Search Results - "Natale, Darren"

InterPro in 2022 by Paysan-Lafosse, Typhaine, Blum, Matthias, Chuguransky, Sara, Grego, Tiago, Pinto, Beatriz Lázaro, Salazar, Gustavo A, Bileschi, Maxwell L, Bork, Peer, Bridge, Alan, Colwell, Lucy, Gough, Julian, Haft, Daniel H, Letunić, Ivica, Marchler-Bauer, Aron, Mi, Huaiyu, Natale, Darren A, Orengo, Christine A, Pandurangan, Arun P, Rivoire, Catherine, Sigrist, Christian J A, Sillitoe, Ian, Thanki, Narmada, Thomas, Paul D, Tosatto, Silvio C E, Wu, Cathy H, Bateman, Alex

“…The InterPro database (https://www.ebi.ac.uk/interpro/) provides an integrative classification of protein sequences into families, and identifies functionally…”
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OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies by Jackson, Rebecca, Matentzoglu, Nicolas, Overton, James A, Vita, Randi, Balhoff, James P, Buttigieg, Pier Luigi, Carbon, Seth, Courtot, Melanie, Diehl, Alexander D, Dooley, Damion M, Duncan, William D, Harris, Nomi L, Haendel, Melissa A, Lewis, Suzanna E, Natale, Darren A, Osumi-Sutherland, David, Ruttenberg, Alan, Schriml, Lynn M, Smith, Barry, Stoeckert, Jr, Christian J, Vasilevsky, Nicole A, Walls, Ramona L, Zheng, Jie, Mungall, Christopher J, Peters, Bjoern

“…Biological ontologies are used to organize, curate and interpret the vast quantities of data arising from biological experiments. While this works well when…”
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Protein Ontology (PRO): enhancing and scaling up the representation of protein entities by Natale, Darren A, Arighi, Cecilia N, Blake, Judith A, Bona, Jonathan, Chen, Chuming, Chen, Sheng-Chih, Christie, Karen R, Cowart, Julie, D'Eustachio, Peter, Diehl, Alexander D, Drabkin, Harold J, Duncan, William D, Huang, Hongzhan, Ren, Jia, Ross, Karen, Ruttenberg, Alan, Shamovsky, Veronica, Smith, Barry, Wang, Qinghua, Zhang, Jian, El-Sayed, Abdelrahman, Wu, Cathy H

“…The Protein Ontology (PRO; http://purl.obolibrary.org/obo/pr) formally defines and describes taxon-specific and taxon-neutral protein-related entities in three…”
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BpForms and BcForms: a toolkit for concretely describing non-canonical polymers and complexes to facilitate global biochemical networks by Lang, Paul F, Chebaro, Yassmine, Zheng, Xiaoyue, P Sekar, John A, Shaikh, Bilal, Natale, Darren A, Karr, Jonathan R

“…Non-canonical residues, caps, crosslinks, and nicks are important to many functions of DNAs, RNAs, proteins, and complexes. However, we do not fully understand…”
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Representative proteomes: a stable, scalable and unbiased proteome set for sequence analysis and functional annotation by Chen, Chuming, Natale, Darren A, Finn, Robert D, Huang, Hongzhan, Zhang, Jian, Wu, Cathy H, Mazumder, Raja

“…The accelerating growth in the number of protein sequences taxes both the computational and manual resources needed to analyze them. One approach to dealing…”
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COVID-19 biomarkers and their overlap with comorbidities in a disease biomarker data model by Gogate, Nikhita, Lyman, Daniel, Bell, Amanda, Cauley, Edmund, Crandall, Keith A, Joseph, Ashia, Kahsay, Robel, Natale, Darren A, Schriml, Lynn M, Sen, Sabyasach, Mazumder, Raja

“…In response to the COVID-19 outbreak, scientists and medical researchers are capturing a wide range of host responses, symptoms and lingering postrecovery…”
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Universal Protein Resource (UniProt): an expanding universe of protein information by Wu, Cathy H, Apweiler, Rolf, Bairoch, Amos, Natale, Darren A, Barker, Winona C, Boeckmann, Brigitte, Ferro, Serenella, Gasteiger, Elisabeth, Huang, Hongzhan, Lopez, Rodrigo, Magrane, Michele, Martin, Maria J, Mazumder, Raja, O'Donovan, Claire, Redaschi, Nicole, Suzek, Baris

“…The Universal Protein Resource (UniProt) provides a central resource on protein sequences and functional annotation with three database components, each…”
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The Immune Epitope Database (IEDB): 2024 update by Vita, Randi, Blazeska, Nina, Marrama, Daniel, Shackelford, Deborah, Zalman, Leora, Foos, Gabriele, Zarebski, Laura, Chan, Kenneth, Reardon, Brian, Fitzpatrick, Sidne, Busse, Matthew, Coleman, Sara, Sedwick, Caitlin, Edwards, Lindy, MacFarlane, Catriona, Ennis, Marcus, Duesing, Sebastian, Bennett, Jason, Greenbaum, Jason, De Almeida Mendes, Marcus, Mahita, Jarjapu, Wheeler, Daniel K, Cantrell, Jason R, Overton, James A, Natale, Darren A, Sette, Alessandro, Peters, Bjoern

“…Abstract Over the past 20 years, the Immune Epitope Database (IEDB, iedb.org) has established itself as the foremost resource for immune epitope data. The IEDB…”
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The COG database: an updated version includes eukaryotes by Tatusov, Roman L, Fedorova, Natalie D, Jackson, John D, Jacobs, Aviva R, Kiryutin, Boris, Koonin, Eugene V, Krylov, Dmitri M, Mazumder, Raja, Mekhedov, Sergei L, Nikolskaya, Anastasia N, Rao, B Sridhar, Smirnov, Sergei, Sverdlov, Alexander V, Vasudevan, Sona, Wolf, Yuri I, Yin, Jodie J, Natale, Darren A

“…The availability of multiple, essentially complete genome sequences of prokaryotes and eukaryotes spurred both the demand and the opportunity for the…”
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UniProt: the Universal Protein knowledgebase by Apweiler, Rolf, Bairoch, Amos, Wu, Cathy H., Barker, Winona C., Boeckmann, Brigitte, Ferro, Serenella, Gasteiger, Elisabeth, Huang, Hongzhan, Lopez, Rodrigo, Magrane, Michele, Martin, Maria J., Natale, Darren A., O’Donovan, Claire, Redaschi, Nicole, Yeh, Lai‐Su L.

“…To provide the scientific community with a single, centralized, authoritative resource for protein sequences and functional information, the Swiss‐Prot, TrEMBL…”
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The Universal Protein Resource (UniProt) by Bairoch, Amos, Apweiler, Rolf, Wu, Cathy H., Barker, Winona C., Boeckmann, Brigitte, Ferro, Serenella, Gasteiger, Elisabeth, Huang, Hongzhan, Lopez, Rodrigo, Magrane, Michele, Martin, Maria J., Natale, Darren A., O'Donovan, Claire, Redaschi, Nicole, Yeh, Lai-Su L.

“…The Universal Protein Resource (UniProt) provides the scientific community with a single, centralized, authoritative resource for protein sequences and…”
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GlyGen data model and processing workflow by Kahsay, Robel, Vora, Jeet, Navelkar, Rahi, Mousavi, Reza, Fochtman, Brian C, Holmes, Xavier, Pattabiraman, Nagarajan, Ranzinger, Rene, Mahadik, Rupali, Williamson, Tatiana, Kulkarni, Sujeet, Agarwal, Gaurav, Martin, Maria, Vasudev, Preethi, Garcia, Leyla, Edwards, Nathan, Zhang, Wenjin, Natale, Darren A, Ross, Karen, Aoki-Kinoshita, Kiyoko F, Campbell, Matthew P, York, William S, Mazumder, Raja

“…Abstract Summary Glycoinformatics plays a major role in glycobiology research, and the development of a comprehensive glycoinformatics knowledgebase is…”
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OMIT: dynamic, semi-automated ontology development for the microRNA domain by Huang, Jingshan, Dang, Jiangbo, Borchert, Glen M, Eilbeck, Karen, Zhang, He, Xiong, Min, Jiang, Weijian, Wu, Hao, Blake, Judith A, Natale, Darren A, Tan, Ming

“…As a special class of short non-coding RNAs, microRNAs (a.k.a. miRNAs or miRs) have been reported to perform important roles in various biological processes by…”
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The InterPro protein families and domains database: 20 years on by Blum, Matthias, Chang, Hsin-Yu, Chuguransky, Sara, Grego, Tiago, Kandasaamy, Swaathi, Mitchell, Alex, Nuka, Gift, Paysan-Lafosse, Typhaine, Qureshi, Matloob, Raj, Shriya, Richardson, Lorna, Salazar, Gustavo A, Williams, Lowri, Bork, Peer, Bridge, Alan, Gough, Julian, Haft, Daniel H, Letunic, Ivica, Marchler-Bauer, Aron, Mi, Huaiyu, Natale, Darren A, Necci, Marco, Orengo, Christine A, Pandurangan, Arun P, Rivoire, Catherine, Sigrist, Christian J A, Sillitoe, Ian, Thanki, Narmada, Thomas, Paul D, Tosatto, Silvio C E, Wu, Cathy H, Bateman, Alex, Finn, Robert D

“…Abstract The InterPro database (https://www.ebi.ac.uk/interpro/) provides an integrative classification of protein sequences into families, and identifies…”
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A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes by Koonin, Eugene V, Fedorova, Natalie D, Jackson, John D, Jacobs, Aviva R, Krylov, Dmitri M, Makarova, Kira S, Mazumder, Raja, Mekhedov, Sergei L, Nikolskaya, Anastasia N, Rao, B Sridhar, Rogozin, Igor B, Smirnov, Sergei, Sorokin, Alexander V, Sverdlov, Alexander V, Vasudevan, Sona, Wolf, Yuri I, Yin, Jodie J, Natale, Darren A

“…Sequencing the genomes of multiple, taxonomically diverse eukaryotes enables in-depth comparative-genomic analysis which is expected to help in reconstructing…”
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Integrative annotation and knowledge discovery of kinase post-translational modifications and cancer-associated mutations through federated protein ontologies and resources by Huang, Liang-Chin, Ross, Karen E., Baffi, Timothy R., Drabkin, Harold, Kochut, Krzysztof J., Ruan, Zheng, D’Eustachio, Peter, McSkimming, Daniel, Arighi, Cecilia, Chen, Chuming, Natale, Darren A., Smith, Cynthia, Gaudet, Pascale, Newton, Alexandra C., Wu, Cathy, Kannan, Natarajan

“…Many bioinformatics resources with unique perspectives on the protein landscape are currently available. However, generating new knowledge from these resources…”
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UniRule: a unified rule resource for automatic annotation in the UniProt Knowledgebase by MacDougall, Alistair, Volynkin, Vladimir, Saidi, Rabie, Poggioli, Diego, Zellner, Hermann, Hatton-Ellis, Emma, Joshi, Vishal, O’Donovan, Claire, Orchard, Sandra, Auchincloss, Andrea H, Baratin, Delphine, Bolleman, Jerven, Coudert, Elisabeth, de Castro, Edouard, Hulo, Chantal, Masson, Patrick, Pedruzzi, Ivo, Rivoire, Catherine, Arighi, Cecilia, Wang, Qinghua, Chen, Chuming, Huang, Hongzhan, Garavelli, John, Vinayaka, C R, Yeh, Lai-Su, Natale, Darren A, Laiho, Kati, Martin, Maria-Jesus, Renaux, Alexandre, Pichler, Klemens

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The InterPro protein families database: the classification resource after 15 years by Mitchell, Alex, Chang, Hsin-Yu, Daugherty, Louise, Fraser, Matthew, Hunter, Sarah, Lopez, Rodrigo, McAnulla, Craig, McMenamin, Conor, Nuka, Gift, Pesseat, Sebastien, Sangrador-Vegas, Amaia, Scheremetjew, Maxim, Rato, Claudia, Yong, Siew-Yit, Bateman, Alex, Punta, Marco, Attwood, Teresa K, Sigrist, Christian J A, Redaschi, Nicole, Rivoire, Catherine, Xenarios, Ioannis, Kahn, Daniel, Guyot, Dominique, Bork, Peer, Letunic, Ivica, Gough, Julian, Oates, Matt, Haft, Daniel, Huang, Hongzhan, Natale, Darren A, Wu, Cathy H, Orengo, Christine, Sillitoe, Ian, Mi, Huaiyu, Thomas, Paul D, Finn, Robert D

“…The InterPro database (http://www.ebi.ac.uk/interpro/) is a freely available resource that can be used to classify sequences into protein families and to…”
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Tutorial on Protein Ontology Resources by Arighi, Cecilia N, Drabkin, Harold, Christie, Karen R, Ross, Karen E, Natale, Darren A

“…The Protein Ontology (PRO) is the reference ontology for proteins in the Open Biomedical Ontologies (OBO) foundry and consists of three sub-ontologies…”
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Protein Ontology: a controlled structured network of protein entities by Natale, Darren A, Arighi, Cecilia N, Blake, Judith A, Bult, Carol J, Christie, Karen R, Cowart, Julie, D'Eustachio, Peter, Diehl, Alexander D, Drabkin, Harold J, Helfer, Olivia, Huang, Hongzhan, Masci, Anna Maria, Ren, Jia, Roberts, Natalia V, Ross, Karen, Ruttenberg, Alan, Shamovsky, Veronica, Smith, Barry, Yerramalla, Meher Shruti, Zhang, Jian, AlJanahi, Aisha, Çelen, Irem, Gan, Cynthia, Lv, Mengxi, Schuster-Lezell, Emily, Wu, Cathy H

“…The Protein Ontology (PRO; http://proconsortium.org) formally defines protein entities and explicitly represents their major forms and interrelations. Protein…”
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