YCGA Bioinformatics

The Yale Center for Genome Analysis is a full-service genomics core lab, providing microarray and next-generation sequencing services and analysis.  The center has a combination of Illumina HiSeqs and MiSeqs and a PacBio RS II instrument for next-generation sequencing, and has Illumina and Affymetrix microarray services.

The YCGA Bioinformatics group provides analysis support services for next-generation sequencing performed at the YCGA.  Members within this unit are a combination of biologists and computer scientists, having many years of experience in bioinformatic data analysis, as well as methodology development.  They are also available to contribute to research design, and grant and manuscript preparations.

Analysis services available:

  • Whole exome sequencing
  • Whole genome sequencing
  • RNA-seq
  • ChIP-seq
  • De novo assembly
  • Custom support for other next-generation sequencing analysis
  • Collaborative work on bioinformatics projects

For Yale Cancer Center members, Francesc Lopez-Giraldez can provide support and analysis at no charge.  For all Yale and non-Yale investigators, the group is available for analysis services at the rate of $195 per lane of sequencing for Yale investigators (and, for non-Yale investigators, $234 per lane for non-profit and $273).  This includes running current best-practice pipelines,  performing data quality evaluation and generating annotated gene lists, as well as pathway and/or GO enrichment, if appropriate.  It also includes some custom scripting to ensure you get the analysis results in a form you can interpret, and to assist in the creation of journal-quality figures for a subsequent paper submission.

Group Members

Dr. James Knight is Director of Bioinformatics and Research Scientist in the Department of Genetics, and started at Yale in June, 2014.  Prior to that, he was an R&D Fellow and Bioinformatics Director at 454 Life Sciences and CuraGen Corporation, and has been active in the bioinformatics field for the last 25 years.

Dr. Francesc López-Giráldez obtained his PhD in Evolutionary Genetics at the Autonomous University of Barcelona in 2006, and has been at Yale since 2007. He has 10 years of bioinformatics experience on a variety of large-scale biological sequence analyses, 5 years on NGS data analysis and pipeline development, and over 35 publications.

Dr. Sameet Mehta joined the group in November, 2014.  He obtained his Ph.D. in Zoology in 2007 and had been performing NGS analysis for the last 5 years, as a Visiting Fellow at the National Cancer Institute.

 

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