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ANTON YURYEV |
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Citizenship:
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Molecular
Biologist |
2001 Certification in project management
Lewis Institute for Project Management systems,
1995-1997 Postdoctoral Research Training,
Molecular and Cellular Biology Research Unit,
Pharmaceutical Division, Novartis
Corporation,
1991-1995 Ph.D. in Molecular Biology and Genetics,
Graduate Program in Biochemistry, Cellular and Molecular Biology,
Johns Hopkins University, School of Medicine , Baltimore, MD
USA
Thesis: C-terminal Domain of RNA polymerase II: Some Insights on its Function in vivo.
1987-1989
MS in Cellular and Molecular
Biology with Honors
Shemyakin’s
Institute of Bioorganic Chemistry, Academy of Sciences, Moscow, USSR
Thesis: Isolation and Physical
Mapping of Gene Encoding a2 isoform of Na,K-ATPase.
1983-1987 BS in Physics and Biophysics with
Honors
Moscow Institute of Physics and Technology ,
Research and Professional Experience
11.2002 - present
Senior Director,
Application Science Department. Ariadne
Genomics Inc.
ACCOMPLISHMENTS
Application Science department supports existing AGI customers, offer technical support for sales and promote AGI software by means of scientific publications, education of scientific community, popularizing AGI technology and scientific collaborations to analyze high-throughput data.
I am involved in the development, testing and supporting of all Ariadne Genomics software products including Pathway Studio applications for pathway analysis, MedScan text-to-knowledge technology utilizing natural language processing algorithms. My research interests include studying the topological and evolutionary properties of the biological networks and developing algorithms for pathway reconstruction and analysis of high-throughput data.
Senior Bioinformatics
Analyst. Orchid Biosciences Inc.,
ACCOMPLISHMENTS
Developed statistical model for SNP-IT primer extension genotyping reaction to predict the success of the single nucleotide polymorphism (SNP) genotyping assay. The model calculates various DNA sequence properties for primers and PCR product and combine them using logistic regression analysis to calculate the success probability (confidence) for the assay. The model is implemented in Orchid’s proprietary software for primer design and marker clustering for multiplex genotyping assay: Autoprimer.com.
I was the project manager for Orchid’s Chromosome Browser project. This Web application is designed to provide customers access to Orchid’s proprietary data for SNP genotyping mapped on human genome. It allows collection of SNPs for genotyping experiment using genome browsing and data-mining. The software has 3-tier architecture with Java JDK 1.4 client, ORACLE 9i database and Orion J2EE application server. I was responsibile for timeline scheduling and effort coordination of two groups of programmers: Java contractors based in India and in-house database development group. I wrote technical specifications, functional requirements documents, use cases and supervised software testing and development of user documentation. The project included 19 people at different times. I participated in the Chromosome Browser database development to import LocusLink, OMIM, Golden Path, GenBank, and RefSeq public databases and apply ORACLE advance text search capabilities for data mining. I also developed SNP spacing algorithm to mine evenly distributed SNPs in user-defined chromosome region. I also worked on implementation of distributed genome annotation system (DAS) into Chromosome Browser.
Developed several small in-house software applications: oligonucleotide tag design for solid phase primer hybridization, repeat masking using BLAST results, and primer design for DNA computer.
Developed algorithm for auto-classification of signal clusters on scatter plots using neural networks. The two-layer neural network was trained using genetic algorithm. The algorithm is used to automatically detect failed SNPs genotyped by SNPStream UHT instrument for high-throughput genotyping.
9.1999 - 8.2001
Senior Research
Scientist/Systems Analyst. InforMax Inc.,
ACCOMPLISHMENTS
Designed and developed the prototype of new software for Genetic Analysis of single nucleotide polymorphism (SNP) and microsatellite markers (STS). I have worked with a team of three software developers. Our software uses Java for client interface, ORACLE back end and C++ to write algorithms and cgi. I was also invloved in the development of the software for genome analysis and designed new algorithms and software for PCR primer design. My responsibilities included writing use cases, developing and implementing algorithms in C++ and software architechure design.
Senior Research Scientist. deCODE
Genetics Inc., Research and Development Group,
ACCOMPLISHMENTS
Developed novel proprietary molecular biological technologies for high throughput amplification and sequencing of large human genome regions. The technology involves amplification of human genomic DNA by long and accurate PCR, subcloning and shotgun sequencing. I was also involved in organizing the high throughput functional analysis of potential drug targets by two-hybrid screen.
Postdoctoral Research Scientist. Novartis Corporation, Molecular and Cellular Biology Research Unit,
ACCOMPLISHMENTS
Studied protein kinase RAF isoform specific functions and mapped
the principal RAF protein-protein interaction domain. Identified RAF isoform
specific protein interactions by two-hybrid screen.
Discovered genes encoding human mitochondrial protein import
receptors. Demonstrated that A-RAF isoform is imported into mammalian
mitochondria.
Expressed in E.coli and purify a novel
growth associated mammalian protein kinase, which interact with RAF cystein-rich domain in the two-hybrid assay. Developed an
in vitro biochemical assay for this kinase.
Graduate Student. Johns Hopkins University, School of Medicine, Department of Molecular Biology
and Genetics, Baltimore, Maryland, USA.
Supervisor: Jeffry L. Corden,
Ph.D.
ACCOMPLISHMENTS
Studied a function of yeast RNA polymerase II C-terminal
domain (CTD) using methods of yeast genetics. Developed the selection
system for mutant hunt, cloned a novel suppressor gene. Analyzed lethal
mutations in yeast by suppression analysis.
Developed a method to search for CTD interacting proteins by
two-hybrid screen and discovered a novel family of splicing-related proteins
that interact with CTD of RNA polymerase II using two-hybrid screen method.
This discovery suggested the existence of the physical link between
transcription and splicing in eukaryotic cells.
1.1992-3.1992
Graduate Student. Johns Hopkins University,
Rotation project. Supervisor: Daniel Nathans, M.D.
ACCOMPLISHMENTS
Phosphopeptide mapping of JunB protein.
9.1990-9.1991
Senior Laboratory Assistant. Johns Hopkins University,
ACCOMPLISHMENTS
Participated in determination of the structural basis for selective binding of Epstein-Barr virus (EBV) to human complement receptor type 2 (CR2) using methods of molecular cloning and tissue culture. The parts of human CR2 receptor were substituted by mouse CR2 and mouse-human CR2 chimeras were assayed for their ability to bind (EBV) using methods of tissue culture transfection or infection with retroviruses.
11.1988 - 9.1990
Research Associate. Shemyakin's
Institute of Bioorganic Chemistry, Academy of Sciences, Moscow, USSR
9/1989 - 9/1990 RESEARCH ASSOCIATE, Supervisor: Prof. N. N. Modyanov
Isolated and physically mapped the 5’-end of the gene, encoding a1 isoform of Na,K-ATPase
11/1988-9/1989 SENIOR LABORATORY ASSISTANT, Supervisor: Prof. N. N. Modyanov
ACCOMPLISHMENTS
Isolated and physically mapped genes encoding different Na,K-ATPase isoforms.
Books – Articles
– Talks – Patents
1. Yuryev A
Pathway analysis for Drug discovery
John Wiley & Sons, Hoboken, New Jersey (2008)
2. Yuryev A
Methods in Molecular Biology: PCR Primer Design
Humana Press,
ARTICLES
1. Yuryev A
In silico pathway analysis: the final frontier towards completely rational drug design.
Expert Opinion on Drug Discovery 2008; v3(8):867-876(10)
2. Dunfield PF, Yuryev A Senin P, Smirnova AV, Stott MB, Hou S, Ly B, Saw JH, Zhou Z, Ren Y, Wang J, Mountain BW, Crowe MA, Weatherby TM, Bodelier PL, Liesack W, Feng L, Wang L, Alam M.
Methane oxidation by an extremely acidophilic bacterium of the phylum Verrucomicrobia.
Nature. 2007 Dec 6;450(7171):879-82
3. Yan KK, Maslov S, Mazo I, Yuryev A
Prediction and verification of indirect interactions in densely interconnected regulatory networks.
arXiv:0710.0892v2 [q-bio.QM]
4. Huang J, Yuryev A
Developing a statistical model for primer design.
Methods Mol Biol. 2007; 402:105-38
5. Yuryev A
PCR primer design using statistical modeling.
Methods Mol Biol. 2007; 402:93-104
6. Kotelnikova
E, Kalinin A, Yuryev A, Maslov S
Prediction of Protein-protein Interactions on
the Basis of Evolutionary Conservation of Protein Functions.
Evolutionary Bioinformatics 2007: 3
7. Sivachenko
AY, Yuryev A, Daraselia N, Mazo I
Molecular networks in microarray analysis.
J Bioinform Comput Biol.
2007 Apr;5(2b):429-56
8. Daraselia
N, Yuryev A, Egorov S, Mazo I, Ispolatov I
Automatic extraction of gene ontology annotation and its
correlation with clusters in protein networks.
BMC Bioinformatics. 2007 Jul 10;8(1):243
9. Sivachenko
A, Kalinin A, Yuryev A.
Pathway analysis for design of
promiscuous drugs and selective drug mixtures.
Curr Drug Discov Technol.
2006 Dec;3(4):269-77
10. Sivachenko
AY, Yuryev A.
Pathway analysis software as a tool for drug
target selection, prioritization and validation of drug mechanism.
Expert Opinion on Therapeutic Targets, 2007 Mar;11(3):411-21
11.
Yuryev A.
Targeting transcription factors in cell
regulation.
Expert opinion on Therapeutic Targets, 2007 Mar;11(3):411-21
12. Ispolatov
I, Mazo I, and Yuryev A.
Finding mesoscopic communities in
sparse networks.
J. Stat. Mech., 2006 P09014
13.
Badretdinov A, Yuryev A.
Pathway Analysis in Drug Development.
Pharma & Bio Ingridients,
March 2006
14.
Yuryev A,
Mulyukov Z, Kotelnikova E, Maslov S, Egorov S, Nikitin A, Daraselia N, Mazo I.
Automatic pathway building in biological association
networks.
BMC Bioinformatics. 2006 Mar 24; 7:171.
15. Ispolatov
I, Yuryev A, Mazo I, Maslov S.
Binding properties and evolution of homodimers in protein-protein interaction networks.
Nucleic Acids Res. 2005 Jun 27;33(11):3629-35.
16. Sivachenko
AY, Yuryev A, Daraselia N, Mazo I.
Identifying Local Gene Expression Patterns in Biomolecular
Networks.
IEEE Computational Systems Bioinformatics
Conference, Aug. 8-11, 2005.
17. Ispolatov I, Krapivsky, Mazo
I, and Yuryev A.
Cliques and duplication-divergence network
growth.
New J.Phys. 7(2005) 145
18. Ispolatov
I,
Duplication-divergence model of protein
interaction network.
Phys Rev E Stat Nonlin
Soft Matter Phys. 2005 Jun;71
19. Daraselia N, Yuryev A,
Egorov S, Novichkova S, Nikitin A, Mazo I.
Extracting human protein interactions
from MEDLINE using a full-sentence parser. (PDF download)
Bioinformatics.
2004 Mar 22; 20(5): 604-11. Epub 2004 Jan 22.
20. Egorov S, Yuryev A, Daraselia N.
A simple and practical dictionary-based
approach for identification of proteins in Medline abstracts.
J Am Med Inform
Assoc. 2004 May-Jun; 11(3):174-8. Epub 2004 Feb 05.
21. Edvardsen H, Irene Grenaker,
Alnaes G, Tsalenko A, Mulcahy T, Yuryev A, Lindersson M, Lien S, Omholt S, Syvanen AC, Borresen-Dale AL, Kristensen V.
Experimental validation of data mined
single nucleotide polymorphisms from several databases and consecutive dbSNP builds.
Pharmacogenet
Genomics. 2006 Mar;16(3):207-217.
22. Yuryev A, Huang J, Scott KE, Kuebler
J, Donaldson M, Phillips MS, Pohl M, Boyce-Jacino MT.
Primer design and marker clustering for
multiplex SNP-IT primer extension genotyping assay using statistical modeling. (PDF download)
Bioinformatics, 2004,Dec 12;20(18):3526-32.
23. Huang CY, Studebaker J, Yuryev A, Huang J, Scott KE, Kuebler
J, Varde S, Alfisi S, Gelfand CA, Pohl M, Boyce-Jacino
MT.
Auto-validation of fluorescent primer extension genotyping
assay using signal clustering and neural networks.
BMC
Bioinformatics. 2004 Apr 02; 5(1): 36.
24. Yuryev A, Huang J, Pohl M, Patch R,
Watson F, Bell P, Donaldson M, Phillips MS, and Boyce-Jacino
MT.
Predicting success of primer extension
genotyping assay using statistical modeling.
Nucleic Acids Research, 2002, Vol. 30, No. 23 e131.
25. Gorelenkov V, Antipov A, Lejnine S, Daraselia N, Yuryev A.
A set of novel tools for PCR primer
design.
Biotechniques. 2001 Dec;31(6):1326
26. Grant SF, Kristjansdottir H,
Steinsson K, Blondal T, Yuryev A, Stefansson K,
Gulcher JR.
Long PCR detection of the C4A null allele
in B8-C4AQ0-C4B1-DR3.
J Immunol Methods. 2000 Oct 20; 244(1-2): 41-7
27. Yuryev A, Wennogle LP.
Novel RAF kinase protein-protein
interactions found by exhaustive yeast two-hybrid analysis.
Genomics. 2003 Feb;81(2):112-25.
28. Yuryev A, Ono M, Goff SA, Macaluso
F, Wennogle LP.
Isoform-Specific Localization of A-RAF in
Mitochondria.
Mol Cell Biol. 2000 Jul 1; 20(13): 4870-4878. PMID: 10848612
29. Allentoff AJ, Mandiyan S, Liang
H, Yuryev A, Vlattas
I, Duelfer T, Sytwu II,
Wennogle LP.
Understanding the cellular uptake of phosphopeptides.
Cell Biochem Biophys:31(2):129-40 (1999)
30. Yuryev A, Wennogle LP.
The RAF family: an expanding network of
post-translational controls and protein-protein interactions (review).
Cell Res (2):81-98 (1998)
31. Pellegrini MC, Liang H, Mandiyan
S, Wang K, Yuryev A, Vlattas
I, Sytwu T, Li Y-C, Wennogle LP.
Mapping the substrate preferences of
protein tyrosine phosphatase PTP-1B using
combinatorial chemistry approaches.
Biochemistry (8):15598-15606 (1998)
32. Mandiyan S, Schumacher C, Cioffi C,
Sharif H, Yuryev A, Lappe R, Monia
B, Hanson S, Goff S, Wennogle LP.
Molecular and cellular characterization
of baboon C-Raf as a target for antiproliferative
effects of antisense oligonucleotides.
Antisense Nuc Acid Drug Dev (6):539-48 (1997)
33. Yuryev A, Patturajan M, Litingtung Y, Joshi RV, Gentile C, Gebara
M, Corden JL.
The C-terminal domain of the largest
subunit of RNA polymerase II interacts with a novel set of serine/arginine-rich proteins. (PDF download)
Proc Natl Acad Sci U S A 93 (14): 6975-6980 (1996)
34. Yuryev A and Corden JL.
Suppression analysis reveals a functional
difference between the serines inpositions
two and five in the consensus sequence of the C-terminal domain of yeast RNA
polymerase II.
Genetics 143 (2): 661-671 (1996)
35. Yuryev A and Corden JL.
A Saccharomyces
cerevisiae gene encoding a potential adenine phosphoribosyltransferase.
Yeast 10 (5): 659-662 (1994)
36.
Determination of the structural
basis for selective binding of Epstein-Barr virus to human complement receptor
type 2.
J Exp Med 174 (6): 1299-1311 (1991)
37. Yuryev AD
Synthesis of Biotin Label and Combining it with oligonucleotide.
Moscow Institute of Physics and Technology, Annual Reports, 1988 (in Russian)
38. Yuryev AD, Makarevich OI.
Molecular Cloning of Na.K-TPase cDNA.
Moscow Institute of Physics and Technology, Annual Reports, 1988 (in Russian)
1. Identification of Major Transcription Factors Responsible for Particular Cellular Regulatory Responses.
Applications
of Gene Regulation and Regulatory Networks ,
2.
Pathway Analysis of Biological
Association Networks.
Second Annual
Oklahoma Bioinformatics Society Symposium ,
3. Identification of Major Metabolism Regulators from metabolic profiles.
Advances in Metabolic Profiling,
4. PathwayExpert: Extraction from Literature and Pathway Analysis.
WorldFusion seminar,
5. Databases And Software For Predicting Molecular Interactions In Newly Sequenced Genomes.
Plant & Animal Genomes XIV Conference, Jan. 17, 2006 (Workshop)
6. Applications for Pathway Analysis in Drug Discovery.
Pathway Analysis for Target and Compound Evaluation, Feb. 23 2006 (Round table discussion)
7. Identification of Defective Signaling Pathways in the Aggressive Melanoma.
Regulomics symposium , Oct. 23 2006
8.
Pathway Studio
A*STAR Bioinformatics Institute,
9. In Silico Pathway Analysis: The Final Frontier Towards Completely Rational Drug Design.
3rd Annual Modern Drug Discovery & Development Summit,
10. In Silico Pathway Analysis: The Final Frontier Towards Completely Rational Drug Design.
1st International Conference On Drug Design & Discovery,
Agent: Marc Karish Sheldon
& Mak -
Inventors: Shobha A. Varde, Mark A. Kunkel, Yuryev A
Contact Information ayuryev@gmail.com
My house in Alburg, VT (you can rent it).
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