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.

Recent Publications

Viets K, Sauria MEG, Chernoff C, Rodriguez Viales R, Echterling M, Anderson C, Tran S, Dove A, Goyal R, Voortman L, Gordus A, Furlong EEM, Taylor J, Johnston RJ. “Characterization of Button Loci that Promote Homologous Chromosome Pairing and Cell-Type-Specific Interchromosomal Gene Regulation”. Developmental Cell. 2019 November; 51(3):341-356.e7. doi:10.1016/j.devcel.2019.09.007

Uritskiy G, Getsin S, Munn A, Gomez-Silva B, Davila A, Glass B, Taylor J, DiRuggiero J. “Halophilic microbial community compositional shift after a rare rainfall in the Atacama Desert”. The ISME Journal. 2019 July; 13:2737–2749. doi:10.1038/s41396-019-0468-y

Jalili V, Afgan E and Taylor J and Goecks, J. “Cloud bursting galaxy: federated identity and access management”. Bioinformatics. 2019 June; doi:10.1093/bioinformatics/btz472

Yardımcı GG, Ozadam H, Sauria MEG, Ursu O, Yan KK, Yang T, Chakraborty A, Kaul A, Lajoie BR, Song F, Zhan Y, Ay F, Gerstein M, Kundaje A, Li Q, Taylor J, Yue F, Dekker J, Noble WS. “Measuring the reproducibility and quality of Hi-C data”. Genome Biology. 2019 March; 20:57. doi:10.1186/s13059-019-1658-7

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. 2018 October; 362(6411):eaau6348. doi:10.1126/science.aau6348

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