STUDENTS & ALUMNI

Current Students in PhD Program

NameAdvisorResearch Area
Philip QueenRoatingI am interested in vision, behavior, and how they are coordinated in the brain, and use machine learning and computer vision techniques to study freely moving animals.
Yonghao ZhaoRotatingI am interested in developing machine learning methods for complex biological systems. Specifically, I focus on representation learning, generative modeling, and multimodal learning for single-cell and spatial omics.
Brandon KohrtRotatingMy main research interest is in computational neuroscience. Specifically, I am excited about utilizing machine learning to create models relating to our sensory systems. I am also interested in analysis of MRI and fMRI data, especially in the context of mental health disorders. 
Hanan WeesRotatingI am interested in unraveling the complexities of disease using statistical and machine learning techniques to drive biological insight. 
Manaswitha EdupalliRotatingI am interested in developing multimodal ML/AI methods that bridge high-dimensional biomedical data and actionable clinical insights, with a focus on explainability and interpretability. I am also interested in extending such methods to secure, federated settings to encourage cross-institutional collaboration. 
Breanna RemigioFan ZhangI am interested in developing and applying machine learning tools to advance precision medicine and deepen our understanding of complex diseases, with a particular focus on the integration and analysis of multi-omics data.

Raymond Lemayana Lesiyon

Natalie Davidson I am interested in developing computational methods to integrate multimodal data and study complex biological and biomedical problems comprehensively. Specifically, I am excited about unifying diverse data types such as different omics or image data, and text for a holistic representation. 
Emily EkstrumDaniel DenmanI am interested in developing data analysis pipelines to identify patterns and structural relationships in complex biological data. My goal is to integrate large-scale datasets with novel computational approaches to deepen the understanding of biological systems.
Christian AndersonFan ZhangI am interested in using high-dimensional multi-omic data integration with statistical methods to understand human diseases. Specifically, I enjoy applying Bayesian methods to identify disease progression patterns.
Saloni DixonNatalie DavidsonI am interested in developing computational and machine learning methods to better understand RNA biology and its role in human disease. My research focuses on studying alternative splicing in large-scale transcriptomic and molecular datasets to uncover biologically and clinically meaningful patterns.
Kat TerwelpJanani Ravi I am interested in applying machine learning on microbial horizontal gene transfer and interaction networks to predict individual and community level phenotypes, such as antibiotic resistance and disease associated dysbiosis.
Weishan LiGregory WayIn progress
Nicholas CordaroJayashree Kalpathy-CramerMy research focuses on developing interpretable AI models to analyze ophthalmic imaging for retinal diseases. I am particularly interested in leveraging longitudinal imaging data and deep learning to enhance clinical decision-making, clinical trial design, and early detection of irreversible vision loss. 
Samantha  ReynosoFan ZhangMy research interests focus on developing benchmarking pipelines that leverage statistical modeling and machine learning techniques for single-cell spatial transcriptomics, with the goal of advancing treatments for human diseases. 
Aishwarya MandavaArjun KrishnanI am interested in applying computational and machine learning algorithms to large-scale molecular interaction networks. I am currently working on inferring tissue-specific functional associations of gene regulators and other non-coding regions. 
Jill HoffmanMilton Pividori I am interested in understanding the edges between genes in a co-expressed module through the lens of the omnigenic model. 
Alexander KotzJames Mitchell My current work involves employing advanced interviewing techniques, large language models, and user-centered design techniques to gather robust feedback for applications and programs in clinical, education, and military settings.  
Kewalin SamartArjun Krishnan and Janani RaviMy research involves applying machine learning models to study infectious diseases with a focus on host-directed drug repurposing.
Talon ArbuckleLarry HunterIn progress
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.
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.
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. 
Sofia Burkhart 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.

PhD Student Alumni

Following graduation, our alumni have pursued exciting careers as post-doctoral fellows, professors, consultants, research staff and lead scientists that span a wide range of environments from academic institutions, research hospitals, government agencies, independent consulting, biotech startups, and industry.

Full NameAdvisorThesisDegree ConferredCurrent Position
Nourah SalemLarry Hunter 2026 
Katherina CortesMelissa Haendel 2026 
Erik SerranoGregory Way 2026 
Connor ElkhillAntonio Porras 2025 
Lucas GillenwaterJim Costello 2025 
Eric PrinceCarsten Goerg 2025 
Brook Santangelo Catherine Lozupone 2025 
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 
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
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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