Matthew MacManes

Genome Enabled Biology
Phone: (603) 862-4052
Office: Molecular, Cellular & Biomedical Sciences, Gregg Hall Room 434, Durham, NH 03824
Pronouns: He/him/his

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.


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

Research Interests

  • Animal Behavior/Ethology
  • Bioinformatics
  • Evolutionary Biology
  • Functional Genomics
  • Genomics
  • Mammalogy
  • Transcriptomics
  • Vertebrate Physiology

Courses Taught

  • 508: Human Anatomy & Physiology II
  • 705/805: Population Genetics
  • 725/825: Population Genetics Lab
  • 999: Doctoral Thesis
  • GEN 604: Principles of Genetics/Honors
  • GEN 705: Population Genetics
  • GEN 705/805: Population Genetics
  • GEN 711/811: Genomics and Bioinformatics
  • GEN 725/825: Population Genetics Lab
  • GEN 790: Undergrad Teaching Experience
  • GEN 795W: Investigations in Genetics
  • GEN 799H: Honors Senior Thesis
  • GEN 805: Population Genetics
  • GEN 999: Doctoral Research
  • INCO 590: Rsrch Exp/MCBS
  • INCO 790: Adv Rsrch Exp/MCBS
  • MCBS 913: Applied Bioinformatics
  • MCBS 999: Doctoral Thesis
  • MESB 999: Doctoral Research

Selected Publications

Rogers, R. L., Zhou, L., Chu, C., Marquez, R., Corl, A., Linderoth, T., . . . Nielsen, R. (2018). Genomic Takeover by Transposable Elements in the Strawberry Poison Frog. MOLECULAR BIOLOGY AND EVOLUTION, 35(12), 2913-2927. doi:10.1093/molbev/msy185

MaManes, M. D. (2018). The Oyster River Protocol: a multi-assembler and kmer approach for de novo transcriptome assembly. PEERJ, 6. doi:10.7717/peerj.5428

Calisi, R. M., Austin, S. H., Lang, A. S., & MacManes, M. D. (2018). Sex-biased transcriptomic response of the reproductive axis to stress. HORMONES AND BEHAVIOR, 100, 56-68. doi:10.1016/j.yhbeh.2017.11.011

MacManes, M. D. (2017). Severe acute dehydration in a desert rodent elicits a transcriptional response that effectively prevents kidney injury. AMERICAN JOURNAL OF PHYSIOLOGY-RENAL PHYSIOLOGY, 313(2), F262-F272. doi:10.1152/ajprenal.00067.2017

Calisi, R., Austin, S., Lang, A., & MacManes, M. (2017). Sex-biased transcriptomic response of the reproductive axis to stress. doi:10.1101/152801

Westbrook, A., Ramsdell, J., Schuelke, T., Normington, L., Bergeron, R. D., Thomas, W. K., & MacManes, M. D. (2017). PALADIN: protein alignment for functional profiling whole metagenome shotgun data. BIOINFORMATICS, 33(10), 1473-1478. doi:10.1093/bioinformatics/btx021