Curriculum Vitae of Andrey A. Ptitsyn, Ph.D.

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Andrey A. Ptitsyn, Ph.D.
CURRICULUM VITAE

INSTITUTE ADDRESS: Colorado State University

Campus delivery 1682
Fort Collins CO 80523
TELEPHONE: (970) 491 0878
FAX: (970) 491-1815
E-MAIL: Andrey.Ptitsyn@colostate.edu
WWW: http://lamar.colostate.edu/~ptitsyn/
CURRENT POSITION: Assistant Professor,
CSU Center for Bioinformatics

EDUCATION
Ph.D. in Bioinformatics, 2001, University of the Western Cape,
Cape Town, South Africa.
Thesis title: "High-performance algorithms for EST clustering".
Master of Science in Biology (special training in ecology and
mathematical biology), 1990, Novosibirsk, Novosibirsk State
University, Russia.
Thesis title: "Computer modeling of biomass flow in ecosystems
incorporating helminthes with complex life cycle"
Long-range wire connection specialist. 1984 - 1986 Army Signals
School, Poltava, Ukraine.
Undergraduate student, 1983 - 1984 Gorky State University, Biology
Department, Russia.

EXPERIENCE
Colorado State University
Time: 2006 - current
Position: Assistant Professor, Special research faculty
Responsibilities: Development of the Center for Bioinformatics

Pennington Biomedical Research Center
Time: 2001 - 2006
Position: Assistant Professor, Research track
Responsibilities: Development of an independent research program
in computational biology, assisting the other research program in
bioinformatics, assistance in building of bioinformatics
facilities at the Pennington Center.

Genomics Institute of the Novartis Research Foundation
Time: 2000 - 2001
Position: Bioinformaticist
Responsibilities: Development of algorithms and tools for analysis
of genomic data, analysis of microarray data.

South African National Bioinformatics Institute
Time: 1997 - 2000
Position: Senior computer programmer, National Bioinformatics
Server Manager.
Responsibilities: Installation and running the SA National WWW
server for bioinformatics. Development of algorithms and software
tools for bioinformatics server. Scientific research in
bioinformatics.

Institute of Cytology and Genetics, Siberian Branch, USSR
Academy of Sciences
Time: 1996 - 1997
Position: Group Leader and Senior Researcher.
Responsibilities: Leading a small group developing tools for DNA
and protein sequence analysis. Design, implementation and
management of LAN for the institute. Consulting on LAN and
Internet. Determining the needs of the institute in the areas of
IT, communications and computing; development of the appropriate
solution and overseeing its implementation. Research in
computational biology, both independent and in collaboration in
experimental teams.

Time: 1993 - 1996
Position: Researcher at the laboratory of Theoretical
Molecular Genetics
Responsibilities: Scientific programming and research. Managing
independent research and software development projects. Managing
local network in the laboratory.

Time: 1992 - 1993
Position: Junior researcher at the laboratory Of Theoretical
Molecular Genetics.
Responsibilities: Scientific programming and research it a team.
Participation in software projects design.

Time: 1990 - 1992
Position: Scientific Programmer, full time
Responsibilities: Scientific programming and research in a team.
Time: 1988 - 1990
Position: Scientific Programmer, part time.
Responsibilities: Scientific programming in research team

PROFESSIONAL ACTIVITY
1990-current Development of independent research projects in
Computational Biology, Bioinformatics and Biomedical Science.
1997 - Russian Foundation for Basic Research Grant for the
development of Siberian Regional Genome Informatics Server
(largest RFBR grant in the institute)
1997 - Visiting researcher at the San Diego Supercomputer Center,
San Diego, CA, USA.
1991 - 1997 Scientific research on the All-Union (later Russian
National) Scientific and Technological Project "HUMAN GENOME"
(Section "Informatics").
1996 - Visiting researcher at the Max Plank Institute for
Molecular Genetics, Berlin, Germany.
1993 - 1997 Computer Networking and System Integration in the
biological research center, Novosibirsk.
1993, 1994 - Visiting researcher at the Institute for Advanced
Biomedical Technologies, Milan, Italy.
1989 - 1993 Development of educational software for Novosibirsk
State University.
2006 - organized 3rd annual MCBIOS Conference in Baton Rouge,
Louisiana.

AREA OF SCIENTIFIC INTERESTS:

Computational Biology, Bioinformatics, Systems Biology. Circadian
oscillation in biological pathways. Etiology of metabolic
syndrome. Algorithm development. High-performance computing.
Sequences analysis. Genome assembly and annotation. EST
clustering. Gene expression analysis, microarray data analysis.
Cluster analysis of biological data. Gene structure and
regulation, genome organization.

SYNERGISTIC ACTIVITIES

* Developed and implemented the first prototype of integrated
system for automatic annotation of genomic sequence fragments
which pipelined separate applications, integrated their results
into an object-oriented database and visualized using interactive
graphic interface (1993-1994)
* Designed and implemented campus-size computer network for the
largest biological research institute in Siberia (Inst. of
Cytology and Genetics, Novosibirsk), including web portals,
central databases, web-based bioinformatics applications, email
and file exchange services (1995-1996)
* Contributed to the development and support of the South
African National Bioinformatics Service, South African National
Node of EMBNet (hosted by formally coloreds-only University of
Western Cape), including support and application development for
the first high-performance bio-computing facility on the African
continent (1997-2000).
* Initiated and led research projects in collaboration with
experimental biologists, which resulted in discovery of novel
molecular mechanisms of insulin resistance in type II diabetes and
discovery of the baseline circadian oscillation in all mammalian
genes; both discoveries were featured by the national and
international news agencies (2005-2007)
* Contributing to the development of Bioinformatics and Systems
Biology capacity at the Colorado State University and Rocky
Mountain Region in general, which includes Bioinformatics core
service, bio-computing facilities, bioinformatics analysis
supplement (1-3 lectures) to a number of "omics" courses taught at
different departments, education of faculty through short courses
and seminars, adding bioinformatics component for multiple
collaborative research projects and grant applications, connecting
individual PIs across colleges and departments to each other and
core facilities (genomics, proteomics, biostatistics) through
experiment planning, data integration and interpretation, etc.
(current).
PROGRAMMING LANGUAGES
C/C++ (preferred)

Assembler (PDP, VAX, Intel x86), Fortran, Pascal, Java, Perl,
HTML/CGI, MPI

LANGUAGES SPOKEN

Russian (native)
English (fluent)
Italian (rarely exercised)

PUBLICATIONS

Smirnova N.P., Ptitsyn A.A., Austin K.J., Bielefeldt-Ohmann H., Van Campen H., Han H., van
Olphen A.L., Hansen T.R. Persistent fetal infection with bovine viral diarrhea virus differentially
affects maternal blood cell signal transduction pathways. Physiological Genomics, 2009, v 36, pp
129-139.

Yossi Gafni, Andrey Ptitsyn, Yoram Zilberman, Gadi Pelled, Jeffrey Gimble, Dan Gazit,
Circadian Rhythm of Osteocalcin in the Maxillomandibular Complex. J Dent Res. 2009
Jan;88(1):45-50

Smirnova N.P., Ptitsyn A.A., Austin K.J., Bielefeldt-Ohmann H., Van Campen H., Hansen T.R.
Fetal persistent infection with bovine viral diarrhea virus causes down-regulation of T cell receptor
and CXCR4 pathways in blood of cows. Journal of Leukocyte Biology, 2008. Supplement:
Leukocytes: Tissue interactions, Homeostasis, and Host Defense. 41st Annual Meeting of the
Society for Leukocyte Biology, Denver, 2008, p. 40

Andrey Ptitsyn Comprehensive analysis of circadian oscillation in plant transcriptome BMC
Bioinformatics 2008, 9(Suppl 9):S18

Andrey Ptitsyn, Michael M. Weil, Douglas Thamm Systems biology approach to identification of
biomarkers for metastatic progression in cancer. BMC Bioinformatics 2008, 9(Suppl 9):S8

Ptitsyn A (2008) Stochastic Resonance Reveals "Pilot Light" Expression in Mammalian Genes.
PLoS ONE 3(3): e1842. doi:10.1371/journal.pone.0001842

Ptitsyn AA, Gimble JM. Analysis of circadian pattern reveals tissue-specific alternative
transcription in leptin signaling pathway. BMC Bioinformatics. 2007 Nov 1;8 Suppl 7:S15.

Ptitsyn, A., Zvonic, S, Gimble, J., Digital signal processing reveals circadian baseline oscillation in
majority of mammalian genes. PLoS Comput Biol. 2007 Jun 15;3(6):e120. Editor's picks, most
viewed

Adrian M. Stutz, Jaroslaw Staszkiewicz, Andrey Ptitsyn, George Argyropoulos Circadian
Expression of genes regulating food intake Obesity (Silver Spring). 2007 Mar;15(3):607-15.

Ptitsyn A, Hulver M, Cefalu W, York D, Smith SR. Unsupervised clustering of gene expression
data points at hypoxia as possible trigger for metabolic syndrome. BMC Genomics 2006, 7:318 (19
Dec 2006) Highly accessed.

Jonathan D Wren, Yuriy Gusev, Andrey Ptitsyn and Stephen Winters-Hilt Proceedings of the
Third Annual Conference of the MidSouth Computational Biology and Bioinformatics Society
BMC Bioinformatics 2006, 7(Suppl 2):S1

Andrey A. Ptitsyn, Sanjin Zvonic, Jeffrey M. Gimble Permutation test for periodicity in short time
series data BMC Bioinformatics 2006, 7(Suppl 2):S10

Andrey A. Ptitsyn, Sanjin Zvonic, Steven A. Conrad, L. Keith Scott, Randall L. Mynatt, and
Jeffrey M. Gimble Circadian Clocks are Resounding in Peripheral Tissues. PLoS Comput Biol.
2(3): e16. 2006

Sanjin Zvonic, Andrey A. Ptitsyn, Steven A. Conrad, L. Keith Scott, Z. Elizabeth Floyd, Gail
Kilroy, Xiying Wu, Brian C. Goh, Randall L. Mynatt, Jeffrey M. Gimble Characterization of
Peripheral Circadian Clocks in Adipose Tissues. Diabetes. 2006 Apr;55(4):962-70.

Ptitsyn, A. Hide W. CLU: a new algorithm for EST clustering, BMC Bioinformatics. 2005 Jul 15;6
Suppl. 2:S3.

Hide, W., Ptitsyn, A. What is an EST? ENCYCLOPEDIA OF GENETICS, GENOMICS,
PROTEOMICS & BIOINFORMATICS 2005 Wiley

Jennings, S., Ptitsyn, A., Wilkins, D., Bruhn, R., Slikker, W., Wren, J. Regional Societies:
Fostering Competitive Research Through Virtual Infrastructures, PLoS Biology 2004
Dec.2(12):2039-40.

Ptitsyn, A. Class Discovery Analysis of the Lung Cancer Gene Expression Data, DNA and Cell
Biology, 2004 Oct;23(10):715-21

Smith, S., Ptitsyn, A., Graunke, D., Xie, H., Koza, R., Solving Clinical Problems in Nutrition
Research with Microarrays Genomics and Proteomics in Nutrition. Marcel Dekker 2004.

Ptitsyn A. Topological adjustments to the Genechip expression values. Methods of Microarray
Analysis III. Kluwer Acad. Publishers 2003. ISBN 1-4020-7582-0

Smith, S., Ptitsyn, A.,Xie, H. Perils, pitfalls and promise: expression profiling to diagnose obesity
subtypes. Progress in Obesity Research John Libbey Eurotext Ltd, 2003, pp. 342-347.

Gamieldien J, Ptitsyn A, Hide W. Eukaryotic genes in Mycobacterium tuberculosis could have a
role in pathogenesis and immunomodulation. Trends Genet. 2002 Jan;18(1):5-8

Miller RT, Christoffels AG, Gopalakrishnan C, Burke J, Ptitsyn AA, Broveak TR, Hide WA A
comprehensive approach to clustering of expressed human gene sequence: the sequence tag
alignment and consensus knowledge base. Genome Res 1999 Nov;9(11):1143-55

Frolov AS, Lavriushev SV, Grigorovich DA, Kel AE, Ptitsyn AA, Kolchanov NA, Podkolodnyi
NL, Solov'ev VV, Milanesi L, Bourne P, et al. WWWMGS: an integrated server for molecular-
genetic studies Biofizika 1999 Sep-Oct; 44(5):832-6 (in Russian)

Fedorova EV, Rogozin IB, Ptitsyn AA, Cheriaukene OV, Kaftanovskaia EM The isolation and
analysis of the highly repetitive DNA from the argali Tsitol. Genet. 1998 Sep-Oct;32(5):67-74 (in
Russian)

A. Kel, A. Ptitsyn, V. Babenko, S. Meier-Ewert and H. Lehrach, A genetic algorithm for designing
gene family-specific oligonucleotide sets used for hybridization: the G protein-coupled receptor
protein superfamily, Bioinformatics, v.14 no. 3 (1998) pp. 259-271;
E.I.Jantsen, A.A.Ptitsyn, M.L.Filipenko, O.A. Baturina, N.P.Mertvetsov, Computer analysis of
nucleotide sequences from the family of interspersed repetitive elements MER1 - another
oligonucleotide primer for the PCR assay of human DNA. Genetika. 1997 Feb; 33(2):243-8. (in
Russian).

Gruntenko NE, Kochetov AV, Makarova KS, Mishin VP, Lukasheva VV, Ptitsyn AA, Kokoza VA
Gene Nc73EF of Drosophila melanogaster encodes a protein highly homologous to E1 subunit of
human 2-oxoglutarate dehydrogenase (in Russian) Genetika 1998 Jan;34(1):32-7

A. A. Ptitsyn, I. B. Rogozin, D. A. Grigorovich, V. B. Strelets, A. E. Kel, L. Milanesi, and N. A.
Kolchanov, AutoGene: A Computer System for Nucleotide Sequence Analysis, Molekulyarnaya
Biologiya, v.30 no.2 (1996) pp.436-445;
Ptitsyn, A.A., Grigorovich D.A., Object-oriented data handler for the sequence analysis software
development, Comp. Appl. Biosci. V.11 no. 6 (1995) pp. 583-589;

Strelets, V.B., Ptitsyn, A.A., Milanesi, L., Lim, H.A. (1994) Data bank homology search algorithm
with linear computation complexity. Comp. Appl. Biosci., v.10, n. 3 (1994), pp. 319-322;

Ptitsyn, A.A., Strelets, V.B., Rogozin, I.B., Kel, A.E., Milanesi L., Kolchanov, N.A. "The
AutoGene v1.0: a computer system for automatic molecular genetic analysis", Novosibirsk, 47 pp.
1994;

SCIENTIFIC CONFERENCES

1990 -International Symposium "Modelling and Computer Methods in Molecular
Biology and Genetics", Novosibirsk, -2 posters.
1993 -I International course of computer methods in molecular genetics, IMB,
Moscow, practical workshops.
1994 -IV annual conference of Russian National Program "Human Genome",
Chernogolovka (Moscow region), poster.
1995 -II International course of computer methods in molecular genetics, IMB,
Moscow, practical workshops.
1996 -ISMB-96, poster
1996 -II Siberian Congress on Applied and Industrial Mathematics -4 oral
presentations.
1996 -German Conference on Bioinformatics, Leipzig -poster
1996 -Bioinformatics-Structure, Jerusalem -posters
1999 -EBG meeting, University of Cape Town, oral presentation.
1999 -RECOMB99, Lyon, poster
1999 -ISMB99, Heidelberg, tutorial (one of the authors), poster
2000 -CSHL Genome sequencing and biology, poster
2000 -EBI Genome Based Gene Structure Determination, Poster
2000 -ISMB2000, San Diego, poster
2001 -RECOMB01 Satellite Meeting on sequence assembly, oral presentation.
2001 - ISMB2001, Copenhagen, poster.
2002 - ISMB2002, Edmonton, poster.
2002 - Microarray Analysis Coordination Network Retreat, Lake Mohonk NY, oral
presentation.
2002 - Critical Assessment of Microarray Data Analysis, Duke Univ., oral
presentation.
2003 - ISMB2003, Brisbane, Australia, poster.
2003 - Open Bioinformatics Consortium BOSC2003, Brisbane, Australia, oral
presentation.
2003 - Affymetrix Low-Level Analysis Workshop, UC Berkeley, oral presentation.
2003 - MCBIOS (Mid-South Bioinformatics Society) First Annual Meeting, Little
Rock, Arkansas, oral presentation.
2004 - Bioinformatics Symposium, University of Louisiana at Lafayette, oral
presentation
2004 - MCBIOS (Mid-South Bioinformatics Society) First Annual Meeting, Little
Rock, Arkansas, oral presentation.
2005 - Keystone Symposium X3 Systems Biology "Mechanisms of insulin resistance
revealed by high-dimension expression pattern analysis".
2005 - Bioinformatics Symposium at UL Lafayette, LA "High-performance "booster"
matching algorithm for EST clustering".
2005 - American Diabetes Association, San Diego, CA "New mechanisms of insulin
resistance in skeletal muscle".
2005 - 2nd Moscow Conference on Computational Molecular Biology (MCCMB'05)
"Algorithm GRAD for selection of informative genetic characteristics"
2006 - MCBIOS 3rd Annual Meeting (Chair), poster.
2006 - CSHL Systems Biology, poster
2006 - BGRS2006, poster
2006 - Bioinformatics Rocky 2006, keynote
2007 - MCBIOS07, New Orleans, oral presentation
2007 - Keystone symposium on systems Biology (X5), poster
2007 - Graybill Conference 2007, Fort Collins, CO. Tutorial.
2007 - ISMB/ECCB, Highlights Track presentation, poster
2007 - Bioinformatics Rocky 2007, keynote
2008 - MCBIOS, oral presentation, poster
2008 -IADR Israeli Division Meeting "Circadian Rhythm of Osteocalcin in the
Maxillomandibular Complex", contributor
2008 - Biopathways 2008, oral presentation
2008 - ISMB, Highlight Track presentation

MENTORING EXPERIENCE

Grigorovich Dmitriy, B.Sci. in Computer Science, 1996

Novosibirsk State University,
odip@bionet.nsc.ru
Anindya Poddar, Louisiana State University Computer Science Dept.,
Ph.D. candidate
Corby Martin Ph.D. Department of Health Behavior, Instructor
co-mentor on K23 (Mentored Patient-Orientated

Research Career Development Award) grant entitled

Energy Expenditure: Relation with Body Mass over Time,

awarded by NIH in 2005.

PROFESSIONAL ASSOCIATIONS

International Society for Computational Biology - member since 1999.
MidSouth Computational BIOlogy Society (MCBIOS) - Board of Directors, 2003-2007,
Chair of the 2005 MCBIOS Bioinformatics Conference
American Diabetes Association - professional section member since 2005.