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I-Min (Amy) Chen

Dr. I-Min Amy Chen, JGI

Dr. I-Min A. Chen received her Ph.D. in Computer Science from University of Southern California. Her research has been focused on semantic and object-oriented data modeling, and biological data management. Amy was one of the co-authors and key developers of the Object-Protocol Model (OPM) data management tools for scientific applications developed at Berkeley Lab. Dr. Chen is currently the Microbiome Computational Resource Lead at JGI, responsible for the data management infrastructure of the Integrated Microbial Genomes (IMG) family of systems. Before joining LBNL in 2006, she was Director of Application Development Systems at Gene Logic, Inc. from 1997 to 2005, responsible for the development of key components of Gene Logic’s flagship Genesis data management platforms for gene expression data, one of the most successful data management systems of their kind, deployed to tens of pharmaceutical and biotech companies.

Education

  • BA, Computer Science, National Taiwan University
  • PhD, Computer Science, University of Southern California

Software

Integrated Microbial Genomes and Microbiomes

Publications

  1. Chen I-MA, Chu K, Palaniappan K, Ratner A, Huang J, Huntemann M, Hajek P, Ritter S, Varghese N, Seshadri R et al. The IMG/M data management and analysis system v.6.0: new tools and advanced capabilities. Nucleic acids research Oct 2020
  2. Roux S, Páez-Espino D, Chen I-MA, Palaniappan K, Ratner A, Chu K, Reddy TBK, Nayfach S, Schulz F, Call L et al. IMG/VR v3: an integrate ecological and evolutionary framework for interrogating genomes of uncultivated viruses. Nucleic acids research Nov 2020
  3. Chen IA, Markowitz V, Palaniappan K, Szeto E, Chu K, Huang J, Ratner A, Pillay M, Hadjithomas M, Huntemann M, Mikhailova N, Ovchinnikova G, Ivanova NN, and  Kyrpides NC. Supporting community annotation and user collaboration in the integrated microbial genomes (IMG) system, BMC Genomics 17:307, doi:10.1186/s12864-016-2629-y, April 2016
  4. Chen IA, Markowitz V, Szeto E, Palaniappan K, and Chu K. Maintaining a Microbial Genome & Metagenome Data Analysis System in an Academic Setting, SSDBM 14, July 2014