User:Ybukhman
Scientist, Computational Biology Core Group, Great Lakes Bioenergy Research Center, University of Wisconsin - Madison, USA
RESUME
SUMMARY
Computational Biologist with 15 years of relevant experience in academia and biotech industry. Experience in data management and statistical analysis of high-throughput biological data, such as gene expression, array CGH, LC-MS, and HTS. Expertise in statistics, databases, computer programming. Skills include S+/R statistical software; programming in Perl, Python and other languages; SQL, MySQL, FileMaker Pro, MS Access; Unix/Linux, Windows, Mac OS X. Ph.D. in Chemistry from Johns Hopkins, 1998.
EXPERIENCE
Associate Scientist, Computational Biology Core Group. October 2008 – present Great Lakes Bioenergy Research Center, University of Wisconsin – Madison, USA Participated in all key activities of the Computational Biology Core Group provides bioinformatics consultation, data analysis, application development/maintenance/support and data management services to the Center. Analyzed gene expression, metabolomics, microbial growth curves, and proteomics data Participated in design, development and deployment of bioinformatics software and databases. This includes a web-based tool for the analysis of robotic screens of microbial growth curves, deployment of a Galaxy server and integration of in-house tools into the same, and a specialized computational biology database (under development) Participated in the development of strategic plans, reports, presentations and an ITIL Service Catalog Recruited and managed scientific and software development staff Received training in RNA-seq data analysis, SRI Pathway Tools and other technical areas, as well as in project management and staff supervision
Instructor. 2009-present. BioPharmaceutical Technology Center Institute, Madison, WI, USA Lectured at summer courses: Computational Approaches to Analyzing Microarray Data
Bioinformatics Specialist/Architect. January 2006 – September 2008. Campbell Family Institute for Breast Cancer Research, University Health Network, Toronto, Ontario, Canada Participated in early-stage drug discovery for breast cancer. Performed bioinformatics research to facilitate discovery of novel drug targets. Statistical analysis of high-throughput datasets: analyzed in-house array CGH (BAC SMRT and Affymetrix SNP 6.0), siRNA screening, and gene expression data. Cross-platform integration and analysis of in-house and public domain data relevant to breast cancer genomics and proteomics: downloaded, analyzed and imported into an in-house database relevant publicly available gene expression datasets. Development of databases in cooperation with off-site consultants: developed an extensive in-house database including array CGH, gene expression, and siRNA data, results of statistical analyses, and biological annotations from a variety of sources.
Bioinformatics Scientist (Sep 2003 – May 2004), Senior Bioinformatics Scientist (May 2004 – Sep 2005). MDS Proteomics/Protana Inc., Toronto, Ontario, Canada. Participated in biomarker discovery and platform development Performed statistical design and analysis of LC-MS proteomics experiments Acted as a lead bioinformatician and data analyst for the biomarker discovery program. Interacted with project leaders and wet lab scientists to help with experimental design and determine data analysis objectives. Coordinated efforts of other bioinformatics personnel.
Scientist, Bioinformatics. Oct 2001 – Sep 2003. Psychiatric Genomics, Inc., Gaithersburg, MD, USA. Participated in early-stage drug discovery for psychiatric disorders, particularly schizophrenia, bipolar disorder and autism. Conducted bioinformatics research to facilitate discovery of novel disease markers and drug targets. Designed and maintained the company database of microarray data, including schema design and implementation of data input/output scripts. Performed statistical analyses of microarray data. Served as a liaison between bioinformatics and microarray groups. Closely interacted with experimental scientists and research project leaders, helped design microarray experiments, provided customized analyses, summaries of most significant results and advice on statistical issues.
Post-doctoral Research Associate. Oct 1998 – Sep 2001 Laboratory of Computational Genomics, PI: Dr. Jeffrey Skolnick (started in October 1998 at Scripps Research Institute, La Jolla, CA, USA; moved with the Skolnick group in July 1999 to the Donald Danforth Plant Science Center, St. Louis, MO, USA; finished in September 2001) Participated in bioinformatics research related to structural biology Developed BioMolQuest, an integrated database and search engine for protein structure, function and classification utilizing a novel search algorithm. This involved designing and implementing a relational database and programming a web-interfaced application using the database as the back end. Developed and maintained relational databases and assisted colleagues in database use.
Junior Research Associate (July 1992 – Aug 1993). Moscow Institute of Tuberculosis, Moscow, Russia. Participated in the development and administration of immunoassays for the detection of tuberculosis antigens in bodily fluids. Carried out a patent search on immunoassays utilizing magnetic particles.
EDUCATION
1998. Ph.D. in Chemistry, Johns Hopkins University, Baltimore, MD, USA. Thesis: Interactions of Ions with Tertiary Structure of a 23S rRNA Fragment. Adviser: David E. Draper. Wet lab molecular biology, experimental thermodynamics, statistics and computer programming
1997 Sarah and Adolph Roseman Award for Outstanding Achievement in Chemistry (Johns Hopkins University Department of Chemistry)
1995. M.A. in Chemistry, Johns Hopkins University, Baltimore, MD, USA. Took advanced classes in molecular biology, biophysics, theoretical and computational chemistry
1992. Diploma in Chemistry, Moscow State University, Moscow, Russia. Diploma thesis: Thermodynamic Modeling of the Liquid Phase and Phase Equilibriums in the Y-Cu-O System. General and computational chemistry curriculum; computer programming.
PROFESSIONAL DEVELOPMENT (recent)
RNA-seq data analysis tutorial (half-day), 2012, ISMB, Long Beach, CA
iPlant Tools and Services Workshop (2 days), 2012, University of Wisconsin – Madison, Madison, WI
R Workshop with Bill Venables (2 days), 2012, MILWASA, Milwaukee, WI
Advanced Pathway Tools Tutorial (3 days), 2012, SRI, Menlo Park, CA
Agile Project Management: Techniques for Iterative Development (2 days), 2013, Executive Education and the Wisconsin School of Business, University of Wisconsin – Madison.
Excellence in Management and Supervision Certificate Program (17 hrs), 2012-2013, University of Wisconsin – Madison, Office of Human Resource Development, Madison, WI
PUBLICATIONS
Sanjaya, Miller, R., Durrett, T.P., Kosma, D.K., Lydic, T.A., Muthan, B., Koo, A.J.K., Bukhman, Y.V., Reid, G.E., Howe, G.A., et al.. Altered Lipid Composition and Enhanced Nutritional Value of Arabidopsis Leaves following Introduction of an Algal Diacylglycerol Acyltransferase 2. Plant Cell 2013; 25:677–693.
Reilly PT, Afzal S, Gorrini C, Lui K, Bukhman YV, Wakeham A, Haight J, Ling TW, Cheung CC, Elia AJ, Turner PV, Mak TW. Acidic nuclear phosphoprotein 32kDa (ANP32)B-deficient mouse reveals a hierarchy of ANP32 importance in mammalian development. Proc Natl Acad Sci U S A. 2011 Jun 21;108(25):10243-8.
Riederer A, Takasuka TE, Makino S, Stevenson DM, Bukhman YV, Elsen NL, Fox BG. Global gene expression patterns in Clostridium thermocellum as determined by microarray analysis of chemostat cultures on cellulose or cellobiose. Appl Environ Microbiol. 2011 Feb;77(4):1243-53.
Cohen B, Shimizu M, Izrailit J, Ng NF, Buchman Y, Pan JG, Dering J, Reedijk M. Cyclin D1 is a direct target of JAG1-mediated Notch signaling in breast cancer. Breast Cancer Res Treat. 2010 Aug;123(1):113-24. Bukhman YV, Dharsee M, Ewing R, Chu P, Topaloglou T, LE Bihan T, Goh T, Duewel H, Stewart II, Wisniewski JR, Ng NF. (2008). Design and analysis of quantitative differential proteomics investigations using LC-MS technology. J Bioinform Comput Biol. 2008 Feb;6(1):107-23.
Ewing RM, Chu P, Elisma F, Li H, Taylor P, Climie S, McBroom-Cerajewski L,Robinson MD, O'Connor L, Li M, Taylor R, Dharsee M, Ho Y, Heilbut A, Moore L, Zhang S, Ornatsky O, Bukhman YV, Ethier M, Sheng Y, Vasilescu J, Abu-Farha M, Lambert JP, Duewel HS, Stewart II, Kuehl B, Hogue K, Colwill K, Gladwish K, Muskat B, Kinach R, Adams SL, Moran MF, Morin GB, Topaloglou T, Figeys D. (2007). Large-scale mapping of human protein-protein interactions by mass spectrometry. Mol Syst Biol. 2007;3:89
Topaloglou T., Dharsee M, Ewing RM and Bukhman Y (2007). A High-Throughput Bioinformatics Platform for Mass Spectrometry-Based Proteomics. In Data Integration in the Life Sciences, 4th International Workshop, DILS 2007, Philadelphia, PA, USA, June 27-29, 2007. Proceedings, Springer Berlin / Heidelberg
LeBihan, T., Goh, T., Stewart, I.I., Salter, A.M., Bukhman, Y.V., Dharsee, M., Ewing, R., and Wisniewski, J.R. (2006). Differential Analysis of Membrane Proteins in Mouse Fore- and Hindbrain Using a Label-Free Approach. J. Proteome Res., 2006 Oct; 5(10):2701-10
Altar CA, Jurata LW, Charles V, Lemire A, Liu P, Bukhman Y, Young TA, Bullard J, Yokoe H, Webster MJ, Knable MB, Brockman JA. (2005). Deficient hippocampal neuron expression of proteasome, ubiquitin, and mitochondrial genes in multiple schizophrenia cohorts. Biol. Psychiatry. 58(2):85-96.
Jurata LW, Bukhman YV, Charles V, Capriglione F, Bullard J, Lemire AL, Mohammed A, Pham Q, Laeng P, Brockman JA, Altar CA. (2004). Comparison of microarray-based mRNA profiling technologies for identification of psychiatric disease and drug signatures. J. Neurosci. Methods. 30;138(1-2):173-88
Altar, C.A., Laeng, P., Jurata, L.W., Brockman, J.A., Lemire, A., Bullard, J., Bukhman, Y.V., Young, T.A., Charles, V., Palfreyman, M.G. (2004). Electroconvulsive Seizures Regulate Gene Expression of Distinct Neurotrophic Signaling Pathways. J. Neurosci., 24:2667-77
Bukhman, Y.V. and Skolnick, J. (2001). BioMolQuest: integrated database-based retrieval of protein structural and functional information. Bioinformatics, 17:468-478.
Draper, D.E., Bukhman, Y.V. and Gluick, T.C. (2000). Thermal methods for the analysis of RNA folding pathways. In Current Protocols in Nucleic Acid Chemistry (Beaucage, S. L., Bergstrom, D. E., Glick, G. D. & Jones, R. A., ed), section 11.3, John Wiley & Sons, New York.
Bukhman, Y.V. and Draper, D.E. (1997). Affinities and selectivities of divalent cation binding sites within an RNA tertiary structure. J. Mol. Biol., 273:1020-1031.
Rogers, M.J., Bukhman, Y.V., McCutchan, T.F., and Draper, D.E. (1997). Interaction of thiostrepton with an RNA fragment derived from the plasmid-encoded ribosomal RNA of the malaria parasite. RNA, 3:815-820.
