Julia V. Ponomarenko, Ph.D.
Scientist, Computational Biology
Skaggs School of Pharmacy & Pharmaceutical
2004 – present Senior Research Scientist
Scientific leadership in the development of the 3D structure component of the Immune Epitope Database (IEDB), including development of data ontology and representation format, benchmark datasets, analysis and visualization (EpitopeViewer) tools, annotation of PDB structures and research on 3D structure-based prediction of immune epitopes.
2002 - 2004 Research Scientist
Research on classification of 3D structures of protein DNA-binding protein domains in PDB.
Protein annotation with GO terms based on structural similarity of protein domains.
1997 - 2002 Research Scientist
Institute of Cytology and Genetics,
Research of eukaryotic transcription factor and nucleosome DNA binding sites, related ontologies, data representation, and prediction methods.
Development of databases and analysis tools on protein-DNA binding sites resulted in four public resources: rSNP_Guide, ACTIVITY, SELEX_DB, B-DNA-VIDEO.
Leading the team of 13 curators and programmers working on these resources.
1991 - 1997 Scientific Programmer
Institute of Cytology and Genetics,
Development of the method for protein 3D structure prediction from sequence based on statistics of inter-atomic contacts. Implementation of the method in Fortran; integration of software developed by others for secondary structure and topology prediction.
Development of the method for analysis of DNA conformational features of gene regulatory regions. Implementation of the method in C. Research on TATA-boxes of eukaryotic and prokaryotic promoters.
PUBLICATIONS AND PRESENTATIONS
Thirty four publications in peer-review journals, including Proteins, Bioinformatics, BMC Structural Biology, BMC Bioinformatics, Nucleic Acids Research, Human Mutation, Journal of Molecular Recognition, BMC Immunome Research, and PLOS Biology.
Posters and twenty oral presentations at thirty five bioinformatics conferences, including PSB, ISMB, RECOMB, HUGO, Cold Spring Harbor and other meetings.
Visiting Scientist, Genaissance
Scientific Consultant, GlaxoSmithKline
A reviewer for the journals Bioinformatics, Proteins, Journal of Molecular Biology, Nature Biotechnology, BMC Bioinformatics, BMC Immunology, BMC Structural Biology, Journal of Molecular Recognition, ISMB and RECOMB conferences.
1. Zhang Q, Wang P, Kim Y, Haste-Andersen P, Beaver J, Bourne PE, Bui HH, Buus S, Frankild S, Greenbaum J, Lund O, Lundegaard C, Nielsen M, Ponomarenko J, Sette A, Zhu Z, Peters B. (2008) Immune epitope database analysis resource (IEDB-AR). Nucleic Acids Res.,36 (Web Server issue), W513-518.
Ponomarenko JV, van Regenmortel MHC (2008) B-cell epitope prediction. Structural Bioinformatics, Ed:
5. Greenbaum JA, Andersen PH, Blythe M, Bui HH, Cachau RE, Crowe J, Davies M, Kolaskar AS, Lund O, Morrison S, Mumey B, Ofran Y, Pellequer JL, Pinilla C, Ponomarenko JV, Raghava GP, van Regenmortel MH, Roggen EL, Sette A, Schlessinger A, Sollner J, Zand M, Peters B. (2007) Towards a consensus on datasets and evaluation metrics for developing B-cell epitope prediction tools. J Mol Recognition, 20(2), 75-82.
6. Vita R, Vaughan K, Zarebski L, Salimi N, Fleri W, Grey H, Sathiamurthy M, Mokili J, Bui HH, Bourne PE, Ponomarenko J, de Castro R Jr, Chan RK, Sidney J, Wilson SS, Stewart S, Way S, Peters B, Sette A. (2006) Curation of complex, context-dependent immunological data. BMC Bioinformatics, 7, 341.
7. Peters B, Sidney J, Bourne P, Bui HH, Buus S, Doh G, Fleri W, Kronenberg M, Kubo R, Lund O, Nemazee D, Ponomarenko JV, Sathiamurthy M, Schoenberger S, Stewart S, Surko P, Way S, Wilson S, Sette A. (2005) The design and implementation of the immune epitope data base and analysis resource. Immunogenetics, 57(5), 326-36.
8. Peters B, Sidney J, Bourne P, Bui HH, Buus S, Doh G, Fleri W, Kronenberg M, Kubo R, Lund O, Nemazee D, Ponomarenko JV, Sathiamurthy M, Schoenberger S, Stewart S, Surko P, Way S, Wilson S, Sette A. (2005) The immune epitope database and analysis resource: from vision to blueprint. PLoS Biology, 3(3), e91.
9. Ponomarenko J.V., Bourne P.E., Shindyalov I.N. (2005) Assigning new GO annotations to protein data bank sequences by combining structure and sequence homology. Proteins, 58(4), 855-865.
Ponomarenko JV, Merkulova TI, Orlova
Ponomarenko JV, Orlova GV, Merkulova
TI, Gorshkova EV,
14. Ponomarenko JV, Merkulova TI, Vasiliev GV, Levashova ZB, Orlova GV, Lavryushev SV, Fokin ON, Ponomarenko MP, Frolov AS, Sarai A (2001) rSNP_Guide, a database system for analysis of transcription factor binding to target sequences: application to SNPs and site-directed mutations. Nucleic Acids Research, 29(1), 312-316.
15. Ponomarenko JV, Furman DP, Frolov AS, Podkolodny NL, Orlova GV, Ponomarenko MP, Kolchanov NA, Sarai A (2001) ACTIVITY: a database on DNA/RNA sites activity adapted to apply sequence-activity relationships from one system to another. Nucleic Acids Research, 29, 284-287.
16. Ponomarenko JV, Orlova GV, Ponomarenko MP, Lavryushev SV, Frolov AS, Zybova SV, Kolchanov NA (2000) SELEX_DB: an activated database on selected randomized DNA/RNA sequences addressed to genomic sequence annotation. Nucleic Acids Research, 28, 205-208.
17. Kolchanov NA, Ponomarenko MP, Frolov AS, Ananko EA, Kolpakov FA, E, Ignatieva EV, Podkolodnaya OA, Goryachkovskaya TN, Stepanenko IL, Merkulova TI, Babenko VV, Ponomarenko YuV, Kochetov AV, Podkolodny NL, Vorobiev DV, Lavryushev SV, Grigorovich DA, Kondrakhin YuV, Milanesi L, Wingender E, Solovyev V, Overton GC (1999) Integrated databases and computer systems for studying eukaryotic gene expression. Bioinformatics, 15, 7/8, 669-686.
JV, Ponomarenko MP,
Ponomarenko MP, Ponomarenko JV,
20. Ponomarenko MP, Ponomarenko JV, Frolov AS, Podkolodnaya OA, Vorobyev DG, Kolchanov NA, Overton GC (1999) Oligonucleotide frequency matrices addressed to recognizing functional DNA sites. Bioinformatics, 15, 7/8, 631-643.
21. Ponomarenko MP, Ponomarenko JV, Frolov AS, Podkolodnaya OA, Vorobyev DG, Kolchanov NA, Overton GC (1999) Oligonucleotide frequency matrices addressed to recognizing functional DNA sites. Bioinformatics, 15, 7/8, 631-643.
Ponomarenko MP, Ponomarenko JV, Kel AE,
Kolchanov NA (1997)
Search for DNA conformational features for functional sites. Investigation of
the TATA box. In: “Biocomputing:
proceedings of the 1997 Pacific Symposium” (Altman, R., et al., eds.),