Browsing by Author "Waldron, Levi"

Now showing items 1-7 of 7

    • Composition of the Adult Digestive Tract Bacterial Microbiome Based on Seven Mouth Surfaces, Tonsils, Throat and Stool Samples 

      Segata, Nicholas; Haake, Susan Kinder; Mannon, Peter; Lemon, Katherine Paige; Waldron, Levi D.; Gevers, Dirk; Huttenhower, Curtis; Izard, Jacques Georges (BioMed Central, 2012)
      Background: To understand the relationship between our bacterial microbiome and health, it is essential to define the microbiome in the absence of disease. The digestive tract includes diverse habitats and hosts the human ...

    • curatedOvarianData: clinically annotated data for the ovarian cancer transcriptome 

      Ganzfried, Benjamin Frederick; Riester, Markus; Haibe-Kains, Benjamin; Risch, Thomas; Tyekucheva, Svitlana; Jazic, Ina; Wang, Xin Victoria; Ahmadifar, Mahnaz; Birrer, Michael James; Parmigiani, Giovanni; Huttenhower, Curtis; Waldron, Levi D. (Oxford University Press, 2013)
      This article introduces a manually curated data collection for gene expression meta-analysis of patients with ovarian cancer and software for reproducible preparation of similar databases. This resource provides uniformly ...

    • A Guide to Enterotypes across the Human Body: Meta-Analysis of Microbial Community Structures in Human Microbiome Datasets 

      Koren, Omry; Knights, Daniel; Gonzalez, Antonio; Waldron, Levi D.; Segata, Nicola; Knight, Rob; Huttenhower, Curtis; Ley, Ruth E. (Public Library of Science, 2013)
      Recent analyses of human-associated bacterial diversity have categorized individuals into ‘enterotypes’ or clusters based on the abundances of key bacterial genera in the gut microbiota. There is a lack of consensus, ...

    • Metagenomic biomarker discovery and explanation 

      Segata, Nicola; Izard, Jacques; Waldron, Levi; Gevers, Dirk; Miropolsky, Larisa; Garrett, Wendy S.; Huttenhower, Curtis (Springer Science + Business Media, 2011)
      This study describes and validates a new method for metagenomic biomarker discovery by way of class comparison, tests of biological consistency and effect size estimation. This addresses the challenge of finding organisms, ...

    • Metagenomic microbial community profiling using unique clade-specific marker genes 

      Segata, Nicola; Waldron, Levi D.; Ballarini, Annalisa; Narasimhan, Vagheesh; Jousson, Olivier; Huttenhower, Curtis (2012)
      Metagenomic shotgun sequencing data can identify microbes populating a microbial community and their proportions, but existing taxonomic profiling methods are inefficient for increasingly large datasets. We present an ...

    • Microbial Community Function and Biomarker Discovery in the Human Microbiome 

      Abubucker, Sahar; Goll, Johannes; Schubert, Alyxandria M; Cantarel, Brandi L; Rodriguez-Mueller, Beltran; Thiagarajan, Mathangi; Henrissat, Bernard; White, Owen; Kelley, Scott T; Methé, Barbara; Schloss, Patrick D; Gevers, Dirk; Mitreva, Makedonka; Izard, Jacques Georges; Waldron, Levi D.; Zucker, Jeremy Daniel Hofeld; Garrett, Wendy S.; Huttenhower, Curtis; Segata, Nicola (BioMed Central, 2011)

    • Report on emerging technologies for translational bioinformatics: a symposium on gene expression profiling for archival tissues 

      Waldron, Levi D.; Simpson, Peter; Parmigiani, Giovanni; Huttenhower, Curtis (BioMed Central, 2012)
      Background: With over 20 million formalin-fixed, paraffin-embedded (FFPE) tissue samples archived each year in the United States alone, archival tissues remain a vast and under-utilized resource in the genomic study of ...