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      The composition and stability of the vaginal microbiota of normal pregnant women is different from that of non-pregnant women.

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          Abstract

          This study was undertaken to characterize the vaginal microbiota throughout normal human pregnancy using sequence-based techniques. We compared the vaginal microbial composition of non-pregnant patients with a group of pregnant women who delivered at term.

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          Metagenomic biomarker discovery and explanation

          Nicola Segata, Jacques Izard, Levi Waldron … (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, genes, or pathways that consistently explain the differences between two or more microbial communities, which is a central problem to the study of metagenomics. We extensively validate our method on several microbiomes and a convenient online interface for the method is provided at http://huttenhower.sph.harvard.edu/lefse/.
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            Differential expression analysis for sequence count data

            Simon Anders, Wolfgang Huber (2010)
            High-throughput sequencing assays such as RNA-Seq, ChIP-Seq or barcode counting provide quantitative readouts in the form of count data. To infer differential signal in such data correctly and with good statistical power, estimation of data variability throughout the dynamic range and a suitable error model are required. We propose a method based on the negative binomial distribution, with variance and mean linked by local regression and present an implementation, DESeq, as an R/Bioconductor package.
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              UCHIME improves sensitivity and speed of chimera detection

              Robert Edgar, Brian Haas, Jose C. Clemente … (2011)
              Motivation: Chimeric DNA sequences often form during polymerase chain reaction amplification, especially when sequencing single regions (e.g. 16S rRNA or fungal Internal Transcribed Spacer) to assess diversity or compare populations. Undetected chimeras may be misinterpreted as novel species, causing inflated estimates of diversity and spurious inferences of differences between populations. Detection and removal of chimeras is therefore of critical importance in such experiments. Results: We describe UCHIME, a new program that detects chimeric sequences with two or more segments. UCHIME either uses a database of chimera-free sequences or detects chimeras de novo by exploiting abundance data. UCHIME has better sensitivity than ChimeraSlayer (previously the most sensitive database method), especially with short, noisy sequences. In testing on artificial bacterial communities with known composition, UCHIME de novo sensitivity is shown to be comparable to Perseus. UCHIME is >100× faster than Perseus and >1000× faster than ChimeraSlayer. Contact: robert@drive5.com Availability: Source, binaries and data: http://drive5.com/uchime. Supplementary information: Supplementary data are available at Bioinformatics online.
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                Author and article information

                Journal
                Journal ID (iso-abbrev): Microbiome
                Title: Microbiome
                Publisher: Springer Science and Business Media LLC
                ISSN: 2049-2618
                ISSN (Print): 2049-2618
                Publication date (Electronic): February 03 2014
                Volume: 2
                Issue: 1
                Affiliations
                [1 ] Perinatology Research Branch, Program for Perinatal Research and Obstetrics, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD and, Detroit, MI, USA. romeror@mail.nih.gov.
                Article
                Publisher Item ID: 2049-2618-2-4
                DOI: 10.1186/2049-2618-2-4
                PMC ID: 3916806
                PubMed ID: 24484853
                SO-VID: 8b05a8ba-7dc7-4165-8c87-35b6ed831da6
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