Although Computational Bioscience is a relatively new program at UCD at Anschutz Medical Campus, the faculty have published in such prestigious publications as Nature, Science, and The Proceedings of the National Academy of Sciences. They have also been awarded millions of dollars in grants from the National Institutes of Health, the National Science Foundation and other highly competitive organizations.

Below are selected ongoing grants for each faculty member. Relevant publications and complete support lists can be found on their individual home pages.

Active Grants:
Dr. Lawrence Hunter

Technology Development For a Molecular Biology Knowledge Base
NIH 2R01 LM008111-04A1 (Principal Investigator)
The goal of this project is to demonstrate that database integration and natural language information extraction technology are adequate to produce in automated fashion a broad, deep knowledge base for molecular biology.

Beyond Abstracts: Issues in Mining Full Texts
NIH 5R01 LM 009254-03 (Principal Investigator)
This research tests the following hypothesis: Creation of large, high-quality, biomedical corpora from full text genres will lead to significant improvement in the performance of biomedical text mining systems and the creation of new approaches to text mining tasks. Specific aims include constructing several large corpora covering a range of genres and incorporating a rich knowledge representation; identifying factors that affect differential performance on full text versus abstracts; and developing new methods for language processing, especially of full text.

Bioscience Training Program
NIH T15 LM009451-02 (Principal Investigator)
This grant supports the Colorado Bioscience Program's outstanding training program with scholarships, travel funds, and other resources.

Ontologies and Biomedical Language Processing

NIH 5R01GM083649-02 (Principal Investigator)

The goal of this project is to explore bot6h the potential for, and obstacles to, the mutual application of biomedical ontologies and biomedical language processing.

Construction of a Full Text Corpus for Biomedical Text Mining

NIH 5G08LM009639-02 (Principal Investigator)

The goal of this project is to build a team that includes the builder of the largest semantically annotated corpus to date, one of the pioneers of the model organism databases, and an already-assembled cadre of experienced linguistic  and domain-expert annotators.

Dr. Aaron Clauset

JSMF220020171 Role: co-PI
J.S. McDonnell Foundation
Statistical Inference and Machine Learning for Complex Networks
The goal of this project is to develop novel statistical and computational algorithms for automatically detecting and characterizing complex structures in large-scale network data.

Dr. Robin Dowell

Butcher Seed Grant, University of Colorado (co-Principal Investigator)
p53 meets genomics: elucidating the p53 transcriptome by global run-on deep sequencing
Time series analysis of GRO-Seq trancriptome data from a human cell line stimulated for p53 by the nongenotoxic
drug Nutlin.

Boettcher Foundation Webb-Waring Biomedical Research Award (Principal Investigator)
Modeling evolution of transcriptional regulation.
Build a computational model of transcription that incorporates noncoding transcripts as regulators. Train and
validate the model using genome-wide RNA-Seq and ChIP-Seq datasets generated in closely related yeast
strains.

Dr. Debra Goldberg

NSF GK-12: Integrating Computer Science into Traditional Studies (Principal Investigator)
This project is called ECSITE (Engaging Computer Science In Traditional Education) Train future researchers
in Computer Science to communicate effectively with the public about their work, and understand the
connections between their work and other disciplines. Educate K-12 students and teachers about the current
ubiquity of computing and the revolution that computing has had on different areas of science and society.

Dr. Carsten Görg

Ontologies and Biomedical Language Processing (Instructor)
The goal of this collaboration with the National Center for Biomedical Ontology is to develop language
processing tools to suggest automated annotations, to evaluate relations between ontologies and concepts in
peer-reviewed publications, and connecting terms within and across ontologies.

NIH HHSN276201000033C (Hunter, PI)
Computational Thinking Contract (Role: Expert in Visual Analytics and Information Visualization)
The goals of this contract are to (a) construct models of the explanatory cognition and cognitive workflows of
molecular biologists analyzing data and constructing hypotheses, (b) analyze full text journal articles for
statements that explain or provide evidence for or against another statement to facilitate the creation of
computer systems that can automatically recognize explanations in texts, and (c) combine and extend the
existing Hanalyzer and Jigsaw computer systems to support generation of explanations and hypotheses.

Dr. Michael Kahn

Colorado Clinical and Translational Science Institute (Role: CCTSI Co-Director & Informatics Core Director)
Goal: Provide the infrastructure for performance of clinical (patient-oriented) translational investigation in
infants, children and adolescents and in pregnant women.

UL1 RR025780-02S3 (Role: Co-Investigator)
Colorado Clinical Translational Sciences Institute Supplement
Goal: Advance Translational (T1 and T2) Research by evaluating Internet-based remote access to electronic
clinical systems to support study monitoring tasks.

R01 HS019908-01 (Role: Informatics Lead)
Scalable Architecture for Federated Therapeutic Inquiries Network (SAFTINet)
This multi-state project will allow researchers, health policy experts, payers, and clinicians to better understand
the impact of a wide variety of health care interventions on health outcomes for minority, underserved and
socioeconomically disadvantage populations. We will assemble a learning community dedicated to the
aforementioned populations and build a secure technology to allow authorized and authenticated stakeholders
to answer important questions regarding issues ranging from treatment options to care delivery options.

1R01 HS020024-01 (Role: Site informatics lead)
Building Modular Pediatric Chronic Disease Registries for QI and CE Research
This multi-institutional project will expand an existing chronic disease quality improvement registry for pediatric
inflammatory bowel disease to support comparative effectiveness research. Specific Aims focus on enlarging
the size and scope of the registry using innovative informatics techniques, improving data quality and
completeness and engaging in advanced CER analysis techniques.

NLM 3T15LM009451-04S1 (Role: Co-Investigator)
Computational Bioscience Program Training Grant
The supplement funding request will extend the existing NLM T15 training curriculum at the University of
Colorado to include three new courses or course materials: (1) a new course in next generation clinical
phenotyping, (2) new materials on the responsible conduct of research, and (3) a mini-series on “Informatics
for non-Informaticians” directed toward translational research investigators.

HHSN2752 0080018C (Role: Co-Investigator)
LOI3-SL-05-A, Neonatal Research Networks Terminology Harmonization
This multi-institutional project will bring three active national neonatal research networks together to harmonize
overlapping data elements and definitions to promote the use of national standards and data sharing across
networks. Linkages to national clinical standards and to the existing NICHD child development common data
elements will be included in harmonization efforts.

1U18HS020508-01 (Role: Site Co-Investigator)
A Pediatric Quality Measurement Center and Testing Laboratory
The Children’s Hospital of Philadelphia is proposing to be a Center of Excellence for the Pediatric Quality
Measures Program (PQMP). Our unique methodological competencies are using the EHR to measure quality,
development of innovative quality and outcome measures, and statistical methods for risk adjustment and
disparity assessment. Based on our extensive experience with outcome and process measure development,
we have suggested a coherent plan for quality measure enhancement and development that we believe will
benefit the entire PQMP consortium, and help guarantee that the metrics developed from this ambitious
initiative will be of the highest caliber and of adequate scale and scope to transform child health.

Dr. Katherina J. Kechris

K01 AA016922 Katherina Kechris-Mays (PI) NIH/NIAAA
Genomic Regulatory Sequence Analysis for Alcohol-Related Phenotypes
The goal of this work is to study mammalian model systems to identify genomic regulatory sequences that
contribute to transcriptional changes in alcohol-related behaviors.

Butcher Seed Grant Proposals Katherina Kechris-Mays (PI) Butcher Foundation/CU-Boulder Chancellor's Office
Genetics of Gene Expression in COPD
The goal of this pilot funding is to combine and analyze data from genome wide association studies and gene
expression profiling in efforts to elucidate the molecular mechanisms controlling gene expression in Chronic
Obstructive Pulmonary Disease. Role: co-Principal Investigator (w/ Russell Bowler & Christopher Coldren)

R01 HL095432 Russell Bowler (Role: Co-Investigator) NIH/NHLBI
Metabolome and Proteome Profiles of Emphysema and Airway Disease
The goals of this work are to (1) use proteomic and metabolomic approaches to identify plasma biomarkers
that are associated with Chronic Obstructive Pulmonary Disease phenotypes and (2) identify the genetic
control of these biomarkers.

Dr. Robin Knight
5P01 DK078669-04 (co-PI) NIDDKD
Metagenomic Studies of the Gut Microbiomes of Obese and Lean Twins
The goal of this project is to develop new methods for detecting lateral gene transfer and for comparing gut
microbial communities.

NNX08AP60G (Principle Investigator) NASA
Measuring the Abudance of the simplest functional RNAs
The goal of this project is to understand how abundant simple aptamers and ribozymes are in randomsequence
pools, with implications for SELEX and the origin of life.

WU-09-72/2905035N (co-PI) Crohn's and Colitis Foundation of America
Metagenomic Studies of the Human Gut Microbiome: An Initial Pilot Study
The goal of this project is to understand how microbial communities change with Crohn’s disease and colitis,
beginning with a sample of healthy individuals.

5 R01 HG004872-03 (PI) HHS NHGRI
Tools for Understanding microbial communities & diversity in human body habitats
The goal of this project is to develop enriched descriptors of microbial community composition and timeseries
methods for analyzing microbial diversity.

DE-AC05-76RL01830 (PI) Batelle (PNNL)
Role of Microenvironments and Transition Zones in Subsurface Reactive Contaminant Transport Research
The goal of this project is to explore the role of subsurface microbial communities in mobilization and
demobilization of radioisotopes at the Hanford nuclear contaminated site.

51678 (co-PI) Bill & Melinda Gates Foundation
Characterizing the human gut microbiota and its microbiome in malnourished children at two sites in the Mal-
ED network
The goal of this project is to understand risk factors for malnutrition, focusing on microbial communities.

3 R01 HG004872-02S1 (PI) HHS NHGRI
New Tools for Understanding the Composition and Dynamics of Microbial Communities
The goal of this project is to develop enriched descriptors of microbial community composition and timeseries
methods for analyzing microbial diversity.

5 R01 HL0090480-03 (co-PI) NIH
Longitudinal Studies of HIV-1 Nef in Pulmonary Hypertension
The goal of this project is to test whether the Nef protein in HIV is associated with heart disease: our role is to
apply bioinformatics methods to the sequence datasets collected by the Flores lab.

5 U01 HG004866-03 (co-PI) NIH
A Quality Assurance, Coordination and Analysis Center for HMP
The goal of this project is to develop a center for data analysis for the Human Microbiome Project. The Knight
lab’s role is to contribute bioinformatics tools and to work on metadata standards.

5 U01 HL098996-02 (co-PI) HHS NHLBI
Alterations in Lung Microbiome in Acute and Chronic HIV Infection
The goal of this project is to characterize changes in bacterial communities in the lung associated with HIV
infection and attendant morbidity.

HHMI Early Career Scientist (PI)
This award provides unrestricted funding to pursue new research directions.

2008-34158-04713 (co-PI) National Science Foundation
Collaborative Research: How are archaeal diversity, abundance, and function regulated in agroecosystems?
The goal of this project is to understand how land use affects the types of archaea present in soils.

CNS 0821794 (co-PI) National Science Foundation
MRI-Consortium: Acquisition of a Supercomputer by the Front Range Computing Consortium
The goal of this project is to acquire, maintain and support a supercomputer for many tasks, including 454 data
analysis.

2010-12-04 (co-PI) ALFRED P. SLOAN FOUNDATION
MoBe DAC-- A data analysis core for the Indoor Environment Microbiology Program
The goal of this project is to develop new standards and software to facilitate interoperability between QIIME,
VAMPS and MG-RAST, allowing users to conveniently visualize their 16S rRNA data and metagenomic data
using a range of tools.

Dr. Sonia Leach

NIH RC2 HL101715 (Role: Co-Investigator )
Lung Genomics Research Consortium
The overall goal of this project is to establish a genetic, molecular, and quantitative clinical phenotyping
warehouse for the lung research community that would enable investigators to develop and test hypotheses to
understand the etiology, pathogenesis, and clinical manifestation of complex, chronic lung diseases.

Dr. Tzu Phang

UL1 RR025780-01 (Role: Education Specialist) NIH
Colorado Clinical Translational Sciences Institute
The program incorporates a broad reaching intra and inter-institutional comprehensive program to enhance
translational clinical research, training of clinical translational scientists, and collaboration with the communities
of the state of Colorado and the surrounding region.

P30 CA 046934 (Role: Bioinformatician) NIH/NCI
Cancer Center Support Grant; Gene Expression Core
The Core aims to offer state-of-the-art cytogenetics methodology support to the members of the University of
Colorado Comprehensive Cancer Center.

CMREF/IPAH (Role: Data Analyst)
Source: Medical Research and Education Fund/American Heart Association Center for Genomics Cardiovascular
This grant provides extensive support to idiopathic pulmonary arterial hypertension (IPAH) researchers for the
incorporation of genomic resources for their research endeavors. This project also will provide extensive
expression analysis in pulmonary samples and a database for normal control lung expression and SNP data.

R01 AA018120-01A2 (Role: Data Analyst) NIH/NIAAA
Genetics of Alcohol Sensitivity in Rats
The goals of this project are to fine-map acute alcohol sensitivity QTLs on rat chromosomes 1 and 2; identify
candidate genes for these QTLs; and begin testing the functional contribution of the candidate genes to acute
alcohol sensitivity and alcohol reward.

Dr. David Pollock
NIH R01 GM083127 (PI)
Modeling evolution of functional context in proteins
Methods will be developed to model differences in evolutionary patterns across positions in proteins, and to model how these patterns change over time. The volutionary patterns at each position will be correlated to known structural features,  and based on these analyses models will be developed that directly incorporate structural and functional information.

NSF EAGER Hillis (co-PI)
A novel genomic sequence enrichment strategy for phylogenomics This is a project to implement my idea of doing targeted high throughput sequencing by hybridization of conserved genes for phylogenomics. This idea is being tested on amphibians as an extension of Hillis’ amphibian Tree of Life grant.

Dr. Michael Strong

NIH Loan Repayment Program (PI)

Award for Health Disparities Research

Dr. Karin Verspoor

R01 LM010120-02 (Principal Investigator) NIH / LM
Automated Literature Mining for Validation of High-Throughput Function Prediction
We will develop methods for automatically mining the full text literature to validate computational predictions of functional sites in proteins. Our overall approach is to integrate predictions of protein functional sites derived from structural modeling with information extraction from text to enable identification of statements supporting or refuting a prediction in the literature.

5R01 LM008111-06 (Hunter, PI) NIH / LM
Technology Development for a Molecular Biology Knowledge-base
The goal of this project is to demonstrate that database integration and natural language information extraction technology are adequate to produce in automated fashion a broad, deep knowledge base of molecular biology.

5R01 GM083649-04 (Hunter, PI) NIH
Ontologies and Biomedical Language Processing
The goal of this project is to explore both the potential for, and obstacles to, the mutual application of biomedical ontologies and biomedical language processing.