We are a computational biology lab in the Biology Department at Johns Hopkins University with research interests in bioinformatics, computational genomics, and data intensive science. Our labs interests are primarily in two areas.
Genomics of gene regulation: we seek to achieve a global understanding of the genomic basis of gene regulation, particularly over time and in development, using functional genomics and machine learning. We have a long standing interest in identification of cis-regulatory modules, particularly long-range enhancers. More recently, we have been focusing on understanding the determinants of 3D genome organization and its role in gene regulation.
Data intensive science: We work to increase access to compute and data intensive methods for the scientific research community, particularly in genomics. We are part of the team that develops Galaxy, a framework for making large scale computational analysis more accessible and reproducible. In the context of Galaxy we have research interests in data visualization and analytics, cloud and high-performance computing, transparent and reproducible scientific publication. We are particularly concerned with improving the reproducibility of published scientific results that depend on complex methods.
Managing and disseminating tools and data in Galaxy: Two new papers describe the Galaxy ToolShed and Data Managers.
James Taylor, 12 March 2014
Moving from Emory to Johns Hopkins University: As of January 1st 2014 James and the lab will move to the Department of Biology and Johns Hopkins University in Baltimore, MD.
James Taylor, 31 October 2013
High resolution mapping of 3D chromatin structure: Cell paper on fine scale 3D organization is mouse ES/NPC cells, features our methods for deriving sensitive high-resolution maps of 3D chromatin structure from 5C datasets.
James Taylor, 25 May 2013
Two articles on analysis of parasitoid wasp venomes: featuring an approach for combining RNA-seq and mass spectrometry to identify peptides in dissected venom gland lumen.
James Taylor, 23 May 2013
Galaxy For Interactive Visual Analysis: Trackster and Sweepster enable visual parameter tuning for RNA-seq analyses and other genomic analyses.
Jeremy Goecks, 20 November 2012
Galaxy Hackathon, 28-30 June, Baltimore MD
Galaxy Community Conference, 30 June - 1 July 2014, Baltimore, MD
Blankenberg D, Johnson JE, The Galaxy Team, Taylor J, Nekrutenko A. “Wrangling Galaxy's Reference Data”. Bioinformatics. March 2014;
Blankenberg, D, von Kuster, G, Bouvier E, Baker, B, Afgan, E, Stoler N, Rebolledo-Jaramillo B, The Galaxy Team, Taylor J, Nekrutenko A. “Dissemination of scientific software with Galaxy ToolShed”. Genome Biology. February 2014; 15:403
Sandve GK, Nekrutenko A, Taylor J, Hovig E. “Ten simple rules for reproducible computational research”. PLoS Computational Biology. October 2013; 9(10):e1003285
LeDuc R, Vaughn M, Fonner JM, Sullivan M, Williams J, Blood PD, Taylor J, Barnett W. “Leveraging the National Cyberinfrastructure for Biomedical Research”. Journal of the American Medical Informatics Association. August 2013;
Goecks J, Eberhard C, Too T, The Galaxy Team, Nekrutenko A, Taylor J. “Web-based Visual Analysis for High-throughput Genomics”. BMC Genomics. June 2013; 14(1):397 more publications