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Publications

  1. Markowitz, V.M., Korzeniewski, F., Palaniappan, K., Szeto, E., Ivanova, N., and Kyrpides, N. “The Integrated Microbial Genomes (IMG) System, A Case Study in Biological Data Management”, Proc. of 31st Int. Conf. on Very Large Data Bases, August 2005.
  2. Markowitz, V.M., Korzeniewski, F., Palaniappan, K., Szeto, E., et al. ”The Integrated Microbial Genomes (IMG) System”, Nucleic Acids Research 34, Special Database Issue, D344-D348, 2006.
  3. Markowitz, V.M., Ivanova, N., Korzeniewski, F., Palaniappan, K., Szeto, E., et al. ”An Experimental Metagenome Data Management and Analysis System”. Bioinformatics 22(14), 359-367, 2006.
  4. Markowitz, V.M. and Kyrpides, N. “Comparative Genome Analysis in the Integrated Microbial Genomes (IMG) System”, chapter in Comparative Genomics Vol. 1, Methods Molecular Biology 395, 35-56.
  5. Markowitz, V.M. “Microbial Genome Resources”. Current Opinion in Biotechnology 2007, 18(3), 267-272.
  6. Markowitz, V.M., Szeto, E.,Palaniappan, K., et al. ”The Integrated Microbial Genomes (IMG) System in 2007: data content and analysis tools extensions”, Nucleic Acids Research 36, Special Issue on Databases, D528-D533, 2008.
  7. Markowitz, V.M., Ivanova, N., Szeto, E., et al. ”IMG/M: a data management and analysis system for metagenomes”, Nucleic Acids Research 36, Special Issue on Databases, D534-D538, 2008.
  8. Dalevi, D. SeSantis, T.Z., Fredslund, J., Anderson, G.L., Markowitz, V.M., and Hugenholtz, P., “automated group assignment in large phylogenetic trees using GRUNT”, BMC Bioinformatics 8(1), 2007.
  9. Dalevi D., Ivanova, N.N., Mavromatis, K., Hooper, S., Szeto, E., Hugenholtz, P., Kyrpides, N.C., and Markowitz, V.M. Annotation of metagenome short reads using proxygenes. Bioinformatics, 2008.
  10. Angiuoli, S.V., Gusmman, A., Klimke, W., Cochrane, G., Field, D., Garrity, G., Kodira, C.D., Kyrpides, N.C., Madupu, R., Markowitz, V.M., Tatusova, T., Thomson, N., White, O. (2008) Toward an Online Repository of Standard Operating Procedures (SOPs) for (Meta)genomic Annotation, OMICS 12 (2).
  11. Hirschman, L., Clark, C., Cohen, B., Mardis, S., Luciano, J., Kottmann, R., Cole, J., Markowitz, V.M., Kyrpides, N.C., Field, D. (2008) Habitat-Lite: A GSC Case Study Based on Free Text Terms for Environmental Metadata, OMICS 12 (2).
  12. Sharon, I., Pati, A., Markowitz, V.M., Pinter R.Y. ”A Statistical Framework for the Functional Analysis of Metagenomes”, Lecture Notes in Computer Science 5541, RECOMB 2009, pp. 570-585, 2009.
  13. Markowitz, V.M., Mavromatis, K., Ivanova, N. et al. ”IMG ER: A System for Microbial Genome Annotation Expert Review and Curation”, Bioinformatics 2009.
  14. Mavromatis, K., Chu, K., Ivanova, N.N., Hooper, S., Markowitz, V.M., Kyrpides, N.C. Mavromatis, K. et al. (2009) Gene Context Analysis in the Integrated Microbial Genomes (IMG) Data Management System, PLoS ONE 4(11): e7979.
  15. Markowitz, V.M. et al. "The integrated microbial genomes system: an expanding comparative analysis resource", Nucleic Acids Research 2010, Vol 38, Database issue D382-390K.
  16. Liolios, K. et al., "The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata", Nucleic Acids Research 2010, Vol 38, Database issue D346-354.
  17. Markowitz VM, Chen IMA, Palaniappan K, Chu K, Szeto E, et al. (2012) IMG: the integrated microbial genomes database and comparative analysis system, Nucleic Acids Res., 40: D115-D122.
  18. Markowitz VM, Chen IMA, Chu K, Szeto E, Palaniappan K, et al. (2012) IMG/M: the integrated metagenome data management and comparative analysis system, Nucleic Acid Res., 40: D123-129.
  19. Markowitz VM, Chen IMA, Chu K, Szeto E, Palaniappan K, et al. (2012) IMG/M-HMP: A metagenome comparative analysis system for the Human Microbiome Project, PLoS ONE 7(7): e40151.
  20. The Human Microbiome Project Consortium, (2012) Structure, function and diversity of the healthy human microbiome, Nature 486: 207-214.
  21. The Human Microbiome Project Consortium, (2012) A framework for human microbiome research, Nature 486: 215-221.
  22. Pagani, I, Liolios, K, Jansson, J, Chen, IMA, Smironova, T, Nosrat, B, Markowitz, VM, and Kyrpides, NC. (2012) The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res., 40: D571-D579.
  23. Chen IMA, Markowitz VM, Chu K, Anderson I, Mavromatis K, Kyrpides NC, Ivanova NN (2013) Improving microbial genome annotations in an integrated database context, accepted for publication PLoS ONE.

BDMTC members have also contributed to and appear as co-authors on genome and metagenome analysis publications: see http://img.jgi.doe.gov/publication.html