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Students and Alumni

Current Students

  
  
Research Area
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.
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.
Joel Zylberberg
A self-organizing memory network
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.
Lawrence Hunter
Using semantic knowledge representations to investigate drug-target mechanism
James Costello
The goal of my research is to characterize the molecular and metabolic pathways that become dysregulated in cancer and other diseases. By modeling 1) the transcriptional regulation of enzymes and 2) the flux through metabolic pathways, we aim to accurately mimic the behavior of a cancer cell. With this model, we can simulate in silico how cellular metabolism changes in response to genetic changes or drug treatments. These observations help us understand the perturbed pathways in a disease state and may aid in the identification of novel or combinatorial therapeutic options.
Carsten Goerg
Finding and visualizing multi-omic patterns in human systems biology
Sonia Leach
Visual Analysis and Integration of Knowledge Networks using Genetic Data
Jim Costello
I am interested in identifying molecular signatures within bladder cancer using integrative data approaches coupled with machine learning methods. Ultimately, these signatures will be used in building a predictive model to infer patient outcome or response, i.e. survival or sensitivity and resistance to treatment.
Robin Dowell
I am interested in using various genomic datasets to better understand how transcription is regulated.
Michael Strong
1st Year Student
1st Year Student
1st Year Student

Alumni

  
  
Thesis
  
Current Position
Negacy Hailu
Lawrence Hunter
Investigation of traditional and deep neural sequence models for biomedical concept recognition.
2019
Michael Shaffer
Catherine Lozupone
Using networks to understand microbiome and metabolome interactions
2019
Postdoctoral Fellow, Colorado State University
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
Postdoctoral Fellow, University of Colorado-Boulder
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 Multiple Species
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

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