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.
Being a part of the open source community: means participating and contributing to Sprints, Hackathons and Codefests - a process now captured in a paper.
Enis Afgan, 27 November 2014
Mouse ENCODE Consortium Papers out: comprehensive mapping and comparison of functional genomic data in human and mouse.
James Taylor, 19 November 2014
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.
Enis Afgan, 13 November 2014
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.
James Taylor, 1 July 2014
Managing and disseminating tools and data in Galaxy: Two new papers describe the Galaxy ToolShed and Data Managers.
James Taylor, 12 March 2014
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
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