MM
Matthew MacManes
genomicsPeromyscusevolutionary biologyTranscriptomeRNAseqPhysiologybioinformaticsDehydrationphysiologyReproduction
On Valency
published · living versionsW_w6hykr7c·v1 · currentpublished
W_26xzgw86·v1published
Preprints & journals
56 papers in the corpus · 2009–2026Selection-driven color variation in the aposematic strawberry poison frog, Oophaga pumilio.41713409 · Aguilar-Gómez, Diana, Freeborn, Layla, Yuan, Lin et al.2026 · 5 citationsCurrent biology : CB. 2026;36(6):1355-1372.e8
High total water loss driven by low-fat diet in desert-adapted mice.40206330 · Blumstein, Danielle M, Colella, Jocelyn P, Linder, Ernst et al.2026 · 8 citationsJournal of mammalogy. 2025;106(2):293-303
The multi-tissue gene expression and physiological responses of water deprived Peromyscus eremicus.39118009 · Blumstein, Danielle, MacManes, Matthew2024 · 3 citationsBMC genomics. 2024;25(1):770
What Makes a Mimic? Orange, Red, and Black Color Production in the Mimic Poison Frog (Ranitomeya imitator).38874406 · Rubio, Andrew O, Stuckert, Adam M M, Geralds, BreAnn et al.2024 · 12 citationsGenome biology and evolution. 2024;16(7)
The genomics of mimicry: Gene expression throughout development provides insights into convergent and divergent phenotypes in a Müllerian mimicry system.38923007 · Stuckert, Adam M M, Chouteau, Mathieu, McClure, Melanie et al.2024 · 6 citationsMolecular ecology. 2024;33(14):e17438
Impacts of dietary fat on multi tissue gene expression in the desert-adapted cactus mouse.38746252 · Blumstein, Danielle M, MacManes, Matthew D2025 · 0 citationsbioRxiv : the preprint server for biology. 2024
When the tap runs dry: The multi-tissue gene expression and physiological responses of water deprived Peromyscus eremicus.38328088 · Blumstein, Danielle M, MacManes, Matthew D2026 · 1 citationbioRxiv : the preprint server for biology. 2024
White-nose syndrome restructures bat skin microbiomes.37888992 · Ange-Stark, Meghan, Parise, Katy L, Cheng, Tina L et al.2023 · 29 citationsMicrobiology spectrum. 2023;11(6):e0271523
When the tap runs dry: The physiological effects of acute experimental dehydration in Peromyscus eremicus.37461486 · Blumstein, Danielle M, MacManes, Matthew D2026 · 14 citationsbioRxiv : the preprint server for biology. 2023
Genetic basis of aposematic coloration in a mimetic radiation of poison frogs10.1101/2023.04.20.537757v1 · Linderoth, T., Aguilar-Gomez, D., White, E. et al.2023 · 9 citationsbioRxiv
Correction: Disentangling environmental drivers of circadian metabolism in desert-adapted mice.35921099 · Colella, Jocelyn P, Blumstein, Danielle M, MacManes, Matthew D2025 · 0 citationsThe Journal of experimental biology. 2022;225(15)
Chromosome size affects sequence divergence between species through the interplay of recombination and selection.35271737 · Tigano, Anna, Khan, Ruqayya, Omer, Arina D et al.2022 · 36 citationsEvolution; international journal of organic evolution. 2022;76(4):782-798
Prolactin and prolactin receptor expression in the HPG axis and crop during parental care in both sexes of a biparental bird (Columba livia).34756919 · Farrar, Victoria S, Harris, Rayna M, Austin, Suzanne H et al.2022 · 21 citationsGeneral and comparative endocrinology. 2022;315:113940
Disentangling environmental drivers of circadian metabolism in desert-adapted mice.34495305 · Colella, Jocelyn P, Blumstein, Danielle M, MacManes, Matthew D2021 · 9 citationsThe Journal of experimental biology. 2021;224(18)
Feather Gene Expression Elucidates the Developmental Basis of Plumage Iridescence in African Starlings.33885791 · Rubenstein, Dustin R, Corvelo, André, MacManes, Matthew D et al.2021 · 21 citationsThe Journal of heredity. 2021;112(5):417-429
Limited Evidence for Parallel Evolution Among Desert-Adapted Peromyscus Deer Mice.33686424 · Colella, Jocelyn P, Tigano, Anna, Dudchenko, Olga et al.2021 · 27 citationsThe Journal of heredity. 2021;112(3):286-302
Signal, bias, and the role of transcriptome assembly quality in phylogenomic inference.33726665 · Spillane, Jennifer L, LaPolice, Troy M, MacManes, Matthew D et al.2021 · 13 citationsBMC ecology and evolution. 2021;21(1):43
The Genome of the Softshell Clam Mya arenaria and the Evolution of Apoptosis.32653903 · Plachetzki, David C, Pankey, M Sabrina, MacManes, Matthew D et al.2021 · 8 citationsGenome biology and evolution. 2020;12(10):1681-1693
A total crapshoot? Evaluating bioinformatic decisions in animal diet metabarcoding analyses.33005342 · O'Rourke, Devon R, Bokulich, Nicholas A, Jusino, Michelle A et al.2024 · 72 citationsEcology and evolution. 2020;10(18):9721-9739
Limited evidence for parallel evolution among desert adapted Peromyscus deer mice10.1101/2020.06.29.178392v3 · Colella, J. P., Tigano, A., Dudchenko, O. et al.2020 · 0 citationsbioRxiv
De novo assembly and functional annotation of the heart + hemolymph transcriptome in the Caribbean spiny lobster Panulirus argus.32414680 · Baeza, J Antonio, MacManes, Matthew2021 · 7 citationsMarine genomics. 2020;54:100783
A linked-read approach to museomics: Higher quality de novo genome assemblies from degraded tissues.32153100 · Colella, Jocelyn P, Tigano, Anna, MacManes, Matthew D2021 · 22 citationsMolecular ecology resources. 2020;20(4):856-870
Comparative and population genomics approaches reveal the basis of adaptation to deserts in a small rodent.32130752 · Tigano, Anna, Colella, Jocelyn P, MacManes, Matthew D2021 · 59 citationsMolecular ecology. 2020;29(7):1300-1314
Stress-mediated convergence of splicing landscapes in male and female rock doves.32293250 · Lang, Andrew S, Austin, Suzanne H, Harris, Rayna M et al.2021 · 5 citationsBMC genomics. 2020;21(1):251
Divergent selection and drift shape the genomes of two avian sister species spanning a saline-freshwater ecotone.31871659 · Walsh, Jennifer, Clucas, Gemma V, MacManes, Matthew D et al.2023 · 24 citationsEcology and evolution. 2019;9(23):13477-13494
Variation in pigmentation gene expression is associated with distinct aposematic color morphs in the poison frog Dendrobates auratus.30995908 · Stuckert, Adam M M, Moore, Emily, Coyle, Kaitlin P et al.2019 · 48 citationsBMC evolutionary biology. 2019;19(1):85
A novel CRISPR/Cas9 associated technology for sequence-specific nucleic acid enrichment.30998719 · Stevens, Richard C, Steele, Jennifer L, Glover, William R et al.2020 · 27 citationsPloS one. 2019;14(4):e0215441
Dynamic pigmentary and structural coloration within cephalopod chromatophore organs.30824708 · Williams, Thomas L, Senft, Stephen L, Yeo, Jingjie et al.2019 · 177 citationsNature communications. 2019;10(1):1004
Genomic Takeover by Transposable Elements in the Strawberry Poison Frog.30517748 · Rogers, Rebekah L, Zhou, Long, Chu, Chong et al.2019 · 55 citationsMolecular biology and evolution. 2018;35(12):2913-2927
The Oyster River Protocol: a multi-assembler and kmer approach for de novo transcriptome assembly.30083482 · MacManes, Matthew D2020 · 103 citationsPeerJ. 2018;6:e5428
Sex-biased transcriptomic response of the reproductive axis to stress.29378207 · Calisi, Rebecca M, Austin, Suzanne H, Lang, Andrew S et al.2019 · 32 citationsHormones and behavior. 2018;100:56-68
Transcriptomic analyses reveal tissue-specific selection on genes related to apoptotic processes in the subterranean rodent, Ctenomys sociabilis10.1101/256875v1 · Lang, A., Kordonowy, L., Lacey, E. et al.2018 · 1 citationbioRxiv
Comparative Genomics of Pathogenic and Nonpathogenic Beetle-Vectored Fungi in the Genus Geosmithia.29186370 · Schuelke, Taruna A, Wu, Guangxi, Westbrook, Anthony et al.2018 · 18 citationsGenome biology and evolution. 2017;9(12):3312-3327
Comparative Genomics of Color Morphs In the Coral Montastraea cavernosa.29167578 · Jarett, Jessica K, MacManes, Matthew D, Morrow, Kathleen M et al.2019 · 11 citationsScientific reports. 2017;7(1):16039
Characterizing the reproductive transcriptomic correlates of acute dehydration in males in the desert-adapted rodent, Peromyscus eremicus.28645248 · Kordonowy, Lauren, MacManes, Matthew2018 · 21 citationsBMC genomics. 2017;18(1):473
PALADIN: protein alignment for functional profiling whole metagenome shotgun data.28158639 · Westbrook, Anthony, Ramsdell, Jordan, Schuelke, Taruna et al.2018 · 51 citationsBioinformatics (Oxford, England). 2017;33(10):1473-1478
Widespread patterns of sexually dimorphic gene expression in an avian hypothalamic-pituitary-gonadal (HPG) axis.28417958 · MacManes, Matthew D, Austin, Suzanne H, Lang, Andrew S et al.2018 · 47 citationsScientific reports. 2017;7:45125
Severe acute dehydration in a desert rodent elicits a transcriptional response that effectively prevents kidney injury.28381460 · MacManes, Matthew David2017 · 44 citationsAmerican journal of physiology. Renal physiology. 2017;313(2):F262-F272
Physiological and biochemical changes associated with acute experimental dehydration in the desert adapted mouse, Peromyscus eremicus.28330954 · Kordonowy, Lauren, Lombardo, Kaelina D, Green, Hannah L et al.2017 · 27 citationsPhysiological reports. 2017;5(6)
Brain Transcriptional Profiles of Male Alternative Reproductive Tactics and Females in Bluegill Sunfish.27907106 · Partridge, Charlyn G, MacManes, Matthew D, Knapp, Rosemary et al.2017 · 27 citationsPloS one. 2016;11(12):e0167509
Characterization of a male reproductive transcriptome for Peromyscus eremicus (Cactus mouse).27812417 · Kordonowy, Lauren L, MacManes, Matthew D2023 · 13 citationsPeerJ. 2016;4:e2617
Characterizing the adult and larval transcriptome of the multicolored Asian lady beetle, Harmonia axyridis.27326374 · Havens, Lindsay A, MacManes, Matthew D2016 · 5 citationsPeerJ. 2016;4:e2098
Comparative genomics explains the evolutionary success of reef-forming corals.27218454 · Bhattacharya, Debashish, Agrawal, Shobhit, Aranda, Manuel et al.2017 · 198 citationseLife. 2016;5
De novo genome assembly of Geosmithia morbida, the causal agent of thousand cankers disease.27168971 · Schuelke, Taruna A, Westbrook, Anthony, Broders, Kirk et al.2016 · 8 citationsPeerJ. 2016;4:e1952
Establishing evidenced-based best practice for the de novo assembly and evaluation of transcriptomes from non-model organisms10.1101/035642v2 · Matthew D MacManes2015 · 42 citationsbioRxiv
Optimizing error correction of RNAseq reads10.1101/020123v1 · Matthew D MacManes2015 · 4 citationsbioRxiv
Characterization of the transcriptome, nucleotide sequence polymorphism, and natural selection in the desert adapted mouse Peromyscus eremicus.25374784 · MacManes, Matthew D, Eisen, Michael B2014 · 38 citationsPeerJ. 2014;2:e642
On the optimal trimming of high-throughput mRNA sequence data.24567737 · Macmanes, Matthew D2014 · 210 citationsFrontiers in genetics. 2014;5:13
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species.23870653 · Bradnam, Keith R, Fass, Joseph N, Alexandrov, Anton et al.2014 · 671 citationsGigaScience. 2013;2(1):10
De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis.23845962 · Haas, Brian J, Papanicolaou, Alexie, Yassour, Moran et al.2014 · 8,433 citationsNature protocols. 2013;8(8):1494-512
Career total: at least 141 works. 56 are in this corpus.Showing the 50 most recent.
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