MS Bioinformatics students who have been enrolled full-time for at least one semester and are in good academic standing are eligible to apply for Computational Biology Faculty Research Awards.

Award recipients will be appointed as Graduate Research Assistants, with a monthly stipend and a remission of regular graduate tuition. (Recipients will still have to pay the tuition surcharge and mandatory fees, as outlined on the Bursars' web site.)

Application materials include a 3-page research proposal, a professional resume, and a letter of support from the faculty mentor for the student’s proposed research. Students continuing with a previous GRA project should also submit a 1-page description of their previous research accomplishments.

Application Deadlines:
Spring = November 21
Summer = April 21
Fall = July 21

Computational Biology Faculty Research Awards, Spring 2017
Student Faculty Mentor Title of Project
Adam Dabrowski King Jordan Ancestry-Specific Assortative Mating in Latin America
Aditi Paranjpe Kostas Konstantinidis Quantifying the Role of Recombination in Maintaining Diversity Within Natural Microbial Populations with Metagenomics
Ajay Ramakrishnan Varadarajan Patrick McGrath The Role of Transposable Elements in Gene Regulation in the Sand and Rock Dwelling Cichlids of Lake Malawi
Bowen Yang Lee Cooper Genomic and Histology Analysis of Diffuse Lower-Grade Gliomas
Camila Medrano Trochez King Jordan HLA-omics of Admixed Latin American Populations and Its Impact on Health and Disease
Hannah Hatchell Soojin Yi Relating Tissue-Specific Gene Expression and Drug Killing Indices
Juichang Lu Sam Brown The Dynamic of Death
Junke Wang King Jordan Genetic Canalization and Sex-Specific Protective Model for Diseases
Karan Kapuria Sam Brown Network Analysis of Microbial Communities in Cystic Fibrosis Lung
Krithika Ravindran Naidu Fredrik Vannberg Drug Response Prediction on Cancer Patients Using Support Vector Machines
Meixue Duan Greg Gibson Investigating Personal Differences During Complicated Malaria Development
Michael Finlayson Greg Gibson The Effect of Bone Marrow Transplantation on Peripheral Blood Expression Profiles
Mrunal Dehankar Yuhong Fan Computational Modeling of Neural Stem Cell Differentiation
Ramyasree Madupuri Matt Torres Analysis of 3-Dimensional Structural Features of Eukaryotic Phosphorylation Sites
Rushika Pandya Matt Torres Computational Analysis of PTMs in Domain Families
Shareef Khalid John McDonald Analyzing Allele Specific Expression in Tumor Tissue Samples
Shashwat Deepali Nagar King Jordan Detecting Polygenic Adaptive Introgression
Tian Jin Fredrik Vannberg De novo Genome Assembly Post-assembly Processing
Tyrone Lee Patrick McGrath A System for High Throughput Behavioral Analysis of Lake Malawi Cichlid Fishes using Computer Vision techniques
Venna Wang Joe Lachance Is the Rate of Human Evolution Accelerating?
Computational Biology Faculty Research Awards, Fall 2016
Student Faculty Mentor Title of Project
Andrew Teng Joe Lachance From Genetic Risk Scores to Clinical Disease Risks
Chen Guo Greg Gibson Evaluating Contribution of Rare Variants to Gene Expression in Humans
Devika Singh Joshua Weitz A New Method of Modeling Phage Therapy
Hari Prasanna Subramanian Greg Gibson RNA-Sequencing as a diagnostic tool for Neuromuscular Dystrophy
Harshmi Shah John McDonald Developing an Algorithm to Predict Drug Therapies from Tumor Sample Analysis
James Moore Fredrik Vannberg Forecasting Tuberculosis Emergence Using Agent-based Modeling with Partial Data
Min Yi Fredrik Vannberg Processing, Storing, and Analytics of Electronic Health Records
Niveda Sundararaman Matthew Torres Developing a Scoring and Ranking Scheme for PTM Hotspots
Petar Penev Eric Gaucher The Aroma of Fluorescence
Tannishtha Som King Jordan Suffix Tree Based Approach to Bacterial Typing
Tyrone Lee Patrick McGrath A System for High Throughput Behavioral Analysis of Lake Malawi Cichlid Fishes Using Computer Vision Techniques
Walker Gussler Joshua Weitz Modeling Infectious Disease Spread Over Complex Networks Outside of the SIS Framework
Computational Biology Faculty Research Awards, Summer 2016
Student Faculty Mentor Title of Project
Aroon Chande King Jordan Developing a Typing Scheme for Nontypeable Haemophilus influenzae
Harshmi Shah John McDonald Developing an Algorithm to Predict Drug Therapies from Tumor Sample Analysis
Namrata Kalsi Patrick McGrath Prediction of Chemical Ligands Using Molecular Dynamic Simulations
Niveda Sundararaman Matt Torres Analysis and Comparison of PTM Hotpots between Experimental and Putative PTMs
Peijue Zhang Eva Lee Models for Choosing the Drug-of-Choice in Response to a Biochemical Terrorist Attack
Computational Biology Faculty Research Awards, Spring 2016
Student Faculty Mentor Title of Project
Alicia Francis Fredrik Vannberg De Novo RNA-SEQ Ovarian Cancer Profile Analysis
Andrew Teng Joe Lachance From Genetic Risk Scores to Clinical Disease Risks
Devika Singh Joshua Weitz A New Method of Modeling Phage Therapy
Hari Prasanna Subramanian Greg Gibson Comparative analysis of Conventional RNA-seq and Targeted RNA-seq in Neuromuscular Diseases
Harshmi Shah John McDonald Developing an Algorithm to Predict Drug Therapies from Tumor Sample Analysis
Min Yi Fredrik Vannberg Drug Prediction on Ovarian Cancer Patients
Namrata Kalsi Patrick McGrath Prediction of Chemical Ligands Using Molecular Dynamic Simulations
Niveda Sundararaman Matt Torres SAPH-ire: Structural Analysis of PTM Hotspots
Tannishtha Som King Jordan Machine Learning Based Method for Reporting Antimicrobial Resistance of Fungal Infections in Colombia
Tyrone Lee Patrick McGrath Genomics of Complex Behavior in Lake Malawi Cichlid Fishes
Computational Biology Faculty Research Awards, Fall 2015
Student Faculty Mentor Title of Project
Bhanu Gandham King Jordan Colombian Admixture Studies And Visualization Tools for Population Genomic Health Profiles
Binbin Huang Joe Lachance Dating an ancient African population bottleneck using whole genome sequences from the Simons Genome Diversity Project
Menghan Li Chong Shin Multi-Cellular Crosstalk During Liver Regeneration After Injury
Raghavendra Padmanabhan Patrick McGrath Analysis of Chromosomal Inversions in Cichlids using Next Gneration Sequencing (NGS) data
Roopa Reddy Nagilla Greg Gibson The 'CorRelate' package for understanding correlation between high-throughput genomic data
Shashidhar Ravishankar Fredrik Vannberg Alignment free quantification of gene expression from RNA-Seq experiments
Vaishnavi Venkat Patrick McGrath Prediction of Chemical Ligands Using Molecular Dynamic Simulations
Xin Wu Soojin Yi Non-coding RNA Methylation and Expression during Human Brain Development and Evolution
Yasvanth Kulasekarapandian Fredrik Vannberg Diagnostic Primer Design Tool: Sparrow
Computational Biology Faculty Research Awards, Summer 2015
Student Faculty Mentor Title of Project
Binbin Huang Joe Lachance A Journey of African Genetic Variation
Menghan Li Chong Shin Multi-Cellular Crosstalk During Liver Regeneration After Injury
Roopa Reddy Nagilla Fredrik Vannberg Universal data structures for manipulating clustered k-mers
Computational Biology Faculty Research Awards, Spring 2015
Student Faculty Mentor Title of Project
Anuj Gupta King Jordan A Genome Based Sequence Typing Tool for Bacterial Pathogens
Bhanu Gandham King Jordan Detection of Causal Mutation for Mucopolysaccharidosis by Trio Exome Analysis
Menghan Li Chong Shin Multi-cellular Crosstalk During Liver Regeneration After Injury
Nandida Damaraju Constantine Dovrolis Structural Analysis of Metabolic Networks
Rachel Kutner Greg Gibson Integrative -omic Study of Malaria Virulence and Disease Progression Over Time
Raghavendra Padmanabhan Patrick McGrath A Computational Model to Predict Phenotype from Genotype in Caenorhabditis elegans
Shashidhar Ravishankar Fredrik Vannberg Alignment free quantification of gene expression from RNA-Seq experiments
Taylor Griswold Brian Hammer Identifying Mutations in Novel Genetic Factors that Prevent Natural Competence in the Human Pathogen Vibrio cholerae
Tian Mi Steve Harvey Evolution of Ribosome at Insertion Points
Vaishnavi Venkat Patrick McGrath Prediction of Chemical Ligands Using Molecular Dynamics Simulation
Xin Wu Soojin Yi Investigating the Roles of Non-CpG Methylation of Duplicate Genes during Human Brain Development
Yasvanth Kulasekarapandian Fredrik Vannberg K-mer based solutions for highly dynamic viral geomes
Computational Biology Faculty Research Awards, Fall 2014
Student Faculty Mentor Title of Project
Ali Pirani King Jordan Bordetella Genome Informatics Platform - BGIP
Dhruviben Patel Fredrik Vannberg Comparative Analysis of Plasmodium Parasites P. malariae and P. brasilinum
Emily Norris King Jordan The Genomic Basis of Capsule Switching and its Relationship to Disease in Neisseria meningitidis
Karthikeyan Murugesan Greg Gibson Gene Expression Profiling Workflow for Bioconductor With an Emphasis on SNM
Krutika Satish Gaonkar Eric Gaucher An Experimental Method to Benchmark Ancestral Sequence Reconstruction Methods
Sanjeev Sariya Patrick McGrath Predicting Residues Involved for Ligand Binding in C. elegans Chemoreceptors
Taylor Griswold Brian Hammer Identifying Novel Genetic Factors that Prevent Natural Competence in the Human Pathogen Vibrio cholerae
Ying Sha King Jordan Dynamic Analysis of Nucleosomes of Human Stem Cell
Computational Biology Faculty Research Awards, Summer 2014
Student Faculty Mentor Title of Project
Ali Pirani King Jordan Genome Rearrangement Analysis to Characterize the Emergence of Bordetella pertussis
Dhruviben Patel Fredrik Vannberg Comparative Analysis of Plasmodium Parasites P. malariae and P. brasilinum
Emily Norris Steve Harvey Unusual RNA Secondary Structures
Gayathri Kurup Francesca Storici Genome Wide Mapping and Detailed Analysis of rNMP Incorporation in Yeast
Parimala Devi William Ratcliff Determining the Molecular Basis of Multicellular Complexity in Experimentally-Evolved Saccharomyces cerevisiae and Chlamydomonas reinhardtii
Computational Biology Faculty Research Awards, Spring 2014
Student Faculty Mentor Title of Project
Ali Pirani King Jordan Genome-Based MLST Scheme for Bordetella pertussis
Emily Norris Steve Harvey Unusual RNA Secondary Structures
Karthikeyan Murugesan Greg Gibson Gene Expression as a Predictor of Complex Disease Traits
Krutika Satish Gaonkar Eric Gaucher An Experimental Method to Benchmark Ancestral Sequence Reconstruction Methods
Sanjeev Sariya Patrick McGrath Predicting Residues Involved for Ligand Binding in C. elegans Chemoreceptors
Ying Sha King Jordan Senescence of Human Stem Cell
Computational Biology Faculty Research Awards, Fall 2013
Student Faculty Mentor Title of Project
Cai Huang Fredrik Vannberg Alignment Free Sequence Analysis
Dan Sun Soojin Yi A Global Analysis of DNA Methylation and Aging in Human Brain
Deepak Unni Eric Gaucher To Understand the Interactions Between Elongation Factor - Tu and Other Proteins Within the tufA Network by Using Techniques in Structural Bioinformatics and to Understand How Mutations in These Proteins Affect Protein-Protein Interactions
Esha Jain Yuhong Fan Repeat Analysis of Individual H1 Variants Enriched Regions
Kelley Bullard Yuhong Fan An Investigation of the Relationship Between Linker Histone H1 and the Insulator Binding Protein CTCF
Pramod Mayigowda King Jordan Integration of Bacterial Isolate Genome Sequence database to Meningococcus Genome Informatics Platform
Raghu Chandramohan May Wang Identifying the Detection Threshold and Systematic Assessment of RNA-seq Expression Profiling Using Simulated Data
Siddharth Biswal John McDonald
Smruthy Sivakumar King Jordan Antagonistic Pleiotropy and Cancer
Vartika Agrawal Greg Gibson Analysis of allele specific expression using DNA and RNA-Sequencing
Vivek Sagar Radhakrishna Fredrik Vannberg Developing a Generic Web-Based Framework for to Analyze and Visualize Global Distribution Patterns Pathogen
Computational Biology Faculty Research Awards, Summer 2013
Student Faculty Mentor Title of Project
Cai Huang Fredrik Vannberg K-Mer Based Algorithm for Virus Identification
Dan Sun Soojin Yi A Study of Epigenetic Divergence and Genome Evolution Using Primates
Siddharth Biswal John McDonald Development of a Drug Recommendation Pipeline for Personalized Cancer Treatment
Computational Biology Faculty Research Awards, Spring 2013
Student Faculty Mentor Title of Project
Deepak Unni Eric Gaucher To Use Experimental Systems to Understand Evolution of Proteins in a Protein-Protein Interaction Network (PPIN) and to Use Computer Simulations to Aid Future Laboratory Experiments
Gaurav Sureka Steve Harvey To build a relational database and find unusual features in the secondary structure of RNA or find outliers by comparing various properties
Peter Audano Fredrik Vannberg Rapid Detection of Pathogens in Metagenomic Sequence Data
Pramod Mayigowda King Jordan Meningococcus Genome Informatics Platform
Raghu Chandramohan May Wang Integrated Prediction Modeling for Neuroblastoma Treatment Outcome Using RNA-Seq Data
Siddharth Biswal John McDonald Development of an Integrated Genomic Pipeline for Personalized Cancer Treatment
Vartika Agrawal Greg Gibson Exome-Wide Study of Histiocytoid Cardiomyopathy in a Family-Based Cohort
Vivek Sagar Radhakrishna Fredrick Vannberg R-Tree Based Qualitative K-Merised Metagenomic Analysis and Data Visualization
Xiao Dong Yuhong Fan Bioinformatics Analysis of Linker Histone H1 and DNA Methylation
Computational Biology Faculty Research Awards, Fall 2012
Student Faculty Mentor Title of Project
Ambily Sivadas Greg Gibson The WHOLE Study – An Approach to Personalized Medicine through Integrative Genomic Profiling
Amit Rupani Fredrik Vannberg Expression-based genome-wide association study to identify susceptibility loci linked to HCV infection in liver tissue
Ashwath Kumar Yuhong Fan Analysis of Histone H1 and H3 modifications from CHIP-Seq data
Deepak Purushotham King Jordan Transposable element derived structural variation in human prostate cancer
Haozheng Tian Greg Gibson Methylome in the Role of Regulation of Transcriptome in WHOLE Study
Hema Nagrajan Soojin Yi Genome wide characterization of CpG Islands by Epigenetic properties
Lu Wang King Jordan Transcriptional profiling of non-coding RNA expression in human adult stem cells during aging
Piyush Ranjan Steve Harvey Searching for unusual features in RNA secondary structure
Shengyun Peng Fredrik Vannberg Clinical Metagenomics Using K-Mer Arrays
Shimantika Sharma Joshua Weitz G-DES: an efficient software for microbial gene-level diversity estimation
Computational Biology Faculty Research Awards, Summer 2012
Student Faculty Mentor Title of Project
Hema Nagrajan Soojin Yi Genome-wide characterization of CpG islands by epigenetic properties
Lu Wang King Jordan The relationship between DNA damage and non-coding RNA expression in adult stem cells
Piyush Ranjan Steve Harvey Incorporating Kinetic Information into RNA Secondary Structure Prediction
Computational Biology Faculty Research Awards, Spring 2012
Student Faculty Mentor Title of Project
Ambily Sivadas Greg Gibson Genome Wide Association Study (GWAS) of Human Metabolic profiles to identify common and rare variants-associated metabolic phenotypes
Amit Rupani Fredrik Vannberg Differential RNA dynamics study of exosomes post vaccination: A systems biology approach
Ashwath Kumar Yuhong Fan Analysis of Histone H1 and H3 modifications from CHIP-Seq data
Deepak Purushotham King Jordan Transposable element derived structural variation in human prostate cancer
Hema Nagrajan Soojin Yi Identifying Determinants of Mammalian Non-synonymous and Synonymous Substitution Rates Using Novel Multivariate Principal Component Regression Method
Keerti Surapaneni Greg Gibson Extending functionality of GeneVar to perform eQTL analysis on metabolite data & developing an open source visualization tool for the Fly Database Project
Piyush Ranjan Steve Harvey Incorporating Kinetic Information into RNA Secondary Structure Prediction
Shengyun Peng Fredrik Vannberg Multivariate Analysis of Exosomes Pre- and Post-Stimulation
Shimantika Sharma Joshua Weitz G-DES: an efficient software for microbial gene-level diversity estimation
Computational Biology Faculty Research Awards, Fall 2011
Student Faculty Mentor Title of Project
Kristen Knipe Joshua Weitz DynBio: an Educational Tool to Aid in the Understanding of Modeling Dyamical Systems and to Reduce the Fear of Mathematical Biology
Neha Varghese King Jordan & Nael McCarty Correlation of site-specific evolutionary parameters with mutational effects in Cystic Fibrosis Transmembrane Regulator
Paul Cooper Yuhong Fan Analysis of Histone H1 binding to DNA
Robert Petit Timothy Read & King Jordan Bacterial Pathogen Database and Browser for Clinical Diagnostics
Shaopu "Peter" Qin Greg Gibson & Nicoleta Serban Comparison of different normalization method and application of variable selection methods in microarray data analysis
Shrutii Sarda Soojin Yi Understanding evolution of gene-body methylation in diverse animals using experimentally determined methylation levels
Vani Rajan Mark Borodovsky & Brian Hammer Computational methods to identify genes involved in control of horizontal gene transfer in the bacterial pathogen Vibrio cholerae
Computational Biology Faculty Research Awards, Summer 2011
Student Faculty Mentor Title of Project
Kristen Knipe Joshua Weitz PhageLab: a Matlab-based Java Web Application to Aid in the Understanding of Phage Dynamics
Robert Arthur John McDonald Study and Stent Usage and Restenosis in Sus scrofa
Robert Petit King Jordan and Tim Read Bacterial Pathogen Database and Browser for Clinical Diagnostics
Shaopu Qin Greg Gibson & Nicoleta Serban Application of Variable Selection Methods in Microarray Data Analysis
Computational Biology Faculty Research Awards, Spring 2011
Student Faculty Mentor Title of Project
Kristen Knipe Joshua Weitz PhageLab: a suite of GUIs to aid in the understanding of phage dynamics
Neha Varghese King Jordan & Nael McCarty Comparison of site-specific evolutionary parameters to mutational effects in Cystic Fibrosis Transmembrane Regulator
Paul Cooper Yuhong Fan Analysis of Histone H1 binding to DNA
Racchit Thapliyal Eric Gaucher Benchmarking of ancestral sequence reconstruction tools
Robert Adam Arthur John McDonald Gene expression in coronary arteries exposed to stents eluting synthetic rapamycin derivatives
Robert Petit Timothy Read & King Jordan Bacterial pathogen database and browser for clinical diagnostics
Shaopu Qin Greg Gibson & Nicoleta Serban Gene clustering analysis from human leukocyte gene expression profiles
Shrutii Sarda Soojin Yi Understanding evolution of gene-body methylation in diverse animals using experimentally determined methylation levels
Computational Biology Faculty Research Awards, Fall 2010
Student Faculty Mentor Title of Project
Aarthi Talla Greg Gibson Gene Network Analysis of Human Gene Expression Data
Chandni Desai Brian Hammer Comparative Sequence Analysis to Predict Interspecies Horizontal Gene Transfer among Bacterial Pathogens
Eishita Tyagi King Jordan Epigenetic regulation of cell-type specific gene expression by transposable element derived enhancers
Jay Humphrey King Jordan Assembly and Annotation Pipeline and Scalable Genome Browser
Nadeem Bulsara Yuhong Fan Structural and Functional Analysis of Linker Histone H1
Neha Gupta Greg Gibson Use of Next-Gen Sequencing & Association Based Mapping for dissecting laboratory-based adaptation in Drosophila melanogaster
Phillip Lee Melissa Kemp Mathematical modeling of cellular thioredoxin redox states and cellular signaling
Sandeep Namburi King Jordan InGen: A Suite of Tools to Aid in the Epidemiology of Influenza
Computational Biology Faculty Research Awards, Summer 2010
Student Faculty Mentor Title of Project
Eishita Tyagi King Jordan Epigenetic regulation of cell-type specific gene expression by transposable-element derived enhancers
Jay Humphries King Jordan Scalable multiple genome browser and pipeline
Namburi Sandeep King Jordan InGen: a suite of tools to aid in the epidemiology of influenza
Phillip Lee Melissa Kemp Mathematical modeling of cellular thioredoxin redox states and cellular signaling
Computational Biology Faculty Research Awards, Spring 2010
Student Faculty Mentor Title of Project
Aarthi Talla Greg Gibson Microarray analysis of human gene expression data
Eishita Tyagi King Jordan Epigenetic regulation of cell-type specific gene expression by transposable-element derived enhancers
Kanika Arora Eric Gaucher & Stephen Harvey Heterotachy in ribosomal RNA
Nadeem Bulsara Yuhong Fan Structural and functional analysis of linker histone H1
Neha Gupta Greg Gibson BSA-SFP linkage mapping analysis of Drosophila melanogaster for cardiac dysfunctions
Nitya Sharma King Jordan Investigating the role of IS elements in capsule switching in Neisseria meningitidis
Vinay Vyas Stephen Harvey A study of the structural basis of ribosomal fidelity using MD (Molecular Dynamic) simulations
Computational Biology Faculty Research Awards, Fall 2009
Student Faculty Mentor Title of Project
Abhiram Das Joshua Weitz Duplicate gene fate finder
Jasreet Hundal Yuhong Fan I. Genome-wide DNA methylation analysis II. Histone H1 structure modeling
Jeffrey Martin Mark Borodovsky Machine learning algorithms for inferring bacterial genome function from RNA-Seq data
Kanika Arora Stephen Harvey Dependence of 3D size of single-stranged RNA molecules on sequence length, secondary structure and presence of condensing agents
Khanjan Ghandi Timothy Read, Emory University Design of database of bacterial pathogen genomes for PCR primer design and ongoing validation
Nitya Sharma King Jordan Using SNPs to discriminate virulent and carriage strains in Neisseria meningitidis
Viswateja Nelakuditi King Jordan Neisseria Base: a comparative genomics database and genome browser for species of the Neisseria genus