Lawrence Berkeley National Lab
Environmental Genomics & Systems Biology
Principal Investigator
jmchandonia@lbl.gov
(510) 292-9495
John-Marc Chandonia is a computational biologist with a background in protein structure prediction, structure classification, and evolutionary analysis of proteins. His team develops novel methods to analyze genome-scale datasets in order to predict biological networks and annotate gene functions. He leads the ENIGMA Data Management team, working on the Data Clearing House, a platform that we developed to organize all ENIGMA data in a FAIR way (the FAIR principles require that all data be Findable, Accessible, Interoperable and Reusable, both for machines and for people). FAIR data management is critical to enabling the large-scale team science that distinguishes projects like ENIGMA from the kind of research that can be conducted in individual labs. This features much smoother uploading and plotting of multi-dimensional datasets, to fit into the ENIGMA data management ecosystem.
Relevant Publications
Examining adaptations of a dominant bacterial species at a contaminated subsurface site - Leveraging comparative genomics, community analysis, and geochemical data to understand adaptations that facilitate survival of a dominant community member in the contaminated Oak Ridge Reservation subsurface. More →
The Contextual Ontology-based Repository Analysis Library (CORAL) facilitates FAIR ENIGMA datasets - Novichkov, PS*; Chandonia, J-M*; Arkin, AP. (2022) CORAL: A framework for rigorous self-validated data modeling and integrative, reproducible data analysis. GigaScience [DOI]:10.1093/gigascience/giac089 OSTI ID: 1888047 The Contextual Ontology-based Repository Analysis Library (CORAL) platform greatly facilitates adherence to the FAIR principles, including the especially difficult challenge of making heterogeneous datasets Interoperable and Reusable across all parts of a large, long-lasting… More →
Host Bacteria Are Helped By Viral Genomes - Kothari, Ankita.; S. Roux, H. Zhang, A. Prieto, J-M Chandonia, S. Spencer, X. Wu, A M. Deutschbauer, A. P. Arkin, E J. Alm, R. Chakraborty, A Mukhopadhyay (2021) Ecogenomics of groundwater viruses suggests niche differentiation linked to specific environmental tolerance. mSystems [doi]:1128/mSystems.00537-21 {PMID}: 34184913 PMCID: PMC8269241 OSTI:1807913 Niche Specific Genes from Phage Genomes are Advantageous for Communities of Groundwater Bacteria Ground water… More →