Works by Natale, Darren A

Results: 38

Computational clustering for viral reference proteomes.

Published in:

Bioinformatics, 2016, v. 32, n. 13, p. 2041, doi. 10.1093/bioinformatics/btw110

By:

Chuming Chen;
Hongzhan Huang;
Mazumder, Raja;
Natale, Darren A.;
McGarvey, Peter B.;
Jian Zhang;
Polson, Shawn W.;
Yuqi Wang;
Wu, Cathy H.

Publication type:

Article

BpForms and BcForms: a toolkit for concretely describing non-canonical polymers and complexes to facilitate global biochemical networks.

Published in:

Genome Biology, 2020, v. 21, n. 1, p. 1, doi. 10.1186/s13059-020-02025-z

By:

Lang, Paul F.;
Chebaro, Yassmine;
Zheng, Xiaoyue;
P. Sekar, John A.;
Shaikh, Bilal;
Natale, Darren A.;
Karr, Jonathan R.

Publication type:

Article

Correction: Toll-Like Receptor Signaling in Vertebrates: Testing the Integration of Protein, Complex, and Pathway Data in the Protein Ontology Framework.

Published in:

PLoS ONE, 2015, v. 10, n. 6, p. 1, doi. 10.1371/journal.pone.0131148

By:

Arighi, Cecilia;
Shamovsky, Veronica;
Masci, Anna Maria;
Ruttenberg, Alan;
Smith, Barry;
Natale, Darren A.;
Wu, Cathy;
D’Eustachio, Peter

Publication type:

Article

Toll-Like Receptor Signaling in Vertebrates: Testing the Integration of Protein, Complex, and Pathway Data in the Protein Ontology Framework.

Published in:

PLoS ONE, 2015, v. 10, n. 4, p. 1, doi. 10.1371/journal.pone.0122978

By:

Arighi, Cecilia;
Shamovsky, Veronica;
Masci, Anna Maria;
Ruttenberg, Alan;
Smith, Barry;
Natale, Darren A.;
Wu, Cathy;
D’Eustachio, Peter

Publication type:

Article

OMIT: Dynamic, Semi-Automated Ontology Development for the microRNA Domain.

Published in:

PLoS ONE, 2014, v. 9, n. 7, p. 1, doi. 10.1371/journal.pone.0100855

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

Publication type:

Article

Representative Proteomes: A Stable, Scalable and Unbiased Proteome Set for Sequence Analysis and Functional Annotation.

Published in:

PLoS ONE, 2011, v. 6, n. 4, p. 1, doi. 10.1371/journal.pone.0018910

By:

Chuming Chen;
Natale, Darren A.;
Finn, Robert D.;
Hongzhan Huang;
Jian Zhang;
Wu, Cathy H.;
Mazumder, Raja

Publication type:

Article

OmniSearch: a semantic search system based on the Ontology for MIcroRNA Target (OMIT) for microRNA-target gene interaction data.

Published in:

Journal of Biomedical Semantics, 2016, v. 7, p. 1, doi. 10.1186/s13326-016-0064-2

By:

Jingshan Huang;
Gutierrez, Fernando;
Strachan, Harrison J.;
Dejing Dou;
Weili Huang;
Smith, Barry;
Blake, Judith A.;
Eilbeck, Karen;
Natale, Darren A.;
Yu Lin;
Bin Wu;
de Silva, Nisansa;
Xiaowei Wang;
Zixing Liu;
Borchert, Glen M.;
Ming Tan;
Ruttenberg, Alan

Publication type:

Article

The Non-Coding RNA Ontology (NCRO): a comprehensive resource for the unification of non-coding RNA biology.

Published in:

Journal of Biomedical Semantics, 2016, v. 7, p. 1, doi. 10.1186/s13326-016-0066-0

By:

Jingshan Huang;
Eilbeck, Karen;
Smith, Barry;
Blake, Judith A.;
Dejing Dou;
Weili Huang;
Natale, Darren A.;
Ruttenberg, Alan;
Jun Huan;
Zimmermann, Michael T.;
Guoqian Jiang;
Yu Lin;
Bin Wu;
Strachan, Harrison J.;
Yongqun He;
Shaojie Zhang;
Xiaowei Wang;
Zixing Liu;
Borchert, Glen M.;
Ming Tan

Publication type:

Article

Protein ontology on the semantic web for knowledge discovery.

Published in:

Scientific Data, 2020, v. 7, n. 1, p. N.PAG, doi. 10.1038/s41597-020-00679-9

By:

Chen, Chuming;
Huang, Hongzhan;
Ross, Karen E.;
Cowart, Julie E.;
Arighi, Cecilia N.;
Wu, Cathy H.;
Natale, Darren A.

Publication type:

Article

A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology.

Published in:

Journal of Biomedical Semantics, 2022, v. 13, n. 1, p. 1, doi. 10.1186/s13326-022-00279-z

By:

He, Yongqun;
Yu, Hong;
Huffman, Anthony;
Lin, Asiyah Yu;
Natale, Darren A.;
Beverley, John;
Zheng, Ling;
Perl, Yehoshua;
Wang, Zhigang;
Liu, Yingtong;
Ong, Edison;
Wang, Yang;
Huang, Philip;
Tran, Long;
Du, Jinyang;
Shah, Zalan;
Shah, Easheta;
Desai, Roshan;
Huang, Hsin-hui;
Tian, Yujia

Publication type:

Article

Perspectives on tracking data reuse across biodata resources.

Published in:

Bioinformatics Advances, 2024, v. 4, n. 1, p. 1, doi. 10.1093/bioadv/vbae057

By:

Ross, Karen E;
Bastian, Frederic B;
Buys, Matt;
Cook, Charles E;
D'Eustachio, Peter;
Harrison, Melissa;
Hermjakob, Henning;
Li, Donghui;
Lord, Phillip;
Natale, Darren A;
Peters, Bjoern;
Sternberg, Paul W;
Su, Andrew I;
Thakur, Matthew;
Thomas, Paul D;
Bateman, Alex;
Consortium, and the UniProt

Publication type:

Article

COVID-19 biomarkers and their overlap with comorbidities in a disease biomarker data model.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 6, p. 1, doi. 10.1093/bib/bbab191

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

Publication type:

Article

Novel sequence feature variant type analysis of the HLA genetic association in systemic sclerosis.

Published in:

Human Molecular Genetics, 2010, v. 19, n. 4, p. 707, doi. 10.1093/hmg/ddp521

By:

Karp, David R.;
Marthandan, Nishanth;
Marsh, Steven G.E.;
Ahn, Chul;
Arnett, Frank C.;
DeLuca, David S.;
Diehl, Alexander D.;
Dunivin, Raymond;
Eilbeck, Karen;
Feolo, Michael;
Guidry, Paula A.;
Helmberg, Wolfgang;
Lewis, Suzanna;
Mayes, Maureen D.;
Mungall, Chris;
Natale, Darren A.;
Peters, Bjoern;
Petersdorf, Effie;
Reveille, John D.;
Smith, Barry

Publication type:

Article

OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies.

Published in:

Database: The Journal of Biological Databases & Curation, 2021, v. 2021, p. 1, doi. 10.1093/database/baab069

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

Publication type:

Article

PIRSitePredict for protein functional site prediction using position-specific rules.

Published in:

Database: The Journal of Biological Databases & Curation, 2019, v. 2019, p. N.PAG, doi. 10.1093/database/baz026

By:

Chen, Chuming;
Wang, Qinghua;
Huang, Hongzhan;
Vinayaka, Cholanayakanahalli R;
Garavelli, John S;
Arighi, Cecilia N;
Natale, Darren A;
Wu, Cathy H

Publication type:

Article

Recent advances in biocuration: Meeting Report from the fifth International Biocuration Conference.

Published in:

2012

By:

Gaudet, Pascale;
Arighi, Cecilia;
Bastian, Frederic;
Bateman, Alex;
Blake, Judith A.;
Cherry, Michael J.;
D’Eustachio, Peter;
Finn, Robert;
Giglio, Michelle;
Hirschman, Lynette;
Kania, Renate;
Klimke, William;
Martin, Maria Jesus;
Karsch-Mizrachi, Ilene;
Munoz-Torres, Monica;
Natale, Darren;
O’Donovan, Claire;
Ouellette, Francis;
Pruitt, Kim D.;
Robinson-Rechavi, Marc

Publication type:

Proceeding

Selective instability of Orc1 protein accounts for the absence of functional origin recognition complexes during the M-G<sub>1</sub> transition in mammals.

Published in:

EMBO Journal, 2000, v. 19, n. 11, p. 2728, doi. 10.1093/emboj/19.11.2728

By:

Natale, Darren A.;
Cong-Jun Li;
Wei-Hsin Sun;
DePamphilis, Melvin L.

Publication type:

Article

Initiation of eukaryotic DNA replication: conservative or liberal?

Published in:

Journal of Cellular Physiology, 2000, v. 184, n. 2, p. 139, doi. 10.1002/1097-4652(200008)184:2<139::AID-JCP1>3.0.CO;2-8

By:

Bogan, Joseph A.;
Natale, Darren A.;
Depamphilis, Melvin L.

Publication type:

Article

The Immune Epitope Database (IEDB): 2024 update.

Published in:

Nucleic Acids Research, 2025, v. 53, n. D1, p. D436, doi. 10.1093/nar/gkae1092

By:

Vita, Randi;
Blazeska, Nina;
Marrama, Daniel;
Members, IEDB Curation Team;
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

Publication type:

Article

InterPro in 2022.

Published in:

Nucleic Acids Research, 2023, v. 51, n. D1, p. D418, doi. 10.1093/nar/gkac993

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

Publication type:

Article

InterPro in 2019: improving coverage, classification and access to protein sequence annotations.

Published in:

Nucleic Acids Research, 2019, v. 47, n. D1, p. D351, doi. 10.1093/nar/gky1100

By:

Mitchell, Alex L;
Attwood, Teresa K;
Babbitt, Patricia C;
Blum, Matthias;
Bork, Peer;
Bridge, Alan;
Brown, Shoshana D;
Chang, Hsin-Yu;
El-Gebali, Sara;
Fraser, Matthew I;
Gough, Julian;
Haft, David R;
Huang, Hongzhan;
Letunic, Ivica;
Lopez, Rodrigo;
Luciani, Aurélien;
Madeira, Fabio;
Marchler-Bauer, Aron;
Mi, Huaiyu;
Natale, Darren A

Publication type:

Article

The Universal Protein Resource (UniProt).

Published in:

Nucleic Acids Research, 2005, v. 33, n. suppl 1, p. d154

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.

Publication type:

Article

UniProt: the Universal Protein knowledgebase.

Published in:

Nucleic Acids Research, 2004, v. 32, n. suppl 1, p. d115

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.

Publication type:

Article

PIRSF: family classification system at the Protein Information Resource.

Published in:

Nucleic Acids Research, 2004, v. 32, n. suppl 1, p. d112

By:

Wu, Cathy H.;
Nikolskaya, Anastasia;
Huang, Hongzhan;
Yeh, Lai‐Su L.;
Natale, Darren A.;
Vinayaka, C. R.;
Hu, Zhang‐Zhi;
Mazumder, Raja;
Kumar, Sandeep;
Kourtesis, Panagiotis;
Ledley, Robert S.;
Suzek, Baris E.;
Arminski, Leslie;
Chen, Yongxing;
Zhang, Jian;
Cardenas, Jorge Louie;
Chung, Sehee;
Castro‐Alvear, Jorge;
Dinkov, Georgi;
Barker, Winona C.

Publication type:

Article

Congruent evolution of different classes of non‐coding DNA in prokaryotic genomes.

Published in:

Nucleic Acids Research, 2002, v. 30, n. 19, p. 4264, doi. 10.1093/nar/gkf549

By:

Rogozin, Igor B.;
Makarova, Kira S.;
Natale, Darren A.;
Spiridonov, Alexey N.;
Tatusov, Roman L.;
Wolf, Yuri I.;
Yin, Jodie;
Koonin, Eugene V.

Publication type:

Article

The COG database: new developments in phylogenetic classification of proteins from complete genomes.

Published in:

Nucleic Acids Research, 2001, v. 29, n. 1, p. 22, doi. 10.1093/nar/29.1.22

By:

Tatusov, Roman L.;
Natale, Darren A.;
Garkavtsev, Igor V.;
Tatusova, Tatiana A.;
Shankavaram, Uma T.;
Rao, Bachoti S.;
Kiryutin, Boris;
Galperin, Michael Y.;
Fedorova, Natalie D.;
Koonin, Eugene V.

Publication type:

Article

The COG database: a tool for genome-scale analysis of protein functions and evolution.

Published in:

Nucleic Acids Research, 2000, v. 28, n. 1, p. 33, doi. 10.1093/nar/28.1.33

By:

Tatusov, Roman L.;
Galperin, Michael Y.;
Natale, Darren A.;
Koonin, Eugene V.

Publication type:

Article

TGF-beta signaling proteins and the Protein Ontology.

Published in:

BMC Bioinformatics, 2009, v. 10, p. 1, doi. 10.1186/1471-2105-10-S5-S3

By:

Arighi, Cecilia N.;
Hongfang Liu;
Natale, Darren A.;
Barker, Winona C.;
Drabkin, Harold;
Blake, Judith A.;
Smith, Barry;
Wu, Cathy H.

Publication type:

Article

Framework for a Protein Ontology.

Published in:

BMC Bioinformatics, 2007, v. 8, p. 1, doi. 10.1186/1471-2105-8-S9-S1

By:

Natale, Darren A.;
Arighi, Cecilia N.;
Barker, Winona C.;
Blake, Judith;
Ti-Cheng Chang;
Zhangzhi Hu;
Hongfang Liu;
Smith, Barry;
Wu, Cathy H.

Publication type:

Article

Computational identification of strain-, species- and genus-specific proteins.

Published in:

BMC Bioinformatics, 2005, v. 6, p. 279, doi. 10.1186/1471-2105-6-279

By:

Mazumder, Raja;
Natale, Darren A.;
Murthy, Sudhir;
Thiagarajan, Rathi;
Wu, Cathy H.

Publication type:

Article

The COG database: an updated version includes eukaryotes.

Published in:

BMC Bioinformatics, 2003, v. 4, p. 41, doi. 10.1186/1471-2105-4-41

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.

Publication type:

Article

GlyGen data model and processing workflow.

Published in:

Bioinformatics, 2020, v. 36, n. 12, p. 3941, doi. 10.1093/bioinformatics/btaa238

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

Publication type:

Article

Independent Evolution of Heavy Metal-Associated Domains in Copper Chaperones and Copper-Transporting ATPases.

Published in:

Journal of Molecular Evolution, 2001, v. 53, n. 6, p. 622, doi. 10.1007/s002390010249

By:

Jordan, I. King;
Natale, Darren A.;
Koonin, Eugene V.;
Galperin, Michael Y.

Publication type:

Article

GlyGen: Computational and Informatics Resources for Glycoscience.

Published in:

Glycobiology, 2020, v. 30, n. 2, p. 72, doi. 10.1093/glycob/cwz080

By:

York, William S;
Mazumder, Raja;
Ranzinger, Rene;
Edwards, Nathan;
Kahsay, Robel;
Aoki-Kinoshita, Kiyoko F;
Campbell, Matthew P;
Cummings, Richard D;
Feizi, Ten;
Martin, Maria;
Natale, Darren A;
Packer, Nicolle H;
Woods, Robert J;
Agarwal, Gaurav;
Arpinar, Sena;
Bhat, Sanath;
Blake, Judith;
Castro, Leyla Jael Garcia;
Fochtman, Brian;
Gildersleeve, Jeffrey

Publication type:

Article

Protein Ontology (PRO): enhancing and scaling up the representation of protein entities.

Published in:

Nucleic Acids Research, 2017, v. 45, n. D1, p. D339, doi. 10.1093/nar/gkw1075

By:

Natale, Darren A.;
Arighi, Cecilia N.;
Blake, Judith A.;
Bona, Jonathan;
Chuming Chen;
Sheng-Chih Chen;
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;
Qinghua Wang;
Jian Zhang

Publication type:

Article

Protein Ontology: a controlled structured network of protein entities.

Published in:

Nucleic Acids Research, 2014, v. 42, n. D1, p. D415, doi. 10.1093/nar/gkt1173

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

Publication type:

Article

The Protein Ontology: a structured representation of protein forms and complexes.

Published in:

Nucleic Acids Research, 2011, v. 39, n. suppl_1, p. D539, doi. 10.1093/nar/gkq907

By:

Natale, Darren A.;
Arighi, Cecilia N.;
Barker, Winona C.;
Blake, Judith A.;
Bult, Carol J.;
Caudy, Michael;
Drabkin, Harold J.;
D’Eustachio, Peter;
Evsikov, Alexei V.;
Huang, Hongzhan;
Nchoutmboube, Jules;
Roberts, Natalia V.;
Smith, Barry;
Zhang, Jian;
Wu, Cathy H.

Publication type:

Article

The Universal Protein Resource (UniProt): an expanding universe of protein information.

Published in:

Nucleic Acids Research, 2006, v. 34, n. suppl 1, p. d187

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

Publication type:

Article