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.

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 and Events

Boris contributed to a new paper from the Johnston Lab on cone subtype specification in human retinal organoids

New work from Gherman on the MetaWRAP metagenome assembly and annotation pipeline, blog post at Nature Microbiology

James is at BioC 2018 and has posted notes here

James, Enis, Dannon, Sam, Dave, and the rest of the Galaxy team were at GCC/BOSC 24-30 June, 2018

James was at the Rocky Mountain Genomics HackCon 18-23 June, 2018

Recent Publications

Eldred KC, Hadyniak SE, Hussey KA, Brenerman B, Zhang P, Chamling X, Sluch VM, Welsbie DS, Hattar S, Taylor J, Wahlin K, DJ Zack, Johnston RJ. Thyroid hormone signaling specifies cone subtypes in human retinal organoids. Science. October 2018; 362(6411):eaau6348

Uritskiy GV, DiRuggiero J, Taylor J. MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis. Microbiome. September 2018; 15(6):158

Zheng X, Hu J, Yue S, Kristiani L, Kim M, Sauria M, Taylor J, Kim Y, Zheng Y. Lamins organize the global three-dimensional genome from the nuclear periphery. Molecular cell. September 2018; 71(5):802-815

Afgan E, Jalili V, Goonasekera N, Taylor J, Goecks J. Federated Galaxy: Biomedical Computing at the Frontier. 2018 IEEE 11th International Conference on Cloud Computing (CLOUD). July 2018;:871-874

Grüning B, Chilton J, Köster J, Dale R, Soranzo N, van den Beek M, Goecks J, Backofen R, Nekrutenko A, Taylor J. Practical computational reproducibility in the life sciences. Cell Systems. June 2018; 6(6):631-635