STUDENTS & ALUMNI
Current Students in PhD Program
| Name | Advisor | Research Area |
|---|---|---|
| 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 | Catherine Lozupone | 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 | Milton Pividori | I am interested in understanding the edges between genes in a co-expressed module through the lens of the omnigenic model. |
Alexander Kotz | James 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. |
Aishwarya Mandava | Arjun Krishnan | I 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. |
Samantha Reynoso | Fan Zhang | My 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. |
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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 Name | Advisor | Thesis | Degree Conferred | Current Position |
|---|---|---|---|---|
| Jennifer Fouquier | Catherine Lozupone | Feature Selection and Exploratory Analysis in Longitudinal Microbiome Studies | 2024 | Independent Bioinformatics Scientist |
| Emily Mastej | Debashis Ghosh | 2024 | ||
| Laura Stevens | Automating Data Harmonization: Resources and methods to improve harmonization of clinical trial and observational study data | 2023 | Chief Technology Officer, Axiom Health | |
| 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 | Bioinformatics Consultant, The Bioinformatics CRO |
| 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 |