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Chaskar CV

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Chaskar CV

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Chaskar CV

  1. 1. Dr. Prasad Chaskar CONTACT DETAILS Avenue de Cour 126 1007 Lausanne, Switzerland Mobile: +41 78 922 38 66 E-mail: prasadchaskar@gmail.com DATE OF BIRTH December 27, 1986 AVAILABILITY Immediately PERMIT Valid residence permit with rights to work in Switzerland. EDUCATION Ph.D. (March 2012 - February 2016) Swiss Institute of Bioinformatics and University of Lausanne, Switzerland M.Tech. (June 2009 - July 2010) Institute of Bioinformatics and Biotechnology, Pune, India M.Sc. (June 2004 - May 2009) Institute of Bioinformatics and Biotechnology, Pune, India WORK EXPERIENCE Data Scientist (March 2016 - Present) Philip Morris International, Neuchâtel, Switzerland • Established data fusion by matrix tri-factorization method for the integration of heterogeneous omics data. Researcher (March 2012 - February 2016) SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland • Developed a high-quality dataset of zinc and heme ligand-bound protein structures. • Successfully developed an on-the-fly quantum mechanical/molecular mechanical (QM/MM) docking algorithm and benchmarked it on diverse datasets. • Modeled the structure of an anticancer target MAP3K8 and performed virtual high-throughput screening (vHTS) of small molecules against it. Researcher (March 2011 - January 2012) National Center for Biological Sciences, Bangalore, India • Successfully investigated substrate recognition by DNA repair enzymes using computational chemistry methods. Junior Researcher (May 2007 - June 2009) National Center for Cell Sciences, Pune, India • Developed a computer application for transcription factor binding site prediction and analysis. • Established ChIP-on-chip assays to investigate role of epigenetics modifications and tran- scription factors in ovarian cancer progression. • Performed gene expression analysis and pathway analysis to identify bio-markers in ovarian cancer progression. EXPERTISE Technical skills: • Bioinformatics data analysis (e.g. sequence analysis, gene expression analysis, omics data integration), molecular modeling (e.g. homology modeling, molecular dynamics and QM/MM simulations), molecular and cell biology experiments (e.g. cell culture, ChIP-on-chip), scien- tific writing, presentation techniques. Computational tools: • Bioinformatics tools, R Studio, Gene Set Enrichment Analysis (GSEA), molecular modeling tools, Microsoft Office Excel.
  2. 2. Computer Programming: • Perl, UNIX shell scripting, R, Python, CHARMM. Operating Systems: • Linux and other UNIX variants, Microsoft Windows family. PUBLICATIONS 1. Chaskar, P.; Zoete, V.; Röhrig, U. F., On-the-Fly Quantum Mechanical/Molecular Mechani- cal (QM/MM) Docking with Attracting Cavities. (Submitted J. Chem Inf. Model-July2016) 2. Zoete, V.; Thierry, S.; Bovigny, C.; Daina, A.; Röhrig, U. F.; Chaskar, P.; Michielin, O. Attract- ing Cavities For Docking. Replacing The Rough Energy Landscape Of The Protein By A Smooth Attracting Landscape. J. Comput. Chem. 2016, 5, 437-47. doi:10.1002/jcc.24249 3. Chaskar, P.; Zoete, V.; Röhrig, U. F., Toward on-the-Fly Quantum Mechanical/Molecular Mechanical (QM/MM) Docking: Development and Benchmark of a Scoring Function. J. Chem Inf. Model. 2014, 54, 3137-3152. doi:10.1021/ci5004152 4. Kurrey, N. K.; Jalgaonkar, S. P.; Joglekar, A. V.; Ghanate, A. D.; Chaskar, P. D.; Doiphode, R. Y.; Bapat, S. A., Snail and Slug Mediate Radioresistance and Chemoresistance by An- tagonizing P53-Mediated Apoptosis and Acquiring a Stem-Like Phenotype in Ovarian Can- cer Cells. Stem Cells. 2009, 27, 2059-2068.doi:10.1002/stem.154 CONFERENCE POSTERS 1. Chaskar, Prasad; Zoete, Vincent; Michielin, Olivier; Röhrig, Ute. On-The-Fly Quantum Mechanical/ Molecular Mechanical (QM/MM) Docking. In: Computational Advances in Drug Discovery, Lausanne, Switzerland, September 22-25, 2015 2. Chaskar, Prasad; Zoete, Vincent; Michielin, Olivier; Röhrig, Ute. On-The-Fly Quantum Mechanical/ Molecular Mechanical (QM/MM) Docking. In: Basel Computational Biology Conference (BC2) 2015, Basel, Switzerland, June 7-10, 2015 3. Chaskar, Prasad; Puranik, Mrinalini. QM/MM Modeling and UVRR studies of DNA repair Enzymes. In: Innovative Approaches to Computational Drug Discovery, CECAM, EPFL, Lausanne, Switzerland, October 2-6, 2011 WORKSHOPS 1. Understanding Molecular Simulations, University of Amsterdam, Netherlands, January 7- 18, 2013 2. International Chemical Design and Discovery Course, Radboud University, Nimegen, Nether- lands, June 18-28, 2012 3. Advances in Biomolecular Modeling and Simulations using CHARMM, University College Dublin, Ireland, June 5-8, 2012 4. Computational Chemogenomics to understand Systems Biology and Computational Medic- inal Chemistry, University of Geneva, Switzerland, May 14-16, 2012 LANGUAGES • English (professional working proficiency) • Marathi (mother tongue) • Hindi (fluent) • French (beginner (A1 Level), taking lessons to improve French language skills).
  3. 3. REFERENCES 1. Prof. Olivier Michielin (MD-PhD) (Ph.D. supervisor at SIB-Lausanne) Department of Oncology, University of Lausanne and Centre Hospitalier Universitaire Vau- dois (CHUV), CH-1011 Lausanne, Switzerland Email: Olivier.Michielin@unil.ch Phone: +41 21 314 01 85 2. Dr. Vincent Zoete (Ph.D. co-supervisor at SIB-Lausanne) Swiss Institute of Bioinformatics Unil, CIG - Quartier Sorge, bâtiment Genopode - 1015 Lausanne Email: vincent.zoete@sib.swiss Phone: +41 21 692 40 82 3. Dr. Ute Röhrig (Ph.D. co-supervisor at SIB-Lausanne) Swiss Institute of Bioinformatics Unil, CIG - Quartier Sorge, bâtiment Genopode - 1015 Lausanne Email: ute.roehrig@sib.swiss Phone: +41 21 692 40 86 4. Dr. Jay Siddharth (Mentor-microbiology at University of Pune, India) Nestle Institute of Health Sciences SA, EPFL Innovation Park, bâtiment H - 1015 Lausanne Email: jaysiddharth@gmail.com Phone: +41 21 632 61 73 5. Dr. Björn Titz (Project supervisor at PMI-Neuchâtel) Philip Morris International, R&D Innovation Cube T1535 08 - 2000 Neuchâtel Email: Bjorn.Titz@pmi.com Phone: +41 58 242 2312

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