CBB Alumni
Chaitanya Acharya
Duke University, PhD., Computational Biology & Bioinformatics, 2016
Faculty Mentor: Andrew Allen, Ph.D. Duke University, Department of Biostatistics & Bioinformatics
Dissertation: Efficient analysis of complex, multi-modal genomic data
Jason belsky
Duke University, PhD., Computational Biology & Bioinformatics, 2015
Funded by T32 training grant 5T32-GM071340
Faculty Mentors: David MacAlpine, Ph.D., Duke University, Department of Pharmacology & Cancer Biology
Dissertation: Genome-wide foot printing uncovers epigenetic regulatory paradigms by revealing the chromatin occupancy landscape
Rotem Ben-Shachar
Funded by T32 training grant 5T32-GM071340
Faculty Mentors: Katia Koelle, Ph.D., Duke University, Department of Biology
Dissertation: Drivers of dengue within-host dynamics and virulence evolution
Ashlee Benjamin
Duke University, PhD., Computational Biology & Bioinformatics, 2013
Funded by T32 training grant 5T32-GM071340
Faculty Mentors: Greg Wray Ph.D., Duke University, Department of Biology (co-advisor) Joseph E. Lucas Ph.D. (co-advisor)
Dissertation: Computational Processing of Omics Data: Implications for Analysis
Brian Bennett
Duke University, Ph.D., Computational Biology & Bioinformatics, 2012
Funded by T32 training grant 5T32-GM071340
Faculty Mentor: Sayan Mukherjee Ph.D., Duke University, Departments of Statistical Science
Dissertation: Intergrative Genomic Modeling of Complex Traits Using Pathway Analysis
Alan Boyle
Duke University, Ph.D., Computational Biology & Bioinformatics, 2009
Faculty Mentor: Terry Furey, Ph.D., Duke University, Department of Biostatistics and Bioinformatics, IGSP
Dissertation: Studies on Human Chromaticn Using High-Throughput DNasel sequencing
Merve Cakir
Duke University, Ph.D., Computational Biology & Bioinformatics, 2018
Faculty Mentor: Kris Wood, Ph.D., Duke University, Department of Pharmacology and Cancer Biology
Dissertation: Graph-based Approaches for Cancer Genomics with Applications to Cancer Signaling and Dependencies
Xianrui Cheng
Duke University, Ph.D., Computational Biology & Bioinformatics, 2012
Faculty Mentors: Josh Socolar Ph.D, Duke University, Department of Physics (co-advisor) Dave McClay Ph.D., Duke University, Department of Biology (co-advisor)
Dissertation: Mechanistic modeling and experiments on cell fate specificiation in the sea urchin embryo
David Crosslin
Duke University, Ph.D., Computational Biology & Bioinformatics, 2009
Faculty Mentor: Elizabeth Hauser, Ph.D., Duke University, Department of Medicine, Medical Genomics
Dissertation: Characterization of Gene Interaction and Assessment of LD Matrix Measures for the Analysis of Biological Pathyway Association
Anastasia Deckared
Duke University, Ph.D., Computational Biology & Bioinformatics, 2014
Funded by T32 training grant 5T32-GM071340
Faculty Mentors: John Harer, Ph.D. (Duke University, Department of Mathematics), Steve Haase, Ph.D. (Duke University, Department of Biology)
Dissertation: Constructing Mathematical Models of Gene Regulatory Networks for the Yeast Cell Cycle and Other Periodic Processes
Peng Dong
Duke University, Ph.D., Computational Biology & Bioinformatics, 2015
Faculty Mentors: Bernard Mathey-Prevot, Ph.D. (Duke University, Department of Pharmacology & Cancer Biology), Lingchong You, Ph.D. (Duke University, Department of Biomedical Engineering)
Dissertation: Explore Rb/E2F Activation Dynamcis to Define the Control Logic of Cell Cycle Entry in Single Cells
Matthew Eaton
Duke University, Ph.D., Computational Biology & Bioinformatics, 2011
Funded by T32 training grant 5T32-GM071340
Faculty Mentor: David M. MacAlpine, Ph.D., Duke University, Pharmacology & Cancer Biology
Dissertation: Chromatin determinants of the eukaryotic DNA replication program
Elena Edelman
Duke University, Ph.D., Computational Biology & Bioinformatics, 2008
Funded by T32 training grant 5T32-GM071340
Faculty Mentor: Sayan Mukherjee, Ph.D., Duke University, Department of Statistical Science, IGSP
Dissertation: Modeling Cancer Progression on the Pathway Level
Kai Fan
Duke University, Ph.D., Computational Biology & Bioinformatics, January 2018
Faculty Mentor: Katherine Heller, Ph.D., Duke University, Department of Statistical Science
Dissertation: Deep Generative Models and Biological Applications
Jacob Frelinger
Duke University, Ph.D., Computational Biology & Bioinformatics, 2013
Funded by T32 training grant 5T32-GM071340
Faculty Mentor: Cliburn Chan Ph.D., Duke University, Department of Biostatistics & Bioinformatics
Dissertation: Computational Methods for Comparative Analysis of Rare Cell Subsets in Flow Cytometry
Diana Fusco
Duke University, Computational Biology & Bioinformatics, 2014
Faculty Mentor: Patrick Charbonneau Ph.D., Duke University, Department of Chemistry
Dissertation: Protein Crystallization: Soft Matter and Chemical Physics Perspectives
Stoyan Georgiev
Duke University, Ph.D., Computational Biology & Bioinformatics, 2011
Faculty Mentors: Uwe Ohler Ph.D., Duke University, Department of Biostatistics & Bioinformatics (co-advisor) Sayan Mukherjee Ph.D., Duke University, Department of Statistical Science (co-advisor)
Dissertation: Computational Methods for Functional Motif Identification and Approximate Dimension Reduction in Genomic Data
Mariana Gomez-Schiavon
Duke University, Ph.D., Computational Biology & Bioinformatics, 2016
Faculty Mentor: Nicolas Buchler Ph.D., Duke University, Department of Biology
Dissertation: Stochastic Dynamics and Epigenetic Regulation of Gene Expression: From Stimulus Response to Evolutionary Adaptation
Justin Guinney
Duke University, Ph.D., Computational Biology & Bioinformatics, 2009
Funded by T32 training grant 5T32-GM071340
Faculty Mentors: Sayan Mukherjee, Ph.D., Duke University, Department of Statistical Science, IGSP (co-advisor) Philip Febbo MD, Duke University, Department of Medicine, IGSP (co-advisor)
Dissertation: The Geometry of Cancer
Ayal Baruch Gussow
Duke University, Ph.D., Computational Biology & Bioinformatics, 2016
Funded by T32 training grant 5T32-GM071340
Faculty Mentor: David Goldstein, Ph.D., Columbia University and Duke University
Dissertation: Population Genetic Annotation of the Human Genome: Identifying Pathogenic Mutations
Jeff Headd
Duke University, Ph.D., Computational Biology & Bioinformatics, 2009
Faculty Mentors: David Richardson, Ph.D., Duke University Department of Biochemistry (co-advisor) Jane Richardson, Ph.D., Duke University, Department of Biochemistry (co-advisor)
Dissertation: "Analysis and Error Correction in Structures of Macromolecular Interiors and Interfaces"
Swati Jain
Duke University, Ph.D., Computational Biology & Bioinformatics, 2015
Faculty Mentors: Jane Richardson, Ph.D. (Duke University, Department of Biochemistry), Bruce Donald, Ph.D. (Duke University, Department of Computer Science)
Dissertation: RNA 3D Structure Analysis and Validation and Design Algorithms for Proteins and RNA
Yu Jiang
Duke University, Ph.D., Computational Biology & Bioinformatics, 2015
Faculty Mentor: Andrew Allen, Ph.D. Duke University, Department of Biostatistics & Bioinformatics
Dissertation: Statistical Methods of Disease-Gene Mapping in Trio-based Next Generation Sequencing
Nicole Johnson
Duke University, Ph.D., Computational Biology & Bioinfomatics, 2010
Faculty Mentor: Lindsay Cowell Ph.D., Duke University, Department of Biostatistics and Bioinformatics
Dissertation: Using Genome-wide Approaches to Charaxterize the relationship between Genomice Variarion and disease: A case study in Oligoodendroglioma and Staphylococcus aureus
Curtis Layton
Duke University, Ph.D., Computational Biology & Bioinformatics, 2010
Faculty Mentor: Homme Hellinga, Ph.D., Duke University, Department of Biochemistry
Dissertation: Protein-Protein Interactions: A Hotspot-Centric View
Jessica Leete
Funded bt T32 training grant 5T32-GM071340
Faculty Mentor: Anita Layton, Department of Mathematics
Dissertation: Sex-specific Computational Models of Blood Pressure Regulation
Parawee Lekprasert
Duke University, Ph.D., Computational Biology & Bioinformatics, 2012
Faculty Mentor: Uwe Ohler Ph.D., Duke University, Departments of Biostatistics and Bioinformatics
Dissertation: MicroRNA Target Prediction via Duplex Formation Features and Direct Binding Evidence
Anna Lowegard
Duke University Ph.D., Computational Biology & Bioinformatics, 2019
Funded by T32 training grant 5T32-GM073140
Faculty Mentor: Bruce Donald, Ph.D., Duke University, Department of Computer Science
Dissertation: Novel Algorithms and Tools for Computational Protein Design with Applications
Phillippe Luedi
Duke University, Ph.D., Bioinformatics & Genome Technology, 2006
Faculty Mentor: Fred Dietrich Ph.D., Duke University, Molecular Genetics & Microbiology
Dissertation: A Machine learning approach to predict epigenetic phenomena in human and mouse
Kaixuan (Kevin) Luo
Faculty Mentors: Alexander Hartemink, Ph.D., Duke University, Department of Computer Science
Dissertation: Modeling Nuclease Digestion Data to Predict the Dynamics of Genome-wide Transcription Factor Occupancy
Daniel Mace
Duke University, Ph.D., Computational Biology & Bioinformatics, 2009
Funded by T32 training grant 5T32-GM071340
Faculty Mentor: Uwe Ohler, Ph.D., Duke University, Department of Biostatistics and Bioinformatics, IGSP
Dissertation: Automated microscopy and high throughput image analysis in Arabidopsis and Drosophila
William Majoros
Duke University, Ph.D., Computational Biology & Bioinformatics, 2017
Funded by T32 training grant 5T32-GM071340
Faculty Mentor: Tim Reddy, Ph.D., Department of Biostatistics and Bioinformatics, GCB
Dissertation: Statistical Modeling of Genetic and Epigenetic Factors in Gene Structures and Transcriptional Enhancers
Dinesh Manandhar
Duke University, Ph.D., Computational Biology & Bioinformatics, March 2018
Faculty Mentor: Raluca Gordân, Ph.D., Duke University, Department of Biostatistics and Bioinformatics
Dissertation: Methods for Comparative Analysis of Chromatin Accessibility and Gene Expression wih Applications to Cellular Reprogramming
Samuel Andres Ramirez Martinez
Duke University, Ph.D., Computational Biology & Bioinformatics, 2015
Faculty Mentors: Daniel Lew, Ph.D., Duke University, Department of Pharmacology & Cancer Biology
Dissertation: Modeling the Effect of Cell Shape on Spatial Information Flow in Neurons
Michael Mayhew
Duke University, Ph.D., Computational Biology & Bioinformatics, 2014
Funded by T32 training grant 5T32-GM071340
Faculty Mentors: Alexander Hartemink, Ph.D. Duke University, Department of Computer Science, Steve Haase, Ph.D. Duke University, Department of Biology
Dissertation: Computational Systems Biology of Saccharomyces cerevisiae Growth and Division.
Ian McDowell
Duke University, Ph.D., Computational Biology & Bioinformatics, 2017
Funded by T32 training grant 5T32-GM071340
Faculty Mentor: Tim Reddy, Ph.D., Department of Biostatistics and Bioinformatics, GCB
Dissertation: Integrative Analysis of the Genomics of the Human Glucocorticoid Response
Firas Midani
Duke University, Ph.D., Computational Biology & Bioinformatics, June 2018
Funded by T32 training grant 5T32-GM071340
Faculty Mentor: Lawrence David, Ph.D., Duke University Department of Molecular Genetics & Microbiology
Dissertation: Predicting colonization of microbes in the human gut
Andrea Moffit
Duke University, Ph.D., Computational Biology & Bioinformatics, 2016
Faculty Mentor: Sandeep Dave, M.D., MS, Duke University, Department of Medicine
Dissertation: Integrative Computational Genomics Defines the Molecular Orgins and Outcomes of Lymphoma
Brad Thomas Moore
Duke University, Ph.D., Computational Biology & Bioinformatics, 2017
Funded by T32 training grant 5T32-GM071340
Faculty Mentor: Ryan Baugh, Ph.D., Duke University, Department of Biology
Dissertation: Population Sequencing for Studying Natural and Artificial Variation in C. elegans
Supriya Munshaw
Duke University, PhD., Computational Biology & Bioinformatics, 2010
Faculty Mentor: Tom Kepler, Ph.D., Duke University, Department of Biostatistics and Bioinformatics
Dissertation: Computational Methods to Study Diversification in Pathogens, and Invertebrate and Vertebrate Immune System
Anirudh Natarajan
Duke University, Ph.D., Computational Biology & Bioinformatics, 2014
Faculty Mentors: Blanche Capel Ph.D., Duke University, Deparment of Cell Biology (co-advisor) Uwe Ohler Ph.D., Max-Delbruck-Centrum Fur Molekulare Medizin (MDC), Berlin-Buch, Computational Regulatory Genomics (co-advisor)
Dissertation: Uncovering the Transcription Factor Network Underlying Mammalian Sex Determination
Adegoke Ojewole
Duke University, Ph.D., Computational Biology & Bioinformatics, March 2018
Funded by T32 training grant 5T32-GM071340
Faculty Mentor: Bruce Donald, Ph.D., Duke University, Department of Computer Science
Dissertation: Efficient New Computational Protein Design Algorithms with Application to Drug Resistance Prediction and HIV Antibody Design
David Orlando
Duke University, Ph.D., Computational Biology & Bioinformatics, 2009
Faculty Mentors: Philip Benfey, Ph.D., Duke University, Department of Biology, Institute of Genome Science and Policy (co-advisor) Steve Haase Ph.D., Duke University, Department of Biology (co-advisor)
Dissertation: Regulation of Global Transcription Dynamics During Cell Division and Root Development
Razvan Panea
Duke University, Ph.D., Computational Biology & Bioinformatics, 2020
Faculty Mentor: Sandeep Dave, Department of Medicine
Dissertation: A Cloud-based Infrastructure for Cancer Genomics
Andreas Pfenning
Duke University, Ph.D., Computational Biology & Bioinformatics, 2012
Funded by T32 training grant 5T32-GM071340
Faculty Mentors: Erich Jarvis Ph.D., Duke University, Department of Neurobiology (co-advisor) Alex Hartemink Ph.D., Duke University, Department of Computer Science (co-advisor)
Dissertation: A Computational Synthesis of Genes, Behavior, and Evolution Provides Insights into the Molecular Basis of Vocal Learning
Elizabeth Rach
Duke University, Ph.D., Computational Biology & Bioinformatics, 2010
Faculty Mentor: Uwe Ohler, Ph.D., Duke University, Department of Biostatistics and Bioinformatics, IGSP
Dissertation: The Spacial and Temporal Regulatory Code for Transcription Initiawtion in Drosophila Melanogaster
Kyle E. Roberts
Duke University, Ph.D., Computational Biology & Bioinformatics, May 2014
Funded by T32 training grant 5T32-GM071340
Faculty Mentor: Bruce Donald Ph.D., Duke University, Department of Computer Science
Dissertation: Novel Computational Protein Design Algorithms with Applications to Cystic Fibrosis and HIV
Chetan Rupakheti
Duke University, Ph.D., Computational Biology & Bioinformatics, May 2015
Faculty Mentor: David Beratan, Ph.D., University, Department of Chemistry
Dissertation: Property Biased-Diversity Guided Explorations of Chemical Spaces
Ana PaulA de Oliveira Sales
Duke University, Ph.D., Computational Biology & Bioninformatics, 2011
Faculty Mentor: Thomas B. Kepler, Ph.D., Duke University, Department of Biostatistics & Bioinformatics & Duke Human Vaccine Institute
Dissertation: Computational Methods for Investigating Dendritic Cell Biology
Zachary Scholl
Duke University, Ph.D., Computational Biology & Bioinformatics, 2016
Faculty Mentor: Piotr Marszalek, Ph.D., Duke University, Department of Mecahnical Engineering & Material Science & Weitao Yang, Ph.D., Duke University, Department of Chemistry
Dissertation: The (un)folding of multidomain proteins through the lens of single-molecule force-spectroscopy and computer simulation
Nathan C. Sheffield
Duke University, Ph.D., Computational Biology & Bioinformatics, 2013
Funded by T32 training grant 5T32-GM071340
Faculty Mentor: Gregory Crawford, Ph.D., Duke University, Department of Pediatrics
Dissertation: Regulatory Elements and Gene Expression in Primates and Diverse Human Cell-types
Haige Shen
Duke University, Ph.D., Computational Biology & Bioinformatics, 2007
Faculty Mentors: Mike West, Ph.D., Department of Statistical Science, Duke Center for Genomic and Computational Biology Science and Policy (co-advisor) Jen-Tsan Ashley Chi, MD, Ph.D., Duke University IGSP, Program in Cell and Molecular Biology (co-advisor)
Dissertation: Bayesian Analysis in Cancer Pathway Studies and Probabilistic Pathyway Annotation
Justin silverman
Duke University, Ph.D., Computational Biology & Bioinformatics, 2019
Faculty Mentor: Lawrence David, Ph.D., Duke University, Department of Molecular Genetics and Microbiology (MGM)
Dissertation: Bayesian Multivariate Count Models for the Analysis of Microbiome Studies
Peter Tonner
Duke University, Ph.D., Computational Biology & Bioinformatics, 2017
Faculty Mentor: Amy Schmid, Ph.D., Department of Biology, GCB
Dissertation: Bayesian Modeling of Microbial Physiology
Diana Vera-Cruz
Duke University, Ph.D., Computational Biology & Bioinformatics, 2020
Faculty Mentor: Katia Koelle, Department of Biology at Emory University
Dissertation: Understanding the Interplay Between Viral and Host Dynamics
Joseph Volpe
Duke University, Ph.D., Computational Biology & Bioinformatics, 2008
Faculty Mentor: Tom Kepler, Ph.D., Duke University, Department of Biostatistics and Bioinformatics
Dissertation: Mechanistic and Genetic Biases in Human Immunoglobulin Heavy Chain Development
Florian Wagner
Duke University, Ph.D., Computational Biology & Bioinformatics, 2017
Faculty Mentor: Sandeep Dave, M.D. M.S., Duke University, Department of Medicine
Dissertation: Methods for Systematic Exploratory Analysis of Gene Expression Data with Applications to Cancer Genomics
Hanghang Wang
Duke University, Ph.D., Computational Biology & Bioinformatics, 2017
Faculty Mentor: Svati Shah, M.D., Duke University, Department of Medicine
Dissertation: Improving Mass Spectrometry-Based Metabolite Identification and Quantification and Application to Cardiovascular Disease
Rui Wang
Duke University, Ph.D., Computational Biology & Bioinformatics, 2011
Faculty Mentors: Erich Jarvis Ph.D., Duke University, Department of Neurobiology (co-advisor) Alex Hartemink Ph.D., Duke University, Department of Computer Science (co-advisor)
Dissertation: Dissecting the genetic basis of convergent complex traits based on molecular homoplasy
Cavin Ward-Caviness
Duke University, Ph.D., Computational Biology & Bioinformatics, 2014
Funded by T32 training grant 5T32-GM071340
Advisor: Elizbeth Hauser Ph.D., Duke University, Department of Medicine and The Center for Human Genetics
Dissertation: Gene-Environment Interactions in Cardiovascular Disease
Todd Wasson
Duke University, Ph.D., Computational Biology & Bioinformatics
Funded by T32 training grant 5T32-GM071340
Faculty Mentor: Alexander Hartemink Ph.D., Duke University, Department of Computer Science
Dissertation: Modeling Multi-Factor binding of the Genome
David Winski
Duke University, Ph.D., Computational Biology & Bioinformatics
Faculty Mentor: Nicolas Buchler Ph.D., Duke University, Department of Biology
Dissertation: Single-cell analysis of transcriptional dynamics during cell cycle arrest
Deborah Winter
Duke University, Ph.D., Computational Biology & Bioinformatics, 2013
Faculty Mentor: Greg Crawford Ph.D., Duke University, Departments of Pediatrics/IGSP
Dissertation: Genome-wide Analysis of Chromatin Structure across Diverse Human Cell Types
Galip Gurkan Yardimci
Duke University, Ph.D., Computational Biology & Bioinformatics, 2014
Faculty Mentors: Uwe Ohler Ph.D., Duke University, Department of Biostatistics & Bioinformatics (co-advisor) Gregory Crawford Ph.D., Duke University, Department of Pediatrics (co-advisor)
Dissertation: Tracking Transcription Factors on the Genome by their DNase-seq Footprints
Ken Yokoyama
Duke University, Ph.D., Computational Biology & Bioinformatics, 2010
Funded by T32 training grant 5T32-GM071340
Faculty Mentors: Greg Wray, Ph.D., Duke University, Department of Biology, IGSP (co-advisor) Uwe Ohler Ph.D., Duke University, Department of Biostatistics and Bioinformatics, IGSP (co-advisor)
Dissertation: Studies into Location-specific cis-Regulatory Motifs
Hsiang Yu Yuan
Duke University, Ph.D., Computational Biology & Bioinformatics, 2013
Faculty Mentor: Katia Koellle Ph.D., Duke University, Departments of Biology
Dissertation: The roles of Cellular Receptor Binding Avidity and Other Biral Phenotypes in the Antigenic Drift of Influenza
Mengqi Zhang
Duke University, Ph.D., Computational Biology & Bioinformatics, 2019
Faculty Mentor: Andrew Allen, Ph.D., Duke University, Department of Biostatistics & Bioinformatics; Director, Center for Statistical Genetics and Genomics
Dissertation: Gene Set-Based Signal-Detection Analyses Based on Goodness-of-Fit Statistics and Their Application in Complex Diseases
Yizhe Zhang
Duke University, Ph.D., Computational Biology & Bioinformatics, January 2018
Faculty Mentor: Lawrence Carin, Duke University, Department of Electrical and Computer Engineering
Dissertation: Efficient and Scalable Marakov Chain Monte Carlo Methods and Its Biological Applications
Jingkang Zhao
Duke University, Ph.D., Computational Biology & Bioinformatics, July 2020
Faculty Mentor: Raluca Gordan, Department of Biostatistics & Bioinformatics
Dissertation: Transcription Factor-centric Approaches to Identify Regulatory Driver Mutations in Cancer
Shiwen Zhao
Faculty Mentor: Sayan Mukherjee, Ph.D., Duke University, Department of Statistical Science
Dissertation: New advancements of scalable statistical methods for learning latent structures in big data
Lingling Zheng
Duke University, Ph.D., Computational Biology & Bioinformatics, 2013
Faculty Mentors: Sayan Mukherjee Ph.D., Duke University, Department of Statistical Science (co-advisor) Joseph E. Lucas Ph.D. (co-advisor)
Dissertation: Bayesian Meta Analysis Models for Heterogeneous Omics Data
jianling zhong
Duke University, PhD., Computational Biology & Bioinformatics, 2015
Faculty Mentors: Alexander Hartemink, Ph.D., Duke University, Department ofComputer Science
Dissertation: Computational Inference of Protein-DNA Interactions Using High-throughput Genomic Data