Unifying the analysis of high-throughput sequencing datasets: characterizing RNA-seq, 16S rRNA gene sequencing and selective growth experiments by compositional data analysis von Fernandes, Andrew D, Reid, Jennifer Ns, Macklaim, Jean M, McMurrough, Thomas A, Edgell, David R, Gloor, Gregory B

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Displaying Variation in Large Datasets: Plotting a Visual Summary of Effect Sizes von Gloor, Gregory B., Macklaim, Jean M., Fernandes, Andrew D.

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Microbiome profiling by illumina sequencing of combinatorial sequence-tagged PCR products von Gloor, Gregory B, Hummelen, Ruben, Macklaim, Jean M, Dickson, Russell J, Fernandes, Andrew D, MacPhee, Roderick, Reid, Gregor

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Deep sequencing of the vaginal microbiota of women with HIV von Hummelen, Ruben, Fernandes, Andrew D, Macklaim, Jean M, Dickson, Russell J, Changalucha, John, Gloor, Gregory B, Reid, Gregor

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Comparative meta-RNA-seq of the vaginal microbiota and differential expression by Lactobacillus iners in health and dysbiosis von Macklaim, Jean M, Fernandes, Andrew D, Di Bella, Julia M, Hammond, Jo-Anne, Reid, Gregor, Gloor, Gregory B

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ANOVA-like differential expression (ALDEx) analysis for mixed population RNA-Seq von Fernandes, Andrew D, Macklaim, Jean M, Linn, Thomas G, Reid, Gregor, Gloor, Gregory B

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Solving the Protein Sequence Metric Problem von Atchley, William R., Zhao, Jieping, Fernandes, Andrew D., Drüke, Tanja, Fitch, Walter M.

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No evidence that equations cause impeded communication among biologists von Fernandes, Andrew D

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Identifying and seeing beyond multiple sequence alignment errors using intra-molecular protein covariation von Dickson, Russell J, Wahl, Lindi M, Fernandes, Andrew D, Gloor, Gregory B

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Divalent metal ion differentially regulates the sequential nicking reactions of the GIY-YIG homing endonuclease I-BmoI von Kleinstiver, Benjamin P, Bérubé-Janzen, Wesley, Fernandes, Andrew D, Edgell, David R

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The SWI/SNF protein ATRX co-regulates pseudoautosomal genes that have translocated to autosomes in the mouse genome von Levy, Michael A, Fernandes, Andrew D, Tremblay, Deanna C, Seah, Claudia, Bérubé, Nathalie G

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Sequence Signatures and the Probabilistic Identification of Proteins in the Myc-Max-Mad Network von Atchley, William R., Fernandes, Andrew D., Fitch, Walter M.

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Mutual information is critically dependent on prior assumptions: would the correct estimate of mutual information please identify itself? von Fernandes, Andrew D., Gloor, Gregory B.

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Estimating the evidence of selection and the reliability of inference in unigenic evolution von Fernandes, Andrew D, Kleinstiver, Benjamin P, Edgell, David R, Wahl, Lindi M, Gloor, Gregory B

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Functionally compensating coevolving positions are neither homoplasic nor conserved in clades von Gloor, Gregory B, Tyagi, Gaurav, Abrassart, Dana M, Kingston, Andrew J, Fernandes, Andrew D, Dunn, Stanley D, Brandl, Christopher J

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unified genetic, computational and experimental framework identifies functionally relevant residues of the homing endonuclease I-BmoI von Kleinstiver, Benjamin P, Fernandes, Andrew D, Gloor, Gregory B, Edgell, David R

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Mutual information is critically dependent on prior assumptions: would the correct estimate of mutual information please identify itself? von Fernandes, Andrew D., Gloor, Gregory B.

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Gaussian Quadrature Formulae for Arbitrary Positive Measures von Fernandes, Andrew D., Atchley, William R.

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Site-specific evolutionary rates in proteins are better modeled as non-independent and strictly relative von Fernandes, Andrew D., Atchley, William R.

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Biochemical and Functional Evidence of p53 Homology Is Inconsistent with Molecular Phylogenetics for Distant Sequences von Fernandes, Andrew D, Atchley, William R

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