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

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 Woods, Ph.D., Duke University, Department of Pharmacology and Cancer Bilogy
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

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

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

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

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

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

Shiwen Zhao

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