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Faculty and Research

Larry Hunter, PhD

Professor and Director
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David Pollock, PhD

Graduate Studies Director
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Elizabeth Wethington

Lead Program Administrator
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Our Expertise and Leadership

Our outstanding faculty, staff, trainees and alumni have come to Colorado from around the world. Before joining our program, they trained at Harvard, Yale, Stanford, Johns Hopkins, and other top universities.

The Computational Bioscience core and affiliated faculty work in a wide range of areas, including biomedical text mining, protein structure simulations, RNA sequence and structure analysis, graphical models of protein interactions, and statistical analysis of regulatory sequences. They have appointments in numerous departments on three CU campuses, including Medicine, Pharmacology, Biometrics, Biochemistry & Molecular Genetics, Computer Science, CCTSI; and we have faculty from National Jewish Health.

Research Areas Include:

  • Biological Visualization Data
  • Biomedical Ontology
  • Clinical Research Informatics
  • Computational Pharmacology
  • Gene Expression
  • Genomics
  • Metagenomics
  • Microbiome
  • Molecular Evolution
  • Natural Language Processing
  • Network Analysis
  • Neuroscience
  • Next Generation Sequence Analysis
  • Personalized Medicine
  • Statistical Methods in Genomics
  • Biostatistics
  • Text Mining
  • Translational Bioinformatics
  • Visual Analytics
  • Physical simulations of biological macromolecules and their dynamics

Core Faculty

Entity identification and normalization, information extraction, corpus linguistics, and computational lexical semantics, particularly in the molecular biology domain.
Systems and network biology approaches to disentangle signaling pathways in cancer development; Computational modeling of how therapeutic compounds function across different genomic backgrounds.
Application of machine learning, probabilistic models, and pattern recognition to large high throughput genomic datasets.
My research interests focus on the use of machine learning, multiple comparisons and multivariate statistical methods for the analysis of high-throughput data.  I have focused most of my research on combining genomic data from either multiple datasets or from multiple studies.  I have worked with transcriptomic, copy number, methylation and more recently, metabolomics and imaging data.    Application areas I have worked in include cancer, diabetes, and ophthalmology.    I have advised 12 Ph.D. students and one postdoctoral fellow in Biostatistics and Statistics on these topics.   Students who would work with me in the future could expect to work on new analytical methods for large-scale datasets as well as begin to examine computational issues to enhance scalability.
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.
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.
Dr. Kahn is interested in the integration of clinical research and electronic medical records for clinical quality improvement, decision support and clinical research. As Director of the CCTSI Informatics Core, Dr. Kahn is interested in distributed research networks for comparative effectiveness research. His area of informatics research also includes measures of data quality, data completeness, and data validation, especially across multi-institutional data sharing environments.
Development and application of statistical methods for analyzing molecular sequences and high throughput genomic data.
Research in the area of probabilistic graphical models and genomic data fusion, particularly for the tasks of gene prioritization, developing protein interaction networks and discovery of novel disease-gene associations.
Microbiology of the human gut and impacts on health. The development of bioinformatics techniques for analysis of marker gener and genomic sequence data.
Genome-enabled and bioinformatic approaches to studying microbial communities. Novel experimental methods and computational algorithms for assembly and analysis of high-throughput sequencing data.
VerbNet, ACE-Prop Bank, CLEAR NLP, Chinese Corpus Annotation
Developing computational and statistical algorithms for analyzing microarray data, with special emphasis on time-course experimental design and alternative splicing detection. He works directly with scientists to translate biological concept into algorithm for rapid exploration and discovery. He is also interested in how best to share the vast bioinformatics and genomics resources between multi-disciplinary scientists.
Evolutionary genomics and molecular evolution, particularly the interaction between protein sequence, structure, function, and molecular co-evolution within and between proteins.
Systems biology, genomics, and structural bioinformatics, particularly developing computational strategies to integrate genome sequence, gene expression, protein network, and protein structure information, with applications to respiratory diseases, including tuberculosis.
Translational Bioinformatics, Cancer Systems Biology, Precision Oncology, Drug Repurposing and Repositioning, Kinase Signaling Networks, Biomedical Data Science, Machine Learning, Developmental Therapeutics.
Computational phenotyping and data science using electronic medical records. Pharmacogenomics discovery, translation, and clinical implementation.
Mechanisms underlying sensory perception. My research uses tools from machine learning and statistics to understand (a) how information is represented in the activities of sensory neurons; and (b) the neural circuit mechanisms that shape those representations. Active collaboration with experimenters is a key component of this research.

Associated Faculty

My lab specializes in applications of machine learning in bioinformatics. We are developing methods for predicting protein function and interactions, and are studying the process of alternative splicing in plants.
Professor Choi’s research interests are in computer graphics, scientific visualization and human–computer interaction, with an emphasis on physically–based modeling and simulation for medical and bioinformatics applications.
Development and application of bioinformatics methods for analyzing genomics, epigenomcs and transcriptomic data. Genetic and epigenetic abnormalities incancer and pre-malignant conditions.
Professor Everett’s research interests are in the promoting of the proper use of statistics among scientists and clinicians, including the statistics of multiple testing.
Professor Gardiner's laboratory focuses on the molecular basis of the cognitive deficits seen in Down syndrome. Down syndrome (Trisomy 21) is the most common cause of intellectual disability, and is due to an extra copy of human chromosome 21 and the increased expression of some number of the ~500 genes encoded by it.
Professor Geraci is the Director of the Gene Expression Center, and the Division Chief of Pulmonary and Critical Care Medicine. His research interests are in the role of eicosanoids and pulmonary hypertension and lung cancer, and in the use of gene expression analysis to study disease pathogenesis.
Professor Gill’s research interests are in new tools and theories to study the evolution of microbial genomes, focusing particularly on the evolution of stress tolerance behaviors in E.coli.
Each year approximately 100,000 individuals worldwide endure a spinal cord injury (SCI). In spite of centuries of research no satisfying treatment is available for this disease. This is mainly due to complex systems behavior, which makes it difficult for scientists to comprehend the entire processes. My group has set its dedication to develop new therapeutics via the utilization of a knock down technology called deoxyribozyme to reduce proteins, which are inhibitory to axonal growth. To identify these suitable molecules, so called “key player” my laboratory has additionally developed a prototypic computer program suite. This program provides an overall picture of SCI, its underlying biochemical pathways, potential protein interactions and lays hand on the sheer number of applied substances. Together these two approaches hold promise to find a treatment for paralysis.
Cell determination, developmental patterning and hedgehog signaling in Drosophila.
Translational bioinformatics, Personalization of progonsis and treatment plan, Heart failure/cardiomyopathy, Integration of public data resources,
Professor Pace’s research interests involve the synthesis, structure and function of RNA; and the application of molecular biological tools to problems in environmental microbiology.
Professor Santorico’s research interests are in Statistical Genetics, Genetic Epidemiology, Genetics of Gene Expression, Integrating Genomics Data to Understand Complex Human Traits including Methods involving Genetic Linkage and Linkage Disequilibrium.
Professor Sikela’s research interests are in the development and application of advanced genome technologies, particularly as they apply to understanding of human evolution and human disease.
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.
My research interests are in developing computational methods for metabolomics and proteomics by better utilizing the chemico-physical characteristics of ions as detected in mass spectrometry thus improving the identification of metabolites, peptides and lipids.
The explosion in genomic technology over the past decade has thus far not resulted in concrete applications for global public health problems.  Genomically-informed epidemiologists are needed to design and implement clinically- and epidemiologically-relevant human studies.  My clinical expertise in tuberculosis and experience through years of designing and conducting epidemiologic studies in the developing world enabled me to rapidly establish multi-national, multi-center cohort studies which are collecting specimens for expression profiling. I am refining skills in study design and biostatistics through a PhD in Epidemiology.  Applying genomic tools to gain insight into the epidemiology of tuberculosis demands multi-disciplinary collaboration.  I have help to assemble a team of leading experts in genomics, systems biology, immunology, and study design.  My background and training in combination with my expert collaborators and strong institutional support will enable us to make important contributions to the genomic epidemiology of tuberculosis.
Craniofacial development.
Research and teach HCI issues with societal impacts. Promote emergent literacy for blind children using 3D printing. Study Android apps using Big Data. Automate GUIs using computer vision.

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