Matthew D. MacManes

Assistant Professor
Assistant Professor of Genome Enabled Biology
Office: Molecular, Cellular & Biomedical Sciences, Gregg Hall Room 434, Durham, NH 03824

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

  • BMS 600: Field Experience
  • GEN 604: Principles of Genetics/Honors
  • GEN 711: Genomics and Bioinformatics
  • GEN 790: Undergrad Teaching Experience
  • GEN 999: Doctoral Research
  • INCO 590: Rsrch Exp/MCBS
  • INCO 790: Rsrch Exp/MCBS
  • MCBS 999: Doctoral Thesis
  • MESB 999: Doctoral Research

Selected Publications

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., Austin, S. H., Lang, A. S., Booth, A., Farrar, V., & Calisi, R. M. (2017). Widespread patterns of sexually dimorphic gene expression in an avian hypothalamic–pituitary–gonadal (HPG) axis. Scientific Reports, 7(1). doi:10.1038/srep45125

Schuelke, T. A., Wu, G., Westbrook, A., Woeste, K., Plachetzki, D. C., Broders, K., & MacManes, M. D. (2017). Comparative Genomics of Pathogenic and Nonpathogenic Beetle-Vectored Fungi in the Genus Geosmithia. Genome Biology and Evolution, 9(12), 3312-3327. doi:10.1093/gbe/evx242

Jarett, J. K., MacManes, M. D., Morrow, K. M., Pankey, M. S., & Lesser, M. P. (2017). Comparative Genomics of Color Morphs In the Coral Montastraea cavernosa . Scientific Reports, 7(1). doi:10.1038/s41598-017-16371-9

Bhattacharya, D., Agrawal, S., Aranda, M., Baumgarten, S., Belcaid, M., Drake, J. L., . . . Falkowski, P. G. (2016). Comparative genomics explains the evolutionary success of reef-forming corals. eLife, 5. doi:10.7554/eLife.13288

MacManes, M. D. (2014). On the optimal trimming of high-throughput mRNA sequence data. Frontiers in Genetics, 5. doi:10.3389/fgene.2014.00013

Bradnam, K. R., Fass, J. N., Alexandrov, A., Baranay, P., Bechner, M., Birol, I., . . . Korf, I. F. (2013). Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. GigaScience, 2(1). doi:10.1186/2047-217X-2-10

Haas, B. J., Papanicolaou, A., Yassour, M., Grabherr, M., Blood, P. D., Bowden, J., . . . Regev, A. (2013). De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nature Protocols, 8(8), 1494-1512. doi:10.1038/nprot.2013.084

ROWE, K. E. V. I. N. C., SINGHAL, S. O. N. A. L., MACMANES, M. A. T. T. H. E. W. D., AYROLES, J. U. L. I. E. N. F., MORELLI, T. O. N. I. L. Y. N., RUBIDGE, E. M. I. L. Y. M., . . . MORITZ, C. R. A. I. G. C. (2011). Museum genomics: low-cost and high-accuracy genetic data from historical specimens. Molecular Ecology Resources, 11(6), 1082-1092. doi:10.1111/j.1755-0998.2011.03052.x

Most Cited Publications