STUDENTS & ALUMNI
Current Students
| Name | Advisor | Research Area |
|---|---|---|
| Mayla Boguslav | Larry Hunter | The goal of my research is to create natural language processing tools to help biomedical researchers better contextualize their experimental results within the current biomedical literature and to provide a new way for biomedical researchers to stay up-to-date on the literature both in their own field and others. |
| Tiffany Callahan | Larry Hunter & Michael Kahn | I am interested in investigating novel integration and discovery methods for clinical data and biomedical knowledge linkage and inference. My research pairs Semantic Web technology, network inference, and machine learning techniques in order to better understand the biological mechanisms underlying complex diseases. Currently, I am focusing on developing a computational method that reversibly transforms Web Ontology Language-compliant biomedical knowledge into a representation better suited for network inference. |
| Cody Glickman | Michael Strong | I am exploring the interplay of the virome, microbiome, and human host. Mechanisms such as horizontal gene transfer, evolution, and symbiotic relationships affect the genetic community composition and play a significant role in human health. To understand these mechanisms, I am developing tools to integrate viral and bacterial metagenomics from clinical samples with the explicit goal of expanding the traditional view of metagenomics studies. |
| Harrison Pielke-Lombardo | Lawrence Hunter | Using semantic knowledge representations to investigate drug-target mechanism |
| Janet Siebert | Carsten Goerg | Finding and visualizing multi-omic patterns in human systems biology |
| Laura Stevens | Sonia Leach | Visual Analysis and Integration of Knowledge Networks using Genetic Data |
| Rutendo Sigauke | Robin Dowell | I am interested in using various genomic datasets to better understand how transcription is regulated. |
| Josephina Hendrix | Michael 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 Mastej | Debashis Ghosh | I am interested in combining imaging and radiomics with other -omic data to better understand the progression of disease. |
| Jennifer Fouquier | Catherine Lozupone | I explore computational methods for analyzing gut microbiome data in different disease contexts. Currently, I am working on longitudinal data analyses to study how the microbiome changes over time in HIV+ individuals undergoing dietary intervention. I am also interested in multiomics analyses to see how immune phenotypes (RNA-seq) relate to the gut microbiome. |
| Kendra Meer | Robin 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 Guatney | Chris Miller | |
| Connor Elkhill | Rotating | |
| Lucas Gillenwater | Rotating | |
| Eric Prince | Rotating | |
| Brook Santangelo | Rotating |
Alumni
| Full Name | Advisor | Thesis | Degree Conferred | Current Position |
|---|---|---|---|---|
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 |
| Kelsey (KC) Anderson | Sonia Leach | Prioritizing Candidate Genes in Disjoint Sets using Graph Kernels on Unverlying Protien-protien networks. | 2018 (Masters Degree) | |
| 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 | Big Data Scientist, Arrow Electronics |
| 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 Biodedical 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 Univeristy |
| 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 |
| 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 |