# Bioinformatics Core

> **NIH NIH P60** · OREGON HEALTH & SCIENCE UNIVERSITY · 2021 · $166,672

## Abstract

Bioinformatics Core Summary/Abstract
The Portland Alcohol Research Center (PARC) research projects will generate large amounts of gene
expression and epigenetic data from multiple species and treatment conditions. The Bioinformatics Core
(C002) will play an integral role in the management and analysis of these data, enabling the identification of
genomic markers of alcohol exposure and risk for alcohol abuse. The key functions of C002 will be to provide
foundational analyses to enable the primary endpoints within each project, provide higher-order inference by
integrating data across PARC projects, and to augment these analyses by integration of PARC data with
publicly available data resources.
C002 will work with PARC investigators to design, troubleshoot, and execute best-practices computational
analysis pipelines appropriate for the primary endpoints for each project.The core's experimental design and
analysis services include: 1) Bioinformatics such as DNA- and RNA-seq read alignment, differential
expression and pathway analysis, methylation and epigenetic analyses, data integration, and custom script
writing; and 2) Biostatistics such as biomarker, longitudinal, survival, and high-throughput/high-dimensional
omics analysis. Services under these two categories are often integrated during a given study. Each analysis is
customized to best fit the needs of the project and investigator.
Furthermore, C002 will augment individual PARC projects by bespoke integration of big data resources
available in the public domain. C002 will download and organize available single-cell RNA-sequencing
(scRNA-seq) data from relevant mouse brain regions, creating an atlas of cell type-specific expression that can
be used for fine-mapping the cell types driving differential expression patterns observed in P001 and P002.
Likewise, C002 will host publicly available epigenetic information from human and mouse, which will allow
expression and methylation in P001, P002, P003 and P004 to be annotated and contextualized with a much
larger set of genomic annotations (e.g. ChIP-seq, ATAC-seq, etc). Finally, C002 will perform cross-project
integration by searching for signals that may be shared across species, first by assessing for common gene
sets or pathways identified in mouse and macaque experiments, and, as a final translational step, assessing
the convergence of PARC-based insights with the vast amount of human genetics data emerging on Alcohol
Use Disorder.

## Key facts

- **NIH application ID:** 10056071
- **Project number:** 2P60AA010760-26
- **Recipient organization:** OREGON HEALTH & SCIENCE UNIVERSITY
- **Principal Investigator:** DONALD F. CONRAD
- **Activity code:** P60 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $166,672
- **Award type:** 2
- **Project period:** 1996-12-01 → 2025-12-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10056071

## Citation

> US National Institutes of Health, RePORTER application 10056071, Bioinformatics Core (2P60AA010760-26). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/10056071. Licensed CC0.

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