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Julia V. Ponomarenko, Ph.D. Senior Research
Scientist, Computational Biology Skaggs School of Pharmacy & Pharmaceutical
Science E-mail: jpon@sdsc.edu Video: http://www.scivee.tv/node/5328 EDUCATION
PROFESSIONAL EXPERIENCE 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. SYNERGISTIC ACTIVITIES Visiting Scientist, Visiting Scientist, Genaissance
Pharmaceuticals, Scientific Consultant, GlaxoSmithKline
Pharmaceuticals, 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. SELECTED PUBLICATIONS 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. 2.
Ponomarenko JV, van Regenmortel MHC (2008) B-cell epitope prediction. Structural Bioinformatics, Ed: 3.
Ponomarenko JV, 4.
Beaver JE, 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. 10.
Ponomarenko JV, Merkulova TI, Orlova
GV, 11.
Ponomarenko JV, 12.
Ponomarenko JV, Orlova GV, Merkulova
TI, Gorshkova EV, 13.
Ponomarenko
JV, Orlova
GV, 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. 18.
Ponomarenko
JV, Ponomarenko MP, 19.
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. 22.
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.),
Word Sci. |
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