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Shobha
Potluri
19 Spencer Street, # 314
Tel: 802-683-7133
Lebanon, NH 03766
Email: potluri@cs.dartmouth.edu
http://www.cs.dartmouth.edu/~potluri
Objective
Seeking a challenging position that best utilizes my academic training
and analytical skills in the area of Computational Biology and Computer
Science.
Competency Area
• Experience in the design, development and analysis
of computational algorithms to solve complex biological and chemical
problems.
• Solid programming skills to develop complex
large-scale applications that harness, analyze and present biological
and chemical data.
• Strong knowledge in multivariate statistics,
statistical data mining and application of statistical modeling
techniques
Education
PhD (Computer Sciences),
CGPA (3.9/4.0) Dartmouth College,
Hanover/NH, (Expected: Mar 07)
Thesis: Protein Complex Structural
Inference by a Complete
Configuration Space Analysis.
Advisors: Prof. Chris Bailey-Kellogg (Computer Science), Prof. Bruce R.
Donald (Computer Science, Chemistry and Biological Sciences)
Mutations in membrane proteins lead to
a vast array of inherited and acquired diseases including Alzheimer’s.
Understanding structure of membrane proteins helps design drugs to
combat these diseases. This project allows for structural inference of
symmetric membrane proteins.
• Chose targets
on which traditional structure determination protocols fail due to
sparseness and ambiguity in experimental data (NMR, mutagenesis,
cross-linking)
• Developed
algorithms that analyze protein complex configuration space to identify
data-consistent regions
• Developed a
probabilistic framework to infer structures of symmetric membrane
proteins and identify information content in the data
• Developed a
Java package that could be used by biologists for structure
determination of symmetric homo-oligomers by NMR
• Adapted and
extended an open source project, KStar, to handle uncertainty in
monomer structure of the symmetric homo-oligomer
MS (Computer Sciences),
CGPA (3.9/4.0) Purdue University, West
Lafayette/IN, Aug 03
Thesis: Geometric Algorithms for High
Throughput Protein Structure
Determination
Advisors: Prof. Chris Bailey-Kellogg (Computer Science), Prof.
Alan M.
Friedman (Biological Sciences)
This work facilitates rapid protein
structure determination essential for key post-genomic tasks such as
modeling molecular cell functionality and applications like drug
design.
• Obtained
experimental data (from cross-linking and mutagenesis) for target
protein
• Developed
geometric algorithms to obtain corresponding data from each of the
target protein models
• Discriminated
protein models by comparing experimental data with computational data
• Developed a
C++ package using Computational Geometry Algorithm Library (CGAL)
BTech (Computer Sciences), CGPA
(4.0/4.0) KLCE, India, April 01
Work Experience
Research Assistant,
Computational Biology Laboratory, Dartmouth College (Jul 04-present)
• In collaboration with Prof. James Chou, Dept. of
Biological Chemistry and Molecular Pharmacology, Harvard Medical School.
Teaching Assistant, Computer
Science Department, Dartmouth College (Winter 06)
• Programming Languages: grading of course projects
Co-advisor, Women in Science
Project (WISP) intern, Dartmouth College (Fall and Spring 05)
• Supervised a freshman student on a research project
involving prediction of complex structure by analysis of intermolecular
distances
Research Assistant, Computational Biology Laboratory, Purdue
University (May 02-Jun 04)
• In collaboration with Prof. Alan Friedman, Dept. of
Biological Sciences, Purdue University
Research Assistant, project funded by the Center for Education
and Research in Information Assurance and Security (CERIAS), Purdue
University (Aug 01– May 02)
• Developed and implemented “An Integrated
Agent-based Architecture for Optimal Security Profile Generation”. In
collaboration with Krannert School of Management.
Computer Skills
Languages:
C/ C++, Java, Python, Oz, Tcl/Tk
Operating Systems: Linux, Xinu,
Windows, Mac OS X
Databases:
SQL, MySQL, Oracle
Statistical Tools:
R, Matlab
Visualization Tools: VMD, Rasmol, Pymol,
Molmol
Libraries:
Posix Threads, BSD
Sockets
Profilers:
GDB
IDE:
Netbeans, Visual Studio
UI:
Java Swing, QT
Course Work
Core Computer Science:
Algorithm Design, Analysis and Implementation, Operating Systems,
Compilers, Numerical Linear Algebra, Internetworking, Advanced
Cryptography
Computational Biology related:
Computational Biology, Machine Learning and Data Mining, Database
Systems, Distributed Database Systems, Simulation and Modeling of
Computer Systems, Statistical Issues in Data Mining, Statistical
Pattern Recognition, Analytical Informatics, Computational biology
journal club
Publications
S. Potluri,
A.K. Yan, J.J. Chou, B.R. Donald, C. Bailey-Kellogg. Structure
Determination of Symmetric Homo-oligomers by a Complete Search of
Symmetry Configuration Space Using NMR Restraints and van der Waals
Packing, Proteins,
65(1), 2006.
S. Potluri,
A.K. Yan, B.R. Donald, C. Bailey-Kellogg. A Complete Algorithm to
Resolve Ambiguous NOE Restraints in Structure Determination of
Symmetric Homo-oligomers, Protein Science,
2006. (Submitted for review.)
S. Potluri,
A.K. Yan, J.J. Chou, B.R. Donald, C. Bailey-Kellogg. Structure
Determination of Symmetric Homo-oligomers by a Complete Search of
Symmetry Configuration Space Using NMR Restraints and van der Waals
Packing, Workshop
on the Algorithmic Foundations of Robotics (WAFR),
2006.
S. Potluri,
A.A Khan, A. Kuzminykh, J.M. Bujnicki, A.M. Friedman, and C.
Bailey-Kellogg. Geometric analysis of cross-linkability for protein
fold discrimination. Pac. Symp. Biocomp (PSB),
2004, 447-58
Posters
“Structure Determination of Symmetric
Homo-oligomers by a Complete SCS Search using NMR Restraints and vdW
Packing”, PSI
(Protein Structure Initiative), NIH, Bethesda, Apr 06
“Molecular Symmetry as an Aid to Homo-oligomeric
Protein Structure Determination by NMR, using Sparse Inter-molecular
NOE Restraints”, 13th annual International
Conference on Intelligent
Systems for Molecular Biology (ISMB), Detroit, Jun 05
“Protein Structure Discrimination by Clustering of
Mutagenesis Data”, 26th annual Midwest
Biopharmaceutical Statistics
Workshop, Ball State University, May 2003.
“Algorithms for Protein Structure Determination
using Cross Linking and Mass Spectrometry”, INGEN (Indiana Genomics
Initiative) Proteomics Symposium, Nov 02
“Behavior Based System for Generation of Security
Solutions”, Annual CERIAS
Research Symposium, Apr 02
Achievements and Awards
Submitted structure of Phospholamban, a cardiac muscle protein
to the Protein Data Bank (PDB) with PDB ID 2HYN, 06
Referee for IEEE Computational Systems Bioinformatics (CSB), 05
Talk on “Geometric algorithms for measuring distances in protein
cross-linking", 9th Purdue University Biophysics Symposium (PUBS-9),
Oct 03
“Ice Miller Graduate Student Scholarship Award”, 03, awarded to one in
a class of over a hundred students
Representative of the Computer Science Dept at the Graduate Student
Board (GSB), Purdue University (Aug’02 – Aug’04)
Chairman of the IEEE Chapter, KLCE, India (Jul 00 – Apr 01)
(responsible for its organization)
“Best Outgoing Undergraduate Student Award”, India, 01, awarded to one
in a class of 60 students
Chief Coordinator of “Infovision”, a national level technical symposium
organized at KLCE, India, 01
References
Available on request