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Jeanette Baran-Gale

PhD Defense Date: April 4, 2016
Advisor(s): Praveen Sethupathy and Jeremy Purvis
Degree Type: PhD Curriculum, PhD Program: Bioinformatics and Computational Biology
Thesis Title: Dynamics of mRNA and microRNA expression in the estrogen response of breast cancer cells
Current Position: Postdoctoral Research Fellow at Institute of Genetics and Molecular Medicine, University of Edinburgh


Martin Buchkovich

PhD Defense Date: May 7, 2015
Advisor(s): Karen Mohlke and Terry Furey
Degree Type: PhD Curriculum, PhD Program: Bioinformatics and Computational Biology
Thesis Title: Identifying genetic mechanisms of cardiometabolic traits and diseases using quantitative sequence data
Current Position: Manager, Bioinformatics at Q² Solutions


Yanwei Cai

PhD Defense Date: October 7, 2020
Advisor(s): William Valdar
Degree Type: PhD Curriculum, PhD Program: Bioinformatics and Computational Biology
Thesis Title: Analysis of Genetic and Gene-by-Treatment Effects in the Collaborative Cross mice
Current Position: Postdoctoral Research Associate at the Fred Hutchinson Cancer Research Center


Shengjie Chai

PhD Defense Date: September 18, 2019
Advisor(s): Jonathan S. Serody and Benjamin Vincent
Degree Type: PhD Curriculum, PhD Program: Bioinformatics and Computational Biology
Thesis Title: Bioinformatics Methods for Prediction of Splice Variant Neoantigens
Current Position: Data Scientist at Conversant


Sherry Chao

PhD Defense Date: December 3, 2018
Advisor(s): Jeremy Purvis
Degree Type: MD/PhD Curriculum, PhD Program: Bioinformatics and Computational Biology
Thesis Title: Modeling Cell Cycle Phase Transitions and Arrest Decisions upon DNA Damage
Current Position: Medical Student


Kyla Collins

PhD Defense Date: April 5, 2017
Advisor(s): Shawn Gomez and Gary Johnson
Degree Type: PhD Curriculum, PhD Program: Bioinformatics and Computational Biology
Thesis Title: Data-Driven Computational Modeling of the State and Architecture of the Breast Cancer Kinome
Current Position: Research Scientist at Eli Lilly and Company


Meredith Corley

PhD Defense Date: December 14, 2016
Advisor(s): Alain Laederach
Degree Type: PhD Curriculum, PhD Program: Bioinformatics and Computational Biology
Thesis Title: The functional effects of RNA structure: from riboSNitches to translational control
Current Position: Senior Scientist at Ionis Pharmaceuticals


Robert Corty

PhD Defense Date: May 29, 2018
Advisor(s): William Valdar
Degree Type: MD/PhD Curriculum, PhD Program: Bioinformatics and Computational Biology
Thesis Title: Variance Heterogeneity in Genetic Mapping
Current Position: Medical Student


Wes Crouse

PhD Defense Date: November 13, 2019
Advisor(s): Samir Kelada and William Valdar
Degree Type: PhD Curriculum, PhD Program: Bioinformatics and Computational Biology
Thesis Title: Bayesian Inference of the Allelic Series in Multiparental Populations with Applications
Current Position: Postdoctoral Research Associate at the University of Chicago


Kevin Currin

PhD Defense Date: October 2, 2020
Advisor(s): Karen Mohlke
Degree Type: PhD Curriculum, PhD Program: Bioinformatics and Computational Biology
Thesis Title: Chromatin accessibility changes and genomic integration identify genetic regulatory mechanisms
Current Position:


Julia DiFiore

PhD Defense Date: March 13, 2020
Advisor(s): Brian Strahl
Degree Type: BCB Certificate, PhD Program: Genetics and Molecular Biology
Thesis Title: Examining the Role of Histone H3 Lysine 36 Methylation in Preventing Aberrant Transcription
Current Position: Medical Writing Fellow at Impact Pharmaceutical Services


Qing Duan

PhD Defense Date: May 5, 2016
Advisor(s): Yun Li
Degree Type: PhD Curriculum, PhD Program: Bioinformatics and Computational Biology
Thesis Title: Imputation-Based Genetic Association Analysis of Complex Traits in Admixed Populations
Current Position: Research Associate at University of Cincinnati Evaluation Services Center


Ozgun Erdogan

PhD Defense Date: April 26, 2016
Advisor(s): Xian Chen
Degree Type: BCB Certificate, PhD Program: Biochemistry & Biophysics
Thesis Title: Proteomic dissection of LPS-inducible PHF8-dependent secretome reveals novel roles of PHF8 in TLR4-induced acute inflammation and activation of adaptive immunity
Current Position: Postdoctoral Research Associate at Duke University


Andrew Fant

PhD Defense Date: December 13, 2015
Advisor(s): Alex Trophsa
Degree Type: BCB Certificate, PhD Program: Medicinal Chemistry
Thesis Title: The effect of data curation on the accuracy of Quantitative Structure-Activity Relationship models
Current Position: Computational Biologist at Publicis Sapient


Sherif Farag

PhD Defense Date: June 3, 2019
Advisor(s): Alex Tropsha
Degree Type: PhD Curriculum, PhD Program: Bioinformatics and Computational Biology
Thesis Title: Computational Design of Novel Non-Ribosomal Peptides
Current Position: Bioinformatics Scientist at UNC Lineberger Comprehensive Cancer Center


Dayne Filer

PhD Defense Date: November 16, 2020
Advisor(s): Kirk Wilhelmsen
Degree Type: MD/PhD Curriculum, PhD Program: Bioinformatics and Computational Biology
Thesis Title: Tools and statistical approaches for integrating DNA sequencing into clinical care
Current Position: Medical Student


Ray Haggerty

PhD Defense Date: November 11, 2019
Advisor(s): Jeremy Purvis
Degree Type: PhD Curriculum, PhD Program: Bioinformatics and Computational Biology
Thesis Title: Motif Inference from Single Cell Dynamics
Current Position: Postdoctoral Researcher at University of North Carolina at Chapel Hill


Susanna Harris

PhD Defense Date: May 13, 2020
Advisor(s): Elizabeth Shank and Jeff Dangl
Degree Type: BCB Certificate, PhD Program: Microbiology and Immunology
Thesis Title: Building Complex Communities to Promote Individual Members’ Persistence and Affect Behaviors
Current Position: Founder and CEO, PhD Balance


Austin Hepperla

PhD Defense Date: August 7, 2020
Advisor(s): Ian Davis
Degree Type: BCB Certificate, PhD Program: Genetics and Molecular Biology
Thesis Title: Integrative Genomic Analyses of Chromatin and Epigenetic Regulation Across Eukaryotes: A Journey from Yeast Transcription to Human Cancer
Current Position: Bioinformatics Scientist at UNC Neuroscience Center


Sur Herrera Paredes

PhD Defense Date: April 5, 2017
Advisor(s): Jeff Dangl and Corbin Jones
Degree Type: PhD Curriculum, PhD Program: Bioinformatics and Computational Biology
Thesis Title: Understanding the plant microbiome
Current Position: Postdoctoral Research Fellow at Stanford University


Charles Hodgens

PhD Defense Date: July 1, 2020
Advisor(s): Joe Kieber
Degree Type: BCB Certificate, PhD Program: Genetics and Molecular Biology
Thesis Title: Innovations in cloning genes identified in genetic screens and their application to cytokinin signaling in Arabidopsis thaliana
Current Position:


Reed B. Jacob

PhD Defense Date: March 20, 2017
Advisor(s): Nikolay Dokholyan
Degree Type: PhD Curriculum, PhD Program: Bioinformatics and Computational Biology
Thesis Title: Developing a Bioscavenger Against Organophosphate Nerve Agents
Current Position: Computational Biochemist at UPL, Head of In-silico research


Tim Jacobs

PhD Defense Date: October 6, 2015
Advisor(s): Brian Kuhlman
Degree Type: PhD Curriculum, PhD Program: Bioinformatics and Computational Biology
Thesis Title: De novo proteins designed from evolutionary principles
Current Position: Senior Scientist at AbCellera


Ivan Jimenez-Ruiz

PhD Defense Date: July 30, 2020
Advisor(s): Alain Laederach
Degree Type: PhD Curriculum, PhD Program: Bioinformatics and Computational Biology
Thesis Title: Regulation of SERPINA1 UTR isoforms by Alternative polyadenylation in A1AT
Current Position: Integration Engineer at Medaxion


Shannon Jones

PhD Defense Date: March 21, 2016
Advisor(s): Laura Miller and Ty Hedrick
Degree Type: PhD Curriculum, PhD Program: Bioinformatics and Computational Biology
Thesis Title: A computational fluid dynamics study of the smallest flying insects
Current Position: Research Associate at North Carolina State University


Greg Keele

PhD Defense Date: March 16, 2018
Advisor(s): William Valdar
Degree Type: PhD Curriculum, PhD Program: Bioinformatics and Computational Biology
Thesis Title: Handling uncertainty in haplotype descent for QTL mapping and other adventures with multiparental populations
Current Position: Postdoctoral Associate at The Jackson Laboratory


Benjamin Keith

PhD Defense Date: April 1, 2020
Advisor(s): Terry Furey, Shehzad Sheikh, and Praveen Sethupathy
Degree Type: PhD Curriculum, PhD Program: Bioinformatics and Computational Biology
Thesis Title: Molecular stratification and prognostic determinants of adult and pediatric Crohn’s disease
Current Position: Senior Bioinformatics Scientist at AstraZeneca


Patrick Kimes

PhD Defense Date: May 5, 2015
Advisor(s): Yufeng Liu, Steve Marron and D. Neil Hayes
Degree Type: BCB Certificate, PhD Program: Statistics & Operations Research
Thesis Title: New Statistical Learning Approaches with Applications to RNA-seq Data
Current Position: Principal Scientist I, Bioinformatics at Roche Sequencing


Jessime Kirk

PhD Defense Date: March 29, 2019
Advisor(s): Mauro Calabrese
Degree Type: PhD Curriculum, PhD Program: Bioinformatics and Computational Biology
Thesis Title: Functional classification of long non-coding RNAs by k-mer content
Current Position: Bioinformatics Engineer at Invitae


Katrina Kutchko

PhD Defense Date: April 5, 2017
Advisor(s): Alain Laederach
Degree Type: PhD Curriculum, PhD Program: Bioinformatics and Computational Biology
Thesis Title: Viruses and the evolution of RNA structure
Current Position: Data Scientist at Verizon


Vinal Lakhani

PhD Defense Date: November 11, 2015
Advisor(s): Timothy Elston
Degree Type: PhD Curriculum, PhD Program: Bioinformatics and Computational Biology
Thesis Title: Testing the Theoretical Limit of Gradient Sensing in Yeast
Current Position: Scientist at DILIsym Services Inc


Nicole Lama

PhD Defense Date: April 29, 2020
Advisor(s): Alain Laederach and Kevin Weeks
Degree Type: PhD Curriculum, PhD Program: Bioinformatics and Computational Biology
Thesis Title: Detection of Ligandable Pockets in RNA
Current Position: Senior Consultant/Data Scientist at SickleSoft Inc.


Gen Li

PhD Defense Date: August 4, 2015
Advisor(s): Haipeng Shen and Andrew Nobel
Degree Type: BCB Certificate, PhD Program: Statistics & Operations Research
Thesis Title: Integrated analysis of multiple data sets with biomedical applications
Current Position: Assistant Professor in the Department of Biostatistics at Columbia University


Jin Li

PhD Defense Date: May 12, 2015
Advisor(s): Ethan Lange
Degree Type: PhD Curriculum, PhD Program: Bioinformatics and Computational Biology
Thesis Title: Genetic Association Studies: Application in the Investigation of Biomarkers Related to Cardiovascular Diseases and Study Design
Current Position: Postdoctoral Researcher at Stanford University


Jack Maguire

PhD Defense Date: January 24, 2020
Advisor(s): Brian Kuhlman
Degree Type: PhD Curriculum, PhD Program: Bioinformatics and Computational Biology
Thesis Title: Improving Computational Methods for Designing Polar Protein-Protein Interfaces
Current Position: Senior Computational Scientist at Menten AI


Paul Maurizio

PhD Defense Date: January 9, 2018
Advisor(s): William Valdar and Mark Heise
Degree Type: PhD Curriculum, PhD Program: Bioinformatics and Computational Biology
Thesis Title: Uncovering the Genetic Architecture of the Host Response to Influenza Virus in Mice
Current Position: NIH / NIA F32 Postdoctoral Fellow at the University of Chicago


Patrick McCarter

PhD Defense Date: July 7, 2017
Advisor(s): Timothy Elston and Henrik Dohlman
Degree Type: PhD Curriculum, PhD Program: Bioinformatics and Computational Biology
Thesis Title: Decoding the yeast osmotic stress response through comprehensive mathematical modeling
Current Position: Data Scientist at Cone Health


Kimiko McGirr

PhD Defense Date: June 19, 2020
Advisor(s): Tim Elston and Henrik Dohlman
Degree Type: PhD Curriculum, PhD Program: Bioinformatics and Computational Biology
Thesis Title: Identifying signaling pathway architecture using model-driven experimental design
Current Position: Senior Scientist -- Mathematical Modeler at Applied BioMath


Duncan McPherson

PhD Defense Date: May 8, 2016
Advisor(s): Joe Kieber
Degree Type: BCB Certificate, PhD Program: Genetics and Molecular Biology
Thesis Title: Using FAIRE in Arabidopsis and Rice to study change of chromatin conformation in response to cytokinin
Current Position: Application Support Engineer at Metabolon, Inc.


John Mellnik

PhD Defense Date: April 30, 2015
Advisor(s): M. Greg Forest
Degree Type: PhD Curriculum, PhD Program: Bioinformatics and Computational Biology
Thesis Title: Microrheology and Heterogeneity in Biological Fluids: Approaches, Models and Applications
Current Position: CTO, Path BioAnalytics, Inc.


Andrew P. Morgan

PhD Defense Date: November 30, 2016
Advisor(s): Fernando Pardo-Manuel de Villena
Degree Type: MD/PhD Curriculum, PhD Program: Bioinformatics and Computational Biology
Thesis Title: Structural variation and the evolution of the mouse genome
Current Position: Medical Student


Daniel Oreper

PhD Defense Date: March 23, 2018
Advisor(s): William Valdar
Degree Type: PhD Curriculum, PhD Program: Bioinformatics and Computational Biology
Thesis Title: Computational methods for studying parent-of-origin effects via reciprocal mouse crosses
Current Position: Bioinformatician at Genentech


Amy Pomeroy

PhD Defense Date: June 16, 2020
Advisor(s): Tim Elston and Henrik Dohlman
Degree Type: PhD Curriculum, PhD Program: Bioinformatics and Computational Biology
Thesis Title: Mechanistic models of interactions within and between MAPK pathways
Current Position:


Bryan Quach

PhD Defense Date: July 21, 2017
Advisor(s): Terry Furey
Degree Type: PhD Curriculum, PhD Program: Bioinformatics and Computational Biology
Thesis Title: Computational approaches to studying gene regulation using chromatin accessibility and gene expression assays
Current Position: Bioinformatics Scientist at RTI International


Chelsea K Raulerson

PhD Defense Date: November 6, 2019
Advisor(s): Karen Mohlke and Terry Furey
Degree Type: PhD Curriculum, PhD Program: Bioinformatics and Computational Biology
Thesis Title: Effects of adipose tissue transcriptome on cardiometabolic traits in RNA-sequencing data
Current Position: Computational Biologist II at UT Southwestern Medical Center


Sara Selitsky

PhD Defense Date: August 20, 2015
Advisor(s): Praveen Sethupathy and Stanley M. Lemon
Degree Type: PhD Curriculum, PhD Program: Bioinformatics and Computational Biology
Thesis Title: Small RNA transcriptomic analysis during chronic viral hepatitis and associated cancer
Current Position: Senior Bioinformatics Scientist at Data Driven Bioscience


Joseph J. Shaffer Jr.

PhD Defense Date: March 25, 2015
Advisor(s): Aysenil Belger
Degree Type: BCB Certificate, PhD Program: Neurobiology
Thesis Title: Title: Functional MRI Correlates of Schizophrenia Negative Symptoms during Auditory Oddball Task and Resting State
Current Position: Assistant Research Scientist at University of Iowa


Nur M. Shahir

PhD Defense Date: March 31, 2020
Advisor(s): Terry Furey and Shehzad Sheikh
Degree Type: PhD Curriculum, PhD Program: Bioinformatics and Computational Biology
Thesis Title: IBD Differentially Affects Region Specific Composition and Aerotolerance Profiles of Mucosally-Adherent Bacteria
Current Position:


Andy Shapiro

PhD Defense Date:
Advisor(s): Ivan Rusyn
Degree Type: BCB Certificate, PhD Program: Public Health
Thesis Title:
Current Position: Data Scientist at National Institute of Environmental Health Sciences (NIEHS)


Jenny Shi

PhD Defense Date: June 23, 2015
Advisor(s): Jan Hannig and Corbin Jones
Degree Type: BCB Certificate, PhD Program: Statistics & Operations Research
Thesis Title: Bayesian modeling for viral sequencing data and covariance estimation via fiducial inference
Current Position: Quantitative Strategist at MassMutual


Grace Silva

PhD Defense Date: June 2, 2015
Advisor(s): Charles Perou
Degree Type: PhD Curriculum, PhD Program: Bioinformatics and Computational Biology
Thesis Title: Comprehensive Characterization of DNA Copy Number Alterations in Mouse and Human Breast Tumors
Current Position: Associate Director, Computational Biology at Tessera Therapeutics


Mariesa Slaughter

PhD Defense Date: September 26, 2018
Advisor(s): Ian Davis
Degree Type: BCB Certificate, PhD Program: Genetics and Molecular Biology
Thesis Title: Understanding the relationship between histone acetylation and bromodomain targeting
Current Position: Review Analyst at GeneDx


Jeff Snell

PhD Defense Date:
Advisor(s): Ned Sharpless and Tim Elston
Degree Type: PhD Curriculum, PhD Program: Bioinformatics and Computational Biology
Thesis Title:
Current Position: Principal Physician Data Scientist at Rad AI


Natalie Stanley

PhD Defense Date: March 19, 2018
Advisor(s): Peter Mucha
Degree Type: PhD Curriculum, PhD Program: Bioinformatics and Computational Biology
Thesis Title: Adapting community detection approaches to large, attributed, and multilayer networks
Current Position: Postdoctoral Fellow at Stanford University


Frank Teets

PhD Defense Date: November 1, 2019
Advisor(s): Klaus Hahn and Brian Kuhlman
Degree Type: PhD Curriculum, PhD Program: Bioinformatics and Computational Biology
Thesis Title: Function-Driven Approaches to the Design of Optogenetic Tools
Current Position: Postdoctoral Fellow at the Institute for Protein Innovation, Harvard University


Chanin Tolson Woods

PhD Defense Date: March 27, 2017
Advisor(s): Alain Laederach
Degree Type: PhD Curriculum, PhD Program: Bioinformatics and Computational Biology
Thesis Title: Computational tools for exploring RNA structure change in experimental data
Current Position: Machine Learning Engineer at Apple


Yi-hsuan Tsai

PhD Defense Date: March 4, 2015
Advisor(s): Zefeng Wang and Shawn Gomez
Degree Type: PhD Curriculum, PhD Program: Bioinformatics and Computational Biology
Thesis Title: Transcriptome-wide study of alternative splicing across multiple cancer types
Current Position: Bioinformatician at Lineberger Comprehensive Cancer Center


William Weir

PhD Defense Date: March 26, 2020
Advisor(s): Peter Mucha
Degree Type: PhD Curriculum, PhD Program: MD/PhD
Thesis Title: Modularity-Based Approaches To Community Detection In Multilayer Networks With Applications Toward Precision Medicine
Current Position: Medical Student


Matt Weiser

PhD Defense Date: August 4, 2015
Advisor(s): Terry Furey
Degree Type: PhD Curriculum, PhD Program: Bioinformatics and Computational Biology
Thesis Title: Probing the architecture of complex traits: functional genomics methods and applications
Current Position: Bioinformatician, Equinome/PlusVital


Joshua Welch

PhD Defense Date: May 12, 2017
Advisor(s): Jan Prins
Degree Type: BCB Certificate, PhD Program: Computer Science
Thesis Title: Computational Methods for Inferring Transcriptome Dynamics
Current Position: Assistant Professor at University of Michigan


Youli Xia

PhD Defense Date: August 26, 2020
Advisor(s): Charles Perou
Degree Type: PhD Curriculum, PhD Program: Bioinformatics and Computational Biology
Thesis Title: Integrative Genomics Approaches to Identify Genetic Drivers of Human Breast Cancer
Current Position: Computational Biology Scientist at Cellarity


Scott Yourstone

PhD Defense Date: September 17, 2018
Advisor(s): Jeff Dangl and Corbin Jones
Degree Type: PhD Curriculum, PhD Program: Bioinformatics and Computational Biology
Thesis Title: The taxonomic and functional nature of plant-associated microbiomes
Current Position: Bioinformaticist at Q² Solutions


Guosheng Zhang

PhD Defense Date: April 7, 2016
Advisor(s): Yun Li
Degree Type: PhD Curriculum, PhD Program: Bioinformatics and Computational Biology
Thesis Title: Bioinformatics Tools for Exploring Regulatory Mechanisms
Current Position: Software Engineer at Google