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
| Student | Faculty Mentor | Title of Project |
|---|---|---|
| Ahmad, Maria | King Jordan | Genetic susceptibility and risk prediction for SARS-CoV-2 infection and COVID-19 progression |
| Gan, Shuheng | Sam Brown | Random Forest to Predict COPD Exacerbations with Microbiome Data |
| Lin, Shuting | Peng Qiu | Identifying potential biomarkers that are predictive of patient drug response to cancer therapies |
| Pfennig, Aaron | Mark Borodovsky | Identification of a type of genetic code in an anonymous, prokaryotic DNA sequence |
| Sharma, Rhiya | Patrick McGrath | Employing Neural Network Models to Obtain Accurate Positional Coordinates of Malawi Cichlids |
| Student | Faculty Mentor | Title of Project |
|---|---|---|
| Gupta, Sonali | King Jordan | Web-Based Platform for Approximation of Pulse Field Gel Electrophoresis Pattern Identifiers from Whole Genome Sequences |
| Hazra, Ujani | John McDonald | A Strategy for Identification of Cryptic Promoters in Human Genome Based on the Presence of Transcription Factor Binding Motifs |
| Kesar, Devishi | King Jordan | Exploring the Genetic Diversity in Hispanic/Latino Populations |
| Kumar, Sachin | Eliver Ghosn | Validation and Optimization of Multiple Batch Integration Methods for Single Cell Sequencing |
| Lacek, Kristine | Greg Gibson | Generation and Comparison of Polygenic Risk Scores for Medical Conditions in the North and South of England—Continuation: PRS, PXS, and Ancestry |
| Mora, Laura | Deqiang Qiu | Locus Coeruleus and Its Relationship to Alzheimer’s Disease |
| Parekh, Paarth | Francesca Storici | Determining the Firing Time of Autonomous Replication Site (ARS) Based on Ribo-Nucleotide Incorporation Using Machine Learning |
| Rozanski, Allison | John Varga | Identification of Virulence Factors in Burkholderia cenocepacia Through Large Scale Comparative Genomics |
| Sharma, Rhiya | Patrick McGrath | Improving the Accuracy of DeepLabCut to Obtain Accurate Positional Coordinates of Malawi Cichlids |
| Sharma, Shivam | John McDonald | Understanding the Role of Aberrant Alternative Splicing in Loss of Regulatory Control of Gene Expression by Micro-RNAs in Cancer |
| Sharma, Siddhartha | Joe Lachance | Development and Testing of STRUCTUREpainter: A Local Ancestry Inference Algorithm |
| Singu, Swetha | Yuhong Fan | Single Cell RNA-seq Identifies Expression Signatures Associated with Histone Hyperacetylation in Embryonic Stem Cells |
| Temples, Danielle | Tim Cope | Encoding of Information of Limb Position from Distinctive Muscles to Successfully Form a Movement |
| Vegesna, Manasa | Matthew Torres | Feature Extraction for Enhancing the Predictive Power of the SAPH-ire Model |
| Xiao, Yiqiong | Sam Brown | Cystic Fibrosis Data Integration and Front-End Database Development |
| Yang, Ruize | Le Song | Design Lipid Nanoparticles Using Machine Learning |
| Student | Faculty Mentor | Title of Project |
|---|---|---|
| Aljapur, Vineeth | Patrick McGrath | Understanding Natural Social Behaviors of Cichlids using Convolutional Neural Networks and Depth Sensing |
| Arrojwala, Manu Tej Sharma | Patrick McGrath | Automated Analysis of Sand Topology and Image Data to Study Natural Courtship Behavior in Malawi Cichlids |
| Bharanikumar, Ramit | John McDonald | Optimization and Comparison of Machine Learning Approaches for Ovarian Cancer Diagnosis |
| Feldman, Jacob | James Dahlman | A Nanoinformatics Approach to Predicting Lipid Nanoparticle Formation |
| Fisher, Margaret | Greg Gibson | Quantitative Comparisons Between Fine-Mapping Methods and Defining Credible Intervals with Multi-Objective Optimization |
| Gerald, Nishant | Joe Lachance | Leveraging Local Ancestry of the MADCaP Pilot Dataset to Identify Strong Selection Signals |
| Gruenhagen, George | Todd Streelman | RNA-Seq Analysis of Stem Cells Involved in Tooth Repair |
| Jain, Mani | King Jordan | Approximation of PulseNet PFGE Banding Pattern Identifiers from Whole Genome Sequences using Machine Learning |
| Jain, Prerna | Sam Brown | Machine Learning Approaches to Predict Antibiotic Resistance in Pseudomonas Aeruginosa |
| Kothandaraman, Sachin | Eliver Ghosn | A Gene-Set Library for Immune Cell Type Classification from Expression Analysis of Single-Cell RNA-Sequence Data |
| Lacek, Kristine | Greg Gibson | Generation and Comparison of Polygenic Risk Scores for Medical Conditions in the North and South of England |
| Leventhal-Douglas, Gabriel | Yuhong Fan | ChIP-seq Analysis Pipeline for Quantifying Histone Modifications |
| Li, Tianci | Todd Streelman | Variants in Conserved Region Between Rock-Sand Dwelling and Different Tooth Shape of Cichlids in Lake Malawi |
| Lu, Yinquan | Concettina Guerra | Development of Computational Methods for Gene Prioritization via Rank Aggregation |
| Ma, Jialin | Joe Lachance | Quantify Natural Selection Strength of Human SNPs with Ancestral and Primate Allele |
| Neary, Bridget | Peng Qiu | Identifying Molecular Signatures that are Predictive of Patient Response to Cancer Therapies |
| Pan, Hanying | Sam Brown | Cystic Fibrosis Related Clinical and Experimental Data Cleaning and Integration |
| Raut, Priyam | Raquel Lieberman | Identification of Biological Substrates for Signal Peptide Peptidase in Archaea and Elucidating their Substrate Specificity |
| Sharma, Shrinkhla | John McDonald | Prediction of Personalized Chemotherapies for Cancer Patients Based on Genomic Profiles |
| Yang, Junkai | Eliver Ghosn | Implementation of a New Clustering Algorithm (Exhaustive Projection Pursuit) to Automatically Identify Immune Cell Subsets in Multi-Omics Single-Cell Sequencing Datasets |
| Student | Faculty Mentor | Title of Project |
|---|---|---|
| Cao, Mingming | Raquel Lieberman | An In Silico Phylogenetic and Structural Analysis of Olfactomedins and Comparison with Existing Protein Subfamilies |
| Fisher, Margaret | Greg Gibson | A Novel Conditional Analysis Approach to Fine Map eQTLs Associated with Autoimmune Diseases |
| Gupta, Mansi | Brian Hammer | Identifying Novel Type VI Secretion System Genomic Loci in Diverse Bacterial Species |
| Hutwagner, Will | Fredrik Vannberg and Joe Lachance | From Genotype to Phenotype: Analyzing Breed and Physical Characteristics of the Domestic Dog |
| Li, Tianci | Todd Streelman | Variant Calling for 198 Cichlid Species in Lake Malawi and Conservation Scores for Cichlids |
| Neary, Bridget | Peng Qiu | Identifying Molecular Signatures that are Predictive of Patient Response to Cancer Therapies |
| Raut, Priyam | Raquel Lieberman | Identification of Biological Substrates for Signal Peptide Peptidase in Archaea. |
| Student | Faculty Mentor | Title of Project |
|---|---|---|
| Aljapur, Vineeth | Patrick McGrath | Using Neural Networks to study Natural Social Behaviors of Cichlids |
| Arrojwala, Manu Tej Sharma | Patrick McGrath | Automated approach to study the courtship behavior in Malawi Cichlids |
| Bharanikumar, Ramit | John McDonald | A Machine Learning approach towards diagnosing Ovarian Cancer |
| Duan, Jiachen | Alberto Stolfi | Identifying Progenitors of CNS Cells in the Tunicate Ciona Robusta by scRNAseq Technology |
| Feldman, Jacob | James Dahlman | A Nanoinformatics Approach to Predicting Lipid Nanoparticle Formation |
| Fisher, Margaret | Greg Gibson | Fine Mapping eQTLs and Causal Variants |
| Gerald, Nishant | Joe Lachance | Benchmarking & Optimizing STRUCTUREpainter - A Pipeline for Local Ancestry Inference |
| Gowrishankar, Preethi | Joe Lachance | Differences in polygenic risk scores between populations |
| Gruenhagen, George | Todd Streelman | Genetic Basis of Tooth Shape in Lake Malaŵi Cichlids |
| Gupta, Sinjini | John McDonald | Analysis of the Impact of P-53 Loss-of-Function in an Ovarian Cancer Cell Line |
| Huang, Tzu-Chuan | King Jordan | Evaluating the effects of alternative splice isoforms regulated by transposable elements in cancer |
| Hutwagner, Will | Fredrik Vannberg | From Genotype to Phenotype: Analyzing Breed and Physical Characteristics of the Domestic Dog |
| Jain, Mani | King Jordan | Prediction of PulseNet PFGE Banding Pattern Identifiers from core-genome Multi-Locus Sequence Type allelic profiles using Random Forest classification |
| Jain, Prerna | Sam Brown | Prediction of Antibiotic Resistance Development in Pseudomonas aeruginosa |
| Kothandaraman, Sachin Sarath Yadav | Fredrik Vannberg | An Automated Software Pipeline for Multi-dimensional Analysis of Patient Cancer Data |
| Leventhal-Douglas, Gabriel | Yuhong Fan | ChIP-seq Analysis Pipeline for Quantifying Histone Ubiquitination |
| Li, Tianci | Todd Streelman | Bower behavior in Cichlid fish, pit-digging and castle-building F1 hybrids Allele-specific expression in the specific brain region |
| Ma, Jialin | Joe Lachance | Large scale ancestral allele inference and quantifying the strength of purifying selection |
| Neary, Bridget | Peng Qiu | Identifying Molecular Biomarkers that are Predictive of Patient Response to Cancer Therapies |
| Pan, Hanying | Sam Brown | Cystic Fibrosis Related Clinical and Experimental Data Cleaning and Integration |
| Raut, Priyam | Raquel Lieberman | Identification of biological substrates for Signal Peptide Peptidase in Archaea |
| Zhang, Linglin | Matt Torres | Analysis and mapping of PTM hotspots occurring near biological motifs of protein families |
| Student | Faculty Mentor | Title of Project |
|---|---|---|
| Ban, Dongjo | John McDonald | Assessing the Impact of Aberrant Epigenetic Changes on Allele-Specific Expression in Cancer Cells and the Therapeutic Value of Altering its Mechanisms |
| Brandt, Genevieve | Kostas Konstantinidis | Metagenomic Analysis of the Response of Coastal Microbial Communities to Extreme Weather Pertubations |
| Gulati, Saurabh | King Jordan | Evaluating the Oncogenic Properties of a Novel Histone H2B Modification that Regulates Transposable Element Expression |
| Harvey, William | Kostas Konstantinidis | Transcriptome and Proteome Insights into the Physiology of Dehalococcoides sp. BAV1 During Active Dehalogenation and Differences Compared to Model Organisms |
| Jin, Rong | Joshua Weitz | Examination of Phages as a Biocontrol Approach for Citrus HLB Disease |
| Li, Junyu | Patrick McGrath | Machine Learning on Sand-Manipulating Behaviors of Cichlids |
| Long, Jiani | Matt Torres | Analysis of Post-Translational Modification Hotspots in Domain Families |
| Mathur, Shrey | May Wang | Predicting Underlying Cause of Death Using Electronic Death Records |
| Merritt, Brian | Lily Cheung | Balancer Chromosome and Viral Immunity Design Using CRISPR/Cas9 |
| Nagpal, Sini | Greg Gibson | Pervasive Modulation of Obesity Risk by the Environmental and Genomic Background |
| Ou, Yihao | Fredrik Vannberg | The Epidemiological Dynamics of Highly Mutable Viruses |
| Prabhu, Prachiti | Yuhong Fan | Differential Allelic Expression Regulated by Linker Histone Variants in Development |
| Raghuram, Vishnu | Brian Hammer | Understanding VgrG-Effector Pairs: A Bioinformatics Approach |
| Saldana Farias, Beatriz | King Jordan | Comparing the Effects of Ancestry Versus Admixture on Autozygosity Associated Disease Burden |
| Semwal, Ayush | Soojin Yi | Variation in X Chromosome Inactivation: Can it be Directly Linked to Variation in DNA Methylation? |
| Shah, Nirav | King Jordan | Effects of Ancestry on Prostate Cancer |
| Sharma, Sarthak | Alberto Stolfi | Software for Custom Analysis of Non-Model Organism Single-Cell RNA Sequencing Data from the ddSeq Platform |
| Thakur, Mohit | Joe Lachance | STRUCTUREpainter: A Local Ancestry Inference Algorithm |
| Yue, Qinyu | Sam Brown | C.elegans Tracking and Image Processing with Deep Learning |
| Zhuang, Qinwei | Peng Qiu | Pipeline Construction for Optimal Experimental Design in Tackling Problems of Limited Available Experimental Data in a Multiple-Substgrates-Multiple-Proteases System |
| Student | Faculty Mentor | Title of Project |
|---|---|---|
| Li, Junyu | Patrick McGrath | Machine learning on sand-manipulating behaviors of cichlids |
| Long, Jiani | Matt Torres | Analysis of Post-Translational Modification Hotspots in Domain Families |
| Raghuram, Vishnu | Brian Hammer | Understanding VgrG - effector pairs: A bioinformatics approach |
| Saldana Farias, Beatriz | King Jordan | Genetic risk and disease burden in admixed American populations; The effect of ancestry on the risk of disease |
| Zhuang, Qinwei | Peng Qiu | Pipeline Construction for Optimal Experimental Design in Tackling Problems of Limited Available Experimental Data in a Multiple-Substrates-Multiple-Proteases System |
| Student | Faculty Mentor | Title of Project |
|---|---|---|
| Ban, Dongjo | King Jordan | A Computational Method for Predicting Down-regulated Metabolites in Cancer Which May Constitute Potential Therapeutic Targets |
| Brandt, Genevieve | Kostas Konstantinidis | A Comparison of the Tara Oceans Metagenome Assembled Genomes |
| Gulati, Saurabh | King Jordan | Evaluating the oncogenic properties of a novel histone H2B modification that regulates transposable element expression |
| Jin, Rong | Joshua Weitz | Examination of marine virus and microbial host abundance correlation with metagenomics data |
| Long, Jiani | Matt Torres | Analysis of 3-Dimensional Structural Features as Potential Predictors of PTM Function |
| Mathur, Shrey | May Wang | Predicting Underlying Cause of Death Using Electronic Death Records |
| Mavura, Yusuph | John McDonald | Analysis of Mutations in Cancer Driver Genes in Primary, Metastatic, and recurrent Ovarian Cancer While-Exome Sequecing (WES) Samples |
| Merritt, Brian | Lily Cheung | Engineering the First Balancer Chromosomes in Arabidopsis thaliana |
| Nagpal, Sini | Greg Gibson | Gene Environment Interaction Study for BMI to study the Association of FTO gene with Risk of Obesity |
| Ou, Yihao | Fredrik Vannberg | The Epidemiological Dynamics of Highly Mutable Viruses |
| Prabhu, Prachiti | Yuhong Fan | Differential Allelci Expression Regulated by Linker Histone Variants in Development |
| Raghuram, Vishnu | Brian Hammer | Understanding VgrG – Effector Pairs: A Bioinformatics Approach |
| Ramakrishnan, Ajay | Patrick McGrath | Detecting Subpopulations in Mouse Brain Cells Using Single Cell RNA Sequencing Data |
| Saldana Farias, Beatriz | King Jordan | Genetic Risk and Disease Burden in Genetically Diverse Admixed American Populations |
| Shah, Nirav | James Dahlman | Studying Nanoparticle-Based Changes in Heterochromatin to Improve In Vivo Gene Editing |
| Sharma, Sarthak | Alberto Stolfi | Identification of Ciona Larval Brain Cell Subpopulations Using Single-Cell RNA-Seq |
| Thakur, Mohit | Joe Lachance | Consequences of Admixture in Modern Humans |
| Wist, Stephen | John McDonald | Genotyping Primary, Metastatic, and Recurrent Ovarian Tumors to Inform Treatment |
| Yue, Qinyu | Sam Brown | Using Quantitative Measurement of Fluorescence Intensity to Estimate the Pathogen Load in the Intestine of C. elegans |
| Zhuang, Qinwei | Peng Qiu | Optimal Experimental Design in Tackling Problems of Limited Available Experimental Data in a Multiple-Substrates-Multiple-Proteases System |
| Student | Faculty Mentor | Title of Project |
|---|---|---|
| Adam Dabrowski | King Jordan | Genetics of Sex Difference in Human Mate Preference |
| Aditi Paranjpe | Kostas Konstantinidis | Understanding the Underlying Mechanisms of Genome-Wide Selective Sweeps in Natural Microbial Populations Using Time-Series Metagenomic Analysis |
| Chris Monaco | James Dahlman | Technology Development for High Throughput Analysis of the Nanoparticles |
| Hannah Hatchell | Soojin Yi | CpG Island Identification in Mus musculus Using Whole Genome Bisulfite Sequencing Data from Multiple Tissues |
| Jacob Boswell | Frank Rosenzweig | Phylogenomic Analysis of Multiple Recent Origins of Cellular Differentiation |
| Juichang Lu | Sam Brown | The Dynamics of Death |
| Junke Wang | King Jordan | A Genome-Wide Screen for Genetic Modifiers of Human Transposable Element Expression |
| Kalyani Patankar | Fredrik Vannberg | Microarray Based Gene Expression Analysis to Predict Cancer Tissue of Origin |
| Karan Kapuria | Sam Brown | "Inferring Interactions in the Cystic Fibrosis Microbiome with Dynamic Modeling and Machine Learning" |
| Meixue Duan | Greg Gibson | Single-Cell RNA Sequencing Data Analysis and Pipeline Construction |
| Michael Finlayson | Greg Gibson | An RNA-Seq Based Characterization of Immune Reconstitution in Bone Marrow Transplants |
| Mrunal Dehankar | Yuhong Fan | Computational Modeling of Neural Stem Cell Differentiation |
| Ramya 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 (ASE) in paired Tumor Normal Tissue Samples |
| Shashwat D. Nagar | King Jordan | Exploring Ancestry-Specific Differences in Human Mate Preference |
| Su Jun Zhao | Concettina Guerra | A Distributed Alignment-Free Algorithm to Determine Sequence Similarity Based on Bounded Hamming Distance |
| Venna Wang | Joe Lachance | Ancestral State Reconstruction |
| Xinrui Zhou | Concettina Guerra | Development of Computational Methods for Classifying Permutations with Applications to Rank Aggregation Based Gene Prioritization |
| Student | Faculty Mentor | Title of Project |
|---|---|---|
| Brandon Smith | Soojin Yi | Comparative Analysis of DNA Methylation from Whole Genome Bisulfite Sequencing Maps of Hymenopteran Insects |
| Camila Medrano Trochez | King Jordan | HLA-omics of Admixed LatinAmerican Populations and Its Impact on Health and Disease |
| Chris Monaco | James Dahlman | An Analytical Pipeline for High Throughput Nanoparticle Screening |
| Meixue Duan | Greg Gibson | Longitudinal Evaluation of Human Physiological Conditions Based on Geographical Information System (GIS) and Clinical Outcomes |
| Rohini Mopuri | Patrick McGrath | Study of Single Nucleotide Polymorphisms Arising in East African Lakes |
| Rushika Pandya | Matt Torres | Computational Analysis of PTMs in Domain Families |
| Xinrui Zhou | Concettina Guerra | Development of Computational Methods for Classifying Permutations with Applications to Rank Aggregation Based Gene Prioritization |
| 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? |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |