Publications by authors named "Andrew D Fernandes"

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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.
Andrew D Fernandes, Jennifer Ns Reid, Jean M Macklaim, Thomas A McMurrough, David R Edgell

Microbiome· June 2014

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

PLoS One· January 2014

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

Microbiome· April 2013

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

Proc Natl Acad Sci U S A· November 2012

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

PLoS One· February 2012

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

Algorithms Mol Biol· November 2010

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

PLoS One· October 2010

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Deep sequencing of the vaginal microbiota of women with HIV.
Ruben Hummelen, Andrew D Fernandes, Jean M Macklaim, Russell J Dickson, John Changalucha

PLoS One· August 2010

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

PLoS One· June 2010

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

Mol Biol Evol· May 2010

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

Bioinformatics· May 2010

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

Nucleic Acids Res· April 2010

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

Bioinformatics· October 2008

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

BMC Genomics· October 2008

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Biochemical and functional evidence of p53 homology is inconsistent with molecular phylogenetics for distant sequences.
Andrew D Fernandes, William R Atchley

J Mol Evol· July 2008

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Gaussian quadrature formulae for arbitrary positive measures.
Andrew D Fernandes, William R Atchley

Evol Bioinform Online· February 2007

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Solving the protein sequence metric problem.
William R Atchley, Jieping Zhao, Andrew D Fernandes, Tanja Drüke

Proc Natl Acad Sci U S A· May 2005

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Sequence signatures and the probabilistic identification of proteins in the Myc-Max-Mad network.
William R Atchley, Andrew D Fernandes

Proc Natl Acad Sci U S A· May 2005

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