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Jonathan Epstein, MS, Head

We provide end-user scientific software support for laboratories within the NICHD’s Division of Intramural Research (DIR). As a core facility, we perform most of our work in conjunction with or on behalf of these laboratories.

Mass spectrometry

We continue to work in collaboration with the Mass Spectrometry Core Facility to develop software and original algorithms for the de novo identification of peptides from mass spectra.

Campbell JM, Stein SE, Blank PS, Epstein JA, Vestal ML, Yergey AL. Fragmentation of leucine enkephalin as a function of laser fluence in a MALDI TOF-TOF. J Am Soc Mass Spectrom 2007;18:607-16.

Protein sequence analysis

We developed software that performs extensive proteome-wide analysis of protein tails, searching for highly charged amino-terminal and carboxyl-terminal regions. The focus of the analysis is structural proteins such as tubulins and histones. Aspects of the analysis include several metrics for tagging protein-ends as charged and designation of associated coding genes by using the Gene Ontology database.

Microarrays

We continue to act as a core facility for microarray analysis for several NICHD laboratories. On behalf of the Program in Genomics of Differentiation, we have performed extensive analysis of Affymetrix® microarrays, providing information derived from the Gene Ontology database for selected upregulated and downregulated genes and extensive statistical analysis and development of Web-based software tools. The current focus of the analysis is Gene Set Enrichment Analysis and the mapping of zebrafish probeset identifiers to human gene annotations and their associated biological pathways.

We provided statistical consultation on microarray analysis for the Section on Molecular Genetics of Immunity in the Program in Developmental Endocrinology and Genetics. We performed similar consultation and analysis for the Section on Molecular and Cellular Biology in the Program in Genomics of Differentiation.

General bioinformatics

We provided ongoing consultation on DNA and protein sequence analysis and general bioinformatics issues to the Program in Genomics of Differentiation and have advised on evolving high-throughput DNA sequencing technology.

For further information, contact Jonathan_Epstein@nih.gov.