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Darren Natale

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Publications

TOP 3
Karen E Ross; Cecilia N Arighi; Hongzhan Huang; Darren A Natale; Jia Ren; Cathy H Wu
Use of the protein ontology for multi-faceted analysis of biological processes: a case study of the spindle checkpoint.
Carol Bult; Peter D'Eustachio; Harold Drabkin; Alexei Evsikov; Darren A Natale; Natalia Roberts; Alan Ruttenberg; Barry Smith; Cecilia N Arighi; Judith A Blake; Cathy Wu
The representation of protein complexes in the Protein Ontology (PRO).
Chuming Chen; Darren A Natale; Robert D Finn; Hongzhan Huang; Jian Zhang; Cathy H Wu; Raja Mazumder
Representative proteomes: a stable, scalable and unbiased proteome set for sequence analysis and functional annotation.

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All Publications

2013: Karen E Ross; Cecilia N Arighi; Hongzhan Huang; Darren A Natale; Jia Ren; Cathy H Wu
Use of the protein ontology for multi-faceted analysis of biological processes: a case study of the spindle checkpoint.
Frontiers in genetics 2013;4():62.
2011: Carol Bult; Peter D'Eustachio; Harold Drabkin; Alexei Evsikov; Darren A Natale; Natalia Roberts; Alan Ruttenberg; Barry Smith; Cecilia N Arighi; Judith A Blake; Cathy Wu
The representation of protein complexes in the Protein Ontology (PRO).
BMC bioinformatics 2011;12():371.
2011: Chuming Chen; Darren A Natale; Robert D Finn; Hongzhan Huang; Jian Zhang; Cathy H Wu; Raja Mazumder
Representative proteomes: a stable, scalable and unbiased proteome set for sequence analysis and functional annotation.
PloS one 2011;6(4):e18910.
2011: Peter B McGarvey; Jian Zhang; Darren A Natale; Cathy H Wu; Hongzhan Huang
Protein-centric data integration for functional analysis of comparative proteomics data.
Methods in molecular biology (Clifton, N.J.) 2011;694():323-39.
2011: Sona Vasudevan; CR Vinayaka; Darren A Natale; Hongzhan Huang; Robel Y Kahsay; Cathy H Wu
Structure-guided rule-based annotation of protein functional sites in UniProt knowledgebase.
Methods in molecular biology (Clifton, N.J.) 2011;694():91-105.
2011: Darren A Natale; Cecilia N Arighi; Winona C Barker; Judith A Blake; Carol Bult; Michael Caudy; Harold J Drabkin; Peter D'Eustachio; Alexei V Evsikov; Hongzhan Huang; Jules Nchoutmboube; Natalia V Roberts; Barry Smith; Jian Zhang; Cathy H Wu
The Protein Ontology: a structured representation of protein forms and complexes.
Nucleic acids research 2011;39(Database issue):D539-45.
2010: Raja Mazumder; Darren A Natale; Jessica Anne Ecalnir Julio; Lai-Su Yeh; Cathy H Wu
Community annotation in biology.
Biology direct 2010;5():12.
2009: Cecilia N Arighi; Hongfang Liu; Darren A Natale; Winona C Barker; Harold Drabkin; Judith A Blake; Barry Smith; Cathy H Wu
TGF-beta signaling proteins and the Protein Ontology.
BMC bioinformatics 2009;10 Suppl 5():S3.
2007: Darren A Natale; Cecilia N Arighi; Winona C Barker; Judith Blake; Ti-Cheng Chang; Zhangzhi Hu; Hongfang Liu; Barry Smith; Cathy H Wu
Framework for a protein ontology.
BMC bioinformatics 2007;8 Suppl 9():S1.
2006: Cathy H Wu; Rolf Apweiler; Amos Bairoch; Darren A Natale; Winona C Barker; Brigitte Boeckmann; Serenella Ferro; Elisabeth Gasteiger; Hongzhan Huang; Rodrigo Lopez; Michele Magrane; Maria J Martin; Raja Mazumder; Claire O'Donovan; Nicole Redaschi; Baris E Suzek
The Universal Protein Resource (UniProt): an expanding universe of protein information.
Nucleic acids research 2006;34(Database issue):D187-91.
2005: Raja Mazumder; Darren A Natale; Sudhir Murthy; Rathi Thiagarajan; Cathy H Wu
Computational identification of strain-, species- and genus-specific proteins.
BMC bioinformatics 2005;6():279.
2005: Amos Bairoch; Rolf Apweiler; Cathy H Wu; Winona C Barker; Brigitte Boeckmann; Serenella Ferro; Elisabeth Gasteiger; Hongzhan Huang; Rodrigo Lopez; Michele Magrane; Maria J Martin; Darren A Natale; Claire O'Donovan; Nicole Redaschi; Lai-Su L Yeh
The Universal Protein Resource (UniProt).
Nucleic acids research 2005;33(Database issue):D154-9.
2004: Eugene V Koonin; Natalie Fedorova Abrams; John D Jackson; Aviva R Jacobs; Dmitri M Krylov; Kira S Makarova; Raja Mazumder; Sergei L Mekhedov; Anastasia N Nikolskaya; B Sridhar Rao; Igor Rogozin; Sergei Smirnov; Alexander V Sorokin; Alexander V Sverdlov; Sona Vasudevan; Yuri I Wolf; Jodie Yin; Darren A Natale
A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes.
Genome biology 2004;5(2):R7.
2004: Rolf Apweiler; Amos Bairoch; Cathy H Wu; Winona C Barker; Brigitte Boeckmann; Serenella Ferro; Elisabeth Gasteiger; Hongzhan Huang; Rodrigo Lopez; Michele Magrane; Maria J Martin; Darren A Natale; Claire O'Donovan; Nicole Redaschi; Lai-Su L Yeh
UniProt: the Universal Protein knowledgebase.
Nucleic acids research 2004;32(Database issue):D115-9.
2004: Cathy H Wu; Anastasia N Nikolskaya; Hongzhan Huang; Lai-Su L Yeh; Darren A Natale; CR Vinayaka; Zhang-Zhi Hu; Raja Mazumder; Sandeep Kumar; Panagiotis Kourtesis; Robert S Ledley; Baris E Suzek; Leslie Arminski; Yongxing Chen; Jian Zhang; Jorge Louie Cardenas; Sehee Chung; Jorge Castro-Alvear; Georgi Dinkov; Winona C Barker
PIRSF: family classification system at the Protein Information Resource.
Nucleic acids research 2004;32(Database issue):D112-4.
2003: Roman L Tatusov; Natalie Fedorova Abrams; John D Jackson; Aviva R Jacobs; Boris Kiryutin; Eugene V Koonin; Dmitri M Krylov; Raja Mazumder; Sergei L Mekhedov; Anastasia N Nikolskaya; B Sridhar Rao; Sergei Smirnov; Alexander V Sverdlov; Sona Vasudevan; Yuri I Wolf; Jodie Yin; Darren A Natale
The COG database: an updated version includes eukaryotes.
BMC bioinformatics 2003;4():41.
2003: Igor Rogozin; Vladimir N Babenko; Natalie Fedorova Abrams; John D Jackson; Aviva R Jacobs; Dmitri M Krylov; Kira S Makarova; Raja Mazumder; Sergei L Mekhedov; Boris G Mirkin; Anastasia N Nikolskaya; B Sridhar Rao; Sergei Smirnov; Alexander V Sorokin; Alexander V Sverdlov; Sona Vasudevan; Yuri I Wolf; Jodie Yin; Darren A Natale; Eugene V Koonin
Evolution of eukaryotic gene repertoire and gene structure: discovering the unexpected dynamics of genome evolution.
Cold Spring Harbor symposia on quantitative biology 2003;68():293-301.
2002: Igor Rogozin; Kira S Makarova; Darren A Natale; Alexey N Spiridonov; Roman L Tatusov; Yuri I Wolf; Jodie Yin; Eugene V Koonin
Congruent evolution of different classes of non-coding DNA in prokaryotic genomes.
Nucleic acids research 2002;30(19):4264-71.
2002: Alexei I Slesarev; Katja V Mezhevaya; Kira S Makarova; Nikolai Polushin; Olga V Shcherbinina; Vera V Shakhova; Galina I Belova; L Aravind; Darren A Natale; Igor Rogozin; Roman L Tatusov; Yuri I Wolf; Karl O Stetter; Andrei Malykh; Eugene V Koonin; Sergei A Kozyavkin
The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of archaeal methanogens.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(7):4644-9.
2001: Roman L Tatusov; Darren A Natale; I V Garkavtsev; Tatiana Tatusova; Uma Shankavaram; B Sridhar Rao; Boris Kiryutin; Michael Galperin; Natalie Fedorova Abrams; Eugene V Koonin
The COG database: new developments in phylogenetic classification of proteins from complete genomes.
Nucleic acids research 2001;29(1):22-8.
2000: Darren A Natale; Uma Shankavaram; Michael Galperin; Yuri I Wolf; L Aravind; Eugene V Koonin
Towards understanding the first genome sequence of a crenarchaeon by genome annotation using clusters of orthologous groups of proteins (COGs).
Genome biology 2000;1(5):RESEARCH0009.
2000: Darren A Natale; Michael Galperin; Roman L Tatusov; Eugene V Koonin
Using the COG database to improve gene recognition in complete genomes.
Genetica 2000;108(1):9-17.
2000: Roman L Tatusov; Michael Galperin; Darren A Natale; Eugene V Koonin
The COG database: a tool for genome-scale analysis of protein functions and evolution.
Nucleic acids research 2000;28(1):33-6.