Colorado Computational Pharmacology (CPP)
 
   
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Faculty

Postdoctoral Fellows

Research Staff

Students

Staff

Former Lab Members

       
 

Center Director

   
    Lawrence Hunter, Ph.D.
Email: Larry.Hunter@ucdenver.edu
Home Page: http://compbio.ucdenver.edu/hunter/
Research Areas: Development and application of advanced computational techniques for biomedicine, particularly the application of statistical and knowledge–based techniques to the analysis of high–throughput data and of biomedical texts. Also, neurobiologically and evolutionarily informed computational models of cognition, and ethical issues related to computational bioscience.
   
 
Faculty
   
    Kevin Bretonnel Cohen, PhD
Instructor
Email:Kevin.Cohen@gmail.com
Home Page: http://compbio.ucdenver.edu/cohen/
Research Areas: Entity identification and normalization, information extraction, corpus linguistics, and computational lexical semantics, particularly in the molecular biology domain.
   
           
   

Carsten Görg, Ph.D.

Instructor

Email: Carsten.Goerg@ucdenver.edu

Home Page: http://compbio.ucdenver.edu/goerg

Research Areas: Design, development, and evaluation of visualizations and visual analytics tools for supporting biologists in analyzing large and complex datasets. Also, application of text analytics research approaches to the biomedical literature.

   
           
     

Karin Verspoor, Ph.D.

Research Assistant Professor

Email:  Karin.Verspoor@ucdenver.edu

Home Page: http://compbio.ucdenver.edu/Hunter_lab/Verspoor/

Research Areas:  Development of algorithms for natural language processing of biomedical texts, text mining and information extraction methods combining symbolic and statistical representations of linguistic features and biological knowledge.

   
 
Postdoctoral Fellows
   
   

Haibin Liu, PhD

Email: Haibin.Liu@ucdenver.edu

Research Areas: Natural Language Processing, Text Mining and Information Extraction from biomedical literature, and Web Usage and Content Mining.

   
           
   

Kevin Livingston, PhD

Email:Kevin.Livingston@ucdenver.edu

Research Areas: My research investigates how to build intelligent systems that are capable of leveraging large quantities of background knowledge. Specifically I am currently working on knowledge representation and reasoning of biological information to facilitate extracting more information from biomedical journal articles.

   
           
   

Anis Karimpour-fard, PhD

Email: Anis.Karimpour-fard@ucdenver.edu

Research Areas:  My main interest is in protein-protein interaction networks.  I design and use the graph algorithms and integrate information from different sources of annotation to analyze genomic data and predict protein function.  I am also interested in developing algortihms to analyze comparative genomic and functional genomic data

   
           
   

Ravikumar Komandur, PhD

Email: Ravikumar.Komandur@ucdenver.edu

Research Areas: My prime research interest is centered on broad areas such as BioMedical Literature Mining, BioMedical Ontologies and Knowledge representation of BioMedical Semantics.

   
 

Research Staff

   
   

Mike Bada, PhD

Biomedical Ontologist

Email: Mike.Bada@ucdenver.edu

Research Areas: Formal (especially ontology–based) representation of biological data and its applications. The integration and enrichment of existing biological ontologies by mining the component ontologies, generating assertions involving the ontological terms, and adding these assertions to the ontologies as links between terms. Also, the annotation of texts to serve as gold–standard corpora for biomedical text–mining, involving maintenance of the ontologies used, development of the annotation guidelines, and training of the annotators.


   
           
    Bill Baumgartner, Jr. Bill Baumgartner, MSE
Lead Software Engineer, Biomedical and Text Mining Group
Email: William.Baumgartner@ucdenver.edu
Home Page: http://compbio.ucdenver.edu/baumgartner/
Research Areas: Development and evaluation of natural language processing technologies applied in the biomedical domain, particularly with regard to information extraction, semantic parsing, and knowledgebase construction.
   
         
   

Tom Christiansen, MS

Email: tchrist@perl.com

Research Areas: Languages: computer languages, human languages. Automation.

   
         
    Helen Louise Johnson Helen L. Johnson, MS
Computational Linguist, Biomedical Text Mining Group
Email: Helen.Johnson@ucdenver.edu
Home Page: http://compbio.ucdenver.edu/johnson/
Research Areas: Natural language processing on biomedical literature, including entity identification and normalization, relationship and information extraction, and text-to-ontology alignment.
   
           
   

Yuriy Malenkiy

Software Engineer

Email: Yuriy.Malenkiy@ucdenver.edu

Research Areas: Development of software solutions for biomedical domain in areas of automation, high-throughput, analysis and visualization. Ongoing tasks include design, development and testing of lab's software projects in areas of natural language processing and biomedical data analysis.

   
           
   

Chris Roeder, MS

Software Engineer

Email: Chris.Roeder@ucdenver.edu

Research Areas: I work on a variety of software in the lab from shared-tasks to our open source projects hosted on SourceForge. Most of my work centers around UIMA and natural language processing projects written in Java as well as good software engineering practice. I'm currently researching effective ways to scale UIMA processing up to one million documents.

   
   


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Students

   
    Daniel McShan
Email: Daniel.Mcshan@ucdenver.edu
Research Areas: Design and analysis of metabolic pathways.
Advisor: Larry Hunter
   
         
   

Ronald P. Schuyler
Email: Ron.Schuyler@gmail.com
Research Areas: Knowledge-based analysis, data visualization, autoimmunity and the genetics of complex diseases.

Advisor: Larry Hunter

   
   


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Staff

   
    Kathleen Thomas Kathleen R. Thomas
Administrative Coordinator, Computational Bioscience Program
Email: Kathy.R.Thomas@ucdenver.edu
   
         
    Dave Farrell Dave Farrell
Systems Administration / IT Manager
Email: David.Farrell@ucdenver.edu
   
         
    Liz Pruett
Student Coordinator
Email: liz.pruett@ucdenver.edu
   
   


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Former Lab Members:

   
 

Alumns of the Program:

   
   

  Farzin Imani
  Min Hong
  Zhiyong Lu
  Steve Russell
  Ronald Taylor
  Sonia Leach
  Anis Karimpour-fard
  Chai-Yu Yen


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Former Postdocs:

   
   

  George Acquaah-Mensah
  Yiwen He
  William Old
  Tzu Lip Phang

  Hannah Tipney


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Former Lab Members:

   
   

  Jens Eberlin
  Aaron Gabow
  Cary Miller
  David Otteridge

  Andrew Dolbey


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Dr. Hunter's Prior PhD Grads:

   
   

  Myriam Abramson
  Judith Devaney
  Robert Erb
  Jeffrey Krichmar
  Sonia Leach
  Imran Shah
  Lorraine Tanabe
  Barry Zeeberg

  Greg Caporaso

  Tom McTavish

  Anis Karimpour-Fard

  Philip Ogren


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