Expert Details

Bioinformatics, Next-Generation Sequencing, SNP Analysis, Scientific Computing

ID: 726906 India

The world of molecular biology is experiencing a deluge of quantitative data with the advent of new technologies such as high throughput sequencing, chromatin-immunoprecipitation sequencing, and RNA sequencing. New sequencing technologies are now producing sequence data at a very high rate, and this has created a greater need for bioinformatics tools to effectively organize and analyze the data.

One part of Expert's research is on correlating genotypes with phenotypes. He develops methods that can be used to associate a genotype (sequence data) with phenotype (physical traits) while taking the phylogenetic history of the organisms under consideration into account. In short, he is mining datasets of mutational history implied by phylogenetic trees for concurrent changes in phenotype and genotype among lineages to identify candidate loci for phenotypic traits. Another part of his research is related to finding binding sites for transcription factors that regulate gene activity and patterns between different transcription factor binding sites. The results of this can help elucidate regulatory networks in different cell types.

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Education

Year	Degree	Subject	Institution
Year: 2007	Degree: PhD	Subject: Bioinformatics/Physics	Institution: The Ohio State University
Year: 2004	Degree: Master of Science	Subject: Physics	Institution: The Ohio State University
Year: 1999	Degree: Bachelor of Technology	Subject: Engineering Physics	Institution: Indian Institute of Technology, Bombay

Work History

Years	Employer	Title	Department
Years: 2009 to Present	Employer: Undisclosed	Title: Scientist	Department: Center of Excellence in Epigenetics
Responsibilities: Handling bioinformatics queries and developing workflows for next generation sequencing (NGS) data analysis for the Center of Excellence in Epigenetics. In particular, developing pipelines for analysis of transcription factor and histone modification Chip-seq, RNA-seq, and whole genome next generation sequencing. Collaborating with other academic and industry researchers. In detail: • Developed algorithms and workflows for NGS data analysis particularly assembly of genomes, ChIP-seq, and RNA-seq • Developed an algorithm (GePhCorT) for finding genomic regions associated with a phenotype and tested it with HDL Cholesterol levels in mice. • Analyzed the evolution MADF-BESS gene family in dipterans and its expansion in Drosophila (Genetics, 2014) • Developed databases for querying and displaying biological data, among them, development of a Human Histone database (Nucleic Acids Research, 2012) • Collaborating with Persistent Systems Limited on development of SanGenix, a user friendly Next Generation Sequencing data analysis suite • Organized a hands-on workshop on Next Generation Sequencing data analysis • Part of the IISER Information Technology committee which sets policy on use of IT resources in the campus

International Experience

Years	Country / Region	Summary
Years: 2000 to 2007	Country / Region: USA	Summary: Working as a teaching assistant in Physics, Expert took lectures as well as conducted labs for undergraduate pre-medical and pre-engineering courses. His teaching was widely appreciated and his reviews were excellent.

Career Accomplishments

Associations / Societies
American Physical Society

Publications and Patents Summary
Expert has 3 first-author publications and 7 co-authored peer-review publications in bioinformatics and computational biology.

Additional Experience

Training / Seminars
Conducted two courses for large undergraduate classes. One a general course on Introduction to Computation and another a course on Scientific Computing. Organized a workshop on Next Generation Sequencing Bioinformatics Taught undergraduate and graduate courses in Bioinformatics and Biostatistics

Vendor Selection
Participated in various computer hardware sourcing for IISER Pune, in particular for a cluster solution for a 7 TFlop cluster and for High performance general purpose graphics processing unit (GPGPU) machines.

Marketing Experience
A good overview of industry trends in the bioinformatics and computational biology space, especially related to upcoming software as well as hardware required for different tasks and hos they may scale in the coming years.

Language Skills

Language	Proficiency
Hindi

Fields of Expertise

amino acid sequence, bioinformatics, genetic sequencing, genome, pharmacogenetics, protein sequence database, RNA sequencing, amino acid analysis, clinical genetics, computational biology, computer algorithm optimization, medical genetics, nucleotide mapping, pharmacogenomics, human genome, DNA sequencing, genetics, computer algorithm