Recent posts from the lab blog
Posted on 31 October 2013 by James Taylor
As of January 1st 2014 James will be accepting a position as an Associate Professor in the Department of Biology and Johns Hopkins University in Baltimore, MD, with a secondary appointment in the Department of Computer Science. We are extremely excited to be joining a fantastic scientific community at Hopkins. In addition to a rich biomedical research community, Hopkins has a strong and growing group of excellent researchers in machine learning and big data analysis. There will be many new research opportunities in the lab, and we have openings in the lab for both postdocs and graduate students.
High resolution mapping of 3D chromatin structure
Posted on 25 May 2013 by James Taylor
As part of a collaboration with Victor Corces’ and Job Dekker’s groups we have been working on methods for deriving sensitive high-resolution maps of 3D chromatin structure from 5C datasets. The first paper using these methods, “Architectural Protein Subclasses Shape 3D Organization of Genomes during Lineage Commitment” led by Jennifer Phillips-Cremins shows that 3D chromatin architecture changes at the sub-megabase scale during differentiation from mouse ES to NPC cells, and that CTCF, mediator, and cohesin are involved in organizing these interactions, but that different sets of proteins are involved in interactions at different length scales. Importantly, the increased resolution achieved with our 5C approach clearly shows that chromatin is organized in a hierarchical structure, with additional layers of domain organization below the level of “topological domains” as previously described.
Two articles on analysis of parasitoid wasp venomes
Posted on 23 May 2013 by James Taylor
Two new articles in collaboration with Todd Schlenke’s lab on wasp venoms were published this week. The first, “Integrative Approach Reveals Composition of Endoparasitoid Wasp Venoms” in PLoS ONE describes an approach for combining RNA-seq and mass spectrometry to identify peptides in dissected venom gland lumens, allowing the discovery of many new venom proteins in L. boulardi and L. heterotoma The second, “Parasitoid Wasp Venom SERCA Regulates Drosophila Calcium Levels and Inhibits Cellular Immunity” in PNAS uses this approach to describe the venoms of Ganaspis sp.1 (G1), a previously uncharacterized Drosophila parasitoid species. Using this characterization demonstrates plasmatocyte cytoplasmic calcium bursts as an important aspect of ﬂy cellular immunity.