Current Students

NameAdvisorResearch Area
Mayla BoguslavLarry Hunter, Sonia LeachThe goal of my research is to create NLP tools in order to identify, classify, and explore known unknowns in the scientific literature as goals for scientific knowledge. We aim to help students, researchers, funders, and publishers better understand the state of our scientific knowledge and ignorance.
Laura StevensSonia Leach Visual Analysis and Integration of Knowledge Networks using Genetic Data
Rutendo SigaukeRobin Dowell Nascent RNA sequencing data gives an immediate readout on transcription at both enhancers and genes in a single experiment. My research aims at developing tools to better understand transcription and transcription regulation using nascent RNA data. These tools will aid in expanding our understanding of how genes are regulated in various cell types and states.
Josephina HendrixMichael Strong Complete bacterial genome assemblies improve our understanding of microorganisms by revealing the full coding capacity and arrangement of chromosomes and plasmids. My research lies in developing methods to improve and evaluate the quality of bacterial genome assemblies.
Emily MastejDebashis Ghosh I am interested in combining imaging and radiomics with other -omic data using high dimensional mediation methods to better understand mechanistic pathways within biological systems.
Jennifer FouquierCatherine Lozupone My primary research aim is to develop a computational pipeline to select important features from longitudinal microbiome studies using machine learning methods. This tool will help streamline data integration, analytic organization, and result interpretation from different longitudinal study designs.
Kendra MeerRobin Dowell The use of cross-species omics data to study evolution of transcriptional response and regulatory function in primates; and the development of computational tools and algorithms to improve such comparative genomics approaches.
Lucia GuatneyChris MillerMy research aims to improve metagenomic protein annotations with the end goal of better predicting metabolites produced from microbial communities. I hope to develop, validate, and then incorporate novel non-homology methods into present annotation tools and methods.
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 SantangeloLarry HunterI am interested in incorporating knowledge surrounding microbes and biomedical concepts into knowledge bases to understand mechanisms of the gut microbiome in disease.
Talon ArbuckleRotating 
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 Denman 
Nourah SalemLarry Hunter 
Erik SerranoGregory WayI am developing reproducible software and new approaches for analyzing microscopy images of cells.
Keenan ManpearlRotating 
Kewalin SamartRotating 
Jade YoungRotating 


Full NameAdvisorThesisDegree ConferredCurrent Position
Harrison Pielke-LombardoLarry HunterSystematic and scalable computational schematization of biological mechanisms2022 (Masters Degree) 
Tiffany CallahanLarry 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
Kelsey (KC) AndersonSonia Leach Prioritizing Candidate Genes in Disjoint Sets using Graph Kernels on Unverlying Protien-protien networks.2018 (Masters Degree)  
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 Big Data Scientist, Arrow Electronics
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 Biodedical 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 Postdoctoral Fellowwith UCD-AMC Dr. Robert Roach Lab Department of Emergency Medicine
Daniel 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 Univeristy
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
Nicolle WitteJim Costello I 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.2018

Data Analyst at Rose Medical Center

Are you a Computational Bioscience alumnus? We'd love to stay in touch!