Masters Bioinformatics Capstones Page

Projects from 2003-2006

Begun in 2003, our Masters Bioinformatics degree culminates in a yearlong project called the capstone. The project typically involves either genomics or proteomics and some combination of discovery, validation, or tools under the supervision of a core Bioinformatics faculty member and generally a faculty in another area--in biology or chemistry for example. The projects are incredibly diverse and rich in their range of topics and kinds of questions they address.

The graphic thumbnail to the left, when clicked, shows the number of completed projects upto 2006, including the faculty and unit they belong to. The remaining document here lists in chronological order of presentations (top is most recent). We invite you to peruse these presentations. Comments are welcome.






July 15th, 2009

Manasa Balasubramanian

using SMARTS to investigate chemical and biological properties of near neighbors of key compounds

Presentation @ 2pm

Chris Rosenthal

Genome Analysis and Disease Ontologies in Coral Reef Systems

Presentation @ 2:30pm

Nils Schimmelmann

Full Text Literature Mining for Gene Disease Relationships

Presentation @ 3pm

Ryan Rene

Predicting Drug-gene and Drug-disease Networks using Functional Flow

Presentation @ 3:30pm

June 10th, 2009

Vivek Krishnakumar


Presentation @ 2pm

May 22nd, 2009

Jun Ma

Note: Jun Ma is a cheminfo graduate.
Lipid analytical tool (LidpidAT: automated anal ysis of Lipidomic mass spectrometry data

Presentation @ 2pm

Dah Mee Ko

Ubiquitination Sites Prediction

Presentation @ 2:30pm

Rita Desai


Presentation @ 3pm

May 11th, 2009

Ankita Sarangi

Prediction of Protein function based on domain Content

Presentation @ 10:30 am

Ashwini Oke

Identification and Characterization of Regulatory Targets of Drosophila Transcription Factor hzy using Oligonucleotide Arrays

Presentation @ 11:00 am

May 1st, 2009

Kashi Revanna

Developing Novel Web-based bioinformatics analysis tools for comparative genomics

Presentation @ 4:00 pm

Dec 5th, 2008

Hyejin Yoon

Automatic Analysis of Ion Mobility Spectrometry -Mass Spectrometry (IMS-MS) Data

Presentation @ 2:30 pm

Scott Beason

A Smart Card-based Person Health Record: Conceptualization, Design, and Implementation


Aug 15th, 2008

Haleh Ashki

Predicting Biologically Meaningful Gene Sets from Conserved Gene Clusters using Gene Ontology Information

Presentation @ 2:00 pm

Mauli Prasad

Computational Survey of Putative Bidirectional Promoters in Arabidopsis thaliana

Presentation @ 2:30 pm

Sriram Raghuraman

Error Model for Massively Parallel DNA Sequencing Technology

Presentation @ 3:00 pm

May 23rd, 2008

Ankita Bhan

Visualization and Exploration of Gene Clusters

Presentation @ 10:00 am

May 22nd, 2008

Arunima Ram

A Neural Network Predictor for Peptide Fragmentation in Mass Spectrometry

Presentation @ 1:30

May 16th, 2008

Michelle Wynn

A Computational Multi-scale Model of Neural Crest Cell Chain Migration

Presentation @ 9:30 am

Tim Kelley

Discrete Network Models in Bioinformatics

Presentation @ 11:30 am

April 25th, 2008

Meng Li

Exploring the Role of DNA Methylation in the Development of Drug Resistance in Ovarian Cancer Cells

Presentation @ 9:00 am

Sep 28th, 2007

Jasleen Kaur

2:30 – 3:00 Presentation @ 2:30

Harini Gopalakrishnan

3:00 – 3:30 Investigating mRNAs of Intrinsically Disordered Proteins Presentation @ 3:00

Jade Buchanan-Carter

3:30 – 4:00 Using Drosophila Melanogaster Data to Discover Disease-Related Protein Interactions in Humans Presentation @ 3:30

MAY 18th, 2007

Vijetha Vemulapalli

Computational Methods for Biomarker Discovery in Proteomics and Glycomics

Presentation @ 1:30

Preeti Misra

Computational method to analyze tandem repeats in eukaryote genomes

Presentation @ 3:30

MAY 17th, 2007

Sharat Mortha

Prediction of genes involved in influencing terrestrial and aquatic lifestyles in arthropods

Presentation @ 3:30

Sang-Gook Han

Detection of Natural Selection in the Human Genome by Hidden Markov Model

Presentation @ 4:30

Aaron Buechlein

Associating Biomedical Terms: Case Study for Acetylation

Presentation @ 5:30

MAY 11th, 2007

Jang (Jason) Lee

Quantitative analysis of domain interactomes

Presentation @ 2:30

April 20th, 2007

Sean Boyle

Inferring human protein-disease associations from protein-protein interaction networks using shortest path

Presentation @ 9:30

Pedro Alves

Advancement in protein inference from shotgun proteomics using peptide detectibility

Presentation @ 10:30

updating ...2006 May June .....

Junguk Hur

Characterization of transcriptional responses to environmental stress by differential location analysis

Presentation @

updating ...2006 May June .....

June 8, 2006

Narmada Jayasankar

Presentation @ 10:30

April 21, 2006

Keval Mehta

Indigene - Data Mining & Visualization Component

Presentation @3:00pm

Sourav Roy

Unraveling the segmentation clock with bioinformatics tools and techniques

Presentation @3:30pm

April 20, 2006

Huijun Wang

Computational Study of the Diastereoselective Rh-Catalyzed Pauson-Khand Reaction and Data Mining

Presentation @6:30pm (Chemical Informatics)

Divya Rao

Protein Interaction Network Inference Tool

Presentation @3:30pm

December 16, 2005

Jonathan Nowacki

Discovery and Visualization of Germline Genes in a Mushroom with Synchronous Cellular Division

Presentation @2:30pm

Murali Mohan N Rama Podicheti

Information System for Post-translational Modifications

Presentation @3:30pm

Chris Hemmerich

A Study of Residue Correlation within Protein Sequences and its Application to Sequence Classification

Presentation @4:30pm

September 16, 2005

Lalitha Viswanath

Interference Analyzer : tool for analyses of multi loci genetic

Presentation @9:00am

Anital Dalwani

Information System for Comparative Analysis of Legume Genomes

Presentation @9:30am

July 15, 2005

Hardik A. Sheth

Motif Discovery For Proteins Using Subsequence Clustering

Presentation @2:30pm

May 20, 2005

Sumit Middha

Discovery of Regulatory Elements in Drosophila Melanogaster Core Promoters

Presentation @10:00am

Vasanth Singan

Integrating Gene Expression Profiles with Gene Ontology

Presentation @11:00am

April 27, 2005

Yogita Mantri

Statistical Analysis for Word counting in Drosophila Core Promoters

Presentation @3:30pm

Rupali Patwardhan

Motif Discovery in Protein Sequences using Messy de Bruijn Graphs

Presentation @4:00pm

Troy Campbell

Paleontology Discovery System presentation

Presentation @4:30pm

December 17, 2004

Jeffery Mower

PREditorredictive RNA Editor for lant Mitochondrial Genes

Presentation @1:00pm

Kiran Annaiah

ProReP - Protein Results Parser v3.0: A Tool For Handling Tandem Mass Spectrometer Protein Database Search Results

Presentation @1:30pm

Natalya Muzinich

Discovery of Prokaryotic Relationships through Latent Structure

Presentation @2:00pm

Stuart Young

Predicting Deleterious Mutations

Presentation @2:30pm

September 24, 2004

Nihar Sheth

Frequency-based Splice Site Predictor

Presentation @9:00am /p>

Raj Adhikari

Discovering Gene-Disease Association using On-line Scientific Text Abstracts.

Presentation @9:30am

Kranthi K Varala

Cell Model calibration using NMR based metabonomics

Presentation @10:00am

Manish Anand

Effect of polymorphisms on transcriptional regulation in mice: Preliminary study of SNPs in the promoter region of genes with strong cis-eQTL

Presentation @10:30am

July 15, 2004

Angela Burr

Quality Control of Microarrays and the Importance of Human Computer Interaction

Presentation @8:30am

Paul White

A searchable interface as a system component for the Computerization of the IUB Herbarium

Presentation @9:00am

Yi Zou

DNA Sequence Evolution in Sunflower and Lettuce

Presentation @10:30am

Xin Hong

The distribution of introns in the full length cDNA


June 11, 2004

James Costello

BioKnOT: Biological Knowledge through Ontologies and TFIDF

Presentation @1:30pm

Arvind Gopu

A Framework for Sequence Cluster Merging

Presentation @2:00pm

Xiang (Sean) Zhou

The design and implementation of a system that integrates pathway data from KEGG and genome sequence data from NCBI

Presentation @2:30pm

May 13, 2004

Tsukahara Takuma

HISPIG: A Discriminative Model Refinement Approach with Iterations for Detecting Regulatory Regions

Presentation @1:30pm

December 19, 2003

Henry Hyunil Paik

Sequence analysis of CpG islands reveals possible correlation between genes and their CpG island sequences

Presentation @2:00pm

Avinash Kewalramani

BioFilter:An architecture for parallel deployment and dynamic chaining of standalone BioInformatics tools.

Presentation @2:30pm

August 14, 2003

Zhiping Wang

Guiding motif discovery by iterative pattern refinement

Presentation @10:30am

Kwangmin Choi

Improving gene function prediction using conserved gene clusters and genomic context

Presentation @11:00am

April 28, 2003

Sihui Zhao

Clustering and Motif Finding in Kinases of Yeast, Worm, and Arabidopsis thaliana

Presentation @9:00am

Haifeng Zhao

Discovery of Regulatory Motifs of Purine Biosynthetic Genes in E. coli and B. subtillis

Presentation @9:30am

Paul Poole

Whole Genome Repeat Analysis Package: A Preliminary Analysis of the Caenorhabditis elegans Genome

Presentation @10:00am


Irfan Gunduz

Motif Discovery from Large Number of Sequences: A Case Study with Disease Resistance Genes in Arabidopsis thaliana

Presentation @10:30am