Hartwell Center/Research Computing/Bioinformatics Support/Overview

Bioinformatics / Research Computing
Bioinformatics Support

Welcome to the Bioinformatics Support group! We provide bioinformatics and computational biology support for St. Jude research programs. All our staff members have Ph.D.'s in the life sciences as well as publications in bioinformatics and computer programming skills. Our services include analyzing gene expression data, proteomics data, chromatin immunoprecipitation (ChIP)-chip experiments, chromosomal abnormalities, multiple sequence alignments, phylogenetic trees, and any other data types that investigators need our help with. If no standard methods or programs exist to address a given analysis, we can develop them. We also provide training in commonly-used bioinformatics software and advice about methods and experiment design.

Some examples of our main activities include:
•	Identifying significant gene expression differences in Affymetrix or cDNA microarray experiments.
•	Identifying amplified or deleted chromosomal segments in comparative genome hybridization (CGH) arrays or Affymetrix SNP chip arrays, including loss of heterozygosity regions.
•	Building, curating, and maintaining current gene annotations for probes on our custom cDNA microarrays and commercial Affymetrix arrays.
•	Developing methods to analyze protein expression data from proteomics experiments.
•	Associating observed SNPs with disease states or gene expression differences.
•	Scanning promoter regions of genes for transcription factor binding sites, SNPs, CpG islands, or other regulatory signals.
•	Evaluation and visualization of the information generated from regulatory and metabolic pathways using software analysis tools.
•	Prediction of genes targeted by regulatory microRNAs.
•	Analysis of alternate splicing, ORF prediction, and polymorphisms in genomics data.
•	Comparative genomics, including the identification of orthologs and gene families, and phylogenetics analysis.
•	Development of parallel processing programs for computationally intensive analysis methods.
•	Prediction of protein phosphorylation sites and signaling partners.
•	Providing training in the use of bioinformatics applications, including Vector NTI, Ingenuity Pathways Analysis, Spotfire, and PyMOL.
•	Providing advice on the best ways to analyze a new type of data or a new combination of data types.

To use our services, please stop by room DT1030, or call or email one of our staff based on their areas of expertise. If you're not sure who to contact, call or email the bioinformatics section leader, Dr. John Obenauer (x3188).