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Matthew MacManes
PeerJ Author & Reviewer
880 Points

Contributions by role

Author 775
Preprint Author 70
Reviewer 35
Preprint Feedback 15

Contributions by subject area

Bioinformatics
Computational Biology
Genomics
Computational Science
Zoology
Mycology
Evolutionary Studies
Genetics
Animal Behavior
Neuroscience

Matthew MacManes

PeerJ Author & Reviewer

Summary

Animal Behavior Bioinformatics Computational Biology Evolutionary Studies Genomics

Editing Journals

Past or current institution affiliations

UC Berkeley
University of New Hampshire

Work details

Asst. Professor

University of New Hampshire

Websites

  • Lab

PeerJ Contributions

  • Articles 6
  • Preprints 2
  • Feedback 2
  • Answers 1
August 3, 2018
The Oyster River Protocol: a multi-assembler and kmer approach for de novo transcriptome assembly
Matthew D. MacManes
https://doi.org/10.7717/peerj.5428 PubMed 30083482
October 27, 2016
Characterization of a male reproductive transcriptome for Peromyscus eremicus (Cactus mouse)
Lauren L. Kordonowy, Matthew D. MacManes
https://doi.org/10.7717/peerj.2617 PubMed 27812417
June 14, 2016
Characterizing the adult and larval transcriptome of the multicolored Asian lady beetle, Harmonia axyridis
Lindsay A. Havens, Matthew D. MacManes
https://doi.org/10.7717/peerj.2098 PubMed 27326374
May 2, 2016
De novo genome assembly of Geosmithia morbida, the causal agent of thousand cankers disease
Taruna A. Schuelke, Anthony Westbrook, Kirk Broders, Keith Woeste, Matthew D. MacManes
https://doi.org/10.7717/peerj.1952 PubMed 27168971
October 28, 2014
Characterization of the transcriptome, nucleotide sequence polymorphism, and natural selection in the desert adapted mouse Peromyscus eremicus
Matthew D. MacManes, Michael B. Eisen
https://doi.org/10.7717/peerj.642 PubMed 25374784
July 23, 2013
Improving transcriptome assembly through error correction of high-throughput sequence reads
Matthew D. MacManes, Michael B. Eisen
https://doi.org/10.7717/peerj.113 PubMed 23904992
January 21, 2016 - Version: 1
De novo genome assembly of Geosmithia morbida, the causal agent of thousand cankers disease
Taruna Aggarwal, Anthony Westbrook, Kirk Broders, Keith Woeste, Matthew D MacManes
https://doi.org/10.7287/peerj.preprints.1671v1
April 23, 2013 - Version: 1
On the accurate description of social and genetic mating systems
Matthew D MacManes
https://doi.org/10.7287/peerj.preprints.10

Provided feedback on

20 Mar 2014

Brain transcriptome sequencing and assembly of three songbird model systems for the study of social behavior

Chris et. al., I would consider deemphasizing (e.g. eliminating) N50 as a way to evaluate assembly quality. There is plenty of evidence that maximizing N50 may lead us astray, give...

05 Nov 2014

Transcriptome analyses of Anguillicola crassus from native and novel hosts

If I were reviewing (or reading) this manuscript, I'd want to know some more details about how you did your assembly (flags used in Trinity for instance). Also, were raw reads real...

1 Answer

0
Where is GRCm37.71 available from?