Bioinformatics Core

The Bioinformatics Core Facility at UPMC Children's Hospital of Pittsburgh (BCF@CHP) is a resource to support the bioinformatics analysis needs of investigators for datasets generated by the Sequencing Core at Rangos (HSSC@CHP ), by outside sequencing resources, or by using publicly available datasets. 

SERVICES

The Core helps investigators in building standardized workflows as well as customized, in-depth analyses with emphasis on quality control and statistical rigor. The services listed below should give you an impression of the most commonly performed analyses - we are by no means limited to them and are happy to tackle new challenges. We can provide extensive reports with publication-ready images as well as the analysis source code upon request. If you come across a paper with sequencing data analyses or other statistical methodology you would like to use (or think the Core should be aware of), please email it our way! 

 NGS data analysis

GENOMICS (WGS, WES) EPIGENOMICS (CHIP-seq, ATAC-seq)
  •  De novo assembly of eukaryotic and prokaryotic genomes 

  • Whole genome comparison at the genome architecture, and gene level (Evolutionary bioinformatics analysis) 

  • Genome functional annotation: Estimation, and analysis of repeat content, ab initio gene prediction, annotation of genes at three levels via protein domains and motifs, orthology search, and homology search 

  • Whole exome and whole genome analysis: variant calling, and annotation

  • CHIP-seq of transcription factors, and histone modifications

  • Measurements of open chromatin via ATAC-seq 

  • Basic analysis includes peak calling, and creation of enrichment tracks, in addition to raw data quality control, and genome alignment 

  • Additional analysis includes de novo motif detection, motif enrichment analysis, annotation of proximal and distal genes, and integration of peaks with expression data (from RNA-seq or microarray) for inference of regulatory effects

TRANSCRIPTOMICS (Arrays, RNAseq) OTHER  ANALYSIS
  • Analysis of commercial and custom microarrays: differentially expressed genes, group comparison

  • RNA-seq for mRNA: Gene or transcript quantification, differential analysis, and alternative splicing analysis

  • Functional analysis of differentially expressed genes: Gene Ontology terms, motif analysis, and pathways enrichment analysis

  • RNA-seq for small and non-coding RNA: Discovery of new microRNAs, microRNA target prediction

  • Simultaneous/Dual-RNA seq time-course analysis for host-pathogen interaction studies

  • Single cell transcriptomics - Bioinformatics support for processing, quality control, analysis, and interpretation. Additional analysis include identifying subpopulations, differential expression, data visualization, and statistical analysis

  • Metagenomics - Taxonomic identification and quantification for 16S amplicon sequencing, metagenome or metatranscriptome assembly, diversity and differential analysis

  • CRISPR-Cas systems - Off target prediction in gene editing, end-end analysis of pooled CRISPR-Cas9 screens

Statistical support

  • Supervised machine learning approaches for classification purposes, and feature prediction
  • Establish novel analysis pipelines using multivariate-, multiblock-, and network-based analysis for systems-level integration of -omics data across platforms 
  • Data visualization including heatmaps, violin plots, and other types of plots as well as custom visualizations
  • Automation of analysis pipelines using Nextflow 
  • Literate programming using Rmarkdown

Collaboration

Planning a data-intensive project? We are available for long-term collaborations on projects that require a higher level of analysis or the development of custom analysis pipelines. We can also co-mentor students who are interested in performing their own analysis or developing their own methods. 

Grant Support

The BCF@CHP is dedicated to supporting grant applications for  researchers at Rangos Research Center, and other external users. In addition to Letters of Support detailing Core capabilities as they relate to a proposed project, we can also assist with crafting the study design and research strategy, and devising the budget for informatics analysis. Please also consider including a member of the Core as a Co-Investigator in your application, which can strengthen your application by showing the collaborative involvement and support of an informatics expert.

If you expect to use particular Bioinformatics services to carry out your research project and would like our assistance with your application, please contact us. Please note that the time necessary to develop this plan may vary based on the complexity of your project.

To request a Letter of Support, please email dhr11@pitt.edu with the following details:

  • PI first and last name
  • Requestor name, if not PI
  • Draft letter, including your project title and a brief description of the proposed impact of the work.
  • Deadline
  • Specific aims (a draft copy is fine)
  • Name of funding agency
  • Any additional details about your project or other services

 Training

Although not currently deployed, we will be developing training events/workshops to enable researchers to do their own analysis.

ACKNOWLEDGING CORE SUPPORT

Please acknowledge Core staff where appropriate and consider authorship inclusion when scientific contributions merit.  In cases, where extensive bioinformatics analyses have been customized for your research project, we can assist with manuscript preparation, and preparation of figures. Please find more details at the School of Medicine's Authorship policy

CONTACT AND DIRECTIONS

Email: dhr11@pitt.edu

Phone: 412-692-8120

Mailing address: Rangos Research Center Rm. 8132

UPMC Children's Hospital of Pittsburgh

4401 Penn Avenue .

Pittsburgh PA 15224