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HOME / About / Staff Members / Darren Natale
Darren Natale, Ph.D.
Team Lead, Protein Science, and Research Assistant Professor
Georgetown University Medical Center
dan5@georgetown.edu
Primary Expertise
Dr. Natale ensures the validity of the relationships between proteins classified by sequence similarity. He is responsible for providing these protein classes with names and detailed functional, structural and evolutionary descriptions.

Education
B.S., Recombinant Gene Technology, State University of New York, Fredonia, NY. 1986
Ph.D., Molecular and Cellular Biology, Roswell Park Cancer Institute, SUNY Buffalo, NY. 1993
Post Doctorate, Roche Institute of Molecular Biology, Nutley, NJ. 1996
Post Doctorate, Nat'l Institute of Child Health and Human Dev., National Institutes of Health, Bethesda, MD. 1999

Publications
Protein-centric data integration for functional analysis of comparative proteomics data.
McGarvey PB, Zhang J, Natale DA, Wu CH, Huang H.
Methods Mol Biol. 694:323-39. 2011.
Structure-guided rule-based annotation of protein functional sites in UniProt Knowledgebase.
Vasudevan S, Vinayaka CR, Natale DA, Huang H, Kahsay RY, Wu CH.
Methods Mol Biol. 694:91-105. 2011.
Ongoing and future developments at the Universal Protein Resource.
UniProt Consortium.
Nucleic Acids Res. 39(Database issue):D214-9. 2011.
The Protein Ontology: a structured representation of protein forms and complexes.
Natale DA, Arighi CN, Barker WC, Blake JA, Bult CJ, Caudy M, Drabkin HJ, D'Eustachio P, Evsikov AV, Huang H, Nchoutmboube J, Roberts NV, Smith B, Zhang J, Wu CH.
Nucleic Acids Res. 39(Database issue):D539-45. 2011.
From protein sequences to 3D-structures and beyond: the example of the UniProt knowledgebase.
Hinz U; UniProt Consortium.
Cell Mol Life Sci. 67(7):1049-64. 2010.
Community annotation in biology.
Mazumder R, Natale DA, Julio JA, Yeh LS, Wu CH.
Biol Direct. 5:12. 2010.
Novel sequence feature variant type analysis of the HLA genetic association in systemic sclerosis.
Karp DR, Marthandan N, Marsh SG, Ahn C, Arnett FC, Deluca DS, Diehl AD, Dunivin R, Eilbeck K, Feolo M, Guidry PA, Helmberg W, Lewis S, Mayes MD, Mungall C, Natale DA, Peters B, Petersdorf E, Reveille JD, Smith B, Thomson G, Waller MJ, Scheuermann RH.
Hum Mol Genet. 19(4):707-19. 2010.
Quantitative organelle proteomics of MCF-7 breast cancer cells reveals multiple subcellular locations for proteins in cellular functional processes.
Qattan AT, Mulvey C, Crawford M, Natale DA, Godovac-Zimmermann J.
J Proteome Res. 9(1):495-508. 2010.
The Universal Protein Resource (UniProt) in 2010.
UniProt Consortium.
Nucleic Acids Res. 38(Database issue):D142-8. 2010.
TGF-beta signaling proteins and the Protein Ontology.
Arighi CN, Liu H, Natale DA, Barker WC, Drabkin H, Blake JA, Smith B, Wu CH.
BMC Bioinformatics. 10 Suppl 5:S3. 2009.
InterPro: the integrative protein signature database.
Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Das U, Daugherty L, Duquenne L, Finn RD, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Laugraud A, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, Mistry J, Mitchell A, Mulder N, Natale D, Orengo C, Quinn AF, Selengut JD, Sigrist CJ, Thimma M, Thomas PD, Valentin F, Wilson D, Wu CH, Yeats C.
Nucleic Acids Res. 37(Database issue):D211-5. 2009.
The Universal Protein Resource (UniProt) 2009.
UniProt Consortium.
Nucleic Acids Res. 37(Database issue):D169-74. 2009.
A procedure to recruit members to enlarge protein family databases--the building of UECOG (UniRef-Enriched COG Database) as a model.
Fernandes GR, Barbosa DV, Prosdocimi F, Pena IA, Santana-Santos L, Coelho Junior O, Barbosa-Silva A, Velloso HM, Mudado MA, Natale DA, Faria-Campos AC, Aguiar SC, Ortega JM.
Genet Mol Res. 7(3):910-24. 2008.
Framework for a protein ontology.
Natale DA, Arighi CN, Barker WC, Blake J, Chang TC, Hu Z, Liu H, Smith B, Wu CH.
BMC Bioinformatics. 8 Suppl 9:S1. 2007.
The Universal Protein Resource (UniProt).
UniProt Consortium.
Nucleic Acids Res. 35(Database issue):D193-7. 2007.
The Universal Protein Resource (UniProt): an expanding universe of protein information.
Wu CH, Apweiler R, Bairoch A, Natale DA, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Mazumder R, O'Donovan C, Redaschi N, Suzek B.
Nucleic Acids Res. 34(Database issue):D187-91. 2006.
Computational identification of strain-, species- and genus-specific proteins.
Mazumder R, Natale DA, Murthy S, Thiagarajan R, Wu CH.
BMC Bioinformatics. 6:279. 2005.
Large-scale, classification-driven, rule-based functional annotation of proteins.
Natale DA, Vinayaka CR, Wu CH.
in: Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics, Part 4 Bioinformatics, Section 3 Protein Function and Annotation, Chpater 36. S Subramaniam (Ed.), John Wiley & Sons, Ltd. 2005.
The Universal Protein Resource (UniProt).
Bairoch A, Apweiler R, Wu CH, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Natale DA, O'Donovan C, Redaschi N, Yeh LS.
Nucleic Acids Res. 33(Database issue):D154-9. 2005.
A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes.
Koonin EV, Fedorova ND, Jackson JD, Jacobs AR, Krylov DM, Makarova KS, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Rogozin IB, Smirnov S, Sorokin AV, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA.
Genome Biol. 5(2):R7. 2004.
UniProt: the Universal Protein knowledgebase.
Apweiler R, Bairoch A, Wu CH, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Natale DA, O'Donovan C, Redaschi N, Yeh LS.
Nucleic Acids Res. 32(Database issue):D115-9. 2004.
PIRSF: family classification system at the Protein Information Resource.
Wu CH, Nikolskaya A, Huang H, Yeh LS, Natale DA, Vinayaka CR, Hu ZZ, Mazumder R, Kumar S, Kourtesis P, Ledley RS, Suzek BE, Arminski L, Chen Y, Zhang J, Cardenas JL, Chung S, Castro-Alvear J, Dinkov G, Barker WC.
Nucleic Acids Res. 32(Database issue):D112-4. 2004.
The COG database: an updated version includes eukaryotes.
Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Smirnov S, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA.
BMC Bioinformatics. 4:41. 2003.
Evolution of eukaryotic gene repertoire and gene structure: discovering the unexpected dynamics of genome evolution.
Rogozin IB, Babenko VN, Fedorova ND, Jackson JD, Jacobs AR, Krylov DM, Makarova KS, Mazumder R, Mekhedov SL, Mirkin BG, Nikolskaya AN, Rao BS, Smirnov S, Sorokin AV, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA, Koonin EV.
Cold Spring Harb Symp Quant Biol. 68:293-301. 2003.
Congruent evolution of different classes of non-coding DNA in prokaryotic genomes.
Rogozin IB, Makarova KS, Natale DA, SPIRidonov AN, Tatusov RL, Wolf YI, Yin J, Koonin EV.
Nucleic Acids Res. 30(19):4264-71. 2002.
The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of archaeal methanogens.
Slesarev AI, Mezhevaya KV, Makarova KS, Polushin NN, Shcherbinina OV, Shakhova VV, Belova GI, Aravind L, Natale DA, Rogozin IB, Tatusov RL, Wolf YI, Stetter KO, Malykh AG, Koonin EV, Kozyavkin SA.
Proc Natl Acad Sci U S A. 99(7):4644-9. 2002.
Independent evolution of heavy metal-associated domains in copper chaperones and copper-transporting atpases.
Jordan IK, Natale DA, Koonin EV, Galperin MY.
J Mol Evol. 53(6):622-33. 2001.
The COG database: new developments in phylogenetic classification of proteins from complete genomes.
Tatusov RL, Natale DA, Garkavtsev IV, Tatusova TA, Shankavaram UT, Rao BS, Kiryutin B, Galperin MY, Fedorova ND, Koonin EV.
Nucleic Acids Res. 29(1):22-8. 2001.
Copper chaperones in bacteria: association with copper-transporting ATPases.
Jordan IK, Natale DA, Galperin MY.
Trends Biochem Sci. 25(10):480-1. 2000.
Initiation of eukaryotic DNA replication: conservative or liberal.
Bogan JA, Natale DA, Depamphilis ML.
J Cell Physiol. 184(2):139-50. 2000.
Selective instability of Orc1 protein accounts for the absence of functional origin recognition complexes during the M-G(1) transition in mammals.
Natale DA, Li CJ, Sun WH, DePamphilis ML.
EMBO J. 19(11):2728-38. 2000.
Selective activation of pre-replication complexes in vitro at specific sites in mammalian nuclei.
Li CJ, Bogan JA, Natale DA, DePamphilis ML.
J Cell Sci. 113 ( Pt 5):887-98. 2000.
Using the COG database to improve gene recognition in complete genomes.
Natale DA, Galperin MY, Tatusov RL, Koonin EV.
Genetica. 108(1):9-17. 2000.
Towards understanding the first genome sequence of a crenarchaeon by genome annotation using clusters of orthologous groups of proteins (COGs).
Natale DA, Shankavaram UT, Galperin MY, Wolf YI, Aravind L, Koonin EV.
Genome Biol. 1(5):RESEARCH0009. 2000.
The COG database: a tool for genome-scale analysis of protein functions and evolution.
Tatusov RL, Galperin MY, Natale DA, Koonin EV.
Nucleic Acids Res. 28(1):33-6. 2000.
A specialized version of the HD hydrolase domain implicated in signal transduction.
Galperin MY, Natale DA, Aravind L, Koonin EV.
J Mol Microbiol Biotechnol. 1(2):303-5. 1999.
Absence of an unusual densely methylated island at the hamster dhfr ori-beta.
Rein T, Natale DA, Gärtner U, Niggemann M, DePamphilis ML, Zorbas H.
J Biol Chem. 272(15):10021-9. 1997.
Ease of DNA unwinding is a conserved property of yeast replication origins.
Natale DA, Umek RM, Kowalski D.
Nucleic Acids Res. 21(3):555-60. 1993.
DNA helical stability accounts for mutational defects in a yeast replication origin.
Natale DA, Schubert AE, Kowalski D.
Proc Natl Acad Sci U S A. 89(7):2654-8. 1992.
Stable DNA unwinding, not breathing, accounts for single-strand-specific nuclease hypersensitivity of specific A+T-rich sequences.
Kowalski D, Natale DA, Eddy MJ.
Proc Natl Acad Sci U S A. 85(24):9464-8. 1988.


Revised 04/06/2011

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