NICHD Bioinformatics and Scientific Programming Core

Eunice Kennedy Shriver National Institute Of Child Health & Human Development

Investigators

Linked publications, trials & patents

Abstract

NICHD's 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 NIH's Biowulf high-performance computing cluster. Projects continued from previous reporting periods include: development of track hubs to visualize genomic data across many different experiment types; variant calling in patients in several rare diseases; insertion of HIV into the human genome and its relationship with LEDGF chromatin binding protein; bulk and single-cell RNA-seq analysis of differentially expressed genes during Xenopus tropicalis development; identification of genome-wide RNA-RNA interactomes in E. coli using RNA-seq and RIL-seq and under various perturbations; scRNA-seq analysis to characterize GABAergic neurons; an integrative analysis of 5' and 3' ends of bacterial transcripts in multiple species and conditions; CUT&RUN analysis in several model systems; reimplementing and extending software for the TRIP assay; various scRNA-seq and snRNA-seq analyses in a wide range of systems; single-cell sequencing of Borrelia cells; germline variant calling to disentangle a complex phenotype in a long-running mouse strain; metabolomics in various celltypes; assessing mutations in a collection of bacterial strains to identify mutational hotspots; identifying protein interactors in multiple model systems and mutants; developing a generalized tool for improved depletion of ribosomal RNA from bacterial RNA-seq samples; RNA-seq in zebrafish models of clinically-relevant lymphatic syndromes; tool and algorithm development for a novel tRNA sequencing protocol; identifying small RNA and mRNA targets in bacterial gene regulation; assessing the role of extracellular vesicles in Cushings disease; spatially-resolved RNA-seq in pituitary tumors; investigating recombination events in the pantry moth model system; identifying the transcriptional effect of mutations affecting neural regeneration; and additional single-cell and bulk RNA-seq analyses in a range of systems and with a range of experimental designs. New projects this year included scRNA-seq of isolated Drosophila gustatory receptor neurons; spatial RNA-seq in a mouse model of a rare bone disease; variant calling to validate cell lines modeling a rare pediatric neurodegenerative disease, in primary ovarian insufficiency, and in Carney triad; comparing proteomics and RNA-seq under perturbations of iron homeostasis; extensive statistical analysis and biomarker discovery with proximal extension assay data from the serum of patients with a rare pediatric disease; metabolomics and lipidomics to assess lipid membrane dynamics; allele-specific micro-C and ATAC-seq; and various other new RNA-seq, scRNA-seq, and ChIP-seq projects in model systems. 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 NIH's Biowulf high-performance computing cluster. We develop custom web applications using R Shiny that allow our collaborators to explore and compare their data in powerful ways without requiring bioinformatics expertise. In particular, this year we publicly released Carnation and cascadeR, our web applications for exploring bulk and single-cell RNA-seq data respectively. We train users in NICHD and other ICs to use these tools and others 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.