Alex Rolfe


I work at EMD Serono, leading a bioinformatics group that supports the Immunology and Immuno-Oncology therapeutic areas.
Past work includes
  • Pathogenica, Inc, developing new methods for infection diagnosis using high-throughput sequencing.
  • Computational Genomics Group at MIT CSAIL. My research focused on the genetic regulatory networks of pancreatic development as part of the SysCODE Project. We used ChIP-Seq (detects protein-DNA interactions), gene expression data, and proteomics data (protein-protein interactions and protein abundance) to understand the steps in development as cells go from stem cells to endoderm and hopefully to pancreatic beta cells.
  • ReadDB, a custom column store database system for short reads (eg, Illumina/Solexa, ABI/SOLiD) that have been mapped to a genome. We currently store several thousand lanes of sequencing data in this system to support ChIP-Seq and RNA-Seq analysis and visualization.
  • Ruler Arrays, a novel method to detect structural variants between two genomes.
  • GSE, a database and codebase for genomic analysis. This is the shared Java environment that our group uses.
  • Joint Binding Deconvolution (pubmed), a method for analyzing ChIP-Chip data that improves the spatial accuracy of the resulting protein-DNA interaction predictions and can detect pairs of closely spaced interactions.
  • Gene regulation in yeast cell size control, yeast chromatin state, yeast chromatin modifiers, and liver.
My bookmarks are public as are those of some of my colleagues. More recently, we've been using Zotero.

Everything Else

My GPG Key for and
LSC: On campus movie theater and lecture series. I have served as Chairman, Treasurer, Publicity director, and Projection director. I've seen a lot of movies and annoy my family with high standards for 35mm projection.
SIPB: I maintain, MIT's Usenet service, and the RTFM/FAQ server. I taught the IAP Perl class.
I've volunteered for Hub on Wheels for several years. This annual ride has 10, 30, and 50 mile loops from Government Center. The 30 mile and 50 mile routes are a fantastic tour of the southern parts of Boston including Forest Hills Cemetary, the Arnold Arboretum, and the waterfront.
Staying up late fun