NICHD Bioinformatics and Scientific Programming Core

Eunice Kennedy Shriver National Institute Of Child Health & Human Development

Investigators

Linked publications, trials & patents

Abstract

NICHDs Bioinformatics and Scientific Programming Core (BSPC) consists of a central core of staff who coordinate with embedded bioinformaticians working directly in laboratories. This results in centralized infrastructure that is reusable across many projects while also providing focused and custom local support. Analyses performed by BSPC make extensive use of NIHs Biowulf high-performance computing cluster. Projects worked on during the reporting period include: identification of expression quantitative trait loci in RNA-seq from the Fetal Growth Study; comparing schizophrenia-associated genes with a proteomics screen to identify functional overlap; identification of 3 ends of bacterial transcripts; identification of mouse strain-specific variants rescuing an embyronic lethal phenotype; single-cell RNA-seq analysis of cave fish and surface fish and also of zebrafish meninges; RNA immunoprecipitation enrichment analysis of a neuronal membrane protein; quantification of histone incorporation and turnover kinetics during interferon stimulation; integration of single-cell ATAC-seq and single-cell RNA-seq to identify poised enhancers related to neuronal development; detection of random monoallelic expression using single-cell RNA-seq in zebrafish brain; coexpression network modeling of gene expression in a mouse model of Niemann-Pick disease; differential mass-spec analysis of exosomes to look for candidate disease markers; validation of CUT&RUN peak-detection algorithms and scaling up the analysis to run on hundreds of samples, development of track hubs to visualize genomic data across many different experiment types; development and deployment of a web site to visualize and aggregate many different transcriptomic studies; differential methylation in Cushings disease patients and Carney triad patients; variant calling in patients in several rare diseases; localization of an incorporated transgene in a mouse model; proteomic analysis of juvenile neuronal ceroid lipofuscinosis; and development and testing of a software tool for NICHDs Zebrafish Core that identifies optimal CRISPR/Cas9 oligos for designing custom zebrafish models for rare diseases. We performed RNA-seq analysis to detect differentially expressed genes in a wide variety of experimental designs, model systems, and biological perturbations, including depletion of nuclear pore proteins in fly; RNase mutants in mouse; various perturbations related to diurnal cycle in mouse, rat, zebrafish, human, macaque, and chicken; tRNA overrexpression in yeast; non-coding RNA mutants and loss-of-imprinting mutants in mouse; and maternal to zygotic transition in zebrafish. We also performed RNA-seq analysis on osteogenesis imperfecta, pheochromocytoma, Carney triad, Cushings disease, primary macronodular adrenal hyperplasia patients. BSPC continues to develop and maintain lcdb-wf, a system of workflows and pipelines to process high-throughput sequencing data, run extensive quality control, and perform differential ChIP-seq or RNA-seq analyses and which runs on NIHs Biowulf high-performance computing cluster. We train users in NICHD and other ICs to use these tools on their own data. We have also continued to contribute to the Bioconda project, a system used by bioinformaticians worldwide to easily install biology-related software tools.