Saras Saraswathi

Room 108, Office and Lab Bld.
Laurence H. Baker Center for Bioinformatics and Biological Statistics
Iowa State University
Ames, IA 50011
E-mail: saras@iastate.edu

Education

• Graduate student in the Ph.D program for Bioinformatics and Computational Biology, ISU. 08/2007 ~ present
• M.Sc., Bioinformatics, Nanyang Technological University, Singapore. 03/2006 ~ 06/2007
• M.S., Computer Science, Old Dominion University, Norfolk, USA. 03/1984~12/1985
• B. A., Mathematics, University of Delhi, India. 06/1972~05/1977
• CCNA Certification, CISCO, USA. 09/2003
• E-Commerce Engineering Certification, UC Santa Cruz, USA. 01/2000~12/2000
• ACCA, Certified Accountant, Singapore/UK. 01/1995~12/2000

Research interests

• Investigating use of protein physical properties in structure prediction , using machine learning techniques.
• Investigating use of Position Specific Preferences of Amino Acids in structure prediction , using machine learning techniques.

Current interests

Protein secondary structure prediction.
i) Combine several protein physical properties to predict protein sequence and structure.
ii) Use several Machine Learning techniques to predict protein structure.
iii) Use Position Specific Amino Acid Propensities to predict protein structure.

Skills

1. Experienced in several programming languages : C, Ada, C++, Java, ASP, JSP, Perl.
2. Several years of industrial experience developing web pages and application software.
3. Application areas include various industries in Finance, Engineering and Quality control.
4. Several years of expeirence in Technical writing and Training personnel in IT applications.

Publications

Saraswathi.S., Suresh S., Sundararajan N. An Improved Gene Selection Method for Accurate Classification of Microarray Gene Expression Data. INCOB conference, Dec 2006.

Suresh S., Saraswathi.S., Sundararajan N. Performance Enhancement of Extreme Learning Machine for Multi-category Sparse Data Classification. ICONIP conference April 2007. Pattern Analysis and Applications.

Sundararajan,S., Pang, A., Wild, C. Analysis of Executable Specifications for Testing and Monitoring Abstract Data Types. Software Testing Workshop New Jersy, July 1986.

Poster Presentations

Saras Saraswathi, Suresh Sundaram, Narasimhan Sundararajan, Michael Zimmermann. A Three-Step approach for Multi-Class cancer classification using Machine Learning - A biological Approach.
Extracellular and Membrane Proteases in Cell Signaling Symposium, Ames, IA x September 18-21, 2008

W. Allen Miller, Randy Beckett, Saras Saraswathi , Nikki Krueger , Stewart M. Gray Sequences of diverse Barley yellow dwarf and Cereal yellow dwarf viruses reveal that CYDV is highly recombinant and BYDV-RMV is neither BYDV nor CYDV.
XIVth International Congress of Virology in Istanbul, Turkey, August 10-15, 2008

Saraswathi.S., Kloczkowski Andrej , Jernigan Robert. Protein Secondary Structure Prediction based on physical properties of amino acids in multiple sequence alignments, ISMB Conference, July 2008.

Saraswathi.S., Suresh S., Sundararajan N., Zimmermann M. A three-step approach for multi-class cancer classification using Genetic Algorithm, Particle Swarm Optimization and Extreme Learning Machine.
ISMB - SCS4 Symposium, July 2008.

Saraswathi.S., Suresh S., Sundararajan N. An Improved Gene Selection Method for Accurate Classification of Microarray Gene Expression Data with PSO. CRA - W Workshop March 2008.

Research Experience

• Research assistant: Dec. 2007 ~ present.
  L.H. Baker Center for Bioinformatics and Biological Statistics, Iowa State University, USA
• Rotation: Aug. 2007 ~ Dec 2007
  Allen Miller Lab, Center for Plant Responses to Environmental Stresses , IaState. Working on Phylogenic trees (for placement of newly found viruses) and virus DNA extraction (wet lab).
• Rotation: Sept. 2007 ~ Dec 2007
  Honovar Lab, Computer Science Dept., IaState. Developed statistical analytical techniques to determine protein DNA interaction.
• Visiting Researcher: Feb. 2006 - June 2007
  Bioinformatics Research Center, School of Computer Engineering,
  Advisor: Dr. Jagath Rajapakse, Nanyang Technological University, Singapore.
  Worked on Machine learning techniques to solve Bioinformatics problems in classification of cancer data and protein structure prediction.
• Visiting Researcher: Jan 2005 - Jan-2006
  Advisor: Dr. K. Soman. Center for Networking and Excellence, Amrita University, Coimbatore, India.
  Worked on Machine learning (SVM) techniques, and Parallel processing using grid computing and MPI.
• Research Engineer: Jan. 1992- Jan. 1993.
  Advisor: Prof. Robert Gay, GINTIC Institute, Nanyang Technological University, Singapore.
  Developed Finite Element analysis modeling software package in C++. The ultimate objective of the software was to simulate material behavior under extreme conditions. Implemented code migration of a geometrical Finite Element Analysis package from ADA to C.
• Research Assistant: Mar. 1984- Apr. 1986.
  Advisor Prof. Chris Wild: Old Dominion University, Hampton,VA.
  During my MS studies in Computer Science.
• summer internship: May. 1985- Aug. 1985.
  Advisor: Dr. Lansing and Dr. Chris Wild, Langley Research Center. During my MS studies at ODU.
  NASA Student Voluntary Program: Worked on space station animations using Chromatics Graphics computers.

Work Experience

Software Engineer, Amritha Viswa Vidya Peetham, Coimbatore, India July 2004 - Dec 2004

• Project Lead for development of financial modules.
• Developed software in Java.
• Enterprise Resource Planning Software developed for Konkan Railway System.
• Software Engineer, ValueLabs, Hyderabad, India June 2002 – June 2003
• Test development and quality assurance for mobile portal applications.
• Web page and web page application development for mobile portal applications such as interactive TV and multimedia messaging
• Software Consultant, , CEO, Techsoft Consultants, USA. Feb. 2000 – Aug. 2007
• Developed and administered website for a major shipping company, Air7Seas.
• Developed test tracking application for a multimedia software vendor, Margi Systems.
• Computer security consultant for VPN Dynamics.
• Familiar with web technology, Microsoft Office packages.
• E-commerce engineering and database concepts, Scripting and MySQL.
• Working knowledge of Unix and expert knowledge in Windows environment.

Teaching Experience

Tutor - June 1991 - June 2000
Nanyang Technological University, National University of Singapore and Ngee Ann Polytechnic, Singapore.

Professional activities and Honor Societies

Fellow: NSF-IGERT Fellowship from Iowa State University's Bioinformatics and Computational Biology Program (2008).
Reviewer and Program committee member: Computational Intelligence in Bioinformatics and Computational Biology -CIBCB 2008
Reviewer: Bioinformatics to Systems Biology – 2008
Reviewer and Program committee member: ISCB-Student Council Symposiums - 2006-2008
Member : Organizing Committee, ISCB-Student Council Symposiums 2006-2008

Chairperson: ISCB-SC, Regional Student Groups (2006-2008)
Founder and Chairperson, ISCB-SC – RSG – Singapore – (founded 2006 Nov.)
Founder, ISCB-SC – RSG – India – (founded 2006 Nov.)
Founder and President, ISCB-SC- RSG – USA – Sept. 2007 in USA.

Member: ISCB - International Society for Computational Biology.
Member, Finance and Education Committee – ISCB
Senior Member, IEEE
Member, IEEE - Computational Intelligence Society
Member, IEEE - Women in Engineering
Member, SYSTERS
Fellow (2005-2007), Association of Chartered Certified Accountants (UK) – Retired due to PhD studies.
Member Cisco Certified Network Associate (CCNA-2003)

Other Interests

Interested in vocal and instrumental classical Indian music.
Tinkered with several Indian musical Instruments - Violin, Flute, Tabla.
Actively involved in the advancement of student interests in the computational biology field through ISCB.
Interested advancement of Education for women.