TimeLogic,
Applications

Metagenomics

The emerging area of metagenomics enables scientists to explore species diversity in a host of challenging environments, such as ocean water at a particular longitude, latitude and depth; copper-mine runoff that measures pH 1; and the human gut or mouth.

In collaboration with a customer at The Salk Institute, TimeLogic® provided access to an 8-card DeCypher® system for analysis of the Global Ocean Survey sequence data. After one month of test searching and two weeks of continuous analysis time, over 30 million sequences were compared to a battery of protein classification databases (Pfam, TIGRfam, and Superfamily) using Hidden Markov Model analysis methods.

Related Scientific Citations

Below is a short list of some recent DeCypher citations for Metagenomics. For the complete list, please vist our citations page here.

  1. Analysis of 23S rRNA genes in metagenomes-A case study from the Global Ocean Sampling Expedition
    Pelin Yilmaza, Renzo Kottmanna, Elmar Pruessea, Christian Quasta and Frank Oliver Glöckner
  2. Applying graph theoretic approaches to microbial metagenomes: ecological perspectives on function.
    Wolfgang Hankeln, Pier Luigi Buttigieg, Ivaylo Kostadinov, Renzo Kottmann, Pelin Yilmaz, Melissa Beth Duhaime, and Frank Oliver Glöckner.
  3. Metagenomic Analysis of Lysogeny in Tampa Bay: Implications for Prophage Gene Expression
    Lauren McDaniel, Mya Breitbart, Jennifer Mobberley, Amy Long, Matthew Haynes, Forest Rohwer, and John H. Paul
  4. Structural and Functional Diversity of the Microbial Kinome
    Kannan N, Taylor SS, Zhai Y, Venter JC, Manning G
  5. The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families
    Shibu Yooseph, Granger Sutton, Douglas B. Rusch, Aaron L. Halpern, Shannon J. Williamson, Karin Remington, Jonathan A. Eisen, Karla B. Heidelberg, Gerard Manning, Weizhong Li, Lukasz Jaroszewski, Piotr Cieplak, Christopher S. Miller, Huiying Li, Susan T. Mashiyama, Marcin P. Joachimiak, Christopher van Belle, John-Marc Chandonia, David A. Soergel, Yufeng Zhai, Kannan Natarajan, Shaun Lee, Benjamin J. Raphael, Vineet Bafna, Robert Friedman, Steven E. Brenner, Adam Godzik, David Eisenberg, Jack E. Dixon, Susan S. Taylor, Robert L. Strausberg, Marvin Frazier, J. Craig Venter