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Unifying the analysis of high-throughput sequencing datasets: characterizing RNA-seq, 16S rRNA gene sequencing and selective growth experiments by compositional data analysis
- A. Fernandes, J. Reid, Jean M. Macklaim, T. A. McMurrough, D. R. Edgell, G. Gloor
- 5 May 2014
Statistical analysis of high-throughput sequencing datasets composed of per feature counts showed that the ALDEx2 R package is a simple and robust tool, which can be applied to RNA-seq, 16S rRNA gene sequencing and differential growth datasets, and by extension to other techniques that use a similar approach.
ANOVA-Like Differential Expression (ALDEx) Analysis for Mixed Population RNA-Seq
ALDEx, an ANOVA-like differential expression procedure, is developed to identify genes with greater between- to within-condition differences and it is shown that the presence of differential expression and the magnitude of these comparative differences can be reasonably estimated with even very small sample sizes.
Solving the protein sequence metric problem.
- W. Atchley, Jieping Zhao, A. Fernandes, Tanja Drüke
- BiologyProceedings of the National Academy of Sciences…
- 3 May 2005
Multivariate statistical analyses on almost 500 amino acid attributes are used to produce a small set of highly interpretable numeric patterns of amino acid variability that reflect polarity, secondary structure, molecular volume, codon diversity, and electrostatic charge.
Comparative meta-RNA-seq of the vaginal microbiota and differential expression by Lactobacillus iners in health and dysbiosis
- Jean M. Macklaim, A. Fernandes, J. M. Di Bella, John A Hammond, G. Reid, G. Gloor
- 12 April 2013
A proof-of-principle analysis is presented to uncover the function of the microbiota using meta-RNA-seq to uncover genes and pathways that potentially differentiate healthy vaginal microbial communities from those in the dysbiotic state of bacterial vaginosis.
Microbiome Profiling by Illumina Sequencing of Combinatorial Sequence-Tagged PCR Products
A low-cost, high-throughput microbiome profiling method that uses combinatorial sequence tags attached to PCR primers that amplify the rRNA V6 region is developed, showing that the short reads are sufficient to assign organisms to the genus or species level in most cases.
Deep Sequencing of the Vaginal Microbiota of Women with HIV
The vaginal microbiota among women living with HIV in Sub-Saharan Africa constitutes several profiles associated with a normal microbiota or BV, and recurrence of BV frequently constitutes a different BV-associated profile than before antibiotic treatment.
Side-by-Side Comparison of Five Commercial Media Systems in a Mouse Model: Suboptimal In Vitro Culture Interferes with Imprint Maintenance1
Comparing side-by-side comparisons of five commercial embryo culture systems shows that embryo culture in all commercial media systems resulted in imprinted methylation loss compared to in vivo-derived embryos, although some media systems were able to maintain imprintedmethylation levels more similar to those of in vitro embryos in comparison to embryos cultured in Whitten medium.
Functionally compensating coevolving positions are neither homoplasic nor conserved in clades.
We demonstrated that a pair of positions in phosphoglycerate kinase that score highly by three nonparametric covariation measures are important for function even though the positions can be occupied…
Identifying and Seeing beyond Multiple Sequence Alignment Errors Using Intra-Molecular Protein Covariation
It is demonstrated that removing alignment errors due to 1) improper structure alignment, 2) the presence of paralogous sequences, and 3) partial or otherwise erroneous sequences, improves contact prediction by covariation analysis, providing increased confidence in contact prediction when analyzing alignments with erroneous regions.
Sequence signatures and the probabilistic identification of proteins in the Myc-Max-Mad network.
A small set of amino acid sites from the N-terminal portion of the basic helix-loop-helix (bHLH) domain are described that provide very accurate sequence signatures for the Myc-Max-Mad transcription factor network and three of its member proteins.