Microbial Program at JGI-Home

Informatics Publications

2010

  1. The genomes online database (GOLD) in 2009: status of genomic and metagenomics projects and their associated metadata. Liolios, K, Chem, IM, Mavromatis, K et al. Nucleic Acids Research. 2010; 38, Database Issue.
  2. GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes. Pati, A, Ivanova, NN, Mikhailova N, et al. Nature Methods. 2010; 7(6): 455-457.
  3. A catalog of reference genomes for the Human Microbiome. Nelson, KE, Weinstock, GM, et al. Sceince. 2010: 328: 994-999.
  4. The Integrated Microbial Genomes system: an expanding comparative analysis resource. Markowitz, VM, Chen, IA, Palaniappan K, et al. Nucleic Acids Research 2010; 38, Database Issue

2009

  1. Integration of phenotypic metadata and protein similarity in Archaea using a spectral bipartitioning approach. Hooper, SD, Anderson, IJ, Pati, A, Dalevi, D, Mavromatis, K, Kyrpides, NC. Nucleic Acids Research. 2009; 37(7):2096-2104
  2. IMG ER: A System for Microbial Genome Annotation Expert Review and Curation. Markowitz, VM., Mavromatis, K., Ivanova, N. et al. Bioinformatics. 2009; 25(17):2271-2278.
  3. Standard Operating Procedure for the Annotations of Microbial Genomes by the Production Genomic Facility of the DOE JGI. Mavromatis, K., Ivanova, N.N. et al. Standards in Genomic Sciences. 2009; 1(1).
  4. Gene Context Analysis in the Integrated Microbial Genomes (IMG) Data Management System. Mavromatis, K. et al. PLoS ONE. 2009; 4(11): e7979.

2008

  1. The Integrated Microbial Genomes (IMG) system in 2007: data content and analysis tool extensions. Markowitz, VM, Szeto, E, Palaniappan, K, Grechkin, Y, Chu, K, Chen, I-M, Dubchak, I, Anderson, I, Lykidis, A, Mavromatis, K, Ivanova, N, Kyrpides, NC. Nucleic Acids Research. 2008; 36.
  2. Toward an Online Repository of Standard Operating Procedures (SOPs) for (Meta)genomic Annotation. Angiuoli, SV, Gusmman, A, Klimke, W, Cochrane, G, Field, D, Garrity, G, Kodira, CD, Kyrpides, NC, Madupu, R, Markowitz, VM, Tatusova, T, Thomson, N, White, O. OMICS. 2008; 12 (2)..
  3. Habitat-Lite: A GSC Case Study Based on Free Text Terms for Environmental Metadata. Hirschman, L, Clark, C, Cohen, B, Mardis, S, Luciano, J, Kottmann, R, Cole, J, Markowitz, VM, Kyrpides, NC, Field, D. OMICS. 2009; 12 (2).

2007

  1. Microbial Genome Resources. Markowitz, VM. Current Opinion in Biotechnology. 2007; 18(3): 267-272.
  2. Comparative Genome Analysis in the Integrated Microbial Genomes (IMG) System. Chapter in Comparative Genomics Vol. 1. Markowitz, VM and Kyrpides, NC. Methods Molecular Biology. 2007; 395, 35-56.

2006

  1. The Integrated Microbial Genomes (IMG) system. Markowitz VM, Korzeniewski F, Palaniappan K, Szeto E, Werner G, Padki A, Zhao X, Dubchak I, Hugenholtz P, Anderson I, Mavromatis K, Ivanova N, Kyrpides NC. Nucleic Acids Research. 2006; 34: D344-D348.

2005

  1. The Integrated Microbial Genomes (IMG) System, A Case Study in Biological Data Management (.pdf). Markowitz VM, Korzeniewski F, Palaniappan K, Szeto E, Ivanova N, Kyrpides NC. Proc. of 31st Int. Conf. on Very Large Data Bases.