Matthew MacManes, Ph.D.

Matthew MacManes, Ph.D.

Assistant Professor, Undergraduate Program Coordinator

Educational Background:

Ph.D., University of California, Berkeley. Berkeley, CA, Integrative Biology, 2011
AAS, Broome Community College. Binghamton, NY, Nursing 1999
B.S., Universty of Michigan. Ann Arbor, MI, Natural Resources 2005

General Area of Interest and/or Specialty:

Genomics, Genome and Transcriptome Assembly, Population Genetics, Evolution

Description of Current Research and/or Professional Activities: 

For biologists interested in understanding the relationship between fitness, genotype, and phenotype, these are exciting times. New sequencing technologies now afford evolutionary biologists an unprecedented opportunity to gain a deep understanding of genome level processes that together, underlie evolutionary change. My primary research interests involve leveraging these new technologies to better understand adaptation. One of my main interests is in understanding how natural selection has acted on desert animals, allowing them to survive intense heat and extreme drought.

I am currently in the process of bringing the Desert to Durham-- I'm constructing an environmental chamber that will replicate desert conditions and will maintain a colony of desert mice (Peromyscus eremicus). Through careful manipulation of environmental conditions, measurement of physiological state, and Illumina sequencing I'll begin to better understand how these animals survive despite never drinking water. I'm looking for talented students to help with all aspects of the project, from animal care to molecular lab work, to work analyzing sequence data. Please contact me if interested! 

In addition to this project, I'm also involved in several other projects-- Understanding the genomics of color polymorphism in Dendrobatid Frogs (Poison Dart Frogs) and The Genomics of mammalian social behavior to name a few. I also work on some purely computational projects including continued development of the de novo transcriptome assembler Trinity, and other projects developing pipelines for the optimal analysis of Illumina sequence data.   


  1. MacManes, M.D. (2014) On the optimal trimming of high-throughput mRNA sequence data. Front. Genet. 5:13. doi: 10.3389/fgene.2014.00013
  2. M. D. MacManes and M.B. Eisen.  Characterization of the transcriptome, nucleotide sequence polymorphism, and natural selection in the desert adapted mouse Peromyscus eremicus.  Peer J
  3. MacManes, M. D. and M. B. Eisen (2013) Improving transcriptome assembly through error correction of high-throughput sequence reads. PeerJ 1:e113
  4. Korf, I., K. Bradham, M. D. MacManes and 89 others 2013 Assemblathon 2: genome assembly in three vertebrate species. GigaScience 2013, 2:10
  5. Haas, B., A. Papanicolaou, Regev, A., M. D. MacManes and others 2012 De novo transcript sequence reconstruction from RNA-Seq: reference generation and analysis with Trinity. Nature Protocols 8, 1494–1512 (2013)
  6. MacManes, M. D. (2013) On the accurate description of social and genetic mating systems. PeerJ PrePrints 1:e10v1
  7. MacManes, M. D. and E. A. Lacey (2012). The social brain: Transcriptome assembly and characterization of the hippocampus from a social subterranean rodent, the tuco-tuco (Ctenomys sociabilis). PLOS ONE 7(9): e45524.
  8. MacManes, M. D. and E. A. Lacey (2012). Is Promiscuity Associated with Enhanced Selection on MHC-DQ? in Mice (genus Peromyscus)? PLOS ONE 7(5): e37562.
  9. MacManes, M. D. (2011). Promiscuity in mice is associated with increased Vaginal Bacterial Diversity. Naturwissenschaften 98: 951–960.  PMID.
  10. Rowe, K., S. Singhal, M. D. MacManes, J. Ayroles, T. L. Morelli, E. M. Rubridge, K. Bi, and C. C. Moritz. (2011) Museum genomics: Low cost and high accuracy genetic data from historical specimens. Molecular Ecology Resources. 
  11. Benedict, L., M. D. MacManes, J. Fuchs and R. C. K. Bowie, 2010 When non-coding is non- neutral: the role of CHD1 gene polymorphism in sexing, in phylogenetics and as a correlate of fitness in birds. Ibis: 1-3.
  12. Quan, Y. F., M. D. MacManes, L. A. Ebensperger, E. A. Lacey and L. D. Hayes, 2009 Isolation and characterization of polymorphic microsatellite loci from Octodon degus. Molecular Ecology Resources: 3.
Matthew McManes
Gregg Hall 434
Durham, NH 03824
(603) 862-4052