Reetal Pai

Department of Computer Science
Texas A&M University
Email: reetalp@cs.tamu.edu

I am currently pursuing my Ph.D. at TAMU with Dr. Thomas Ioerger . My research interests include the development of pattern recognition and machine learning algorithms with particular application to problems in Computational Biology. My dissertation looks at an important open reserach problem in the field of Proteomics: Annotation of Protein Function Based on the 3-Dimensional Protein Structure.

Current CV

Education

Doctor of Philosophy in Computer Science, Jan 2002-Present

Dissertation Topic: Annotation of Protein Function Based on the Protein 3-Dimensional Structure: A Feature-Based Analysis
Texas A&M University, College Station, TX, USA GPA: 3.8 / 4.0

Master of Science in Computer Engineering, December 2001

Clemson University, Clemson, SC, USA
Thesis: Automated Diagnosis of Retinal Images Using Evidential Reasoning. (GPA: 3.7 / 4.0)

Bachelor of Engineering in Electrical & Electronic Engineering, September 1998

University of Mysore, Mysore, India (GPA: 3.5 / 4.0)

Work Experience

Research Assistant, Department of Biochemsitry and Biophysics, Texas A&M University (May'07 - Present)

Developed computational biology tools for research related to Mycobacterium tuberculosis (Mtb)
Worked with biochemists on developing strategies for inhibitor design using docking algorithms for various targets in Mtb
Developed an interactive webtool that allows scientists in the TB community to experiment with various target selection criteria and explore ways to prioritize gene tragets
Configured and maintained scientific software packages
Trained biochemists to use various computational data analysis software

Teaching Assistant, Department of Computer Science, Texas A&M University (Aug '06 - May '07)

Aided in the developement of assignments, exams and projects for an undergraduate introductory course in Artificial Intelligence

Summer Internship, Google Inc. (May '06 . Aug '06)

Created a demo version of an attribute search tool for Google Base

Research Assistant, Department of Computer Science, Texas A&M University ('02 - May '06, May '07 - Aug '07)

Developed AI algorithms for TEXTAL and PHENIX crystallography packages
Presented research at various regional, national and international conferences
Aided in grant proposal preparation

Research Assistant, Department of Electrical & Computer Engg., Clemson University ('99 - '01)

Developed AI algorithms for STARE, a medical expert system
Developed web-based tutorial for AI algorithms in STARE

Research Projects

Dissertation Project

Developing a feature-based analysis of the structure-funtion relationship in proteins
Developing an approach to deal with conformational flexibility present with large ligands
Developing various tools to analyse large amount of structural data available from the Protein Data Bank
Found conclusive evidence that the feature-based approach is a valid approach to the analysis of diverse active sites

Inhibitor Design

Worked with biochemists to explore possible inhibitors for various M.tuberculosis targets
Worked with DOCK6, OpenEye, CHARMM, Sybyl etc. to explore the various facets of protein-small molecule interaction
Developed a novel ranking function to reduce the number of false positives from large-scale virtual screens and increased recall by over 20% in test cases

Data Mining Software Tool: Target Explorer

Designed an interactive web site that allows the TB research community to experiment with different target selection criteria
Allows researchers to examine correlations between different sources of experimental data
Improves the turnabout time involved in analyzing different drug targets
Presently deployed on the TB website www.webtb.org

Automated Identification of Non-Crystallographic Symmetry

Designed a brute-force algorithm that used local density calculations as a metric to identify NCS relationships
Improved time-performance of the brute-force algorithm significantly using a set of features based on electron density
Obtained operators with an accuracy comparable to and better than the operators obtained by existing methodologies
Developed a web-based interface for this algorithm
Python interface currently deployed in TEXTAL and PHENIX packages

Automated Recognition of Co-Factor Binding Sites

Designed a database containing examples of various co-factor binding sites ensuring diversity of example set
A feature-based approach to the identification and prediction of co-factor binding sites
Methodology had an accuracy of 85% when applied to four groups of co-factors

Stitch

A fragment database approach to correcting chain breaks in the backbones built by TEXTAL, an automated protein model building software.
Stitch increased accuracy of the generated models on an average by 10-15%
Currently implemented as a part of TEXTAL and PHENIX software packages

Probabilistic approach to the prediction of side-chain identity

Developed a multinomial approach to assessing side-chain identity based on the top k matches obtained from a database search
Accuracy of methodology was equivalent to previous estimates based on local density correlations

STARE

Designed and developed an automated diagnostic system using Bayesian reasoning to diagnose retinal images
Diagnostic system was able to differentiate between 13 diagnoses based on a probabilistic analysis with an accuracy of 75%

Publications

Pai, R., Sacchettini, J.C. and Ioerger, T.R. Fragment-Based Analysis of Protein-Ligand Interactions Using Localized Stereochemical Features ( Accepted BIOCOMP, July 2008 )
Pai, R., Sacchettini, J.C. And Ioerger, T.R. Specificity Normalization for Identifying Selective Inhibitors in Virtual Screening ( Accepted BIOCOMP, July 2008 )
Pai, R., Sacchettini, J.C. And Ioerger, T.R. Fragment-Based Analysis of Protein-Ligand Interactions Using Localized Stereochemical Features, ( Accepted as a poster at RECOMB 2008 )
Gopal, K., McKee, E., Romo, T., Pai, R., Smith, J., Sacchettini, J.C. and Ioerger, T.R. (2007). Crystallographic Protein Model-Building on the Web. Bioinformatics , 23:375-377.
Pai, R., Sacchettini, J.C. and Ioerger, T.R. (2006). Identifying Non-Crystallographic Symmetry in Macromolecular Electron Density Maps: A Feature-Based Approach. Acta Cryst D , Volume 62, Part 9, 1012-1021.
Romo, T.D., Gopal, K., McKee, E., Kanbi, L., Pai, R., Smith, J., Sacchettini, J.C., and Ioerger, T.R. (2005). TEXTAL: AI-based Structural Determination for X-ray Protein Crystallography. IEEE Intelligent Systems , 20(6): 59-63.
Gopal, K., Romo, T., Mckee, E., Childs, K., Pai, R., Smith, J., Sacchetini, J.C., Kanbi, L. and Ioerger, T.R. (2005) TEXTAL: Automated Crystallographic Protein Structure Determination. IAAI , 1483-1490.
Pai, R., Sacchettini, J. C. and Ioerger, T. R. Identifying Non-Crystallographic Symmetry: A Feature Based Approach. (2005) XX Congress, International Union of Crystallography
Adams, P. D., Gopal, K., Grosse-Kunstleve, R. W., Hung, L. W., Ioerger, T. R., McCoy, A. J., Moriarty, N. W., Pai, R., Read, R. J., Romo, T. D., Sacchettini, J. C., Sauter, N. K., Storoni, L. C., Terwilliger, T. C. (2004). Recent developments in the PHENIX software for automated crystallographic structure determination. Journal of Synchrotron Radiation , 11:53-55.
Gopal, K., Pai, R., Ioerger, T.R., Romo, T., and Sacchettini, J.C. (2003). TEXTAL: Artificial Intelligence Techniques for Automated Protein Structure Determination. Proceedings of the Fifteenth Conference on Innovative Applications of Artificial Intelligence Conference (IAAI) , 93-100.
Pai, R. Hoover, A. and Goldbaum, M. (2002) Automated Diagnosis of Retinal Images Using Evidential Reasoning, 15th International Conference on Systems Engineering , Las Vegas, NV.
Pai. R. (2001) Automated Diagnosis of Retinal Images Using Evidential Reasoning, M.S. Thesis , ECE Department, Clemson University.

Posters

RECOMB, Singapore, Fragment-Based Analysis of Protein-Ligand Interactions Using Localized Stereochemical Features, Mar 2008
Bioinformatics Workshop, Texas A&M University, Fragment-Based Analysis of Protein-Ligand Interactions Using Localized Stereochemical Features, Feb 2008
Grace Hopper Conference, Orlando, Feature-based Analysis of Protein Active Sites, Oct 2007
Grace Hopper Conference, San Diego, Identifying Non Crystallographic Symmetry in Electron Density Maps: Artificial Intelligence Techniques in X-ray Crystallography, Oct 2006
International Union of Crystallography, Florence, Italy, Identification of Non Crystallographic Symmetry, Aug 2005
Lost Pines, TX, Poster presentation, The TEXTAL System: Artificial Intelligence Techniques for Automated Protein Model Building, Oct 2002

Presentations

Grace Hopper Conference, San Diego, Riding the Technology Wave: Computer Scientists Building a Better Tomorrow, Panel Presentation, Oct 2006
PHENIX, Houston, TX, Identifying Non-Crystallographic Symmetry: A Feature Based Approach, Mar 2005
PHENIX, Texas A&M, Stitch: A Bioinformatics Approach to joining CAPRA chains, Sep 2003
Texas A&M, STARE: Automated Diagnosis of Retinal Images Using Evidential Reasoning, Jan 2002
Journal Club, Texas A&M
- Seminar Presentation on the Structure-Function Relationship in Human Tissue Plasminogen Activator (Therapy for Heart Attacks and Strokes), Oct 2007
- Seminar Presentation on Structural Similarity Enhances Interaction Propensity of Proteins, Feb 2007
- Seminar Presentation on From protein structure to biochemical function?, Oct 2006
- Seminar Presentation on Novel Statistical-Thermodynamic Methods to Predict Protein-Ligand Binding Positions Using Probability Distribution Functions, Feb 2006
- Seminar Presentation on Protein Function Prediction Using Local 3D Templates, Aug 2005
- Seminar Presentation on Anatomy of protein pockets and Cavities: Measurement of Binding Site Geometry and Implications to Ligand Design, Feb 2005

Software Development

Participated in the design and implementation of TEXTAL, an automated protein model building software commercially available
Implemented TEXTAL tasks for PHENIX, an automated X-ray crystal structure determination software
Created a web-based algorithm, PRANCS, to identify NCS relationships in electron density maps using a pattern recognition approach
Developing a web based report system for Brazos County Rape Crisis Center
Developed an interactive web based tool presently used by scientists in the Tuberculosis community (www.webtb.org)

Activities and Leadership Roles

Participant, Grace Hopper Conference, Oct 2007 (Volunteer, Registration Grant received)
Google Ambassador Aug 2006 - Present
AWICS Mentoring Officer Aug 2006 -Feb 2008, Distinguished Lecture Officer 2004 - 2006
Participant, Grace Hopper Conference, Oct 2006 (All expenses scholarship received)
Reviewer, Frontiers in Education 2006
Particpant, Google Workshop for Women Engineers, Jan 2006
Volunteered at ISMB Conference, Detroit, Michigan July 2005 (Registration grant received)
Participant, IUCR Conference, Florence, Italy Aug 2005 (Registration and accommodation grant received)
Department of Computer Science Mentor 2005 - Present
Participant, Graduate Teaching Academy 2005 - Present
Computer Science Graduate Student Association (CSGSA) President 2005 - 2006 (Awarded the Graduate Leadership Award)
Volunteer, Brazos County Rape Crisis Center 2004 - Present (Awarded the Volunteer of the Year for 2005, 2006)
Computer Science Departmental Scholarship 2004
Particpant, 3 Workshops held as a part of the Gender Equity Project 2003 - 2004