Anup ***** , Ph. D.
Summary of Qualifications
Experienced scientist with a strong background in translational research and 10+ years of leadership/project management experience.
Experience in genomic & clinical data integration for supporting multiple aspects of R&D pipeline (early discovery, diagnostics and clinical development).
Experience with application of bioinformatics and genomic technologies towards target and biomarker discovery for disease risk and patient segmentation for targeted therapies in clinical development.
Strong planning, management and organizational skills. Highly effective in managing complex projects across global, virtual and cross-departmental teams.
Extensive experience in development of novel assays using cutting edge technologies (Next generation sequencing etc. ) to support clinical trials.
Demonstrated ability to work independently and collaboratively with bench biologists, statisticians and computational scientists.
Experience in supervision of personnel with diverse background and experience in matrixed work environments.
Invited speaker at premier national conference and international conferences, Published 40+ articles in peer-reviewed journals.
Reviewer for scientific journals and NIH study sections.
Responsible for managing budgets (more than $25 million), products and services.
Senior Scientist, Genomics/Sequencing Group Lead
Covance Genomics Lab, Seattle, WA 2010 to Present
Responsible for developing Next generation sequencing platform for providing sequence based assays as core services by Covance Genomic Laboratory and managing daily operations of three laboratories (8 scientists). Responsible for developing novel MDx assays to support various clinical trials. Played a key role in getting genomics laboratory CLIA approved. Developed business plan for providing sequence based services based on interactions with KOLs at various pharmaceutical companies. Identified potential external collaborators within scientific area and initiated research programs within focus areas. Conducted presentations for customers, participated in setting booths at conferences and interacted with customers to present the results.
Swedish Neuroscience Institute, Seattle, WA 2006 to 2009
Planned and executed the formation of state of the art research center. Influenced and guided the research activities of Center for Advanced Brain Tumor Treatment at executive level to enable healthcare professionals personalize treatments for brain cancers. Managed 5 research scientists and 3 associates. Participated in fund raising effort, writing and evaluating scientific proposals.
• Used systems biology tools and analyzed genomic and epigenomic profiles-gene expression patterns (microarrays and Next-Generation sequencing), mutational analysis and promoter methylation status associated with the tumor samples to identify perturbed networks in brain tumors. Genomic lesions occupying important nodes of these pathways were used to develop a biomarker panel for disease management.
• Received funding by NIH to isolate cancer stem cells by fluorescence activated cell sorter for evaluating novel drugs that target tumor initiating cells. Identified genomic aberrations that play a role in differentiation of tumor initiating cancer cells using Next Generation sequencing technologies.
• Identified 43 putative tumor suppressor genes by comparative analysis of global methylation data (ChIP-chip) and gene expression changes due to silencing of DNA methyl transferases. Two identified genes SDC2 and TMTC1 were found to suppress growth of tumor cell lines.
• Performed micro-dosing experiments and used cell culture techniques to optimize drug dosage requirements for treating brain tumors.
University of Iowa, Iowa City, IA 2003 to 2006
Initiated various collaborative projects to identify and investigate the role of genetic and epigenetic aberrations in human diseases-brain cancers, preterm pregnancies and psychiatric disorders. Managed a group of 9 researchers including students, post-docs, research associates and bio-informaticians.
• Identified epigenetically regulated genes in brain cancer cells by microarray analysis and tested 30 genes for their ability to suppress tumor growth in nude mice and tumor cell lines. Evaluated promoter regions of 60 genes for lesions in their promoter regions to develop a panel of molecular markers for tumor stratification.
• Identified molecular signatures that correlate with psychiatric disorders using various genomic technologies-microarrays and bisulfite sequencing. A panel of markers is being developed for predicting individuals susceptible to alcohol or nicotine dependence.
• Evaluated the ability of epigenetic aberrations to predict women susceptible to pre-term pregnancies using ChIP-chip technology.
Sr. Research Scientist/Director Sequencing facility
Institute for Systems Biology, Seattle, WA 2000 to 2003
Responsible for setting up sequencing infrastructure at the Institute for Systems Biology and participated in several genomic sequencing projects. Managed a group of 20 researchers-post-docs, bio-informaticians and research associates. Wrote and evaluated scientific proposals.
• Co-lead a team of investigators to sequence and analyze 20 mega bases of human chromosome 14 (3Mb) and 15 (17Mb).
• Received grant funding by NCI as Principal investigator to sequence, finish and analyze 6, 00 full length cDNA clones (Mammalian Gene Collection program).
• Funded by NIAID to sequence and analyze various microbial genomic projects. The analysis led to identification molecular markers for rickettsial diseases.
University of Washington, Seattle, WA 1995 to 2000
• Used genomic sequencing tools to understand inter- and intra- patient diversity in HIV.
• Co-lead a team of investigators to generate sequence and analyze mouse MHC cluster.
• Participated in generating rough draft of 20 megabases of human chromosome 14 (3Mb) and 15 (17Mb) ***** cation and Training
Tata Institute of Fundamental Research, Mumbai, India 1989 to 1995
Ph. D. (Biochemical Genetics)
Indian Institute of Technology, Delhi, India 1987 to 1989
1. ***** A, Hosur RV. Triplex formation between d-CGCTCT and the self complimentary oligonucleotide d-CAATCTCGCGAGATT spectroscopic investigations. Current Science 62: ***** , 1992.
2. Radha PK, ***** A, Hosur RV. Unique pair-to-loop dynamism due to GG mismatch at the N site in d-GTTATNATTAAC: NMR characterization. J Chem Soc Chem Commun 19: ***** , 1993.
3. Modi S, ***** A, Saxena A, Behere DV, Mitra S. Circular dichrosim studies of acid=alkaline transition in heme proteins. Proc Indian Acad Sci (Chem Sci) 105: ***** , 1993.
4. Radha PK, ***** A, Padhy LC, Hosur RV. The DNA binding domain of cMyb: over-expression and NMR characterization. Current Science 66: ***** , 1994.
5. ***** A, Hosur RV, Padhy LC. Sequence specific DNA displaces TNS bound to a hydrophobic site on the DNA binding domain of drosophila c-Myb. Biochemistry 33: ***** , 1994.
6. Suckow M, ***** A, Kisters-Woike B, Bergmann B, Buller-Hill B. Creating new DNA binding specificities in the yeast transcriptional factor GCN4 by combining selected amino acid substitutions. Nucleic Acids Res 22: ***** , 1994.
7. Radha PK, ***** A, Padhy LC, Hosur RV. Heternuclear two and three dimensional NMR studies on R1-R2-R3 domain of drosophila melanogaster c-Myb protein: spin system identification. Proc Indian Acad Sci (Chem Sci) 106: ***** , 1994.
8. Radha PK, ***** A, Nibedita R, Hosur RV. Solution structure of the Myb cognate DNA sequence by 2D NMR, spectral simulations, restrained energy minimization and distance geometry calculations. Biochemistry 34: ***** , 1995.
9. ***** A, Radha PK, Srivastava A, Padhy LC, Hosur RV. The DNA binding domain of drosophila melanogaster c-Myb undergoes a multistate denaturation: spectroscopic investigations. Eur J Biochem 230: ***** , 1995.
Radha PK, ***** A, Padhy LC, Hosur RV. NMR studies on the Myc-DNA system. Current Science 69: ***** , 1995.
11. ***** A, Radha PK, Hosur RV, Padhy LC. Bacterial expression, characterization and DNA binding studies on the DNA binding domain of the drosophila melanogaster c-Myb protein. Eur J Biochem 232: ***** , 1995.
12. Singh S, ***** A, Hosur RV. Conformational dynamism in d-(CAATTCCGTTATT) containing the complementary Myb responsive element D-CCGTTA: NMR and MD investigations. Indian J Biochem Biophys 4: ***** , 1995.
13. ***** A, Sonawat HM. Purification and spectroscopic investigation of glucose dehydrogenase from halobacterium salinarium. Physiol Chem Phys & Med NMR 28: ***** , 1996.
14. Hosur RV, Radha PK, ***** A, Padhy LC. NMR of Myb-DNA system. Biophys Chem 68: ***** , 1997.
15. Frenkel LM, Mullins JI, Learn GH, Manns-Acruino L, Herring BL, Kalish ML, Steketee RW, Thea DM, Nicholas JE, Liu S-L, Harmache A, He X, Muthui D, ***** A, Hood L, Haase AT, Zupancic M, Staskus K, Coombs SRW, Pahwa S, Roberts NJ Jr. Genetic evolution of suspected cases of transient HIV-1 infection of infants. Science 280: ***** , 1998.
16. Huang X, ***** A. CAP3: A DNA sequence assembly program. Genome Res 9: ***** , 1999.
17. Aguado B, Bahram S, Beck S, Campbell RD, Forbes S, Geraghty D, Guillaudeux T, Hood L, Horton R, Inoko H, Janer M, Jasoni C, ***** A, et al Complete sequence and gene map of a human major histocompatibility complex (MHC). Nature 401: ***** , 1999.
18. Panchal SC, ***** A, Hosur RV. Cloning, expression and purification of the DNA binding domain of RFX protein. Indian J Biochem Biophys 36: ***** , 1999.
19. Deng Y, ***** A Banta A, Friedman C, Trask B, Hood L, Li L. Characterization, chromosomal localization and the complete 30-kilobase DNA sequence of the human jagged2 gene. Genome Res 63: ***** , 2000.
20. Anderson JP, Rodrigo AG, Learn GH, ***** A, Delahunty C, Coon M, Girard M, Osmanov S, Hood L, Mullins JI. Testing the hypothesis of a recombinant origin of human immunodeficiency virus type I subtype E. Virology 74: ***** , 2000.
21. International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature 409: ***** , 2001.
22. Rowen L, Young J, Birditt B, Kaur A, ***** A, Philipps DL, Qin S, Minx P, Wilson R, Hood L, Graveley BR. Analysis of the human neurexin genes: alternative splicing and the generation of protein diversity. Genomics 79: ***** , 2002.
23. Kumánovics A, ***** A, Qin S, Rowen L, Hood L, Lindahl KF. QUOD ERAT FACIENDUM: sequence analysis of the H2-D and H2-Q regions of 129/SvJ mice. Immunogenetics 54: ***** , 2002.
24. Fahey J, Helton E, Ketteman M, ***** A, Rodrigues S, Sanchez A, Whiting M, ***** A, and the rest of the MGC Consortium. Generation and initial analysis of more than 14, 00 non-redundant, full-length human and mouse cDNA sequences by the NIH mammalian gene collection program. PNAS 99: ***** , 2002.
25. Foltz G, ***** , A and Hood L. Cancer Proteomics: Methodologies for the selection of Immunotherapy targets. Biological Therapy of Cancer, 3(4): ***** , 2002.
26. Heilig R, Eckenberg R, Petit JL, Fonknechten N, Da Silva C, Cattolico L, Levy M, Barbe V, De Berardinis V, Ureta-Vidal A, Pelletier E, Vico V, Anthouard V, Rowen L, ***** A, et al. The DNA sequence and analysis of human chromosome 14. Nature 421(6923): ***** , 2003.
27. Papazisi L, Gorton TS, Kutish G, Markham PF, Browning GF, Nguyen DK, Swartzell S, ***** A, Mahairas G, Geary SJ. The complete genome sequence of the avian pathogen mycoplasma gallisepticum strain RIow. Microbiology 149: ***** , 2003.
28. Xie T, Rowen L, Aguado B, Ahearn ME, ***** A, Qin S, Campbell RD, Hood L. Analysis of the gene-dense major histocompatibility complex class III region and its comparison to mouse. Genome Res 13(12): ***** , 2003.
29. Reeg R and ***** A. Transposon-mediated sequencing. Meth Mol Biol 255: ***** , 2004.
30. Fahey J, Helton E, Ketteman M, ***** A, Rodrigues S, Sanchez A, Whiting M, ***** A, and the rest of the MGC Consortium. The NIH mammalian gene collection of full length cDNAs: Update and the inclusion of additional species. Genome Res 14(10b): ***** , 2004.
31. Cieslewicz MJ, Chaffin D, Glusman G, Kasper D, ***** A, Rodrigues S, Fahey J, Wessels MR, Rubens CE. Structural and genetic diversity of group B streptococcus capsular polysaccharides. Infect Immun. 73(5): ***** (2005).
32. ***** A, Eremeeva, ME, Shaw C, Tang K. , and Dasch, GA. New Perspectives on Rickettsial Evolution from New Genome Sequences of Rickettsia, particularly R. Canadensis, and Orientia tsutsugamushi. Annals of the New York Academy of Sciences 1063: ***** (2005).
33. Rowen L. , ***** A, Qin S, Abbasi N, Baradarni L, Birditt B, Bloom S, Dors M, Fahey J, Fleetwood P, Friedman C, Hensley G, Johnson E, Kaur A, ***** A, Ratcliffe A, Nesbitt R, Steward S, Vincent D, Hood L and rest of chromosome 15 consortium. Analysis of the DNA sequence and duplication history of human chromosome 15. Nature 440 (7084): ***** (2006).
34. Wise KS, Foecking MF, Roske K, Lee JY, Lee YM, ***** A and Calcutt, MJ. A Distinctive Repertoire of Contingency Genes Conferring Mutation-based Phase Variation and Combinatorial Expression of Surface Lipoproteins in Mycoplasma capricolum subsp. Capricolum of the Mycoplasma mycoides Phylogenetic Cluster. J. Bacteriol. 188 (13) ***** (2006).
35. Foltz G, Ryu G, Yoon JG, Nelson T, Fahey J, Frakes A, Hwahyung L, Field R, Zander K, Sibenaller Z, Ryken TC, Vibhakar R, Hood L and ***** A. Genome-wide analysis of epigenetic silencing identifies BEX1 and BEX2 as candidate tumor suppressor genes in malignant glioma. Cancer Res. 66 (13): ***** (2006).
36. Dokras A, Coffin J, Field L, Frakes A, Lee H, ***** A, NelsonT, Ryu G, Yoon JG and ***** A. Epigenetic regulation of maspin expression in the human placenta. Molecular Human Reproduction 12 (10): ***** (2006).
37. Vibhakar R, Foltz G, Yoon JG, Lee H, Ryu G, Pierson J, Davidson B and ***** A. Dickkopf-1 is an epigenetically silenced candidate tumor suppressor gene in medulloblastoma. Neuro-Oncology 9 (2): ***** (2007).
38. Philibert R, ***** A, Andersen A, Cadoret R, Packer H, Sandhu H. Serotonin transporter mRNA levels are associated with the methylation of an upstream CpG island. Am J Med Genet B Neuropsychiatr Genet. 144 (1): ***** (2007).
39. Philibert RA, Crowe R, Ryu GY, Yoon JG, Secrest D, Sandhu H, ***** A. Transcriptional profiling of lymphoblast lines from subjects with panic disorder. Am J Med Genet B Neuropsychiatr Genet. 144 (5): ***** (2007).
40. Philibert RA, Ryu GY, Yoon JG, Sandhu H, Hollenbeck N, Gunter T, Barkhurst A, Adams W, ***** A. Transcriptional profiling of subjects from the Iowa adoption studies. Am J Med Genet B Neuropsychiatr Genet. 144 (5): ***** (2007).
41. Philibert RA and ***** A. Role of MED12 in transcription and human behavior. Pharmacogenomics. 8(8): ***** (2007)
42. Price N, Foltz G, ***** A, Hood L, Tian Q. Systems biology of cancer stem cells. J Cell Mol Med, 12(1): ***** (2008).
43. Philibert RA, Sandhu H, Hollenbeck N, Gunter T, Adams W and ***** A. The relationship of 5HTT (SLC6A4) methylation and genotype on mRNA expression and liability to major depression and alcohol dependence in subjects from the Iowa Adoption Studies. Am J Med Genet B Neuropsychiatr Genet. 147B(5): ***** (2008).
44. Philibert RA, Gunter TD, Beach SR, Brody GH and ***** A. MAOA methylation is associated with nicotine and alcohol dependence in women. Am J Med Genet B Neuropsychiatr Genet. 147B(5): ***** (2008).
45. Ealy M, Chen W, Ryu GY, Yoon JG, Welling DB, Hansen M, ***** A, Smith RJ. Gene expression analysis of human otosclerotic stapedial footplates. Hear Res. 240(1-2):80-6 (2008).
46. Foltz G, Yoon JG, Lee H, Ryken TC, Sibenaller Z, Ehrich M, Hood L, ***** A. DNA methyltransferase-mediated transcriptional silencing in malignant glioma: a combined whole-genome microarray and promoter array analysis. Oncogene 28(29): ***** (2009).
47. Philibert RA, Beach SR, Gunter TD, Brody GH, ***** A, Gerrard M
The effect of smoking on MAOA promoter methylation in DNA prepared from lymphoblasts and whole blood. Am J Med Genet B Neuropsychiatr Genet. 2009 Sep 23 [Epub ahead of print]
Anup ***** , Ph. D.