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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 5R01 LM008111-08 (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.

Biomedical Language Processing Writing Large Scaling to All of Pubmed Central
NIH 5R01 LM 009254-06 (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.

Colorado Biomedical Informatics Training Program
NIH 2T15 LM009451-06 (Principal Investigator)
This grant supports the Colorado Bioscience Program's outstanding training program with scholarships, travel funds, and other resources.


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 enerated 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. 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.

NIH1R2 1HS019726-01A1 (Principal Investigator)

Enhancing Fulfillment Data in Community Practices for Clinical Care and Research

This project will use the Distributed Ambulatory Research in Therapeutics Network (DARTNet) to assess and improve the accessibility and utility of fulfillment (dispensing) data in community practices. While prescribing data represent what clinicians have prescribed for patients (ideally, the intended prescription medication regimen), fulfillment data represent what patients have received from the pharmacy (ideally, the actual prescription medication regimen). Fulfillment data may help clinicians provide better coordination of care (by revealing what other clinicians have prescribed for a patient) and better informed care (by revealing whether a patient has been able to adhere to prescribed drug regiments).

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, under-served 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.

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 DK078669-05 (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.

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
5 R01 GM083127-04 (PI) NIGMS
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.

1R01 GM097251-01A1 (PI) NIGMS
Genome-Wide Mutation Models To Decipher Function

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.

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