the taylor lab at johns hopkins university

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.

News

Mouse ENCODE Consortium Papers out: comprehensive mapping and comparison of functional genomic data in human and mouse.

Two articles at Supercomputing 2014: were published (1) describing a Galaxy federation model and (2) providing an overview of the current Big Data analysis tools.

Welcome Enis Afgan to the lab: Enis Afgan, cloud and distributed computing expert, had joined the lab as an Associate Research Scientist as of July 2014.

Managing and disseminating tools and data in Galaxy: Two new papers describe the Galaxy ToolShed and Data Managers.

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.

older news

Events

Biological Data Science 5-8 November, Cold Spring Harbor Lab

Galaxy Hackathon, 28-30 June, Baltimore MD

Galaxy Community Conference, 30 June - 1 July 2014, Baltimore, MD

Recent Publications

The Mouse ENCODE Consortium. “A comparative encyclopedia of DNA elements in the mouse genome”. Nature. November 2014; 515:355–364

Pope BD, Ryba T, Dileep V, Yue F, Wu Q, Denas O, Vera DL, Wang Y, Hansen RS, Canfield TK, Thurman RE, Cheng Y, Gülsoy G, Dennis JH, Snyder MP, Stamatoyannopoulos JA, Taylor J, Hardison RC, Kahveci T, Ren B, Gilbert DM. “Topologically associating domains are stable units of replication-timing regulation”. Nature. November 2014; 515:402–405

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

more publications