Welcome
to Amol Prakash's homepage.
I graduated in June 2006, and I am now working with Thermo Fisher Scientific as a senior research scientist. My email below is still valid.
Ph.D. student,
Department of Computer Science & Engineering,
University of Washington, Seattle, WA-98195
Affiliate Research Staff Member,
Early Detection Initiative,
Fred Hutchinson Cancer Research Center, Seattle, WA-98109
Affiliate Research Staff Member,
Systems Biology,
Institut Pasteur, Paris, France
Objective
I am planning to graduate in May/June 2006. Currently I am looking for a full-time position that provides me with exciting research problems and an excellent team of colleagues.
My main focus is computational biology (in particular, algorithms for mass spectrometry and genomic sequence analysis), but any Computer Science problem that has algorithmic
aspects or aims to impact the next-generation technology intrigues me.
References
Please send me an email : amol[AT]cs.washington.edu
Publications
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Re-analysing yeast through comparative genomics. (with M. Tompa, J. Maurer, J. Hughes, T. Roseman).
Work in progress , 2007
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Computing the significance of multiple sequence alignments using SigMA. Amol Prakash and Martin Tompa.
Submitted to IEEE Transactions, 2007 Abstract
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Assessing bias in experiment design for large-scale mass spectrometry-based quantitative proteomics. (with B. Piening, J. Whiteaker, H. Zhang, A. Paulovich and B. Schwikowski).
Molecuar and Cellular Proteomics , 2007.PDF Work covered in Journal of Proteomics Research
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Measuring the Accuracy of Genome-Size Multiple Alignments. Amol Prakash and Martin Tompa.
Genome Biology, 2007 PDF
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Quality Control Metrics for LC-MS Feature Detection Tools Demonstrated on Saccharomyces cerevisiae Proteomic Profiles. B. Piening, P. Wang, C. S. Bangur, J. Whiteaker, H. Zhang, L. Feng, J. Keane, J. Eng, H. Tang, A. Prakash, M. McIntosh and A. Paulovich.
Journal of Proteome Research, 2006.PDF
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Signal Maps for Mass Spectrometry-based Comparative Proteomics. A. Prakash, P. Mallick, J. Whiteaker, H. Zhang, A. Paulovich, M. Flory, H. Lee, R Aebersold, and B. Schwikowski.
Molecular and Cellular Proteomics published online November 3, 2005, 10.1074/mcp.M500133-MCP200. Expected journal publication date : March 2006.PDF Art selected for cover page
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Discovery of regulatory elements in vertebrates through comparative genomics. Amol Prakash and Martin Tompa.
Nature Biotechnology, vol. 23, no. 10, October 2005, 1249 - 1256.PDF
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Statistics of local multiple alignments. Amol Prakash and Martin Tompa.
13th Annual International Conference on Intelligent Systems for Molecular Biology, Detroit, MI, June 2005. Bioinformatics,vol. 21, June 2005, i344 - i350.PDF
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Motif Discovery in Heterogeneous Sequence Data. Amol Prakash, Mathieu Blanchette, Saurabh Sinha, and Martin Tompa.
Pacific Symposium on Biocomputing, Hawaii, January 2004, 348-359.PDF
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Performance Modeling and Analysis of a Handover Channel Exchange Scheme in Mobile Cellular Communication Systems. Manpreet Dang, Amol Prakash, Rajeev Shorey, Natwar Modani and Dinesh Anvekar
IEEE International Conference on Communications, New Orleans, USA, June 2000.PDF
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Fuzzy Logic Based Handoff in indoor Wireless Networks. Manpreet Dang, Amol Prakash, Dinesh Anvekar, Manika Kapoor and Rajeev Shorey.
IEEE Vehicular Technology Conference, Japan, May 2000, 2375-2379.PDF
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Patents
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Maintaining Data Communication through Neighboring Mobile Units During Handoff. (with Dinesh K. Anvekar (IBM), Manpreet S. Dang and Rajeev Shorey (IBM))
Patent Number US6377805, Issued by USPTO on April 23, 2002.
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Mobile Battery Discharge Minimization in Indoor Wireless Networks by Antenna Switching. (with Dinesh K. Anvekar (IBM) and Manpreet S. Dang)
Patent Number US6594475, Issued by USPTO on July 15, 2003.
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Research/Work Experience
| Research Assistant | Tompa Lab, Department of Computer Science, University of Washington, Seattle, WA | June 2002 - present |
| Research Intern | Schwikowski Lab, Institute for Systems Biology, Seattle, WA | June 2003 - Jan 2004 |
| Teaching Assistant | Department of Computer Science, University of Washington, Seattle, WA | Sept 2001- June 2002 |
| Software Developer | Sapient Corp., New Delhi, India | June 2001 - Sept 2001 |
| Summer Intern | Algorithms and Complexity Group, Max-Planck-Institut für Informatik, Germany | May 2000 - July 2000 |
| Research Intern | IBM, India Research Labs, India | Feb 1999 - March 2000 |
Educational Background
2003
Master of Science,
Department of Computer Science and Engineering,
University of Washington, Seattle, WA-98195
2001
Bachelor of Technology,
Computer Science & Engineering
Indian Institute of Technology, New Delhi
1997
All India Senior Secondary Examination
St. Xavier's School, Delhi
Academic Awards/Scholarships
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Recipient of Institute Merit Award for securing 1st position in Computer Science Department of IIT Delhi in semester 5. 2000
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Awarded Silver medals for Excellent performance in Manav Sthali Inter-School Mathematics Talent Test. 1993, 1994, 1995.
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Recipient of the National Talent Search Examination Scholarship (NTSE) conducted by the National Council for Educational Research and Training (NCERT). 1995
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Recipient of Merit Certificate in National Mathematics Olympiad Contest, by Delhi Association of Mathematics Teachers. 1994
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Recipient of Open Merit Scholarship by Govt. of the National Capital Territory of Delhi, Directorate of Education, Delhi. 1994
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Extra Curricular Activities
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Percussionist, Pratidhwani (A light music band based in Seattle), 2004-present
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President, UWdesi (Registered organisation with University of Washington serving students coming from India) 2002-2004
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Member, Orientation Committee and Prospective Student Committee, Department of Computer Science, University of Washington during 2002-2003.
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General Secretary, Association of Computer Scientists and Engineers, Computer Science Dept., IIT Delhi during 2000-2001.
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Recipient of President's Award for being a member of Delhi State Scouts, India, in 1994.
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Represented Delhi State in Tennis during 38th National School Games for Lawn Tennis & Table Tennis held at Surat, India in 1993.
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