Current Students in PhD Program

NameAdvisorResearch Area
Connor ElkhillAntonio PorrasMy research interests involve using imaging and deep learning for translational research and clinical decision making. I am currently working on the quantification of surgical outcomes of craniosynostosis along with the Children's Hospital of Colorado. 
Lucas GillenwaterJim CostelloThe goal of my research is to identify and visualize molecular mechanisms causing heterogeneous phenotypes in complex disease. As a Blumenthal Fellow, I work with the Linda Crnic Institute for Down Syndrome to understand co-occurring conditions in the context of trisomy 21.
Eric PrinceCarsten GoergI leverage artificial intelligence and human-centered computing methods to develop clinical and basic science tools to improve care for pediatric cancer patients.
Brook SantangeloCatherine LozuponeI am interested in incorporating knowledge surrounding microbes and biomedical concepts into knowledge bases to understand mechanisms of the gut microbiome in disease.
Sofia ColoradoCatherine LozuponeI am interested in investigating the effects that diet can have on the human gut microbiome in healthy and sick patients using new workflows and software in QIIME.
Katherina CortesMelissa HaendelI am interested in leveraging knowledge graphs and EHR data to predict potential mechanisms of rare diseases.
Nick GarciaDan DenmanThe neural computations required for visual perception require the spatiotemporal coordination of millions of neurons. I am developing computational methods to probe how information is represented and transformed across areas. In particular, I am interested in the dynamics of inter-area communication subspaces. 
Nourah SalemLarry HunterWe aim at resolving at the biomedical knowledge goals through connecting research results with biomedical ignorance-base using concept mapping from knowledge graphs as well as hypothesis generation by deep learning text generation models.
Erik SerranoGregory WayI am developing reproducible software and new approaches for analyzing microscopy images of cells.
Talon ArbuckleLarry HunterIn progress
Keenan ManpearlArjun Krishnan I am interested in developing machine learning methods and tools that leverage molecular interaction networks to predict novel genes associated with cellular functions, physiological traits, and complex diseases.
Kewalin SamartArjun Krishnan and Janani RaviMy research involves applying machine learning models to study infectious diseases with a focus on host-directed drug repurposing
Jade YoungFan ZhangI am interested in developing computational methods to decipher autoimmune disease gene programs with single-cell -omics data. I am also interested in using explainable AI techniques to elucidate the underlying biological factors for more transparent precision medicine.

Jill Hoffman

Milton Pividori  

Alexander Kotz

James Mitchell  

Aishwarya  Mandava

Arjun Krishnan  

Samantha Reynoso

Fan Zhang 

PhD Student Alumni

Full NameAdvisorThesisDegree ConferredCurrent Position
Jennifer FouquierCatherine LozuponeFeature Selection and Exploratory Analysis in Longitudinal Microbiome Studies2024Independent Bioinformatics Scientist
Emily MastejDebashis Ghosh 2024 
Laura Stevens Automating Data Harmonization: Resources and methods to improve harmonization of clinical trial and observational study data2023Chief Technology Officer, Axiom Health
Jo HendrixMichael StrongBacterial Genome Assembly Quality Assessment and Annotation Analysis2023 
Rutendo SigaukeRobin DowellGene regulation inference with nascent RNA transcription2023Postdoctoral Associate, BioFrontiers Institute at the University of Colorado Boulder
Mayla BoguslavLawrence Hunter & Sonia LeachRevealing and Exploring the Literature’s Known Unknowns: Ignorance and How It Drives Science2023Postdoctoral Fellow at Colorado State University, Dept. of Mathematics
Tiffany CallahanLawrence Hunter & Michael KahnLearning Deep Translational Patient Representations: Systematic Integration of Clinical Records and Biomedical Knowledge2021Postdoctoral Fellow at Columbia University, Dept. of Biomedical Informatics

Cody Glickman

Michael StrongThe Influence of Viruses in Non-tuberculous Mycobacterial Infections2021Bioinformatics Scientist at Endolytix Technology, Inc
Janet SiebertCarsten GoergFinding and visualizing network-based multi-omic predictive models2021Founder, CytoAnalytics

Callie Federer

Joel ZylberbergMy thesis work was in the intersection of machine learning and neuroscience: how can we use the brain to develop better machine learning algorithms, and how can we use machine learning algorithms to better understand the brain?2019Associate Research Scientist at RadiaSoft, LLC
Negacy HailuLawrence Hunter Investigation of traditional and deep neural sequence models for biomedical concept recognition.2019  
Rani PowersJames Costello Gene set enrichment analysis for understanding context-specific gene expression2019 Senior Staff Scientist, Wyss Institute
Michael ShafferCatherine Lozupone Using networks to understand microbiome and metabolome interactions2019 Postdoctoral Fellow, Colorado State University
Nicolle WitteJim CostelloI worked on developing new tools for T-cell receptor (TCR) sequencing data. My aims involve improving error correction algorithms for novel gene/allele identification and analysis methods to classify groups of TCR clonotypes that correlate to disease state.2018Data Analyst at Rose Medical Center
Kyle SmithDebashis Ghosh Somatic Evolution in Cancer2017 Bioinformatics Scientist at St. Jude Children's Research Hospital
Gargi DattaSonia Leach & Michael Strong Machine Learning and genomic analysis to predict drug resistance in mycobacterium tuberculosis2016 Bioinformatics Scientist at SomaLogic
Charlotte SiskaKaterina Kechris Determining Differentially Correlated Feature Pairs in High-Throughput Data2016 Senior Applied Machine Learning Researcher, Microsoft
William BaumgartnerLawrence Hunter Enhancing ontology concept enrichment through deductive entailment2015 Research Instructor, University of Colorado-Anschutz Medical Campus
Christopher FunkLawrence Hunter Recognition and Normalization of Terminology from Biomedical Ontologies and their Application for Pharmacogene and Protein Function Prediction2015 Medical Informatics with Wolter Kluwer Health/Health Language in the Denver Tech Center
David KnoxRobin Dowell A simulation modeling framework to study transcriptional regulation through the dynamic changes in the configuration of DNA binding factors.2015 Instructor, Department of Computer Science, University of Colorado-Boulder
Megan PirrungCarsten Goerg Effective Data Visualization for Communication and Analysis of Microbiome Data2015 Visualization Scientist with the Visual Analytics Group for the Pacific Northwest National Laboratory in Richland, Washington
Daniel DvorkinKaterina Kechris Graphical model methods for integrating diverse sources of genome-scale data.2013 Bioinformatics Consultant, The Bioinformatics CRO
McShanLawrence Hunter Computational Bioalchemy, Optimal Pathway Search for the Analysis and Synthesis of Metabolic Systems2012 Complex Systems Architect, Simulation and Test Expert for Syzygyx, Incorporated, BRYXco, CdK, Ltd.
Ronald SchuylerLawrence Hunter Multi-Marker Tests and Proxy Association for Functional Rare Variants2012 Assistant Research Professor, Department of Immunology and Microbiology, University of Colorado-Anschutz Medical Campus
Vijetha VemulapalliDavid Pollock Delineating the Evolutionary Dynamics of Mutation and Selection2012 Informatics Scientist, Berg Biosystems in Boston, MA
Philip OgrenLawrence Hunter Coordination Resolution in Biomedical Texts2010 Software Developer for Oracle in Broomfield, Colorado
Elizabeth (Betsy) SiewertKaterina Kechris Prediction of Transcription Factor Binding Sites Using Information From2010 Statistical Consultant at Statistically Speaking
J. Gregory CaporasoLawrence Hunter Extracting signal from noise in biological data : evaluations and applications of text mining and sequence coevolution2009 Assistant Professor of Biology, Assistant Director Center for Microbial Genetics and Genomics, Northern Arizona University
Todd GibsonDebra Goldberg Modeling the Evolution of Protein Interaction networks2009 Assistant Professor, California State University, Chico
Hyun-Min KimDavid Pollock Evolution and detection of transcription factors. Transcription and ChIP-chip assays. Analysis of hydrophobiicty profiles.2009 Postdoctoral Fellow: University of Colorado- Pollock Lab
Thomas McTavishLawrence Hunter Modeling long-range synchrony in the olfactory bulb2009 Senior Research Scientist at NCS Pearson, Denver Colorado
Anis Karimpour-FardLawrence Hunter Prediction of protein-protein interactions and function in bacteria2008 Research Associate: University of Colorado- Hunter Lab
Zhiyong LuLawrence Hunter Text mining on GeneRIFs2007 Assoc Investigator, Computational Biology Branch NCBI, NLM, NIH
Min HongLawrence Hunter Implicit constraint enforcement to control the physically-based biomedical simulation2005 Assistant Professor: Soon Chun Hyang University, Korea
Steven RussellLawrence Hunter Machine learning and in silico modeling for improved identification of peptides from shotgun proteomic MS/MS Spectra2005 Consultant, KM at Siemens Corporate Research, Greater New York City Area
Farzin ImaniDennis Lezotte Simulation of medical ultrasound images using linear systems theory2003 Assoc. Professor U. of Pittsburg Medical Center

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