ANTON YURYEV

 

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self-portrate1

Citizenship: United States of America
Nationality: Russian
cell: 732-735-8071
FAX: 270-912-6658
E-mail: ayuryev@gmail.com

self-portrate 2


Molecular Biologist

EDUCATION - EXPERIENCE - PUBLICATIONS                                              



Educational Background

2001            Certification in project management

  Lewis Institute for Project Management systems, Princeton, NJ USA

 

1995-1997  Postdoctoral Research Training, Molecular and Cellular Biology Research Unit,
                    Pharmaceutical Division, Novartis Corporation, Summit, NJ USA

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 , Moscow, USSR. (about PhysTech)


Research and Professional Experience

11.2002 - present

            Senior Director, Application Science Department. Ariadne Genomics Inc. Rockville, Maryland, USA

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.

my publications of this period


8.2001 - 11.2002

            Senior Bioinformatics Analyst. Orchid Biosciences Inc., Princeton, New Jersey, USA

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.

my publications of this period


9.1999 - 8.2001

Senior Research Scientist/Systems Analyst. InforMax Inc., Research Department, Maryland, USA.

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.

my publications of this period


5.1998 - 9.1999

Senior Research Scientist. deCODE Genetics Inc., Research and Development Group, Iceland .

ACCOMPLISHMENTS

click here for more details or read Synopsis of my Research at the bottom of this pageDeveloped 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.

my publications of this period


9.1995-9.1997

Postdoctoral Research Scientist. Novartis Corporation, Molecular and Cellular Biology Research Unit, Summit, New Jersey, USA. Supervisor: Lawrence P. Wennogle, Ph.D.

ACCOMPLISHMENTS

click here for more details or read Synopsis of my Research at the bottom of this pageStudied 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.
click here for more details or read Synopsis of my Research at the bottom of this pageDiscovered genes encoding human mitochondrial protein import receptors. Demonstrated that A-RAF isoform is imported into mammalian mitochondria.
click here for more details or read Synopsis of my Research at the bottom of this pageExpressed 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.

my publications of this period


9.1991-7.1995

Graduate Student. Johns Hopkins University, School of Medicine, Department of Molecular Biology
and Genetics, Baltimore, Maryland, USA. Supervisor: Jeffry L. Corden, Ph.D.

ACCOMPLISHMENTS

click here for more details or read Synopsis of my Research at the bottom of this pageStudied 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.
click here for more details or read Synopsis of my Research at the bottom of this pageDeveloped 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.

my publications of this period


1.1992-3.1992

Graduate Student. Johns Hopkins University, School of Medicine, Department of Molecular Biology and Genetics
Rotation project.
Supervisor: Daniel Nathans, M.D.

ACCOMPLISHMENTS
click here for more details or go to the bottom of this page to read Synopsis of my researchPhosphopeptide mapping of JunB protein.


9.1990-9.1991

Senior Laboratory Assistant. Johns Hopkins University, School of Medicine, Rheumatology Division. Supervisor: Joseph M. Ahearn, M.D.

ACCOMPLISHMENTS

click here for more details or read Synopsis of my Research at the bottom of this pageParticipated 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.

my publications of this period


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

click here for more details or read Synopsis of my research at the bottom of this pageIsolated and physically mapped genes encoding different Na,K-ATPase isoforms.

my publications of this period


BooksArticlesTalksPatents

BOOKS

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, Totowa, New Jersey (2007)

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, Krapivsky PL , Yuryev A.
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.  Martin DR , Yuryev A, Kalli KR, Fearon DT, Ahearn JM.
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)

 


TALKS

1.      Identification of Major Transcription Factors Responsible for Particular Cellular Regulatory Responses. 

               Applications of Gene Regulation and Regulatory Networks , Boston USA , Oct 17 2005

2.      Pathway Analysis of Biological Association Networks.

               Second Annual Oklahoma Bioinformatics Society Symposium , Oklahoma USA, Oct. 28 2005

3.      Identification of Major Metabolism Regulators from metabolic profiles.

                Advances in Metabolic Profiling, London UK , Nov. 2 2005

4.      PathwayExpert: Extraction from Literature and Pathway Analysis.

               WorldFusion seminar, Tokyo Japan , Dec. 11 2005

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 Enterprise: a Complete Software Solution for Information Extraction from the Literature and Pathway Analysis of High-throughput Data.

               A*STAR Bioinformatics Institute, Singapore , Feb. 2007

9.      In Silico Pathway Analysis: The Final Frontier Towards Completely Rational Drug Design.

               3rd Annual Modern Drug Discovery & Development Summit, San Francisco , November 29, 2007

10.      In Silico Pathway Analysis: The Final Frontier Towards Completely Rational Drug Design.

               1st International Conference On Drug Design & Discovery, Dubai (UAE) , February 5

             


PATENTS

US #20060204971 - Oligonucleotides for multiplexed binding assays

Agent: Marc Karish Sheldon & Mak - Pasadena, CA, US

Inventors: Shobha A. Varde, Mark A. Kunkel, Yuryev A

 


            Synopsis of my Research


            Contact Information ayuryev@gmail.com











































































































Personal and hobbies:

My house in Alburg, VT (you can rent it).








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