Positions

Research Areas research areas

Overview

  • The MacManes lab is interested in understanding how adaptive evolution has shaped animal (mostly mammals, birds, and amphibians) diversity. We are particularly interested in physiology and genetics, and use modern high-throughput sequencing technologies to better understand this. We have several ongoing projects, including [1] understanding how desert mammals survive without water, [2] neurobiology of parental care in birds, and [3] the genomic architecture of the development of color in poison frogs.
  • Publications

    Academic Article

    Year Title
    2018 Sex-biased transcriptomic response of the reproductive axis to stress.Hormones and Behavior.  100:56-68. 2018
    2018 The Oyster River Protocol: a multi-assembler and kmer approach for de novo transcriptome assembly.PeerJ.  6:e5428. 2018
    2017 Comparative Genomics of Pathogenic and Nonpathogenic Beetle-Vectored Fungi in the Genus Geosmithia.Genome Biology and Evolution.  9:3312-3327. 2017
    2017 Comparative Genomics of Color Morphs In the Coral Montastraea cavernosa.Scientific Reports.  7:16039. 2017
    2017 The Oyster River Protocol: A Multi Assembler and Kmer Approach For de novo Transcriptome Assembly 2017
    2017 Severe acute dehydration in a desert rodent elicits a transcriptional response that effectively prevents kidney injury.American Journal of Physiology - Renal Fluid and Electrolyte Physiology American Journal of Physiology - Renal Physiology.  313:F262-F272. 2017
    2017 Sex-biased transcriptomic response of the reproductive axis to stress 2017
    2017 PALADIN: protein alignment for functional profiling whole metagenome shotgun data.Bioinformatics Computer Applications in the Biosciences.  33:1473-1478. 2017
    2017 Widespread patterns of sexually dimorphic gene expression in an avian hypothalamic-pituitary-gonadal (HPG) axis.Scientific Reports.  7:45125. 2017
    2017 Physiological and biochemical changes associated with acute experimental dehydration in the desert adapted mouse, Peromyscus eremicus.Physiological Reports.  5:e13218-e13218. 2017
    2016 Characterizing the reproductive transcriptomic correlates of acute dehydration in males in the desert-adapted rodent,Peromyscus eremicus 2016
    2016 Widespread patterns of sexually dimorphic gene expression in an avian hypothalamic-pituitary-gonadal (HPG) axis 2016
    2016 Comparative genomics explains the evolutionary success of reef-forming corals.eLife.  5. 2016
    2016 Characterization of a Male Reproductive Transcriptome for Peromyscus eremicus (Cactus mouse) 2016
    2016 PALADIN:Protein Alignment for Functional Profiling Whole Metagenome Shotgun Data 2016
    2016 Physiological and biochemical changes associated with experimental dehydration in the desert adapted cactus mouse, Peromyscus eremicus 2016
    2016 De novo genome assembly of Geosmithia morbida, the causal agent of thousand cankers disease 2016
    2016 Brain Transcriptional Profiles of Male Alternative Reproductive Tactics and Females in Bluegill Sunfish.PLoS ONE.  11:e0167509. 2016
    2016 Characterization of a male reproductive transcriptome for Peromyscus eremicus (Cactus mouse).PeerJ.  4:e2617. 2016
    2016 Characterizing the adult and larval transcriptome of the multicolored Asian lady beetle, Harmonia axyridis.PeerJ.  4:e2098. 2016
    2016 De novo genome assembly of Geosmithia morbida, the causal agent of thousand cankers disease.PeerJ.  4:e1952. 2016
    2015 Establishing evidenced-based best practice for the de novo assembly and evaluation of transcriptomes from non-model organisms 2015
    2015 Characterizing the Adult and Larval Transcriptome of the Multicolored Asian Lady Beetle, Harmonia axyridis 2015
    2015 RNAseq-ing a more integrative understanding of animal behaviorCurrent Opinion in Behavioral Sciences.  6:65-68. 2015
    2015 Optimizing error correction of RNAseq reads 2015
    2014 Characterization of the transcriptome, nucleotide sequence polymorphism, and natural selection in the desert adapted mouse Peromyscus eremicus.PeerJ.  2:e642. 2014
    2014 On the optimal trimming of high-throughput mRNA sequence data.Frontiers in Genetics.  5:13. 2014
    2013 On the optimal trimming of high-throughput mRNAseq data 2013
    2013 De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis.Nature Protocols.  8:1494-1512. 2013
    2013 Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species.GigaScience.  2:10. 2013
    2013 Improving transcriptome assembly through error correction of high-throughput sequence reads.PeerJ.  1:e113. 2013
    2012 Is promiscuity associated with enhanced selection on MHC-DQα in mice (genus Peromyscus)?PLoS ONE.  7:e37562. 2012
    2012 The social brain: transcriptome assembly and characterization of the hippocampus from a social subterranean rodent, the colonial tuco-tuco (Ctenomys sociabilis).PLoS ONE.  7:e45524. 2012
    2011 Museum genomics: low-cost and high-accuracy genetic data from historical specimens.Molecular Ecology Resources.  11:1082-1092. 2011
    2011 Promiscuity in mice is associated with increased vaginal bacterial diversity.Die Naturwissenschaften.  98:951-960. 2011
    2010 When non-coding is non-neutral: the role of CHD1 gene polymorphism in sexing, in phylogenetics and as a correlate of fitness in birdsIbis.  152:223-225. 2010
    2009 Isolation and characterization of polymorphic microsatellite loci from Octodon degus.Molecular Ecology Resources.  9:999-1001. 2009
    Divergent selection and drift shape the genomes of two avian sister species spanning a saline-freshwater ecotoneMolecular Ecology
    Hostile genomic takeover by transposable elements in the Strawberry poison frogGenome Biology
    Transcriptomic analy- ses reveal tissue-specific selection on genes related to apoptotic processes in the subterranean rodent,CtenomyssociabilisMolecular Biology and Evolution

    Conference Proceeding

    Year Title
    2018 Sequencing and Assembly of Field Collected Sponge GenomesIntegrative and Comparative Biology American Zoologist. E424-E424. 2018
    2015 Brain Transcriptional Profiles of Male Alternative Reproductive Tactics and Females in Bluegill SunfishIntegrative and Comparative Biology American Zoologist. E347-E347. 2015

    Patents And Disclosures

    Year Title
    METHODS FOR SEQUENCING NUCLEIC ACID MOLECULES

    Teaching Activities

  • Doctoral Thesis Taught course 2018
  • Genomics and Bioinformatics Taught course 2018
  • Genomics and Bioinformatics Taught course 2018
  • Genomics and Bioinformatics Taught course 2018
  • Rsrch Exp/MCBS Taught course 2018
  • Doctoral Research Taught course 2018
  • Doctoral Research Taught course 2018
  • Principles of Genetics Taught course 2018
  • Principles of Genetics/Honors Taught course 2018
  • Rsrch Exp/MCBS Taught course 2018
  • Undergrad Teaching Experience Taught course 2018
  • Doctoral Research Taught course 2017
  • Doctoral Research Taught course 2017
  • Field Experience Taught course 2017
  • Genomics and Bioinformatics Taught course 2017
  • Genomics and Bioinformatics Taught course 2017
  • Genomics and Bioinformatics Taught course 2017
  • Doctoral Research Taught course 2017
  • Principles of Genetics Taught course 2017
  • Doctoral Research Taught course 2016
  • Genomics and Bioinformatics Taught course 2016
  • Genomics and Bioinformatics Taught course 2016
  • Genomics and Bioinformatics Taught course 2016
  • Doctoral Research Taught course 2016
  • Principles of Genetics Taught course 2016
  • Principles of Genetics Taught course 2016
  • Rsrch Exp/MCBS Taught course 2016
  • Rsrch Exp/MCBS Taught course 2016
  • Undergrad Teaching Experience Taught course 2016
  • Doctoral Research Taught course 2015
  • Genomics and Bioinformatics Taught course 2015
  • Genomics and Bioinformatics Taught course 2015
  • Rsrch Exp/MCBS Taught course 2015
  • Principles of Genetics Taught course 2015
  • Rsrch Exp/MCBS Taught course 2015
  • Adv Rsrch Exp/MCBS Taught course 2014
  • Genomics and Bioinformatics Taught course 2014
  • Principles of Genetics Taught course 2014
  • Rsrch Exp/MCBS Taught course 2014
  • Rsrch Exp/MCBS Taught course 2014
  • Education And Training

  • A.A.S. Nursing, Broome Comm College
  • B.S. Natural Resources, University of Michigan
  • Ph.D. Integrative Biology, University of California - Berkeley
  • Full Name

  • Matthew Macmanes