Curriculum Vitae

Email: fhabib@iiserpune.ac.in

Interests: Bioinformatics, modeling of biological systems, mathematical biology

Education

PhD, Physics (jointly with Biomedical Informatics), The Ohio State University, Columbus, OH	2007
Thesis Topic: Large Scale Genotype-Phenotype Correlations Using Phylogenetic Trees Advisors: Professor Daniel Janies (Biomedical Informatics), Professor Ralf Bundschuh (Physics)
MS, Physics, The Ohio State University, Columbus, OH	2004
Thesis Topic: Modeling of DNA unzipping including DNA-protein interactions
B.Tech., Engineering Physics, Indian Institute of Technology (IIT) Bombay, India	1999

Research Experience

Scientist C, Center of Excellence in Epigenetics, Indian Institute of Science Education and Research, Pune	October 2010 – present
IISER Fellow, Indian Institute of Science Education and Research, Pune	February 2009 – October 2010
Performing motif analysis in ChIP-chip sequencing data Developing visualization software for genotypic data Supervising undergraduate students in research projects
Postdoctoral Research: Department of Plant Pathology, Kansas State University	April 2008 – January 2009
Performing comparative genomic studies and identifying SNPs Developing pipelines for aligning short reads obtained from the Illumina platform to the Sorghum genome Setting up SQL databases for querying genomic data Supervised a graduate assistant to develop a website for dynamically displaying research results
Doctoral Research:Department of Biomedical Informatics and Department of Physics, OSU	June 2004 – August 2007
Developed and implemented algorithms (in Perl, AWK, and TNT scripting languages) to perform genome wide association between genotypes and phenotypes taking phylogenetic history into account Discovered novel and known genes responsible for resistance to anthrax in mice to test the developed algorithms Identified candidate locations for mutations in the flu virus responsible for avian to human transmission Results published in Bioinformatics and Systematic Biology Proposed, built, and administered a cluster of 8 headless, diskless Linux servers for computations
Masters Research: Department of Physics, OSU	June 2002 – May2004
Developed a mathematical model for stretching and unzipping of DNA with bound proteins Determined a lower limit for the protein-DNA binding energy that can be detected with force spectroscopy Results published in Physical Review E
Research Project: Department of Physics, OSU	April 2002 – January 2003
Modeled neural activity in the visual cortex of primates after exposure to natural images Implemented a neural network in Mathematica to test the model developed
Research Project: Department of Physics, OSU	June 2001 – March 2002
Performed statistical analysis of RNA sequences to find biologically relevant regions in random sequences Developed software for RNA folding in C to understand the statistics of long energetically stable subregions within a random RNA sequence

Teaching Experience

Interdisciplinary course: Indian Institute of Science Education and Research, Pune	Fall 2010
Introduction to Computation to first year undergraduates.
Biology course: Indian Institute of Science Education and Research, Pune	Spring 2010, Fall 2011
Bioinformatics and Computational Biology to third and fourth year undergraduates.
Interdisciplinary course: Indian Institute of Science Education and Research, Pune	Fall 2009, Fall 2010
Scientific Computing to second year undergraduates. Introduction to Computation to first year undergraduates.
Department of Physics: The Ohio State University	September 2000 – June 2007
Lectured undergraduate pre-medical and pre-engineering students in algebra and calculus based introductory Physics courses Supervised undergraduate students in introductory Physics labs

Awards

Departmental Fellowship, merit-based one year fellowship for graduate study at The Ohio State University, 1999
National Talent Search Scholarship, given by Government of India, 1992

Journals Refereed

Peer reviewer for Physical Review E (Statistical, Nonlinear, and Soft Matter Physics)

Peer reviewer for Bioinformatics and Briefings in Bioinformatics

Invited Talks

Genome Assembly of Hydra vulgaris from short reads, presented at Bioinformatics symposium titled “Accelerating Biology 2012 : Computing to Decipher”, Pune, India. February 16, 2012

Bioinformatics challenges and opportunities of massively parallel sequencing, presented at Indian Academy of Sciences Discussion Meeting on “Computational Biology in India: status and prospects”, Coorg, India. February 28, 2011

Using high performance computing to manage the data deluge in biology, at Workshop on Next Generation Application Challenges on PARAM Yuva at Center for Development of Advanced Computing, Pune. February 25, 2011.

Reproducible Research in Bioinformatics Using Galaxy, Advanced Centre for Treatment, Research and Education in Cancer, Navi Mumbai, India. February 18, 2011.

Genotype-phenotype correlation in the presence of phylogeny, Tata Institute of Fundamental Research (TIFR), Mumbai, India. August 19, 2009.

Next Generation Sequencing and Sequence Alignment, Genotypic Technology Pvt. Ltd., Bangalore, Karnataka, India. May 16, 2009.

Large Scale Genotype-Phenotype Correlations Using Phylogenetic Trees, Centre for Cellular and Molecular Biology (CCMB), Hyderabad, India. Mar 23, 2009.

Large Scale Genotype-Phenotype Correlations Using Phylogenetic Trees, Indian Institute of Science Education and Research, Pune, India. Jan 23, 2009.

Sequence Alignment and its Applications, Physical Research Laboratory, Ahmedabad, Gujarat, India. January 15, 2009.

Sequence Alignment and its Applications, Mohanlal Sukhadia University, Udaipur, Rajasthan, India. Nov 22, 2008.

Selected Posters and Presentations

Habib, F., Genome-wide Identification of transcription factor binding sites of Hox protein Ultrabithorax in Drosophila. Presented at the International Conference on Mathematical and Theoretical Biology, Pune, India, January 2012.

Agrawal, P., Habib, F., Yelagandula, R., Shashidhara, L. S., Genome-wide Identification and analysis of direct targets of the Hox protein Ultrabithorax in Drosophila. Presented at Asia Pacific Drosophila Research Conference, Taipei, Taiwan, May 2011.

Agrawal, P., Habib, F., Yelagandula, R., Shashidhara, L. S., Genome-wide Identification and analysis of direct targets of the Hox protein Ultrabithorax in Drosophila. Presented at the Annual Meeting for Japanese Society of Developmental Biologists, Okinawa, Japan, May 2011.

Habib, F., Johnson, A., Bundschuh, R., and Janies, D., Correlating continuous phenotypes with genotypes using phylogenetic trees. Presented at The Ohio Collaborative Conference for BIOinformatics (OCCBIO) at Miami, OH, July 2007.

Habib, F., Johnson, A., Bundschuh, R., and Janies, D., Genotype-Phenotype Correlations Using Phylogenetic Trees for Large Datasets. Presented at The Ohio Collaborative Conference for BIOinformatics (OCCBIO) at Athens, OH, June 2006.

Johnson, A., Habib, F., Camerlengo, T., Ervin, D., and Janies, D., Systems Biology integration of large mouse SNP datasets and physiological biomarker data to discover cardiovascular disease candidate genes. Poster at BioOhio, October 2006.

Habib, F., Janies, D., and Bundschuh, R., Phylogenetic methods for computationally correlating genotypes and phenotypes. Presented at the Ohio Section of the American Physical Society meeting in Cleveland, OH, October 2005.

Habib, F. and Janies, D., Intersection and Exclusion Analysis of Genomic Changes Implied by Phylogenetic Trees. Poster at the Ohio Section of the American Physical Society meeting, April 2005.

Johnson, A., Habib, F., and Janies, D., Novel Method for Inferring Genotype-Phenotype Associations to Identify Disease Susceptibility Loci. Poster at the Complex Trait Meeting Jackson Lab, Bar Harbor, ME, July 2004.

Habib, F. and Janies, D., Intersection and Exclusion Analysis of Genomic Changes Implied by Phylogenetic Trees. Poster at the Ohio State University Medical Center Research Day, April 2004.

Publications

Agrawal P, Habib F, Yelagandula R, Shashidhara LS. Genome-level identification of targets of Hox protein Ultrabithorax in Drosophila: novel mechanisms for target selection. Scientific Reports. 2011 Dec;1.

Khare SP^*, Habib F^*, Sharma R, Gadewal N, Gupta S, Galande S; HIstome: a relational knowledgebase of human histone proteins and histone modifying enzymes (Nucleic Acids Research (2011) Database issue doi:10.1093/nar/gkr1125).

Janies, D., Treseder, T., Alexandrov, B., Habib, F., Chen, J. C., Ferreira, R., Ҫatalyürek, Ü., Varón, A., Wheeler, W.C., The Supramap Project: Linking Pathogen Genomes with Geography to Fight Emergent Infectious Diseases. Cladistics. 2011, 27(1), 61-66.

Hill, A.W., Guralnick, R., Wilson, M. J. C., Habib, F., Janies, D., Evolution of Drug Resistance in Multiple Distinct Lineages of Influenza A/H5N1. Infection, Genetics and Evolution. 2009, 9(2), 169-178.

Janies, D., Habib, F., Alexandrov, B., and Pol, D., Evolution of genomes, host shifts, and the geographic spread of SARS-CoV and related coronaviruses. Cladistics. 2008, 24(2), 111-130.

Habib, F., Johnson, A.D., Bundschuh, R., and Janies, D., Large scale genotype-phenotype correlation analysis based on phylogenetic trees. Bioinformatics. 2007, 23, 785-788.

Janies, D., Hill, A.W., Guralnick, R., Habib, F., Waltari, E., and Wheeler, W., Genomic Analysis and Geographic Visualization of the Spread of Avian Influenza. Systematic Biology. 2007, 56, 321-329.

Kurc, T., Janies, D.A., Johnson, A.D., Langella, S., Oster, S., Hastings, S., Habib, F., Camerlengo, T., Ervin, D., Catalyurek, U.V., and Saltz, J.H., An XML-based system for synthesis of data from disparate databases. Journal of American Medical Informatics Association, May-Jun 2006; 13(3), 289-301.

Habib, F. and Bundschuh, R., Modeling DNA unzipping in the presence of bound proteins. Physical Review E, Statistical and Nonlinear Soft Matter Physics, Sep 2005; 72(3 Pt 1):031906.

* – Equal Contribution

Farhat Habib