Babru Bahan Samal
*******@*****.***
Summary
I am a bioinformatics specialist with extensive hands on experience in molecular and cellular biology. I have managed research in health care industry for more than 20 years. My expertise is in knowledge extraction from high throughput gene expression and protein array data, databases, extension of knowledge about novel genes or phenomena by data mining and motif analysis, data integration from a systems biology point of view using pathways and ontology for therapeutic product development.
Education and Training:
Post-doctoral training (functional genomics)
• Princeton University, Princeton, NJ. (1979 - 1981)
• Baylor College of Medicine, Houston, TX. (1977-1979)
PH.D. cellular and molecular biology (functional genomics)
• University of Southern California, Los Angeles, CA, USA 1977
Honors and awards:
• Phi Sigma award for best Ph.D. thesis, USC, Los Angeles,1977
• National Scholarships from the Government of India, 1965-1971, 1973-1977
Membership in Professional Organization
• Society for Neuroscience
Employment History and accomplishment
NIAID, NIH, Rockville, MD
Staff Scientist, Bioinformatics Core (2011-2012)
• Identified and annotated genes modulated in malaria patient PBMC from high throughput gene expression data.
• Defined the impact of TLR7 on gene expression in transgenic mice from Illumina microarray data
• Identified genes modulated by agonist antibodies in NK cells.
• Worked on standardization of protein array normalization and statistical analysis.
• Identified immunogenic proteins in Plasmodium falciparum protein array experiments.
• Assigned P. falciparum proteins expression to different stages by combining MASS spec and transcriptome data.
• Identified cytokines whose profile changed by malaria infection by analyzing Luminex data.
NIMH, NIH, Bethesda, MD
Bioinformatics Core Specialist (2005- 2011)
Special volunteer scientist in Bioinformatics (2003 – 2005)
• Interacted with a number of principal investigators to identify the targets of specific genes in CNS in gene knockout experiments.
• Identified genes which are modulated by neuropeptide PACAP in bovine chromaffin cells, in PC12 cells or in mice with ischemia.
• Identified genes which are modulated by TNF in bovine chromaffin cells.
• Designed methods for functional annotation of novel genes
• Managed Science Signaling website for connection map for PC12 differentiation
• Developed a database by compiling all microarray gene expression studies done at SMN.
• Developed a database for the effect of different antidepressants on gene expression.
NeuralStem Inc, Rockville, MD
Consultant on Bioinformatics and Molecular Biology (2006-2011)
Principal Scientist, Gene Discovery (2000-2002)
• Identified differentiation stage specific gene expression in human neural stem cells and also as a response to specific chemicals (Affymetrix and Agilent microarrays).
• Provided molecular biology expertise for optimal expression of therapeutically relevant foreign genes in transfected neural stem cells in vivo.
• Identified more than 12000 novel brain stem cell specific transcript tags by developing a novel 5’ SAGE technology.
H J Foundation for the Advancement of Military Medicine, Inc, Rockville, MD
Staff Scientist, Neurotrauma Gene Discovery Program (2010-2011)
• Created a neurotrauma database by text mining the effect of different traumatic brain injuries on different brain regions at the transcription level (http://www.molecularbrain.org/TBI/
• Studied the impact of trauma on microRNA and transcriptome by analyzing microarray and deep seq data.
Johns Hopkins University, School of Medicine, Baltimore
Staff Scientist, Oncology (2004 – 2005)
• Identified the genes modulated during hematopoietic stem cells undergoing differentiation in vitro.
ISU chemicals, Seoul, Korea (Biotechnology Division, Rockville, MD)
Consultant in bioinformatics, genomics and molecular biology (2003 – 2004)
• Identified genes modulated during inflammation induced by cytokines and other reagents.
• Submitted two patent drafts for which the company received $25 million dollars to develop the products at their Seoul facility
Psychiatric Genomics, Gaithersburg, MD
Director, Neurogenomics (2002 - 2003)
• Derived a geneset for high throughput screening of novel therapeutics by analyzing gene expression data from post mortem brain, cell culture and animal model systems for various psychiatric diseases (depression. Schizophrenia, bipolar)
Imgenex Inc, San Diego, CA
Director of Bioinformatics and Molecular Biology (1999 - 2000)
• Identified novel therapeutic molecules by mining public databases,cloning and expression studies.
• Submitted R01 grants for research.
Amgen Inc, Thousand Oaks, CA
Research Scientist I, II and III (1981 - 1999)
• Developed a signal trap procedure and used it for identifying genes encoding secreted proteins.
• Cloned, expressed and studied the functions of PBEF (Visfatin), LIF, Proteinase T and TNF and quite a few other novel secreted proteins in both in vitro and in vivo model systems.
• Cloned and expressed different spliced forms of human thrombopoietin.
Certificates
• German language proficiency, 1972 (Goethe Institut)
• Novel techniques in data analysis, 2003-2011(NIH sponsored classes)
Research Management Experience:
NeuralStem Inc.
• Managed the gene discovery department with bioinformatics, molecular Biology and DNA sequencing groups (2000-2002).
Amgen Inc.
• Managed the committee overseeing the process of discovery and functional characterization of novel genes identified in Amgen genome project (1996-1999).
• Managed the interaction between the computational biology and molecular biology group for implementing computational tools in molecular biology research and improving computational tools by testing them in wet labs.
• Managed of collaborations with professors at UCI, UCSD etc. for delineating the biological function of different cytokines ( 1992-1999)
• Managed research in molecular and cellular biology for new therapeutic drug development (1981-1999)
Technical Expertise
Data analysis and data mining (1995-present)
• Analysis of large biological datasets (gene expression, protein array, sequences)
• Derivation of ontological, pathway, network and signal transduction information from complex high dimensional data.
• Knowledge extraction from public databases at NCBI, EBI, UCSC genome browser.
• Identification of co-regulation of genes by promoter analysis..
• Integration of microRNA and gene expression data (Affymetrix, Agilent, Illumina).
• Designing work flows for genome, transcriptome analysis for data integration
• Relational database creation and content management using SQL, PHP and HTML.
• Data and text mining for assignment of function to novel genes.
• Experience in utilizing R and Python and Perl scripts.
Molecular Biology (1973-2002)
• Cloning and functional studies of novel genes using bioassay and gene transfer.
• Expression and purification of novel gene products from E. coli, insect and mammalian cells
• Study of the effect of cytokines on cancer cells (TNF, IFN-gamma, IL-6).
• Documentation for GLP and GMP and toxicology studies (SOPs).
Publication and Patents
Please click (http://www.babru.com/SamalPubPat.pdf )