SudhaRani Mamidipalli
sranin@yahoo.com, nsudhara@iupui.edu
3856 Cornwallis Lane, Carmel
IN 46032 Phone (317) 873 4746
Education
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M.S. Bioinformatics, Indiana University, Indianapolis, USA, GPA 3.9 / 4.0, May 2006
Post Graduate Diploma in Computer Applications, Hyderabad, India
B.S. Agricultural Science, Acharya N G Ranga Agricultural University, India
Sun Certified Java2 Programmer, Sun Microsystems, USA
Certificate in Web Markup & style coding and Access End-User, Indiana University, USA
Skills
Scripting Languages
Markup Languages
Languages
Platforms
Databases
Software Tools
Bioinformatics Tools
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Perl, PHP, and Java script
XML, HTML, and XHTML
Java, SQL, PSQL, C, C++, Excel/VBA, COBOL, JCL, CICS
UNIX (Solaris), Linux (Red Hat, Suse), Windows, MVS, DOS
Oracle, MySQL, DB2, PostgreSQL, MS Access, and SQL Server
SSH, Exceed, Toad, Erwin, Endnote, Komodo, Aqua Data Studio
Gene Spring, Ingenuity, Connectivity Map, Affymetrix, Blast, FASTA,
Phase, Vector NTI, and Seattle Center Proteomics Tools
Scientific Data Management: Spot fire, Cyber Lab, Lab Track, TotalChrom
Bioinformatics Databases: String, Ophid, Uniprot, Pfam, Kegg, Ensembl, IPI, Entrez, Refseq,
Gene cards
Professional Experience
* Visiting Research Associate, Indiana University School of Informatics
June, 2007 – Present
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Research on Biomedical Literature Mining and Association Discovery.
Discover direct, directional and transitive biological associations from literature.
Develop association discovery algorithms using machine learning and NLP techniques
Validate biological association networks using statistical methods and evolutionary principles.
Apply valid associations found in specific pathways to help develop valid, testable hypotheses
relevant to investigator’s research questions.
 Contribute to the knowledge in Biomedical Informatics through the publishing of findings.
 Contribute to writing research grant proposals.
* Research Analyst, Indiana University School of Medicine
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June, 2006 – May, 2007
Co-Investigator for Indiana Biomarker Research Alliance in Neuropsychiatry (INBRAIN).
Member for Laboratory of Neurophenomics.
Research on Genomics and Phenomics of Bipolar, Schizophrenia, Anxiety and related disorders.
Developed conceptual (Entity-Relationship diagrams), logical and physical data models by
identifying entities, attributes, relationships, and assigning keys
 Identified candidate genes and biomarkers for neuropsychiatric disorders.
 Applied Expanded Convergent Functional Genomics approach for breaking the genetic code of major
neuropsychiatric disorders.
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Conducted bioinformatics research on behavioral data, micro array data and human genetic datasets.
Phenochipped psychotic disorders for deconstructing and quantitating psychiatric phenotypes.
Defined metadata (Dublin Core standard) for data management and duplicity reduction.
Identified, characterized, and analyzed direct interactions, functions using Ingenuity (IPA) software.
Used Gene Spring for micro array data normalization, statistical inference and clustering analysis.
Maintained, managed and analyzed data and databases.
Wrote web pages and templates using W3C web standards.
Used Connectivity Map to find connections among small molecules, genes, drugs and diseases.
Wrote bioinformatics protocols.
* Research Assistant, Indiana University School of Informatics
Aug, 2004 – May, 2006
 Member for Discovery Informatics and Computing Group and Department of Computer and
Information Science
 Research on Protein Interactomics, Small interfering RNA, and Oligonucleotides.
 Developed Human Annotated Protein-Protein Interaction (HAPPI) Database.
 Developed an application OligoMatcher for analysis and selection of unique Oligonucleotide
sequences for Gene silencing by Antisense or siRNA.
 Warehoused 95,000 unique, good quality protein interaction pairs of 13,601 human proteins from
BIND, OPHID, MINT, IntAct, HPRD and STRING databases including annotation data from NCBI,
Pub Med, UNIPROT, HUGO, KEGG, PFAM and PDB.
 Designed, developed and maintained website with PHP, MySQL, and JavaScript.
 Developed and integrated Sequence Annotated Feature Mapping tool SafMap into HAPPI.
 Downloaded (ftp), parsed (Perl regular expressions) and loaded data into tables (sqlloader)
 Normalized data for data integrity, optimized queries, faster index creation and sorting.
 Used data management tools (Spotfire) to visually and statistically interrogate the data.
 Generated SQL and PL/SQL scripts to install create and drop database objects including
tables, views, primary keys, indexes, constraints, packages, grants and synonyms.
* Research & Development Intern, Dow Agro Sciences
May, 2005 - Aug, 2005
 Member for Discovery Research Information Management.
 Installed, configured and administered EMBOSS suite of Molecular Biology Programs, wrappers for
EMBOSS, and wEMBOSS on DAS Intranet of Bioinformatics that enables project, data and results
management.
 Integrated public biological databases into DAS Bioinformatics environment.
 Established a pipeline for tandem mass spectrometry (MS/MS) data analysis, validation and
quantification for Proteomics.
 Solved thorny problems by communicating with DAS users and external experts.
 Evaluated DAS Bioinformatics website and proposed usability enhancements.
 Promoted work to molecular biologists through seminars, conferences and meetings.
 Influenced Trait Genetics and Technologies scientists in using bioinformatics tools.
* Independent Study, Indiana University School of Medicine
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Jan, 2005 - May, 2005
Member for General Clinical Research Center Pharmacogenetics Core Laboratory.
Research on Single Nucleotide Polymorphisms and haplotypes.
Identified 8 new SNPs of INDO gene using ContigExpress module of Vector NTI Advance.
Estimated 37 haplotype blocks with 20 best reconstructions using PHASE software.
SudhaRani Mamidipalli
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* Web Developer, University Information Technology Services
May, 2004 - Aug, 2004
 Member for Digital Media Services.
 Designed data model and database for the application.
 Used Microsoft Visio to create the sequence and use cases.
 Developed, tested and integrated Music Placement Test for the School of Music at IUPUI.
* Software Engineer, CGI (formerly IMRGlobal), Bangalore, India
Oct, 1997 - May, 2000
 Performed analysis, coding, maintenance, and testing of applications using COBOL, CICS,
VSAM, MVS and JCL.
 Developed test strategy that includes baseline, unit, parallel and integration testing of jobs.
 Interacted with onsite team on a daily basis via conference calls.
 Enhanced the functionality of COBOL programs using embedded SQL
 Planned and conducted peer reviews for all deliverables.
 Converted an IMS online financial system to a DB2 database CICS system.
 Converted from a batch to an interactive environment for improved customer service (TSO/ISPF)
 Conducted project meetings on weekly basis to resolve issues and problems.
 Clients are Michelin Tires, Fleming Foods, and John Hancock Insurance etc.
Publications
 Helen Le-Niculescu, Matthew J McFarland, SudhaRani Mamidipalli, Cory A Ogden, Ronald
Kuczenski, Sunil M Kurian, Daniel R Salomon, Ming T Tsuang, John I Nurnberger, Alexander
Niculescu. (2007) Convergent Functional Genomics of Bipolar Disorder: From Animal Model
Pharmacogenomics to Human Genetics and Biomarkers. Special Issue on Animal Models – Bipolar
Disorder, Neuroscience and Biobehavioral Reviews. To appear.
 Mamidipalli, S. (2006) HAPPI: A Bioinformatics Database Platform Enabling Network Biology Studies.
IUPUI Digital Archive Informatics Graduate Thesis.
 Mamidipalli S, Palakal M, Li, S. (2006) OligoMatcher: Analysis and Selection of Specific
Oligonucleotide Sequences for Gene Silencing by Antisense or siRNA. Applied Bioinformatics, Volume
5, Number 2, pp. 121-124(4).
 Arefayene, Million; Mamidipalli, SudhaRani; Philips, Santosh; Cao, Donghua; Flockhart, David;
Wilkes, David; Skaar, Todd. (2006) Identification of Functional Genetic Variants of the Indoleamine 2, 3
dioxygenase Gene. Abstract #4765, Immunology 7: Immune Modulation in Cancer. American
Association for Cancer Research, Volume 47: 1119.
Papers acknowledged as a Contributor
 Le-Niculescu H, Balaraman Y, Patel S, Tan J, Sidhu K, Jerome RE, Edenberg HJ, Kuczenski R, Geyer
MA, Nurberger JI Jr, Faraone SV, Tsuang MT, Niculescu AB. (2007) Towards Understanding the
Schizophrenia Code: An Expanded Convergent Functional Genomics Approach. American Journal of
Medical Genetics Part B (Neuropsychiatric Genetics) 9999:1-32. Acknowledged in the
Acknowledgements section for excellent help with Bioinformatics.
SudhaRani Mamidipalli
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Book Chapter
 Mamidipalli, SudhaRani; Chen, Jake Yue. (2007) Protein-Protein Interactions: Concepts, Databases,
Software tools, and Biomedical Implications, in Current Topics in Human Genetics: Studies in
Complex Diseases. To appear.
Poster Presentations
 A.B.Niculescu, S.Kurian, H.Le-Niculescu, S.Mamidipalli, N.Yehyawi, C.Dike, M.J.McFarland,
G.Sandusky, C.Felder, H.J.Edenberg, M.T.Tsuang, D.R.Salomon, J.I.Nurnberger Jr. (2007) Towards
Identifying Blood Biomarkers For Mood Disorders. Institute of Psychiatric Research 50th Anniversary
Symposium, Indiana University-Purdue University at Indianapolis, Indianapolis, IN, May 4, 2007.
 M.J.McFarland, H.Le-Niculescu, Y.Balaraman, C.Ogden, J.Tan, S.Patel, M.E.Rich, S.Mamidipalli,
Z.A.Rodd, M.Paulus, M.Geyer, H.J.Edenberg, J.I.Nurnberger, S.Glatt, S.V.Faraone, M.T.Tsuang,
R.Kuczenski, and A.B.Niculescu. (2007) Mice Lacking the Circadian Clock Gene DBP: A StressReactive Animal Model for Bipolar (Manic-Depressive) Disorder and Co-Morbid Alcohol Abuse.
Institute of Psychiatric Research 50th Anniversary Symposium, Indiana University-Purdue University at
Indianapolis, Indianapolis, IN, May 4, 2007.
 Arefayene, Million; Mamidipalli, SudhaRani; Philips, Santosh; Cao, Donghua; Flockhart, David;
Wilkes, David; Skaar, Todd. (2006) Identification of Functional Genetic Variants of the Indoleamine 2, 3
Dioxygenase Gene. Indiana University Cancer Center’s Annual Cancer Research Day, Indiana
University-Purdue University at Indianapolis, Indianapolis, IN, May 10, 2006.
Professional Services
 Reviewer, Bioinformatics Track. ACM Symposium on Applied Computing (SAC 2007), Korea.
 Reviewer, Bioinformatics Track. ACM Symposium on Applied Computing (SAC 2006), France.
Academic Honors
 Nominated by Dean’s Office in Informatics to be featured as a top graduate from School of Informatics
at the IUPUI Commencement ceremony, May 2006.
 Full Tuition Scholarship and Stipend for Research Assistant Position, School of Informatics, Indiana
University, Spring and Fall Semesters 2005.
 Full Tuition Scholarship and Stipend for Research Assistant position, Department of Computer and
Information Science, Indiana University Purdue University Indianapolis, Fall Semester 2004.
Projects, Research Papers and Presentations
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HAPPI: A Bioinformatics Database Platform Enabling Network Biology Studies
Gene Expression Data Management and Analysis
Application of Bioinformatics in SNP discovery of INDO gene
NCBI – Website Analysis
Medical Databases - Electronic Medical Records
Intelligent Electronic Laboratory Notebooks
Querying Multiple Bioinformatics Information Sources- Can Semantic Web Research Help?
Genetic Algorithms for Protein Folding Simulations
Surrostat Biomarker Analysis System
SudhaRani Mamidipalli
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