| Primary Expertise |
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| Dr. Nikolskaya works on protein classification and annotation of protein families for the PIRSF project. Her interests and experience are in developing procedures and methodologies for protein annotation, classification, and functional prediction. Before coming to PIR, she has worked at the Clusters of Orthologous groups (COGs) and Conserved Domain Database (CDD) at NCBI. She is also involved in collaboration with the InterPro protein classification database (EBI) and in UniProt project involving functional annotation of Swiss-Prot and TrEMBL sections of UniProtKB. Recent teaching experience includes participation in developing and teaching bioinformatics courses at the advanced undergraduate and graduate levels at Georgetown University, as well as development and teaching of the bioinformatics section of the National Institute of Health Proteomics Workshop.
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| Education |
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B.S.,Biology, St. Petersburg State University,
St. Petersburg, Russia, 1985 |
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M.S., Biology, St. Petersburg State University,
St. Petersburg, Russia, 1987 |
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Ph.D, Genetics,Michigan State University,
East Lansing, MI. 1999 |
| Appointments |
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| 2000–2002 | Protein Classification Analyst, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health |
| 2002–Present | Assistant Professor (Research) and Senior Bioinformatics Scientist, Protein Information Resource, Georgetown University Medical Center, Washington, D.C. |
| Teaching/Workshops |
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| 2002–Present | Assistant Professor (Research) and Senior Protein Scientist, Protein Information Resource, Georgetown University Medical Center, Washington, D.C. |
| 2005 | BCHB 621 Advanced Bioinformatics, Georgetown University - Protein Functional Annotation and Classification Section (lecture and lab) |
| 2003–Present | NIH Proteomics Workshop, Bioinformatics class |
| 2003–Present | BCHB521 Georgetown University - Protein Functional Annotation and Classification Section (lecture and lab) |
| 2000-2002 | Protein Classification Analyst, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health |
| 1992,1995 | Teaching Assistant, Michigan State University Fundamental Genetics (Zoology/Botany 341) |
| 1984–1986 | Instructor, St Petersburg State University, Russia, Biology Program for High School Seniors. |
| Invited Talks |
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| Argonne National Lab. PIRSF protein classification system and its use for protein annotation
Talks at Scientific Conferences, 2005 |
| Standards and Ontologies For Functional Genomics (SOFG) Conference. Complementing Gene Ontology with PIRSF classification-based protein ontology, 2004 |
| University of Bordeaux, France. PIRSF protein classification system and its use for protein annotation, 2004 |
| Annual InterPro Consortium Meeting, Hinxton, UK. PIRSF protein classification system and its use for protein annotation, 2004 |
| UniProt retreat, Antibes, France. PIRSF protein classification system and its use for protein annotation, 2004 |
| NCI, NIH. From Protein Sequence to Function: functional analysis of sequences and protein classification, 2003 |
| University of Bordeaux, France. The COG database: using it to discover novel signaling domains encoded in bacterial genomes, 2002 |
| Publications |
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Nikolskaya, A.N., Arighi, C.N., Huang, H., Barker, W.C. and Wu, C.H. 2006. PIRSF family classification system for protein functional and evolutionary analysis. Evolutionary Bioinformatics Online (in press).
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Mulder, N.J., Apweiler, R., Attwood, T.K., Bairoch, A., Bateman, A., Binns, D., Bradley, P., Bork, P., Bucher, P., Cerutti, L., Copley, R., Courcelle, E., Das, U., Durbin, R., Fleischmann, W., Gough, J., Haft, D., Harte, N., Hulo, N., Kahn, D., Kanapin, A., Krestyaninova, M., Lonsdale, D., Lopez, R., Letunic, I., Madera, M., Maslen, J., McDowall, J., Mitchell, A., Nikolskaya, A.N., Orchard, S., Pagni, M., Ponting, C.P., Quevillon, E., Selengut, J., Sigrist, C.J., Silventoinen, V., Studholme, D.J., Vaughan, R., Wu, C.H. 2005. InterPro, progress and status in 2005. Nucleic Acids Res. 33 Database Issue: D201-5.
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Wu, C.H., Huang, H., Nikolskaya, A.N., Vinayaka, C.R., Chung, S and Zhang, J. Family Classification and Integrative Associative Analysis for Protein Functional Annotation in Bioinformatics: New Research (2005). Nova Publishers, New York.
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Barker, W.C., Mazumder, R., Nikolskaya, A.N. and Wu, C.H. 2005 The PIR superfamily (PIRSF) classification system. In: Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. Proteomics Volume, Dunn, M. J. (Ed.) John Wiley & Sons, Ltd. (In press)
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Wu, C.H., Huang, H., Nikolskaya, A.N., Hu, Z., and Barker, W.C. 2004. The iProClass integrated database for protein functional analysis. Comp. Biol. & Chem. 28, 87-96.
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Apweiler, R., Attwood, T.K., Bairoch, A., Bateman, A., Binns, D., Bradley, P., Bordoli, L., Bucher, P., Courcelle, E., Das, U., Durbin, R., Flegel, V., Fleischmann, W., Gouzy, J., Griffiths-Jones, S., Haft, D., Harte, N., Hulo, N., Kahn, D., Kanapin, A., Krestyaninova, M., Lonsdale, D., Lopez, R., McDowall, J., Mulder, N., Nikolskaya, A.N. et. al. InterPro - prediction of protein families, domains and functional sites. In: Progress in Genome Research, Nova Science Publishers (in press).
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Wu, C.H., Nikolskaya, A.N., Huang, H., Yeh L.-S., Natale, D.A., Vinayaka, C.R., Hu, Z., Mazumder, R., Kumar, S., Kourtesis, P., Ledley, R.S., Suzek, B.E., Arminski, L., Chen, Y., Zhang, J., Cardenas, J.L., Chung, S., Castro-Alvear, J., Dinkov, G. and Barker, W.C. 2004. PIRSF family classification system at the Protein Information Resource. Nucleic Acids Res., 32, D112-114.
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Rogozin, I.B., Babenko, V.I., Fedorova, N.D., Jackson, J.D., Jacobs, A.R., Krylov, D.M., Makarova, K.S., Mazumder, R., Mekhedov, S.L., Mirkin, B.G., Nikolskaya, A.N., Rao, B.S., Smirnov, S., Sorokin, A.V., Sverdlov, A.V., Vasudevan, S., Wolf, Y.I., Yin, J.J., Natale, D.A., Koonin, E.V. 2003. Evolution of eukaryotic gene repertoire and gene structure: discovering the unexpected dynamics of genome evolution. Cold Spring Harb Symp Quant Biol. 2003. 68:293-301.
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Koonin, E.V., Fedorova, N.D., Jackson, J., Jacobs, A., Krylov, M.K., Mazumder, R., Mekhedov, S.L., Nikolskaya, A.N., Rao, B.S., Rogozin, I.B., Smirnov, S., Sorokin, A.V., Vasudevan, S., Wolf, Y.I., Yin, J., Natale, D.A. 2003. A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes. Genome Biol. 200, 5(2):R7
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Tatusov, R.L., Fedorova, N.D., Jackson, J.D., Jacobs, A.R., Kiryutin, B., Koonin, E.V., Krylov, D.M., Mazumder, R., Mekhedov, S.L., Nikolskaya, A.N., Sridhar Rao, B., Smirnov, S., Sverdlov, A.V., Vasudevan, S., Wolf, Y.I., Yin, J.J., and Natale, D.A. 2003. The COG database: an updated version includes eukaryotes. BMC Bioinformatics, 4:41.
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Nikolskaya, A.N., Mulkidjanian, A.Y., Beech, I.B., and Galperin, M.Y. 2003. MASE1 and MASE2: two novel integral membrane sensory domains. J Molec Microbiol Biotechnol, 5(1): 11-16.
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Zhulin, I.B., Nikolskaya, A.N., and Galperin, M.Y. 2003. Common extracellular sensory domains in transmembrane receptors for diverse signal transduction pathways in Bacteria and Archaea. J Bacteriol, 185(1): 285-294.
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Marchler-Bauer, A., Anderson, J.B., DeWeese-Scott, C., Fedorova, N.D., Geer, L.Y., He, S., Hurwitz, D.I., Jackson, J.D., Jacobs, A.R., Lanczycki, C.J., Liebert, C.A., Liu, C., Madej, T., Marchler, G.H., Mazumder, R., Nikolskaya, A.N., Panchenko, A.R., Rao, B.S., Shoemaker, B.A., Simonyan, V., Song, J.S., Thiessen, P.A., Vasudevan, S., Wang, Y., Yamashita, R.A., Yin, J.J., Bryant, S.H. 2003. CDD: a curated Entrez database of conserved domain alignments. Nucleic Acids Res. 31(1): 383-387.
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Chen, J., Anderson, J.B., DeWeese-Scott, C., Fedorova, N.D., Geer, L.Y., He, S., Hurwitz, D.I., Jackson, J.D., Jacobs, A.R., Lanczycki, C.J., Liebert, C.A., Liu, C., Madej, T., Marchler-Bauer, A., Marchler, G.H., Mazumder, R., Nikolskaya, A.N., Rao, B.S., Panchenko, A.R., Shoemaker, B.A., Simonyan, V., Song, J.S., Thiessen, P.A., Vasudevan, S., Wang, Y., Yamashita, R.A., Yin, J.J., Bryant, S.H. 2003. MMDB: Entrez's 3D-structure database. Nucleic Acids Res. 31(1): 474-477.
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Nikolskaya, A.N., and Galperin, M.Y. 2002. A novel type of conserved DNA-binding domain in the transcriptional regulators of the AlgR/AgrA/LytR family. Nucleic Acids Res. 30(11):2453-9.
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Fedorova, N.D., Nikolskaya, A.N., and Galperin, M.Y. 2002. Using genomic context in the annotation of multi-component systems. In: Frontiers in Computational Genomics. Kaiser academic Press, Wymondham, UK
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Galperin, M.Y., Nikolskaya, A.N., and Koonin, E.V. 2001. Novel domains of the prokaryotic two-component signal transduction systems. FEMS Microbiol Lett. 203(1):11-21. Review.
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Pitkin, J.W., Nikolskaya, A., Ahn, J.-H., and Walton, J.D. 2000. Reduced virulence caused by meiotic instability of the Tox2 chromosome of the maize pathogen Cochliobolus carbonum. Molec Plant Microbe Interact 13(1): 80-87.
(note: the first two authors contributed equally to this work)
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Nikolskaya, A. N., Pitkin, J. W., Schaeffer, H. J., Ahn, J.-H., and Walton, J. D. 1998. EXG1p, a novel exo-B-1,3-glucanase from the fungus Cochliobolus carbonum, contains a repeated motif present in other proteins that interact with polysaccharides. Biochimica et Biophysica Acta 1425: 632-636.
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Scott-Craig, J.S., Apel-Birkhold, P.C., Gorlach, J.M., Nikolskaya, A., Pitkin, J.W., Ransom, R. F., Sposato, P., Ahn, J.-H., Tonukari, N.J., Wegener, S., and Walton, J.D. 1998. Cell wall degrading enzymes in HST-producing fungal pathogens. In: Molecular genetics of host-specific toxins in plant disease. Kohmoto, K., and Yoder, O. C. (eds.), pp. 245-252. Kluwer Academic Publishers, The Netherlands.
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Nikolskaya, A.N., Panaccione, D.G., and Walton, J.W. 1995. Identification of peptide synthetase-encoding genes from filamentous fungi producing host-selective phytotoxins or analogs. Gene 165:207-211.
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Revised 03/25/05
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