GRA Projects

Project Year: Computational Biology Faculty Research Awards, Fall 2021
Student Name Faculty Mentor Title
Gregory, Mia Candace Fleischer Assessing Pain Processing in Temporomandibular Disorder using Functional Magnetic Resonance Imaging, Quantitative Sensory Testing, and Pain Metrics
Hoyt, Taylor Soojin Yi Evaluating the Extent of Enhancer Duplication in Human Evolution
Kintzle, Jennifer Greg Gibson Combined Single-Cell ATAC and RNA Sequencing of Peripheral Blood Mononuclear Cells in African Americans with Crohn’s Disease
Liang, Yifan Greg Gibson Combined Single-Cell ATAC and RNA Sequencing of Peripheral Blood Mononuclear Cells in African Americans with Crohn’s Disease
Meade, Caeden Anton Petrov/Loren Williams Computational Analysis and Visualization of Multiple-Sequence Alignments of Protein Homologs
Natu, Aditya Michael Goodisman Gene Duplication and the Evolution of Sociality in Insects
Shantaraman, Anantharaman King Jordan The Effect of Genetic Ancestry on Clinical Genomic Diagnoses in Colombia
Toporek, Aaron Deqiang Qiu A Pupil Activation Network as a Predictor of Alzheimer’s Disease Risk
Valancius, Marcus Yifei Wang (Sam Brown Lab) Georgia Cystic Fibrosis (CF) Data Warehouse: Collaboration between Emory, Children’s, Georgia Tech, and Augusta University
Emmel, Grace Peng Qiu Construction of Cell Type-Specific Gene Regulatory Networks from Single-Cell RNA-Seq Data
Adepu, Harini Greg Gibson Single-Cell Characteristics in Patients with Crohn’s Disease
Augenbroe, Anneke King Jordan Population-Specific Differences in Tier 1 Genomics Disease Burden
Bharadwaj, Ajay Joe Lachance Understanding the Evolution of Heritable Phenotypes Using Polygenic Risk Scores and Ancient DNA
Bhukar, Rohan King Jordan Clinical Utility of Integrated Polygenic Risk Scores (iPRS)
Chelsea, Fnu Joel Kostka Comparison of the Root Microbiome of Terrestrial Plants vs Wetland Plants Using Existing 16S rRNA Gene Amplicon Sequence Datasets.
Damle, Gargi Joe Lachance Applying Confidence Intervals to Polygenic Risk Scores for Ancient DNA
Eum, Jinyoung Eliver Ghosn Validating and Optimizing Cell Trajectory Algorithms for Single Cell RNA-Sequencing Datasets
Project Year: Computational Biology Faculty Research Awards, Summer 2021
Student Name Faculty Mentor Title
Gregory, Mia Candace Fleischer Assessing Pain Processing in Temporomandibular Disorder using Functional Magnetic Resonance Imaging and 1H-MRS
Shantaraman, Anantharaman King Jordan The Effect of Genetic Ancestry on Clinical Genomic Diagnoses in Colombia
Project Year: Computational Biology Faculty Research Awards, Spring 2021
Student Name Faculty Mentor Title
Bharadwaj, Ajay Joe Lachance Effects of Natural selection on Prostate cancer risk using Ancient European DNA
Bhukar, Rohan King Jordan Genome-wide modelling of polygenic risk scores using Ancestry-specific and Trans-ancestry meta analysis
Chelsea, Fnu Joel Kostka Metagenome-enabled elucidation of the Spartina alterniflora root microbiome
Emmel, Grace Peng Qiu Imputation of Single-Cell RNA-Seq Data for Robust Gene-Gene Correlations
Gregory, Mia Candace Fleischer Assessing Pain Processing in Temporomandibular Disorder using Functional Magnetic Resonance Imaging
Hoyt, Taylor Soojin Yi Evaluating the Extent of Enhancer Duplication in Human Evolution
Kintzle, Jennifer Greg Gibson Combined Single Cell Assay of Transposase Accessible Chromatin and RNA Sequencing of Peripheral Blood Mononuclear Cells in African Americans with Crohn's Disease
Kollapaneni, Sai Suraj Deqiang Qiu Investigation of CSF Ferritin as a Predictive Alzheimer’s Disease Exacerbation Factor
Liang, Yifan Greg Gibson The Use of Single-Cell RNA-seq for Transcriptional Risk Scores in Crohn’s Disease
Narayanan, Priya Patrick McGrath Implementing Multiple Object Tracking for Real-Time Detection of Lake Malawi Cichlids During Bower Building
Natu, Aditya Daniel Cornforth Determining the impact of normalization method and laboratory on model accuracy evaluation for Pseudomonas aeruginosa infection of the Cystic Fibrosis lung
Shantaraman, Anantharaman King Jordan The Effect of Genetic Ancestry on Clinical Genomic Diagnoses in Colombia
Vegesna, Manasa Matt Torres FEATURE EXTRACTION FOR ENHANCING THE PREDICTIVE POWER OF THE SAPH-ire MODEL
Project Year: Computational Biology Faculty Research Awards, Fall 2020
Student Name Faculty Mentor Title
Gupta, Sonali King Jordan Rare Variant Analysis of Health Disparities
Hazra, Ujani John McDonald Studying the Role of Antisense RNA in Mediating Aberrant Alternative Splicing in Cancer
Kesar, Devishi King Jordan Exploring the Genetic Diversity in Hispanic/Latino Populations
Sharma, Rhiya Patrick McGrath Employing Fast R-CNN to Obtain Cichlid Position Before and After Sand Manipulation Events During Bower-Building
Mora, Laura Deqiang Qiu Neuroimaging as a Predictor of Cognitive Decline in Alzheimer’s Disease
Rozanski, Allison John Varga Identification of Virulence Factors in Burkholderia Cenocepacia Through Large Scale Comparative Genomics
Sharma, Shivam John McDonald Analyzing the Role of Aberrant Alternative Splicing Leading to Loss of Micro-RNA Binding Sites in Cancer
Singu, Swetha Yuhong Fan Single Cell RNA-seq Identifies Expression Signatures Associated with Histone Hyperacetylation in Embryonic Stem Cells
Xiao, Yiqiong Sam Brown Cystic Fibrosis Data Integration and Front-End Database Development
Lin, Shuting Peng Qiu Pan-Cancer Analysis of Correlation Patterns Between DNA Methylation and Alternative Splicing in TCGA
Cleland, Sara Ainsley Nicholson Population Structure and Genome Analysis of Elizabethkingia Anophelis
Gan, Shuheng Sam Brown Machine Learning Method to Identify Microbial Biomarkers in COPD Sputum Samples
Project Year: Computational Biology Faculty Research Awards, Summer 2020
Student Name Faculty Mentor Title
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
Ahmad, Maria King Jordan Genetic susceptibility and risk prediction for SARS-CoV-2 infection and COVID-19 progression
Project Year: Computational Biology Faculty Research Awards, Spring 2020
Student Name Faculty Mentor Title
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, 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
Sharma, Shivam John McDonald Understanding the Role of Aberrant Alternative Splicing in Loss of Regulatory Control of Gene Expression by Micro-RNAs in Cancer
Project Year: Computational Biology Faculty Research Awards, Fall 2019
Student Name Faculty Mentor Title
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
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
Project Year: Computational Biology Faculty Research Awards, Summer 2019
Student Name Faculty Mentor Title
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.
Project Year: Computational Biology Faculty Research Awards, Spring 2019
Student Name Faculty Mentor Title
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
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
Project Year: Computational Biology Faculty Research Awards, Fall 2018
Student Name Faculty Mentor Title
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
Project Year: Computational Biology Faculty Research Awards, Summer 2018
Student Name Faculty Mentor Title
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
Raghuram, Vishnu Brian Hammer Understanding VgrG - effector pairs: A bioinformatics approach
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
Saldana Farias, Beatriz King Jordan Genetic risk and disease burden in admixed American populations; The effect of ancestry on the risk of disease
Project Year: Computational Biology Faculty Research Awards, Spring 2018
Student Name Faculty Mentor Title
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
Project Year: Computational Biology Faculty Research Awards, Fall 2017
Student Name Faculty Mentor Title
Chris Monaco James Dahlman Technology Development for High Throughput Analysis of the Nanoparticles
Shashwat D. Nagar King Jordan Exploring Ancestry-Specific Differences in Human Mate Preference
Rushika Pandya Matt Torres Computational Analysis of PTMs in Domain Families
Aditi Paranjpe Kostas Konstantinidis Understanding the Underlying Mechanisms of Genome-Wide Selective Sweeps in Natural Microbial Populations Using Time-Series Metagenomic Analysis
Kalyani Patankar Fredrik Vannberg Microarray Based Gene Expression Analysis to Predict Cancer Tissue of Origin
Junke Wang King Jordan A Genome-Wide Screen for Genetic Modifiers of Human Transposable Element Expression
Venna Wang Joe Lachance Ancestral State Reconstruction
Su Jun Zhao Concettina Guerra A Distributed Alignment-Free Algorithm to Determine Sequence Similarity Based on Bounded Hamming Distance
Xinrui Zhou Concettina Guerra Development of Computational Methods for Classifying Permutations with Applications to Rank Aggregation Based Gene Prioritization
Jacob Boswell Frank Rosenzweig Phylogenomic Analysis of Multiple Recent Origins of Cellular Differentiation
Adam Dabrowski King Jordan Genetics of Sex Difference in Human Mate Preference
Mrunal Dehankar Yuhong Fan Computational Modeling of Neural Stem Cell Differentiation
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
Hannah Hatchell Soojin Yi CpG Island Identification in Mus musculus Using Whole Genome Bisulfite Sequencing Data from Multiple Tissues
Karan Kapuria Sam Brown "Inferring Interactions in the Cystic Fibrosis Microbiome with Dynamic Modeling and Machine Learning"
Shareef Khalid John McDonald Analyzing Allele Specific Expression (ASE) in paired Tumor Normal Tissue Samples
Juichang Lu Sam Brown The Dynamics of Death
Ramya Madupuri Matt Torres Analysis of 3-Dimensional Structural Features of Eukaryotic Phosphorylation Sites
Project Year: Computational Biology Faculty Research Awards, Summer 2017
Student Name Faculty Mentor Title
Meixue Duan Greg Gibson Longitudinal Evaluation of Human Physiological Conditions Based on Geographical Information System (GIS) and Clinical Outcomes
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
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
Brandon Smith Soojin Yi Comparative Analysis of DNA Methylation from Whole Genome Bisulfite Sequencing Maps of Hymenopteran Insects
Xinrui Zhou Concettina Guerra Development of Computational Methods for Classifying Permutations with Applications to Rank Aggregation Based Gene Prioritization
Project Year: Computational Biology Faculty Research Awards, Spring 2017
Student Name Faculty Mentor Title
Karan Kapuria Sam Brown Network Analysis of Microbial Communities in Cystic Fibrosis Lung
Shareef Khalid John McDonald Analyzing Allele Specific Expression in Tumor Tissue Samples
Michael Finlayson Greg Gibson The Effect of Bone Marrow Transplantation on Peripheral Blood Expression Profiles
Tyrone Lee Patrick McGrath A System for High Throughput Behavioral Analysis of Lake Malawi Cichlid Fishes using Computer Vision techniques
Juichang Lu Sam Brown The Dynamic of Death
Ramyasree Madupuri Matt Torres Analysis of 3-Dimensional Structural Features of Eukaryotic Phosphorylation Sites
Camila Medrano Trochez King Jordan HLA-omics of Admixed Latin American Populations and Its Impact on Health and Disease
Shashwat Deepali Nagar King Jordan Detecting Polygenic Adaptive Introgression
Rushika Pandya Matt Torres Computational Analysis of PTMs in Domain Families
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
Krithika Ravindran Naidu Fredrik Vannberg Drug Response Prediction on Cancer Patients Using Support Vector Machines
Junke Wang King Jordan Genetic Canalization and Sex-Specific Protective Model for Diseases
Venna Wang Joe Lachance Is the Rate of Human Evolution Accelerating?
Bowen Yang Lee Cooper Genomic and Histology Analysis of Diffuse Lower-Grade Gliomas
Adam Dabrowski King Jordan Ancestry-Specific Assortative Mating in Latin America
Mrunal Dehankar Yuhong Fan Computational Modeling of Neural Stem Cell Differentiation
Meixue Duan Greg Gibson Investigating Personal Differences During Complicated Malaria Development
Hannah Hatchell Soojin Yi Relating Tissue-Specific Gene Expression and Drug Killing Indices
Tian Jin Fredrik Vannberg De novo Genome Assembly Post-assembly Processing
Project Year: Computational Biology Faculty Research Awards, Fall 2016
Student Name Faculty Mentor Title
Chen Guo Greg Gibson Evaluating Contribution of Rare Variants to Gene Expression in Humans
Walker Gussler Joshua Weitz Modeling Infectious Disease Spread Over Complex Networks Outside of the SIS Framework
Tyrone Lee Patrick McGrath A System for High Throughput Behavioral Analysis of Lake Malawi Cichlid Fishes Using Computer Vision Techniques
James Moore Fredrik Vannberg Forecasting Tuberculosis Emergence Using Agent-based Modeling with Partial Data
Petar Penev Eric Gaucher The Aroma of Fluorescence
Harshmi Shah John McDonald Developing an Algorithm to Predict Drug Therapies from Tumor Sample Analysis
Devika Singh Joshua Weitz A New Method of Modeling Phage Therapy
Tannishtha Som King Jordan Suffix Tree Based Approach to Bacterial Typing
Hari Prasanna Subramanian Greg Gibson RNA-Sequencing as a diagnostic tool for Neuromuscular Dystrophy
Niveda Sundararaman Matthew Torres Developing a Scoring and Ranking Scheme for PTM Hotspots
Andrew Teng Joe Lachance From Genetic Risk Scores to Clinical Disease Risks
Min Yi Fredrik Vannberg Processing, Storing, and Analytics of Electronic Health Records
Project Year: Computational Biology Faculty Research Awards, Summer 2016
Student Name Faculty Mentor Title
Aroon Chande King Jordan Developing a Typing Scheme for Nontypeable Haemophilus influenzae
Namrata Kalsi Patrick McGrath Prediction of Chemical Ligands Using Molecular Dynamic Simulations
Harshmi Shah John McDonald Developing an Algorithm to Predict Drug Therapies from Tumor Sample Analysis
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
Project Year: Computational Biology Faculty Research Awards, Spring 2016
Student Name Faculty Mentor Title
Andrew Teng Joe Lachance From Genetic Risk Scores to Clinical Disease Risks
Tannishtha Som King Jordan Machine Learning Based Method for Reporting Antimicrobial Resistance of Fungal Infections in Colombia
Min Yi Fredrik Vannberg Drug Prediction on Ovarian Cancer Patients
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
Niveda Sundararaman Matt Torres SAPH-ire: Structural Analysis of PTM Hotspots
Devika Singh Joshua Weitz A New Method of Modeling Phage Therapy
Tyrone Lee Patrick McGrath Genomics of Complex Behavior in Lake Malawi Cichlid Fishes
Namrata Kalsi Patrick McGrath Prediction of Chemical Ligands Using Molecular Dynamic Simulations
Alicia Francis Fredrik Vannberg De Novo RNA-SEQ Ovarian Cancer Profile Analysis
Project Year: Computational Biology Faculty Research Awards, Fall 2015
Student Name Faculty Mentor Title
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
Roopa Reddy Nagilla Greg Gibson The 'CorRelate' package for understanding correlation between high-throughput genomic data
Raghavendra Padmanabhan Patrick McGrath Analysis of Chromosomal Inversions in Cichlids using Next Gneration Sequencing (NGS) 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
Project Year: Computational Biology Faculty Research Awards, Summer 2015
Student Name Faculty Mentor Title
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
Project Year: Computational Biology Faculty Research Awards, Spring 2015
Student Name Faculty Mentor Title
Nandida Damaraju Constantine Dovrolis Structural Analysis of Metabolic Networks
Bhanu Gandham King Jordan Detection of Causal Mutation for Mucopolysaccharidosis by Trio Exome Analysis
Taylor Griswold Brian Hammer Identifying Mutations in Novel Genetic Factors that Prevent Natural Competence in the Human Pathogen Vibrio cholerae
Anuj Gupta King Jordan A Genome Based Sequence Typing Tool for Bacterial Pathogens
Yasvanth Kulasekarapandian Fredrik Vannberg K-mer based solutions for highly dynamic viral geomes
Rachel Kutner Greg Gibson Integrative -omic Study of Malaria Virulence and Disease Progression Over Time
Menghan Li Chong Shin Multi-cellular Crosstalk During Liver Regeneration After Injury
Tian Mi Steve Harvey Evolution of Ribosome at Insertion Points
Shashidhar Ravishankar Fredrik Vannberg Alignment free quantification of gene expression from RNA-Seq experiments
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
Raghavendra Padmanabhan Patrick McGrath A Computational Model to Predict Phenotype from Genotype in Caenorhabditis elegans
Project Year: Computational Biology Faculty Research Awards, Fall 2014
Student Name Faculty Mentor Title
Ying Sha King Jordan Dynamic Analysis of Nucleosomes of Human Stem Cell
Sanjeev Sariya Patrick McGrath Predicting Residues Involved for Ligand Binding in C. elegans Chemoreceptors
Dhruviben Patel Fredrik Vannberg Comparative Analysis of Plasmodium Parasites P. malariae and P. brasilinum
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
Ali Pirani King Jordan Bordetella Genome Informatics Platform - BGIP
Taylor Griswold Brian Hammer Identifying Novel Genetic Factors that Prevent Natural Competence in the Human Pathogen Vibrio cholerae
Emily Norris King Jordan The Genomic Basis of Capsule Switching and its Relationship to Disease in Neisseria meningitidis
Project Year: Computational Biology Faculty Research Awards, Summer 2014
Student Name Faculty Mentor Title
Emily Norris Steve Harvey Unusual RNA Secondary Structures
Dhruviben Patel Fredrik Vannberg Comparative Analysis of Plasmodium Parasites P. malariae and P. brasilinum
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
Ali Pirani King Jordan Genome Rearrangement Analysis to Characterize the Emergence of Bordetella pertussis
Project Year: Computational Biology Faculty Research Awards, Spring 2014
Student Name Faculty Mentor Title
Ying Sha King Jordan Senescence of Human Stem Cell
Sanjeev Sariya Patrick McGrath Predicting Residues Involved for Ligand Binding in C. elegans Chemoreceptors
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
Ali Pirani King Jordan Genome-Based MLST Scheme for Bordetella pertussis
Project Year: Computational Biology Faculty Research Awards, Fall 2013
Student Name Faculty Mentor Title
Smruthy Sivakumar King Jordan Antagonistic Pleiotropy and Cancer
Cai Huang Fredrik Vannberg Alignment Free Sequence Analysis
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
Dan Sun Soojin Yi A Global Analysis of DNA Methylation and Aging in Human Brain
Vivek Sagar Radhakrishna Fredrik Vannberg Developing a Generic Web-Based Framework for to Analyze and Visualize Global Distribution Patterns Pathogen
Pramod Mayigowda King Jordan Integration of Bacterial Isolate Genome Sequence database to Meningococcus Genome Informatics Platform
Esha Jain Yuhong Fan Repeat Analysis of Individual H1 Variants Enriched Regions
Raghu Chandramohan May Wang Identifying the Detection Threshold and Systematic Assessment of RNA-seq Expression Profiling Using Simulated Data
Kelley Bullard Yuhong Fan An Investigation of the Relationship Between Linker Histone H1 and the Insulator Binding Protein CTCF
Siddharth Biswal John McDonald Missing title
Vartika Agrawal Greg Gibson Analysis of allele specific expression using DNA and RNA-Sequencing
Project Year: Computational Biology Faculty Research Awards, Summer 2013
Student Name Faculty Mentor Title
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
Project Year: Computational Biology Faculty Research Awards, Spring 2013
Student Name Faculty Mentor Title
Pramod Mayigowda King Jordan Meningococcus Genome Informatics Platform
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
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
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
Peter Audano Fredrik Vannberg Rapid Detection of Pathogens in Metagenomic Sequence Data
Raghu Chandramohan May Wang Integrated Prediction Modeling for Neuroblastoma Treatment Outcome Using RNA-Seq Data
Xiao Dong Yuhong Fan Bioinformatics Analysis of Linker Histone H1 and DNA Methylation
Vivek Sagar Radhakrishna Fredrick Vannberg R-Tree Based Qualitative K-Merised Metagenomic Analysis and Data Visualization
Project Year: Computational Biology Faculty Research Awards, Fall 2012
Student Name Faculty Mentor Title
Ashwath Kumar Yuhong Fan Analysis of Histone H1 and H3 modifications from CHIP-Seq data
Hema Nagrajan Soojin Yi Genome wide characterization of CpG Islands by Epigenetic properties
Shengyun Peng Fredrik Vannberg Clinical Metagenomics Using K-Mer Arrays
Deepak Purushotham King Jordan Transposable element derived structural variation in human prostate cancer
Piyush Ranjan Steve Harvey Searching for unusual features in RNA secondary structure
Amit Rupani Fredrik Vannberg Expression-based genome-wide association study to identify susceptibility loci linked to HCV infection in liver tissue
Shimantika Sharma Joshua Weitz G-DES: an efficient software for microbial gene-level diversity estimation
Ambily Sivadas Greg Gibson The WHOLE Study – An Approach to Personalized Medicine through Integrative Genomic Profiling
Lu Wang King Jordan Transcriptional profiling of non-coding RNA expression in human adult stem cells during aging
Haozheng Tian Greg Gibson Methylome in the Role of Regulation of Transcriptome in WHOLE Study
Project Year: Computational Biology Faculty Research Awards, Summer 2012
Student Name Faculty Mentor Title
Hema Nagrajan Soojin Yi Genome-wide characterization of CpG islands by epigenetic properties
Piyush Ranjan Steve Harvey Incorporating Kinetic Information into RNA Secondary Structure Prediction
Lu Wang King Jordan The relationship between DNA damage and non-coding RNA expression in adult stem cells
Project Year: Computational Biology Faculty Research Awards, Spring 2012
Student Name Faculty Mentor Title
Ashwath Kumar Yuhong Fan Analysis of Histone H1 and H3 modifications from CHIP-Seq data
Hema Nagrajan Soojin Yi Identifying Determinants of Mammalian Non-synonymous and Synonymous Substitution Rates Using Novel Multivariate Principal Component Regression Method
Shengyun Peng Fredrik Vannberg Multivariate Analysis of Exosomes Pre- and Post-Stimulation
Deepak Purushotham King Jordan Transposable element derived structural variation in human prostate cancer
Piyush Ranjan Steve Harvey Incorporating Kinetic Information into RNA Secondary Structure Prediction
Amit Rupani Fredrik Vannberg Differential RNA dynamics study of exosomes post vaccination: A systems biology approach
Shimantika Sharma Joshua Weitz G-DES: an efficient software for microbial gene-level diversity estimation
Ambily Sivadas Greg Gibson Genome Wide Association Study (GWAS) of Human Metabolic profiles to identify common and rare variants-associated metabolic phenotypes
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
Project Year: Computational Biology Faculty Research Awards, Fall 2011
Student Name Faculty Mentor Title
Paul Cooper Yuhong Fan Analysis of Histone H1 binding to DNA
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
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
Vani Rajan Mark Borodovsky & Brian Hammer Computational methods to identify genes involved in control of horizontal gene transfer in the bacterial pathogen Vibrio cholerae
Shrutii Sarda Soojin Yi Understanding evolution of gene-body methylation in diverse animals using experimentally determined methylation levels
Neha Varghese King Jordan & Nael McCarty Correlation of site-specific evolutionary parameters with mutational effects in Cystic Fibrosis Transmembrane Regulator
Project Year: Computational Biology Faculty Research Awards, Summer 2011
Student Name Faculty Mentor Title
Robert Arthur John McDonald Study and Stent Usage and Restenosis in Sus scrofa
Shaopu Qin Greg Gibson & Nicoleta Serban Application of Variable Selection Methods in Microarray Data Analysis
Kristen Knipe Joshua Weitz PhageLab: a Matlab-based Java Web Application to Aid in the Understanding of Phage Dynamics
Robert Petit King Jordan and Tim Read Bacterial Pathogen Database and Browser for Clinical Diagnostics
Project Year: Computational Biology Faculty Research Awards, Spring 2011
Student Name Faculty Mentor Title
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
Paul Cooper Yuhong Fan Analysis of Histone H1 binding to DNA
Kristen Knipe Joshua Weitz PhageLab: a suite of GUIs to aid in the understanding of phage dynamics
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
Neha Varghese King Jordan & Nael McCarty Comparison of site-specific evolutionary parameters to mutational effects in Cystic Fibrosis Transmembrane Regulator
Project Year: Computational Biology Faculty Research Awards, Fall 2010
Student Name Faculty Mentor Title
Chandni Desai Brian Hammer Comparative Sequence Analysis to Predict Interspecies Horizontal Gene Transfer among Bacterial Pathogens
Jay Humphrey King Jordan Assembly and Annotation Pipeline and Scalable Genome Browser
Sandeep Namburi King Jordan InGen: A Suite of Tools to Aid in the Epidemiology of Influenza
Eishita Tyagi King Jordan Epigenetic regulation of cell-type specific gene expression by transposable element derived enhancers
Aarthi Talla Greg Gibson Gene Network Analysis of Human Gene Expression Data
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
Project Year: Computational Biology Faculty Research Awards, Summer 2010
Student Name Faculty Mentor Title
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
Eishita Tyagi King Jordan Epigenetic regulation of cell-type specific gene expression by transposable-element derived enhancers
Phillip Lee Melissa Kemp Mathematical modeling of cellular thioredoxin redox states and cellular signaling
Project Year: Computational Biology Faculty Research Awards, Spring 2010
Student Name Faculty Mentor Title
Nitya Sharma King Jordan Investigating the role of IS elements in capsule switching in Neisseria meningitidis
Kanika Arora Eric Gaucher & Stephen Harvey Heterotachy in ribosomal RNA
Vinay Vyas Stephen Harvey A study of the structural basis of ribosomal fidelity using MD (Molecular Dynamic) simulations
Eishita Tyagi King Jordan Epigenetic regulation of cell-type specific gene expression by transposable-element derived enhancers
Aarthi Talla Greg Gibson Microarray analysis of human gene expression data
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
Project Year: Computational Biology Faculty Research Awards, Fall 2009
Student Name Faculty Mentor Title
Nitya Sharma King Jordan Using SNPs to discriminate virulent and carriage strains in Neisseria meningitidis
Kanika Arora Stephen Harvey Dependence of 3D size of single-stranged RNA molecules on sequence length, secondary structure and presence of condensing agents
Abhiram Das Joshua Weitz Duplicate gene fate finder
Khanjan Ghandi Timothy Read, Emory University Design of database of bacterial pathogen genomes for PCR primer design and ongoing validation
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
Viswateja Nelakuditi King Jordan Neisseria Base: a comparative genomics database and genome browser for species of the Neisseria genus