STUDENTS & ALUMNI
Current Students in PhD Program
| Name | Advisor | Research Area |
|---|---|---|
| Emily Mastej | Debashis 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 Fouquier | Catherine 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. |
| Lucia Guatney | Chris Miller | My 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 Elkhill | Antonio Porras | My 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 Gillenwater | Jim Costello | The 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 Prince | Carsten Goerg | I leverage artificial intelligence and human-centered computing methods to develop clinical and basic science tools to improve care for pediatric cancer patients. |
| Brook Santangelo | Larry Hunter | I am interested in incorporating knowledge surrounding microbes and biomedical concepts into knowledge bases to understand mechanisms of the gut microbiome in disease. |
| Sofia Colorado | Catherine Lozupone | I 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 Cortes | Melissa Haendel | I am interested in leveraging knowledge graphs and EHR data to predict potential mechanisms of rare diseases. |
| Nick Garcia | Dan Denman | The 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 Salem | Larry Hunter | We 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 Serrano | Gregory Way | I am developing reproducible software and new approaches for analyzing microscopy images of cells. |
| Talon Arbuckle | Larry Hunter | In progress |
| Keenan Manpearl | Arjun 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 Samart | Arjun Krishnan and Janani Ravi | My research involves applying machine learning models to study infectious diseases with a focus on host-directed drug repurposing |
| Jade Young | Fan Zhang | I 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 | Rotating | |
Alexander Kotz | Rotating | |
Aishwarya Mandava | Rotating | |
Samantha Reynoso | Rotating | |
| Celin Younan | Rotating |
PhD Student Alumni
| Full Name | Advisor | Thesis | Degree Conferred | Current Position |
|---|---|---|---|---|
| Jo Hendrix | Michael Strong | Bacterial Genome Assembly Quality Assessment and Annotation Analysis | 2023 | |
| Rutendo Sigauke | Robin Dowell | Gene regulation inference with nascent RNA transcription | 2023 | Postdoctoral Associate, BioFrontiers Institute at the University of Colorado Boulder |
| Mayla Boguslav | Lawrence Hunter & Sonia Leach | Revealing and Exploring the Literature’s Known Unknowns: Ignorance and How It Drives Science | 2023 | Postdoctoral Fellow at Colorado State University, Dept. of Mathematics |
| Tiffany Callahan | Lawrence Hunter & Michael Kahn | Learning Deep Translational Patient Representations: Systematic Integration of Clinical Records and Biomedical Knowledge | 2021 | Postdoctoral Fellow at Columbia University, Dept. of Biomedical Informatics |
Cody Glickman | Michael Strong | The Influence of Viruses in Non-tuberculous Mycobacterial Infections | 2021 | Bioinformatics Scientist at Endolytix Technology, Inc |
| Janet Siebert | Carsten Goerg | Finding and visualizing network-based multi-omic predictive models | 2021 | Founder, CytoAnalytics |
Callie Federer | Joel Zylberberg | My 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? | 2019 | Associate Research Scientist at RadiaSoft, LLC |
| Negacy Hailu | Lawrence Hunter | Investigation of traditional and deep neural sequence models for biomedical concept recognition. | 2019 | |
| Rani Powers | James Costello | Gene set enrichment analysis for understanding context-specific gene expression | 2019 | Senior Staff Scientist, Wyss Institute |
| Michael Shaffer | Catherine Lozupone | Using networks to understand microbiome and metabolome interactions | 2019 | Postdoctoral Fellow, Colorado State University |
| Nicolle Witte | Jim 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 |
| Kyle Smith | Debashis Ghosh | Somatic Evolution in Cancer | 2017 | Bioinformatics Scientist at St. Jude Children's Research Hospital |
| Gargi Datta | Sonia Leach & Michael Strong | Machine Learning and genomic analysis to predict drug resistance in mycobacterium tuberculosis | 2016 | Bioinformatics Scientist at SomaLogic |
| Charlotte Siska | Katerina Kechris | Determining Differentially Correlated Feature Pairs in High-Throughput Data | 2016 | Senior Applied Machine Learning Researcher, Microsoft |
| William Baumgartner | Lawrence Hunter | Enhancing ontology concept enrichment through deductive entailment | 2015 | Research Instructor, University of Colorado-Anschutz Medical Campus |
| Christopher Funk | Lawrence Hunter | Recognition and Normalization of Terminology from Biomedical Ontologies and their Application for Pharmacogene and Protein Function Prediction | 2015 | Medical Informatics with Wolter Kluwer Health/Health Language in the Denver Tech Center |
| David Knox | Robin 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 Pirrung | Carsten Goerg | Effective Data Visualization for Communication and Analysis of Microbiome Data | 2015 | Visualization Scientist with the Visual Analytics Group for the Pacific Northwest National Laboratory in Richland, Washington |
| Daniel Dvorkin | Katerina 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 McShan | Lawrence Hunter | Computational Bioalchemy, Optimal Pathway Search for the Analysis and Synthesis of Metabolic Systems | 2012 | Complex Systems Architect, Simulation and Test Expert for Syzygyx, Incorporated, BRYXco, CdK, Ltd. |
| Ronald Schuyler | Lawrence Hunter | Multi-Marker Tests and Proxy Association for Functional Rare Variants | 2012 | Assistant Research Professor, Department of Immunology and Microbiology, University of Colorado-Anschutz Medical Campus |
| Vijetha Vemulapalli | David Pollock | Delineating the Evolutionary Dynamics of Mutation and Selection | 2012 | Informatics Scientist, Berg Biosystems in Boston, MA |
| Philip Ogren | Lawrence Hunter | Coordination Resolution in Biomedical Texts | 2010 | Software Developer for Oracle in Broomfield, Colorado |
| Elizabeth (Betsy) Siewert | Katerina Kechris | Prediction of Transcription Factor Binding Sites Using Information From | 2010 | Statistical Consultant at Statistically Speaking |
| J. Gregory Caporaso | Lawrence Hunter | Extracting signal from noise in biological data : evaluations and applications of text mining and sequence coevolution | 2009 | Assistant Professor of Biology, Assistant Director Center for Microbial Genetics and Genomics, Northern Arizona University |
| Todd Gibson | Debra Goldberg | Modeling the Evolution of Protein Interaction networks | 2009 | Assistant Professor, California State University, Chico |
| Hyun-Min Kim | David 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 McTavish | Lawrence Hunter | Modeling long-range synchrony in the olfactory bulb | 2009 | Senior Research Scientist at NCS Pearson, Denver Colorado |
| Anis Karimpour-Fard | Lawrence Hunter | Prediction of protein-protein interactions and function in bacteria | 2008 | Research Associate: University of Colorado- Hunter Lab |
| Zhiyong Lu | Lawrence Hunter | Text mining on GeneRIFs | 2007 | Assoc Investigator, Computational Biology Branch NCBI, NLM, NIH |
| Min Hong | Lawrence Hunter | Implicit constraint enforcement to control the physically-based biomedical simulation | 2005 | Assistant Professor: Soon Chun Hyang University, Korea |
| Steven Russell | Lawrence Hunter | Machine learning and in silico modeling for improved identification of peptides from shotgun proteomic MS/MS Spectra | 2005 | Consultant, KM at Siemens Corporate Research, Greater New York City Area |
| Farzin Imani | Dennis Lezotte | Simulation of medical ultrasound images using linear systems theory | 2003 | Assoc. Professor U. of Pittsburg Medical Center |