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Current Students
Name
  
Advisor
  
Research Area
Sonia Leach
Inference on protein-protein interaction networks. Multi-loci prioritization.
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.
Sonia Leach & Michael Strong
Computational and genomic approaches to predict drug-resistance in Mycobacterium tuberculosis.
Joel Zylberberg
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.
Kevin Cohen
Applying NLP techniques in biomedical literature more specifically extracting information from unstructured data. Being in a medical domain makes my work exciting and challenging. My goal is to build text mining tools that help researchers in the medical domain access information naturally.
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.
Catherine Lozupone
I am interested in exploring the effects of various diseases on human microbiomes such as the nose and gut. By looking at varying data types, such as 16S sequencing, metabolomics and data from computational techniques, we can get ideas about what functional changes are happening in human microbial communities in response to disease. I seek to develop computational methods and tools in order to integrate this information for better hypothesis generation and discovery of novel functional changes associated with disease.
Debashis Ghosh
Signatures of accelerated somatic evolution in cancer.
Carsten Goerg
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.

Alumni
Full Name
  
Advisor
  
Thesis
Degree Conferred
  
Current Position
William Baumgartner
Lawrence Hunter
Enhancing ontology concept enrichment through deductive entailment
2015
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
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
Postdoctoral Investigator at Centro Nacional de Analisis Genomico--Barcelona, Catalunya, Spain
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
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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