, Colin, Oliferenko, Snezhana, Blake, Judith, Christie, Karen, Corbani, Lori, Dolan, Mary E, Ni, Li, Sitnikov, Dmitry, Smith, Cynthia, Cuzick, Alayne, Seager, James, Cooper, Laurel, Elser, Justin, Jaiswal, Pankaj, Gupta, Parul, Naithani, Sushma, Lera-Ramirez, Manuel, Rutherford, Kim, Wood, Valerie, De Pons, Jeffrey L, Dwinell, Melinda R, Hayman, G Thomas, Kaldunski, Mary L, Kwitek, Anne E, Laulederkind, Stanley JF, Tutaj, Marek A, Vedi, Mahima, Wang, Shur-Jen, D'Eustachio, Peter, Aimo, Lucila, Axelsen, Kristian, Bridge, Alan, Hyka-Nouspikel, Nevila, Morgat, Anne, Engel, Stacia R, Karra, Kalpana, Miyasato, Stuart R, Nash, Robert S, Skrzypek, Marek S, Weng, Shuai, Wong, Edith D, Bakker, Erika, and Baryshnikova, A

Subjects
1.1 Normal biological development and functioning, Proteins, Computational Biology, Molecular Sequence Annotation, knowledgebase, gene annotation, Databases, Gene Ontology Consortium, Gene Ontology, gene function, knowledge graphs, Genetic, Underpinning research, Genetics, Developmental Biology
Abstract

The Gene Ontology (GO) knowledgebase (http://geneontology.org) is a comprehensive resource concerning the functions of genes and gene products (proteins and noncoding RNAs). GO annotations cover genes from organisms across the tree of life as well as viruses, though most gene function knowledge currently derives from experiments carried out in a relatively small number of model organisms. Here, we provide an updated overview of the GO knowledgebase, as well as the efforts of the broad, international consortium of scientists that develops, maintains, and updates the GO knowledgebase. The GO knowledgebase consists of three components: (1) the GO-a computational knowledge structure describing the functional characteristics of genes; (2) GO annotations-evidence-supported statements asserting that a specific gene product has a particular functional characteristic; and (3) GO Causal Activity Models (GO-CAMs)-mechanistic models of molecular "pathways" (GO biological processes) created by linking multiple GO annotations using defined relations. Each of these components is continually expanded, revised, and updated in response to newly published discoveries and receives extensive QA checks, reviews, and user feedback. For each of these components, we provide a description of the current contents, recent developments to keep the knowledgebase up to date with new discoveries, and guidance on how users can best make use of the data that we provide. We conclude with future directions for the project.

Published
2023

18. A human-curated annotation of the Candida albicans genome.

Author

Braun, Burkhard R, van Het Hoog, Marco, d'Enfert, Christophe, Martchenko, Mikhail, Dungan, Jan, Kuo, Alan, Inglis, Diane O, Uhl, M Andrew, Hogues, Hervé, Berriman, Matthew, Lorenz, Michael, Levitin, Anastasia, Oberholzer, Ursula, Bachewich, Catherine, Harcus, Doreen, Marcil, Anne, Dignard, Daniel, Iouk, Tatiana, Zito, Rosa, Frangeul, Lionel, Tekaia, Fredj, Rutherford, Kim, Wang, Edwin, Munro, Carol A, Bates, Steve, Gow, Neil A, Hoyer, Lois L, Köhler, Gerwald, Morschhäuser, Joachim, Newport, George, Znaidi, Sadri, Raymond, Martine, Turcotte, Bernard, Sherlock, Gavin, Costanzo, Maria, Ihmels, Jan, Berman, Judith, Sanglard, Dominique, Agabian, Nina, Mitchell, Aaron P, Johnson, Alexander D, Whiteway, Malcolm, and Nantel, André

Subjects
Genetics, Developmental Biology
Abstract

Recent sequencing and assembly of the genome for the fungal pathogen Candida albicans used simple automated procedures for the identification of putative genes. We have reviewed the entire assembly, both by hand and with additional bioinformatic resources, to accurately map and describe 6,354 genes and to identify 246 genes whose original database entries contained sequencing errors (or possibly mutations) that affect their reading frame. Comparison with other fungal genomes permitted the identification of numerous fungus-specific genes that might be targeted for antifungal therapy. We also observed that, compared to other fungi, the protein-coding sequences in the C. albicans genome are especially rich in short sequence repeats. Finally, our improved annotation permitted a detailed analysis of several multigene families, and comparative genomic studies showed that C. albicans has a far greater catabolic range, encoding respiratory Complex 1, several novel oxidoreductases and ketone body degrading enzymes, malonyl-CoA and enoyl-CoA carriers, several novel amino acid degrading enzymes, a variety of secreted catabolic lipases and proteases, and numerous transporters to assimilate the resulting nutrients. The results of these efforts will ensure that the Candida research community has uniform and comprehensive genomic information for medical research as well as for future diagnostic and therapeutic applications.

Published
2005

19. The Gene Ontology knowledgebase in 2023

Author

Consortium, Gene Ontology, Aleksander, Suzi A, Balhoff, James, Carbon, Seth, Cherry, J Michael, Drabkin, Harold J, Ebert, Dustin, Feuermann, Marc, Gaudet, Pascale, Harris, Nomi L, Hill, David P, Lee, Raymond, Mi, Huaiyu, Moxon, Sierra, Mungall, Christopher J, Muruganugan, Anushya, Mushayahama, Tremayne, Sternberg, Paul W, Thomas, Paul D, Van Auken, Kimberly, Ramsey, Jolene, Siegele, Deborah A, Chisholm, Rex L, Fey, Petra, Aspromonte, Maria Cristina, Nugnes, Maria Victoria, Quaglia, Federica, Tosatto, Silvio, Giglio, Michelle, Nadendla, Suvarna, Antonazzo, Giulia, Attrill, Helen, Dos Santos, Gil, Marygold, Steven, Strelets, Victor, Tabone, Christopher J, Thurmond, Jim, Zhou, Pinglei, Ahmed, Saadullah H, Asanitthong, Praoparn, Buitrago, Diana Luna, Erdol, Meltem N, Gage, Matthew C, Kadhum, Mohamed Ali, Li, Kan Yan Chloe, Long, Miao, Michalak, Aleksandra, Pesala, Angeline, Pritazahra, Armalya, Saverimuttu, Shirin CC, Su, Renzhi, Thurlow, Kate E, Lovering, Ruth C, Logie, Colin, Oliferenko, Snezhana, Blake, Judith, Christie, Karen, Corbani, Lori, Dolan, Mary E, Ni, Li, Sitnikov, Dmitry, Smith, Cynthia, Cuzick, Alayne, Seager, James, Cooper, Laurel, Elser, Justin, Jaiswal, Pankaj, Gupta, Parul, Naithani, Sushma, Lera-Ramirez, Manuel, Rutherford, Kim, Wood, Valerie, De Pons, Jeffrey L, Dwinell, Melinda R, Hayman, G Thomas, Kaldunski, Mary L, Kwitek, Anne E, Laulederkind, Stanley JF, Tutaj, Marek A, Vedi, Mahima, Wang, Shur-Jen, D'Eustachio, Peter, Aimo, Lucila, Axelsen, Kristian, Bridge, Alan, Hyka-Nouspikel, Nevila, Morgat, Anne, Engel, Stacia R, Karra, Kalpana, Miyasato, Stuart R, Nash, Robert S, Skrzypek, Marek S, Weng, Shuai, Wong, Edith D, Bakker, Erika, Berardini, Tanya Z, Reiser, Leonore, Auchincloss, Andrea, Argoud-Puy, Ghislaine, Blatter, Marie-Claude, Boutet, Emmanuel, Breuza, Lionel, Casals-Casas, Cristina, Coudert, Elisabeth, Estreicher, Anne, Famiglietti, Maria Livia, Gos, Arnaud, Gruaz-Gumowski, Nadine, Hulo, Chantal, Jungo, Florence, Le Mercier, Philippe, Lieberherr, Damien, Masson, Patrick, Pedruzzi, Ivo, Pourcel, Lucille, Poux, Sylvain, Rivoire, Catherine, Sundaram, Shyamala, Bateman, Alex, Bowler-Barnett, Emily, Bye-A-Jee, Hema, Denny, Paul, Ignatchenko, Alexandr, Ishtiaq, Rizwan, Lock, Antonia, Lussi, Yvonne, Magrane, Michele, Martin, Maria J, Orchard, Sandra, Raposo, Pedro, Speretta, Elena, Tyagi, Nidhi, Warner, Kate, Zaru, Rossana, Diehl, Alexander D, Chan, Juancarlos, Diamantakis, Stavros, Raciti, Daniela, Zarowiecki, Magdalena, Fisher, Malcolm, James-Zorn, Christina, Ponferrada, Virgilio, Zorn, Aaron, Ramachandran, Sridhar, Ruzicka, Leyla, and Westerfield, Monte

Subjects
Ecology,Evolution & Ethology, Cell Cycle & Chromosomes, Cell Biology
Abstract

The Gene Ontology (GO) knowledgebase (http://geneontology.org) is a comprehensive resource concerning the functions of genes and gene products (proteins and noncoding RNAs). GO annotations cover genes from organisms across the tree of life as well as viruses, though most gene function knowledge currently derives from experiments carried out in a relatively small number of model organisms. Here, we provide an updated overview of the GO knowledgebase, as well as the efforts of the broad, international consortium of scientists that develops, maintains, and updates the GO knowledgebase. The GO knowledgebase consists of three components: (1) the GO-a computational knowledge structure describing the functional characteristics of genes; (2) GO annotations-evidence-supported statements asserting that a specific gene product has a particular functional characteristic; and (3) GO Causal Activity Models (GO-CAMs)-mechanistic models of molecular "pathways" (GO biological processes) created by linking multiple GO annotations using defined relations. Each of these components is continually expanded, revised, and updated in response to newly published discoveries and receives extensive QA checks, reviews, and user feedback. For each of these components, we provide a description of the current contents, recent developments to keep the knowledgebase up to date with new discoveries, and guidance on how users can best make use of the data that we provide. We conclude with future directions for the project.

Published
2023
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22. PHI-base in 2022: a multi-species phenotype database for Pathogen-Host Interactions

Author

Urban, Martin, Cuzick, Alayne, Seager, James, Wood, Valerie, Rutherford, Kim, Venkatesh, Shilpa Yagwakote, Sahu, Jashobanta, Iyer, S Vijaylakshmi, Khamari, Lokanath, De Silva, Nishadi, Martinez, Manuel Carbajo, Pedro, Helder, Yates, Andrew D, Hammond-Kosack, Kim E, Urban, Martin [0000-0003-2440-4352], Cuzick, Alayne [0000-0001-8941-3984], Seager, James [0000-0001-7487-610X], Wood, Valerie [0000-0001-6330-7526], Rutherford, Kim [0000-0001-6277-726X], De Silva, Nishadi [0000-0003-4802-2375], Pedro, Helder [0000-0001-7582-1565], Yates, Andrew D [0000-0002-8886-4772], Hammond-Kosack, Kim E [0000-0002-9699-485X], and Apollo - University of Cambridge Repository

Subjects
Internet, Insecta, Bacteria, Databases, Factual, Nematoda, Virulence, Fungi, Plants, Diplomonadida, User-Computer Interface, Phenotype, Host-Pathogen Interactions, Animals, Apicomplexa, Phylogeny
Abstract

Since 2005, the Pathogen-Host Interactions Database (PHI-base) has manually curated experimentally verified pathogenicity, virulence and effector genes from fungal, bacterial and protist pathogens, which infect animal, plant, fish, insect and/or fungal hosts. PHI-base (www.phi-base.org) is devoted to the identification and presentation of phenotype information on pathogenicity and effector genes and their host interactions. Specific gene alterations that did not alter the in host interaction phenotype are also presented. PHI-base is invaluable for comparative analyses and for the discovery of candidate targets in medically and agronomically important species for intervention. Version 4.12 (September 2021) contains 4387 references, and provides information on 8411 genes from 279 pathogens, tested on 228 hosts in 18, 190 interactions. This provides a 24% increase in gene content since Version 4.8 (September 2019). Bacterial and fungal pathogens represent the majority of the interaction data, with a 54:46 split of entries, whilst protists, protozoa, nematodes and insects represent 3.6% of entries. Host species consist of approximately 54% plants and 46% others of medical, veterinary and/or environmental importance. PHI-base data is disseminated to UniProtKB, FungiDB and Ensembl Genomes. PHI-base will migrate to a new gene-centric version (version 5.0) in early 2022. This major development is briefly described.

Published
2022
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24. Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project

Author

modENCODE Consortium, Gerstein, Mark B., Lu, Zhi John, Van Nostrand, Eric L., Cheng, Chao, Arshinoff, Bradley I., Liu, Tao, Yip, Kevin Y., Robilotto, Rebecca, Rechtsteiner, Andreas, Ikegami, Kohta, Alves, Pedro, Chateigner, Aurelien, Perry, Marc, Morris, Mitzi, Auerbach, Raymond K., Feng, Xin, Leng, Jing, Vielle, Anne, Niu, Wei, Rhrissorrakrai, Kahn, Agarwal, Ashish, Alexander, Roger P., Barber, Galt, Brdlik, Cathleen M., Brennan, Jennifer, Brouillet, Jeremy Jean, Carr, Adrian, Cheung, Ming-Sin, Clawson, Hiram, Contrino, Sergio, Dannenberg, Luke O., Dernburg, Abby F., Desai, Arshad, Dick, Lindsay, Dosé, Andréa C., Du, Jiang, Egelhofer, Thea, Ercan, Sevinc, Euskirchen, Ghia, Ewing, Brent, Feingold, Elise A., Gassmann, Reto, Good, Peter J., Green, Phil, Gullier, Francois, Gutwein, Michelle, Guyer, Mark S., Habegger, Lukas, Han, Ting, Henikoff, Jorja G., Henz, Stefan R., Hinrichs, Angie, Holster, Heather, Hyman, Tony, Iniguez, A. Leo, Janette, Judith, Jensen, Morten, Kato, Masaomi, Kent, W. James, Kephart, Ellen, Khivansara, Vishal, Khurana, Ekta, Kim, John K., Kolasinska-Zwierz, Paulina, Lai, Eric C., Latorre, Isabel, Leahey, Amber, Lewis, Suzanna, Lloyd, Paul, Lochovsky, Lucas, Lowdon, Rebecca F., Lubling, Yaniv, Lyne, Rachel, MacCoss, Michael, Mackowiak, Sebastian D., Mangone, Marco, McKay, Sheldon, Mecenas, Desirea, Merrihew, Gennifer, Miller, David M., Muroyama, Andrew, Murray, John I., Ooi, Siew-Loon, Pham, Hoang, Phippen, Taryn, Preston, Elica A., Rajewsky, Nikolaus, Rätsch, Gunnar, Rosenbaum, Heidi, Rozowsky, Joel, Rutherford, Kim, Ruzanov, Peter, Sarov, Mihail, Sasidharan, Rajkumar, Sboner, Andrea, Scheid, Paul, Segal, Eran, Shin, Hyunjin, Shou, Chong, Slack, Frank J., Slightam, Cindie, Smith, Richard, Spencer, William C., Stinson, E. O., Taing, Scott, Takasaki, Teruaki, Vafeados, Dionne, Voronina, Ksenia, Wang, Guilin, Washington, Nicole L., Whittle, Christina M., Wu, Beijing, Yan, Koon-Kiu, Zeller, Georg, Zha, Zheng, Zhong, Mei, Zhou, Xingliang, Ahringer, Julie, Strome, Susan, Gunsalus, Kristin C., Micklem, Gos, Liu, X. Shirley, Reinke, Valerie, Kim, Stuart K., Hillier, LaDeana W., Henikoff, Steven, Piano, Fabio, Snyder, Michael, Stein, Lincoln, Lieb, Jason D., and Waterston, Robert H.

Published
2010

27. PHI-base in 2022: a multi-species phenotype database for Pathogen–Host Interactions

Author

Urban, Martin, primary, Cuzick, Alayne, additional, Seager, James, additional, Wood, Valerie, additional, Rutherford, Kim, additional, Venkatesh, Shilpa Yagwakote, additional, Sahu, Jashobanta, additional, Iyer, S Vijaylakshmi, additional, Khamari, Lokanath, additional, De Silva, Nishadi, additional, Martinez, Manuel Carbajo, additional, Pedro, Helder, additional, Yates, Andrew D, additional, and Hammond-Kosack, Kim E, additional

Published
2021
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32. JaponicusDB: rapid deployment of a model organism database for an emerging model species.

Author

Rutherford, Kim M., Harris, Midori A., Oliferenko, Snezhana, and Wood, Valerie

Subjects
*GENETICS, *YEAST, *GENOMES
Abstract

The fission yeast Schizosaccharomyces japonicus has recently emerged as a powerful system for studying the evolution of essential cellular processes, drawing on similarities as well as key differences between S. japonicus and the related, well-established model Schizosaccharomyces pombe. We have deployed the open-source, modular code and tools originally developed for PomBase, the S. pombe model organism database (MOD), to create JaponicusDB (www.japonicusdb.org), a new MOD dedicated to S. japonicus. By providing a central resource with ready access to a growing body of experimental data, ontology-based curation, seamless browsing and querying, and the ability to integrate new data with existing knowledge, JaponicusDB supports fission yeast biologists to a far greater extent than any other source of S. japonicus data. JaponicusDB thus enables S. japonicus researchers to realize the full potential of studying a newly emerging model species and illustrates the widely applicable power and utility of harnessing reusable PomBase code to build a comprehensive, community-maintainable repository of species-relevant knowledge. [ABSTRACT FROM AUTHOR]

Published
2022
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33. Fission stories: using PomBase to understand Schizosaccharomyces pombe biology.

Author

Harris, Midori A., Rutherford, Kim M., Hayles, Jacqueline, Lock, Antonia, Bähler, Jürg, Oliver, Stephen G., Mata, Juan, and Wood, Valerie

Subjects
*DATABASES, *DATA curation, *SEQUENCE analysis, *YEAST, *MOLECULAR biology, *GENOMES
Abstract

PomBase (www.pombase.org), the model organism database (MOD) for the fission yeast Schizosaccharomyces pombe, supports research within and beyond the S. pombe community by integrating and presenting genetic, molecular, and cell biological knowledge into intuitive displays and comprehensive data collections.With new content, novel query capabilities, and biologist-friendly data summaries and visualization, PomBase also drives innovation in the MOD community. [ABSTRACT FROM AUTHOR]

Published
2022
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34. PHI-base: the pathogen-host interactions database

Author

Urban, Martin, Cuzick, Alayne, Seager, James, Wood, Valerie, Rutherford, Kim, Venkatesh, Shilpa Yagwakote, De Silva, Nishadi, Martinez, Manuel Carbajo, Pedro, Helder, Yates, Andy D, Hassani-Pak, Keywan, Hammond-Kosack, Kim E, Wood, Valerie [0000-0001-6330-7526], and Apollo - University of Cambridge Repository

Subjects
Crops, Agricultural, Internet, Antifungal Agents, Databases, Factual, Computational Biology, Plants, Communicable Diseases, Search Engine, Phenotype, Host-Pathogen Interactions, Animals, Humans, Biological Assay, Algorithms, Genome, Plant, Data Management
Abstract

The pathogen-host interactions database (PHI-base) is available at www.phi-base.org. PHI-base contains expertly curated molecular and biological information on genes proven to affect the outcome of pathogen-host interactions reported in peer reviewed research articles. PHI-base also curates literature describing specific gene alterations that did not affect the disease interaction phenotype, in order to provide complete datasets for comparative purposes. Viruses are not included, due to their extensive coverage in other databases. In this article, we describe the increased data content of PHI-base, plus new database features and further integration with complementary databases. The release of PHI-base version 4.8 (September 2019) contains 3454 manually curated references, and provides information on 6780 genes from 268 pathogens, tested on 210 hosts in 13,801 interactions. Prokaryotic and eukaryotic pathogens are represented in almost equal numbers. Host species consist of approximately 60% plants (split 50:50 between cereal and non-cereal plants), and 40% other species of medical and/or environmental importance. The information available on pathogen effectors has risen by more than a third, and the entries for pathogens that infect crop species of global importance has dramatically increased in this release. We also briefly describe the future direction of the PHI-base project, and some existing problems with the PHI-base curation process.

Published
2019
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35. A genome‐wide investigation of adaptive signatures in protein‐coding genes related to tool behaviour in New Caledonian and Hawaiian crows

Author

Dussex, Nicolas, primary, Kutschera, Verena E., additional, Wiberg, R. Axel W., additional, Parker, Darren J., additional, Hunt, Gavin R., additional, Gray, Russell D., additional, Rutherford, Kim, additional, Abe, Hideaki, additional, Fleischer, Robert C., additional, Ritchie, Michael G., additional, Rutz, Christian, additional, Wolf, Jochen B. W., additional, and Gemmell, Neil J., additional

Published
2020
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36. Genomic plasticity of the causative agent of melioidosis, Burkholderia pseudomallei

Author

Holden, Matthew T.G., Titball, Richard W., Peacock, Sharon J., Cerdeno-Tarraga, Ana M., Atkins, Timothy, Crossman, Lisa C., Pitt, Tyrone, Churcher, Carol, Mungall, Karen, Bentley, Stephen D., Sebaihia, Mohammed, Thomson, Nicholas R., Bason, Nathalie, Beacham, Ifor R., Brooks, Karen, Brown, Katherine A., Brown, Nat F., Challis, Greg L., Cherevach, Inna, Chillingworth, Tracy, Cronin, Ann, Crossett, Ben, Davis, Paul, DeShazer, David, Feltwell, Theresa, Fraser, Audrey, Hance, Zahra, Hauser, Heidi, Holroyd, Simon, Jagels, Kay, Keith, Karen E., Maddison, Mark, Moule, Sharon, Price, Claire, Quail, Michael A., Rabbinowitsch, Ester, Rutherford, Kim, Sanders, Mandy, Simmonds, Mark, Songsivilai, Sirirurg, Stevens, Kim, Tumapa, Sarinna, Vesaratchavest, Monkgol, Whitehead, Sally, Yeats, Corin, Barrell, Bart G., Oyston, Petra C.F., and Parkhill, Julian

Subjects
Pseudomonas infections -- Research, Science and technology
Abstract

Burkholderia pseudomallei is a recognized biothreat agent and the causative agent of melioidosis. This Gram-negative bacterium exists as a soil saprophyte in melioidosis-endemic areas of the world and accounts for 20% of community-acquired septicaemias in northeastern Thailand where half of those affected die. Here we report the complete genome of B. pseudomallei, which is composed of two chromosomes of 4.07 megabase pairs and 3.17 megabase pairs, showing significant functional partitioning of genes between them. The large chromosome encodes many of the core functions associated with central metabolism and cell growth, whereas the small chromosome carries more accessory functions associated with adaptation and survival in different niches. Genomic comparisons with closely and more distantly related bacteria revealed a greater level of gene order conservation and a greater number of orthologous genes on the large chromosome, suggesting that the two replicons have distinct evolutionary origins. A striking feature of the genome was the presence of 16 genomic islands (GIs) that together made up 6.1% of the genome. Further analysis revealed these islands to be variably present in a collection of invasive and soil isolates but entirely absent from the clonally related organism B. mallei. We propose that variable horizontal gene acquisition by B. pseudomallei is an important feature of recent genetic evolution and that this has resulted in a genetically diverse pathogenic species.

Published
2004

37. Complete genomes of two clinical Staphylococcus aureus strains: evidence for the rapid evolution of virulence and drug resistance

Author

Holden, Matthew T.G., Feil, Edward J., Lindsay, Jodi A., Peacock, Sharon J., Day, Nicholas P.J., Enright, Mark C., Foster, Tim J., Moore, Catrin E., Hurst, Laurence, Atkin, Rebecca, Barron, Andrew, Bason, Nathalie, Bentley, Stephen D., Chillingworth, Carol, Chillingworth, Tracey, Churcher, Carol, Clark, Louise, Corton, Craig, Cronin, Ann, Doggett, Jon, Dowd, Linda, Feltwell, Theresa, Hance, Zahra, Harris, Barbara C., Bishop, Hauser, Heidi, Holroyd, Simon, Jagels, Kay, James, Keith D., Lennard, Nicola, Line, Alexandra, Mayes, Rebecca, Moule, Sharon, Mungall, Karen, Ormond, Douglas, Quail, Michael A., Rabbinowitsch, Ester, Rutherford, Kim, Sanders, Mandy, Sharp, Sarah, Simmonds, Mark, Stevens, Kim, Whitehead, Sally, Barrell, Bart G., Spratt, Brian G., and Parkhill, Julian

Subjects
Drug resistance in microorganisms -- Research, Staphylococcus aureus -- Research, Staphylococcus aureus -- Genetic aspects, Science and technology, National Academy of Sciences -- Research
Abstract

Staphylococcus aureus is an important nosocomial and community-acquired pathogen. Its genetic plasticity has facilitated the evolution of many virulent and drug-resistant strains, presenting a major and constantly changing clinical challenge. We sequenced the [approximately equal to] 2.8-Mbp genomes of two disease-causing S. aureus strains isolated from distinct clinical settings: a recent hospital-acquired representative of the epidemic methicillin-resistant S. aureus EMRSA-16 clone (MRSA252), a clinically important and globally prevalent lineage; and a representative of an invasive community-acquired methicillin-susceptible S. aureus clone (MSSA476). A comparative-genomics approach was used to explore the mechanisms of evolution of clinically important S, aureus genomes and to identify regions affecting virulence and drug resistance. The genome sequences of MRSA252 and MSSA476 have a well conserved core region but differ markedly in their accessory genetic elements. MRSA252 is the most genetically diverse S. aureus strain sequenced to date: [approximately equal to] 6% of the genome is novel compared with other published genomes, and it contains several unique genetic elements. MSSA476 is methicillin-susceptible, but it contains a novel Staphylococcal chromosomal cassette (SCC) mec-like element (designated SC[C.sub.476]), which is integrated at the same site on the chromosome as SCCmec elements in MRSA strains but encodes a putative fusidic acid resistance protein. The crucial role that accessory elements play in the rapid evolution of S. aureus is clearly illustrated by comparing the MSSA476 genome with that of an extremely closely related MRSA community-acquired strain; the differential distribution of large mobile elements carrying virulence and drug-resistance determinants may be responsible for the clinically important phenotypic differences in these strains.

Published
2004

39. Genome sequence of the human malaria parasite Plasmodium falciparum

Author

Gardner, Malcolm J., Hall, Neil, Fung, Eula, White, Owen, Berriman, Matthew, Hyman, Richard W., Carlton, Jane M., Pain, Arnab, Nelson, Karen E., Bowman, Sharen, Paulsen, Ian T., James, Keith, Eisen, Jonathan A., Rutherford, Kim, Salzberg, Steven L., Craig, Alister, Kyes, Sue, Chan, Man-Suen, Nene, Vishvanath, Shallom, Shamira J., Suh, Bernard, Peterson, Jeremy, Angiuoli, Sam, Pertea, Mihaela, Allen, Jonathan, Selengut, Jeremy, Haft, Daniel, Mather, Michael W., Vaidya, Akhil B., Martin, David M. A., Fairlamb, Alan H., Fraunholz, Martin J., Roos, David S., Ralph, Stuart A., McFadden, Geoffrey I., Cummings, Leda M., Subramanian, G. Mani, Mungall, Chris, Venter, J. Craig, Carucci, Daniel J., Hoffman, Stephen L., Newbold, Chris, Davis, Ronald W., Fraser, Claire M., and Barrell, Bart

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Malcolm J. Gardner (corresponding author) [1]; Neil Hall [2]; Eula Fung [3]; Owen White [1]; Matthew Berriman [2]; Richard W. Hyman [3]; Jane M. Carlton [1]; Arnab Pain [2]; [...]

Published
2002
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40. modMine: flexible access to modENCODE data

Author

Contrino, Sergio, Smith, Richard N., Butano, Daniela, Carr, Adrian, Hu, Fengyuan, Lyne, Rachel, Rutherford, Kim, Kalderimis, Alex, Sullivan, Julie, Carbon, Seth, Kephart, Ellen T., Lloyd, Paul, Stinson, E. O., Washington, Nicole L., Perry, Marc D., Ruzanov, Peter, Zha, Zheng, Lewis, Suzanna E., Stein, Lincoln D., and Micklem, Gos

Published
2012
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43. Term Matrix: A novel Gene Ontology annotation quality control system based on ontology term co-annotation patterns

Author

Wood, Valerie, primary, Carbon, Seth, additional, Harris, Midori A., additional, Lock, Antonia, additional, Engel, Stacia R., additional, Hill, David P., additional, Van Auken, Kimberly, additional, Attrill, Helen, additional, Feuermann, Marc, additional, Gaudet, Pascale, additional, Lovering, Ruth C., additional, Poux, Sylvain, additional, Rutherford, Kim M., additional, and Mungall, Christopher J., additional

Published
2020
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45. Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project

Author

Gerstein, Mark B., Lu, Zhi John, Van Nostrand, Eric L., Cheng, Chao, Arshinoff, Bradley I., Liu, Tao, Yip, Kevin Y., Robilotto, Rebecca, Rechtsteiner, Andreas, Ikegami, Kohta, Alves, Pedro, Chateigner, Aurelien, Perry, Marc, Morris, Mitzi, Auerbach, Raymond K., Feng, Xin, Leng, Jing, Vielle, Anne, Niu, Wei, Rhrissorrakrai, Kahn, Agarwal, Ashish, Alexander, Roger P., Barber, Galt, Brdlik, Cathleen M., Brennan, Jennifer, Brouillet, Jeremy Jean, Carr, Adrian, Cheung, Ming-Sin, Clawson, Hiram, Contrino, Sergio, Dannenberg, Luke O., Dernburg, Abby F., Desai, Arshad, Dick, Lindsay, Dosé, Andréa C., Du, Jiang, Egelhofer, Thea, Ercan, Sevinc, Euskirchen, Ghia, Ewing, Brent, Feingold, Elise A., Gassmann, Reto, Good, Peter J., Green, Phil, Gullier, Francois, Gutwein, Michelle, Guyer, Mark S., Habegger, Lukas, Han, Ting, Henikoff, Jorja G., Henz, Stefan R., Hinrichs, Angie, Holster, Heather, Hyman, Tony, Iniguez, Leo A., Janette, Judith, Jensen, Morten, Kato, Masaomi, Kent, James W., Kephart, Ellen, Khivansara, Vishal, Khurana, Ekta, Kim, John K., Kolasinska-Zwierz, Paulina, Lai, Eric C., Latorre, Isabel, Leahey, Amber, Lewis, Suzanna, Lloyd, Paul, Lochovsky, Lucas, Lowdon, Rebecca F., Lubling, Yaniv, Lyne, Rachel, MacCoss, Michael, Mackowiak, Sebastian D., Mangone, Marco, McKay, Sheldon, Mecenas, Desirea, Merrihew, Gennifer, Miller, David M., III, Muroyama, Andrew, Murray, John I., Ooi, Siew-Loon, Pham, Hoang, Phippen, Taryn, Preston, Elicia A., Rajewsky, Nikolaus, Rätsch, Gunnar, Rosenbaum, Heidi, Rozowsky, Joel, Rutherford, Kim, Ruzanov, Peter, Sarov, Mihail, Sasidharan, Rajkumar, Sboner, Andrea, Scheid, Paul, Segal, Eran, Shin, Hyunjin, Shou, Chong, Slack, Frank J., Slightam, Cindie, Smith, Richard, Spencer, William C., Stinson, E. O., Taing, Scott, Takasaki, Teruaki, Vafeados, Dionne, Voronina, Ksenia, Wang, Guilin, Washington, Nicole L., Whittle, Christina M., Wu, Beijing, Yan, Koon-Kiu, Zeller, Georg, Zha, Zheng, Zhong, Mei, Zhou, Xingliang, Ahringer, Julie, Strome, Susan, Gunsalus, Kristin C., Micklem, Gos, Liu, Shirley X., Reinke, Valerie, Kim, Stuart K., Hillier, LaDeana W., Henikoff, Steven, Piano, Fabio, Snyder, Michael, Stein, Lincoln, Lieb, Jason D., and Waterston, Robert H.

Published
2010
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46. The tuatara genome: insights into vertebrate evolution from the sole survivor of an ancient reptilian order

Author

Gemmell, Neil J., primary, Rutherford, Kim, additional, Prost, Stefan, additional, Tollis, Marc, additional, Winter, David, additional, Macey, J. Robert, additional, Adelson, David L., additional, Suh, Alexander, additional, Bertozzi, Terry, additional, Grau, José H., additional, Organ, Chris, additional, Gardner, Paul P., additional, Muffato, Matthieu, additional, Patricio, Mateus, additional, Billis, Konstantinos, additional, Martin, Fergal J, additional, Flicek, Paul, additional, Petersen, Bent, additional, Kang, Lin, additional, Michalak, Pawel, additional, Buckley, Thomas R., additional, Wilson, Melissa, additional, Cheng, Yuanyuan, additional, Miller, Hilary, additional, Schott, Ryan K., additional, Jordan, Melissa, additional, Newcomb, Richard, additional, Arroyo, José Ignacio, additional, Valenzuela, Nicole, additional, Hore, Tim A., additional, Renart, Jaime, additional, Peona, Valentina, additional, Peart, Claire R., additional, Warmuth, Vera M., additional, Zeng, Lu, additional, Kortschak, R. Daniel, additional, Raison, Joy M., additional, Zapata, Valeria Velásquez, additional, Wu, Zhiqiang, additional, Santesmasses, Didac, additional, Mariotti, Marco, additional, Guigó, Roderic, additional, Rupp, Shawn M., additional, Twort, Victoria G., additional, Dussex, Nicolas, additional, Taylor, Helen, additional, Abe, Hideaki, additional, Paterson, James M., additional, Mulcahy, Daniel G., additional, Gonzalez, Vanessa L., additional, Barbieri, Charles G., additional, DeMeo, Dustin P., additional, Pabinger, Stephan, additional, Ryder, Oliver, additional, Edwards, Scott V., additional, Salzberg, Steven L., additional, Mickelson, Lindsay, additional, Nelson, Nicola, additional, Stone, Clive, additional, and Board, Ngatiwai Trust, additional

Published
2019
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47. PHI-base: the pathogen–host interactions database

Author

Urban, Martin, primary, Cuzick, Alayne, additional, Seager, James, additional, Wood, Valerie, additional, Rutherford, Kim, additional, Venkatesh, Shilpa Yagwakote, additional, De Silva, Nishadi, additional, Martinez, Manuel Carbajo, additional, Pedro, Helder, additional, Yates, Andy D, additional, Hassani-Pak, Keywan, additional, and Hammond-Kosack, Kim E, additional

Published
2019
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48. New PomBase Website 2017, Group Leader Survey Summary

Author

Wood, Valerie, Harris, Midori, Lock, Antonia, and Rutherford, Kim

Subjects
Model Organis Database, pombase, user survey
Abstract

PomBase launched a new version of its website on 25th October 2017. Shortly thereafter, 100 fission yeast research group leaders were surveyed to gauge the impact of the site redesign.

Published
2019
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49. ACT: the Artemis comparison tool

Author

Carver, Tim J., Rutherford, Kim M., Berriman, Matthew, Rajandream, Marie-Adele, Barrell, Barclay G., and Parkhill, Julian

Published
2005

50. GeneDB: a resource for prokaryotic and eukaryotic organisms

Author

Hertz-Fowler, Christiane, Peacock, Chris S., Wood, Valerie, Aslett, Martin, Kerhornou, Arnaud, Mooney, Paul, Tivey, Adrian, Berriman, Matthew, Hall, Neil, Rutherford, Kim, Parkhill, Julian, Ivens, Alasdair C., Rajandream, Marie-Adele, and Barrell, Bart

Published
2004

Catalog

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