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http://genomebio.org/

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Scopus Author ID: 26531552200
ResearcherID: B-8303-2011

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Employment (1)

University of New Hampshire: Durham, NH, US

Associate Professor (Molecular, Cellular, and Biomedical Sciences)
Employment
Source: Self-asserted source
Matthew MacManes

Funding (4)

Collaborative Research: Dimensions: Evolutionary Ecology of Sponges and Their Microbiome Drives Sponge Diversity on Coral Reefs

2016-10-01 to 2019-09-30 | Grant
National Science Foundation - Directorate for Geosciences (Arlington, US)
URL: https://grants.uberresearch.com/100000085/1638296/Collaborative-Research-Dimensions-Evolutionary-Ecology-of-Sponges-and-Their-Microbiome-Drives-Sponge-Diversity-on-Coral-Reefs
GRANT_NUMBER: 1638296
Source: Self-asserted source
Matthew MacManes via DimensionsWizard

Collaborative Research: The Neural Basis of Becoming a Parent: From Genotype to Phenotype

2015-07-01 to 2018-06-30 | Grant
National Science Foundation - Directorate for Biological Sciences (Arlington, US)
URL: https://grants.uberresearch.com/100000076/1455960/Collaborative-Research-The-Neural-Basis-of-Becoming-a-Parent-From-Genotype-to-Phenotype
GRANT_NUMBER: 1455960
Source: Self-asserted source
Matthew MacManes via DimensionsWizard

Using genomics to understand physiologic water conservation in desert rodents

2011-07-01 to 2013-08-31 | Grant
National Institute of Diabetes and Digestive and Kidney Diseases (Bethesda, US)
URL: https://grants.uberresearch.com/100000062/F32DK093227/Using-genomics-to-understand-physiologic-water-conservation-in-desert-rodents
GRANT_NUMBER: F32DK093227
Source: Self-asserted source
Matthew MacManes via DimensionsWizard

DISSERTATION RESEARCH: MHC and Mating Systems: Is sexual behavior related to selection on MHC genes?

2009-06-15 to 2011-05-31 | Grant
National Science Foundation - Directorate for Biological Sciences (Arlington, US)
URL: https://grants.uberresearch.com/100000076/0909798/DISSERTATION-RESEARCH-MHC-and-Mating-Systems-Is-sexual-behavior-related-to-selection-on-MHC-genes
GRANT_NUMBER: 0909798
Source: Self-asserted source
Matthew MacManes via DimensionsWizard

Works (50 of 59)

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Page 1 of 2

Impacts of dietary fat on multi tissue gene expression in the desert-adapted cactus mouse

Journal of Experimental Biology
2024-12-15 | Journal article
DOI: 10.1242/jeb.247978
Contributors: Danielle M. Blumstein; Matthew D. MacManes
Source: check_circle
Crossref

High total water loss driven by low-fat diet in desert-adapted mice

Journal of Mammalogy
2024-09-05 | Journal article
DOI: 10.1093/jmammal/gyae093
Contributors: Danielle M Blumstein; Jocelyn P Colella; Ernst Linder; Matthew D MacManes; John Scheibe
Source: check_circle
Crossref

The multi-tissue gene expression and physiological responses of water deprived Peromyscus eremicus

BMC Genomics
2024-08-08 | Journal article
DOI: 10.1186/s12864-024-10629-z
Contributors: Danielle Blumstein; Matthew MacManes
Source: check_circle
Crossref

Impacts of dietary fat on multi tissue gene expression in the desert-adapted cactus mouse

2024-05-05 | Preprint
DOI: 10.1101/2024.05.03.592397
Contributors: Danielle M. Blumstein; Matthew D. MacManes
Source: check_circle
Crossref

When the tap runs dry: The multi-tissue gene expression and physiological responses of water deprivedPeromyscus eremicus

2024-01-24 | Preprint
DOI: 10.1101/2024.01.22.576658
Contributors: Danielle M. Blumstein; Matthew D. MacManes
Source: check_circle
Crossref

When the tap runs dry: the physiological effects of acute experimental dehydration in Peromyscus eremicus

Journal of Experimental Biology
2023-12-01 | Journal article
DOI: 10.1242/jeb.246386
Contributors: Danielle M. Blumstein; Matthew D. MacManes
Source: check_circle
Crossref

When the tap runs dry: The physiological effects of acute experimental dehydration inPeromyscus eremicus

2023-07-03 | Preprint
DOI: 10.1101/2023.07.03.547568
Contributors: Danielle M. Blumstein; Matthew D. MacManes
Source: check_circle
Crossref

High total water loss driven by low-fat diet in desert-adapted mice

2022-04-15 | Preprint
DOI: 10.1101/2022.04.15.488461
Contributors: Danielle M. Blumstein; Jocelyn P. Colella; Ernst Linder; Matthew D. MacManes
Source: check_circle
Crossref

Disentangling environmental drivers of circadian metabolism in desert-adapted mice

Journal of Experimental Biology
2021-09-15 | Journal article
DOI: 10.1242/jeb.242529
Contributors: Jocelyn P. Colella; Danielle M. Blumstein; Matthew D. MacManes
Source: check_circle
Crossref

Feather Gene Expression Elucidates the Developmental Basis of Plumage Iridescence in African Starlings

Journal of Heredity
2021-08-25 | Journal article
DOI: 10.1093/jhered/esab014
Contributors: Dustin R Rubenstein; André Corvelo; Matthew D MacManes; Rafael Maia; Giuseppe Narzisi; Anastasia Rousaki; Peter Vandenabeele; Matthew D Shawkey; Joseph Solomon; Bridgett vonHoldt
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Crossref

Limited Evidence for Parallel Evolution Among Desert-Adapted Peromyscus Deer Mice

Journal of Heredity
2021-05-24 | Journal article
DOI: 10.1093/jhered/esab009
Contributors: Jocelyn P Colella; Anna Tigano; Olga Dudchenko; Arina D Omer; Ruqayya Khan; Ivan D Bochkov; Erez L Aiden; Matthew D MacManes; Beth Shapiro
Source: check_circle
Crossref

Disentangling environmental drivers of circadian metabolism in desert-adapted mice

2020-12-21 | Preprint
DOI: 10.1101/2020.12.18.423523
Contributors: Jocelyn P. Colella; Danielle M. Blumstein; Matthew D. MacManes
Source: check_circle
Crossref

Isolating the role of corticosterone in the hypothalamic-pituitary-gonadal genomic stress response

2020-10-09 | Preprint
DOI: 10.1101/2020.10.08.330209
Contributors: Suzanne H. Austin; Rayna Harris; April M. Booth; Andrew S. Lang; Victoria S. Farrar; Jesse S. Krause; Tyler A. Hallman; Matthew MacManes; Rebecca M. Calisi
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Crossref

A total crapshoot? Evaluating bioinformatic decisions in animal diet metabarcoding analyses

Ecology and Evolution
2020-09 | Journal article
DOI: 10.1002/ece3.6594
Contributors: Devon R. O'Rourke; Nicholas A. Bokulich; Michelle A. Jusino; Matthew D. MacManes; Jeffrey T. Foster
Source: check_circle
Crossref

A linked‐read approach to museomics: Higher quality de novo genome assemblies from degraded tissues

Molecular Ecology Resources
2020-07 | Journal article
DOI: 10.1111/1755-0998.13155
Contributors: Jocelyn P. Colella; Anna Tigano; Matthew D. MacManes
Source: check_circle
Crossref

Signal, bias, and the role of transcriptome assembly quality in phylogenomic inference

2020-07-24 | Other
DOI: 10.1101/2020.07.23.216606
Contributors: Jennifer L Spillane; Troy M LaPolice; Matthew D MacManes; David C Plachetzki
Source: check_circle
Crossref

Limited evidence for parallel evolution among desert adaptedPeromyscusdeer mice

2020-06-30 | Preprint
DOI: 10.1101/2020.06.29.178392
Contributors: Jocelyn P. Colella; Anna Tigano; Olga Dudchenko; Arina D. Omer; Ruqayya Khan; Ivan D. Bochkov; Erez L. Aiden; Matthew D. MacManes
Source: check_circle
Crossref

Comparative and population genomics approaches reveal the basis of adaptation to deserts in a small rodent

Molecular Ecology
2020-04 | Journal article
DOI: 10.1111/mec.15401
Contributors: Anna Tigano; Jocelyn P. Colella; Matthew D. MacManes
Source: check_circle
Crossref

Divergent selection and drift shape the genomes of two avian sister species spanning a saline–freshwater ecotone

Ecology and Evolution
2019-12 | Journal article
DOI: 10.1002/ece3.5804
Contributors: Jennifer Walsh; Gemma V. Clucas; Matthew D. MacManes; W. Kelley Thomas; Adrienne I. Kovach
Source: check_circle
Crossref

Comparative and population genomics approaches reveal the basis of adaptation to deserts in a small rodent

2019-11-26 | Other
DOI: 10.1101/856310
Contributors: Anna Tigano; Jocelyn P. Colella; Matthew D. MacManes
Source: check_circle
Crossref

Stress-mediated convergence of splicing landscapes in male and female Rock Doves

2019-10-08 | Other
DOI: 10.1101/798413
Contributors: Andrew S Lang; Suzanne H Austin; Rayna M Harris; Rebecca M Calisi; Matthew D MacManes
Source: check_circle
Crossref

The Oyster River Protocol: a multi-assembler and kmer approach for de novo transcriptome assembly

PeerJ
2018-08-03 | Journal article
DOI: 10.7717/peerj.5428
Contributors: Matthew D. MacManes
Source: check_circle
Crossref

Transcriptomic analyses reveal tissue-specific selection on genes related to apoptotic processes in the subterranean rodent, Ctenomys sociabilis

2018-01-30 | Other
DOI: 10.1101/256875
Contributors: Andrew Lang; Lauren Kordonowy; Eileen Lacey; Matthew MacManes
Source: check_circle
Crossref

The Oyster River Protocol: A Multi Assembler and Kmer Approach Forde novoTranscriptome Assembly

2017-08-16 | Preprint
DOI: 10.1101/177253
Contributors: Matthew D. MacManes
Source: check_circle
Crossref

Severe acute dehydration in a desert rodent elicits a transcriptional response that effectively prevents kidney injury

American Journal of Physiology-Renal Physiology
2017-08-01 | Journal article
DOI: 10.1152/ajprenal.00067.2017
Contributors: Matthew David MacManes
Source: check_circle
Crossref

Sex-biased transcriptomic response of the reproductive axis to stress

2017-06-20 | Preprint
DOI: 10.1101/152801
Contributors: Rebecca Calisi; Suzanne H. Austin; Andrew S. Lang; Matthew D. MacManes
Source: check_circle
Crossref

Physiological and biochemical changes associated with acute experimental dehydration in the desert adapted mouse, Peromyscus eremicus

Physiological Reports
2017-03 | Journal article
DOI: 10.14814/phy2.13218
Contributors: Lauren Kordonowy; Kaelina D. Lombardo; Hannah L. Green; Molly D. Dawson; Evice A. Bolton; Sarah LaCourse; Matthew D. MacManes
Source: check_circle
Crossref

Severe acute dehydration in a desert rodent elicits a transcriptional response that effectively prevents kidney injury

2017-01-25 | Preprint
DOI: 10.1101/103077
Contributors: MacManes Matthew
Source: check_circle
Crossref

Characterizing the reproductive transcriptomic correlates of acute dehydration in males in the desert-adapted rodent,Peromyscus eremicus

2016-12-21 | Other
DOI: 10.1101/096057
Contributors: Lauren Kordonowy; Matthew MacManes
Source: check_circle
Crossref

Comparative genomics of beetle-vectored fungal pathogens reveals a reduction in genome size and independent evolution of pathogenicity of two tree pathogens

2016-12-13 | Preprint
DOI: 10.1101/093856
Contributors: Taruna A Schuelke; Anthony Westbrook; Keith Woeste; David C. Plachetzki; Kirk Broders; Matthew D. MacManes
Source: check_circle
Crossref

Widespread patterns of sexually dimorphic gene expression in an avian hypothalamic–pituitary–gonadal (HPG) axis

2016-11-03 | Preprint
DOI: 10.1101/085365
Contributors: Matthew D. MacManes; Suzanne H. Austin; Andrew Booth; April Austin; Victoria Farrar; Rebecca M. Calisi
Source: check_circle
Crossref

Comparative genomics explains the evolutionary success of reef-forming corals

eLife
2016-05-24 | Journal article
DOI: 10.7554/eLife.13288
Contributors: Debashish Bhattacharya; Shobhit Agrawal; Manuel Aranda; Sebastian Baumgarten; Mahdi Belcaid; Jeana L Drake; Douglas Erwin; Sylvian Foret; Ruth D Gates; David F Gruber et al.
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Crossref

De novogenome assembly ofGeosmithia morbida, the causal agent of thousand cankers disease

PeerJ
2016-05-02 | Journal article
DOI: 10.7717/peerj.1952
Contributors: Taruna A. Schuelke; Anthony Westbrook; Kirk Broders; Keith Woeste; Matthew D. MacManes
Source: check_circle
Crossref

Characterization of a Male Reproductive Transcriptome for Peromyscus eremicus (Cactus mouse)

2016-04-13 | Other
DOI: 10.1101/048348
Contributors: Lauren Kordonowy; Matthew MacManes
Source: check_circle
Crossref

PALADIN:Protein Alignment for Functional Profiling Whole Metagenome Shotgun Data

2016-04-08 | Preprint
DOI: 10.1101/047712
Contributors: Anthony Westbrook; Jordan Ramsdell; Taruna Aggarwal; Louisa Normington; R. Daniel Bergeron; W. Kelley Thomas; Matthew MacManes
Source: check_circle
Crossref

Physiological and biochemical changes associated with acute experimental dehydration in the desert adapted mouse,Peromyscus eremicus

2016-04-08 | Preprint
DOI: 10.1101/047704
Contributors: Lauren Kordonowy; Kaelina D. Lombardo; Hannah L. Green; Molly Dawson; Evice A. Bolton; Sarah LaCourse; Matthew D. MacManes
Source: check_circle
Crossref

De novo genome assembly of Geosmithia morbida, the causal agent of thousand cankers disease

2016-01-21 | Other
DOI: 10.7287/peerj.preprints.1671
Contributors: Taruna Aggarwal; Anthony Westbrook; Kirk Broders; Keith Woeste; Matthew D MacManes
Source: check_circle
Crossref

De novo genome assembly of Geosmithia morbida, the causal agent of thousand cankers disease

2016-01-21 | Other
DOI: 10.7287/peerj.preprints.1671v1
Contributors: Taruna Aggarwal; Anthony Westbrook; Kirk Broders; Keith Woeste; Matthew D MacManes
Source: check_circle
Crossref

An opinionated guide to the proper care and feeding of your transcriptome

2015 | Report
DOI: 10.1101/035642
Contributors: Matthew D MacManes
Source: Self-asserted source
Matthew MacManes via Crossref Metadata Search
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Characterizing the Adult and Larval Transcriptome of the Multicolored Asian Lady Beetle, Harmonia axyridis

2015 | Report
DOI: 10.1101/034462
Contributors: Lindsay A Havens; Matthew D MacManes
Source: Self-asserted source
Matthew MacManes via Crossref Metadata Search
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RNAseq-ing a more integrative understanding of animal behavior

Current Opinion in Behavioral Sciences
2015 | Journal article
DOI: 10.1016/j.cobeha.2015.09.007
Contributors: Rebecca M Calisi; Matthew D MacManes
Source: Self-asserted source
Matthew MacManes via Crossref Metadata Search
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Brain Transcriptional Profiles of Male Alternative Reproductive Tactics in Bluegill Sunfish

2015-09-02 | Report
DOI: 10.1101/025916
Contributors: Charlyn Partridge; Matthew MacManes; Rosemary Knapp; Bryan Neff
Source: Self-asserted source
Matthew MacManes via Crossref Metadata Search

Optimizing error correction of RNAseq reads

2015-05 | Report
DOI: 10.1101/020123
Contributors: Matthew D MacManes
Source: Self-asserted source
Matthew MacManes via Crossref Metadata Search
grade
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On the optimal trimming of high-throughput mRNA sequence data

Front. Genet.
2014 | Journal article
DOI: 10.3389/fgene.2014.00013
Contributors: Matthew D. MacManes
Source: Self-asserted source
Matthew MacManes via Crossref Metadata Search

Characterization of the transcriptome, nucleotide sequence polymorphism, and natural selection in the desert adapted mouse Peromyscus eremicus

PeerJ
2014-10 | Journal article
DOI: 10.7717/peerj.642
Contributors: Matthew D. MacManes; Michael B. Eisen
Source: Self-asserted source
Matthew MacManes via Crossref Metadata Search

Characterization of the transcriptome, nucleotide sequence polymorphism, and natural selection in the desert adapted mousePeromyscus eremicus

2014-09-15 | Preprint
DOI: 10.1101/009134
Contributors: Matthew D. MacManes; Michael B. Eisen
Source: check_circle
Crossref

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

GigaScience
2013 | Journal article
DOI: 10.1186/2047-217x-2-10
Contributors: Keith R Bradnam; Joseph N Fass; Anton Alexandrov; Paul Baranay; Michael Bechner; Inanç Birol; Sébastien Boisvert; Jarrod A Chapman; Guillaume Chapuis; Rayan Chikhi et al.
Source: Self-asserted source
Matthew MacManes via Crossref Metadata Search

On the optimal trimming of high-throughput mRNAseq data

2013-11 | Report
DOI: 10.1101/000422
Contributors: M. D. MacManes
Source: Self-asserted source
Matthew MacManes via Crossref Metadata Search
grade
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De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis.

2013-08 | Journal article
DOI:

10.1038/nprot.2013.084

PMID:

23845962
Contributors: Blood PD; Bowden J; Couger MB; Dewey CN; Eccles D; Friedman N; Grabherr M; Haas BJ; Henschel R; Leduc RD et al.
Source: Self-asserted source
Matthew MacManes via Europe PubMed Central

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species.

2013-07 | Journal article
PMID:

23870653
Contributors: Alexandrov A; Baranay P; Bechner M; Birol I; Boisvert S; Bradnam KR; Chapman JA; Chapuis G; Chikhi R; Chitsaz H et al.
Source: Self-asserted source
Matthew MacManes via Europe PubMed Central
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