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Matthew D. MacManes - Publications

Affiliations: 
University of California, Berkeley, Berkeley, CA, United States 
Area:
Genetics, Zoology, Genomics,
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41 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Stuckert AMM, Chouteau M, McClure M, LaPolice TM, Linderoth T, Nielsen R, Summers K, MacManes MD. The genomics of mimicry: gene expression throughout development provides insights into convergent and divergent phenotypes in a Müllerian mimicry system. Molecular Ecology. PMID 34145931 DOI: 10.1111/mec.16024  0.35
2021 Rubenstein DR, Corvelo A, MacManes MD, Maia R, Narzisi G, Rousaki A, Vandenabeele P, Shawkey MD, Solomon J. Feather Gene Expression Elucidates the Developmental Basis of Plumage Iridescence in African Starlings. The Journal of Heredity. PMID 33885791 DOI: 10.1093/jhered/esab014  0.577
2021 Colella JP, Tigano A, Dudchenko O, Omer AD, Khan R, Bochkov ID, Aiden EL, MacManes MD. Limited evidence for parallel evolution among desert adapted Peromyscus deer mice. The Journal of Heredity. PMID 33686424 DOI: 10.1093/jhered/esab009  0.32
2020 O'Rourke DR, Bokulich NA, Jusino MA, MacManes MD, Foster JT. A total crapshoot? Evaluating bioinformatic decisions in animal diet metabarcoding analyses. Ecology and Evolution. 10: 9721-9739. PMID 33005342 DOI: 10.1002/Ece3.6594  0.342
2020 Plachetzki D, Pankey S, MacManes MD, Lesser MP, Walker CW. The genome of the softshell clam Mya arenaria and the evolution of apoptosis. Genome Biology and Evolution. PMID 32653903 DOI: 10.1093/Gbe/Evaa143  0.354
2020 Baeza JA, MacManes M. De novo assembly and functional annotation of the heart + hemolymph transcriptome in the Caribbean spiny lobster Panulirus argus Marine Genomics. 100783. PMID 32414680 DOI: 10.1016/J.Margen.2020.100783  0.38
2020 Lang AS, Austin SH, Harris RM, Calisi RM, MacManes MD. Stress-mediated convergence of splicing landscapes in male and female rock doves. Bmc Genomics. 21: 251. PMID 32293250 DOI: 10.1186/S12864-020-6600-6  0.332
2020 Colella JP, Tigano A, MacManes MD. A linked-read approach to museomics: Higher quality de novo genome assemblies from degraded tissues. Molecular Ecology Resources. PMID 32153100 DOI: 10.1111/1755-0998.13155  0.396
2020 Tigano A, Colella JP, MacManes MD. Comparative and population genomics approaches reveal the basis of adaptation to deserts in a small rodent. Molecular Ecology. PMID 32130752 DOI: 10.1111/Mec.15401  0.447
2019 Walsh J, Clucas GV, MacManes MD, Thomas WK, Kovach AI. Divergent selection and drift shape the genomes of two avian sister species spanning a saline-freshwater ecotone. Ecology and Evolution. 9: 13477-13494. PMID 31871659 DOI: 10.1002/Ece3.5804  0.448
2019 Stevens RC, Steele JL, Glover WR, Sanchez-Garcia JF, Simpson SD, O'Rourke D, Ramsdell JS, MacManes MD, Thomas WK, Shuber AP. A novel CRISPR/Cas9 associated technology for sequence-specific nucleic acid enrichment. Plos One. 14: e0215441. PMID 30998719 DOI: 10.1371/Journal.Pone.0215441  0.33
2019 Stuckert AMM, Moore E, Coyle KP, Davison I, MacManes MD, Roberts R, Summers K. Variation in pigmentation gene expression is associated with distinct aposematic color morphs in the poison frog Dendrobates auratus. Bmc Evolutionary Biology. 19: 85. PMID 30995908 DOI: 10.1186/S12862-019-1410-7  0.413
2018 Rogers RL, Zhou L, Chu C, Márquez R, Corl A, Linderoth T, Freeborn L, MacManes MD, Xiong Z, Zheng J, Guo C, Xun X, Kronforst MR, Summers K, Wu Y, et al. Genomic Takeover by Transposable Elements in the Strawberry Poison Frog. Molecular Biology and Evolution. 35: 2913-2927. PMID 30517748 DOI: 10.1093/Molbev/Msy185  0.344
2018 MacManes MD. The Oyster River Protocol: a multi-assembler and kmer approach for de novo transcriptome assembly. Peerj. 6: e5428. PMID 30083482 DOI: 10.7717/Peerj.5428  0.348
2018 Calisi R, Austin SH, Lang AS, MacManes MD. Sex-biased transcriptomic response of the reproductive axis to stress. Hormones and Behavior. PMID 29378207 DOI: 10.1016/J.Yhbeh.2017.11.011  0.355
2017 Schuelke TA, Wu G, Westbrook A, Woeste K, Plachetzki DC, Broders K, MacManes MD. Comparative genomics of pathogenic and non-pathogenic beetle-vectored fungi in the genus Geosmithia. Genome Biology and Evolution. PMID 29186370 DOI: 10.1093/Gbe/Evx242  0.392
2017 Jarett JK, MacManes MD, Morrow KM, Pankey MS, Lesser MP. Comparative Genomics of Color Morphs In the Coral Montastraea cavernosa. Scientific Reports. 7: 16039. PMID 29167578 DOI: 10.1038/S41598-017-16371-9  0.397
2017 Kordonowy L, MacManes M. Characterizing the reproductive transcriptomic correlates of acute dehydration in males in the desert-adapted rodent, Peromyscus eremicus. Bmc Genomics. 18: 473-473. PMID 28645248 DOI: 10.1186/S12864-017-3840-1  0.38
2017 MacManes MD, Austin SH, Lang AS, Booth A, Farrar V, Calisi RM. Widespread patterns of sexually dimorphic gene expression in an avian hypothalamic-pituitary-gonadal (HPG) axis. Scientific Reports. 7: 45125. PMID 28417958 DOI: 10.1038/Srep45125  0.353
2017 MacManes MD. Severe acute dehydration in a desert rodent elicits a transcriptional response that effectively prevents kidney injury. American Journal of Physiology. Renal Physiology. ajprenal.00067.2017. PMID 28381460 DOI: 10.1152/Ajprenal.00067.2017  0.301
2017 Kordonowy L, Lombardo KD, Green HL, Dawson MD, Bolton EA, LaCourse S, MacManes MD. Physiological and biochemical changes associated with acute experimental dehydration in the desert adapted mouse, Peromyscus eremicus. Physiological Reports. 5. PMID 28330954 DOI: 10.14814/Phy2.13218  0.31
2016 Partridge CG, MacManes MD, Knapp R, Neff BD. Brain Transcriptional Profiles of Male Alternative Reproductive Tactics and Females in Bluegill Sunfish. Plos One. 11: e0167509. PMID 27907106 DOI: 10.1371/Journal.Pone.0167509  0.325
2016 Kordonowy LL, MacManes MD. Characterization of a male reproductive transcriptome for Peromyscus eremicus (Cactus mouse). Peerj. 4: e2617. PMID 27812417 DOI: 10.7717/Peerj.2617  0.42
2016 Havens LA, MacManes MD. Characterizing the adult and larval transcriptome of the multicolored Asian lady beetle, Harmonia axyridis. Peerj. 4: e2098. PMID 27326374 DOI: 10.7717/Peerj.2098  0.366
2016 Bhattacharya D, Agrawal S, Aranda M, Baumgarten S, Belcaid M, Drake JL, Erwin D, Foret S, Gates RD, Gruber DF, Kamel B, Lesser MP, Levy O, Liew YJ, MacManes M, et al. Comparative genomics explains the evolutionary success of reef-forming corals. Elife. 5. PMID 27218454 DOI: 10.7554/Elife.13288  0.42
2016 Schuelke TA, Westbrook A, Broders K, Woeste K, MacManes MD. De novo genome assembly of Geosmithia morbida, the causal agent of thousand cankers disease. Peerj. 4: e1952. PMID 27168971 DOI: 10.7717/Peerj.1952  0.351
2016 Bhattacharya D, Agrawal S, Aranda M, Baumgarten S, Belcaid M, Drake JL, Erwin D, Foret S, Gates RD, Gruber DF, Kamel B, Lesser MP, Levy O, Liew YJ, MacManes M, et al. Author response: Comparative genomics explains the evolutionary success of reef-forming corals Elife. DOI: 10.7554/Elife.13288.066  0.358
2016 Lesser Mp, MacManes M. Transcriptomic Resources for the Rocky Intertidal Blue MusselMytilus edulisfrom the Gulf of Maine Journal of Shellfish Research. 35: 435-465. DOI: 10.2983/035.035.0218  0.301
2015 Calisi RM, MacManes MD. RNAseq-ing a more integrative understanding of animal behavior Current Opinion in Behavioral Sciences. 6: 65-68. DOI: 10.1016/J.Cobeha.2015.09.007  0.401
2014 MacManes MD, Eisen MB. Characterization of the transcriptome, nucleotide sequence polymorphism, and natural selection in the desert adapted mouse Peromyscus eremicus. Peerj. 2: e642. PMID 25374784 DOI: 10.7717/Peerj.642  0.377
2014 Macmanes MD. On the optimal trimming of high-throughput mRNA sequence data. Frontiers in Genetics. 5: 13. PMID 24567737 DOI: 10.3389/Fgene.2014.00013  0.347
2014 Havens L, MacManes M, Dickson J. Identification of the genomic underpinnings of spot polymorphism in Harmonia axyridis F1000research. 5. DOI: 10.7490/F1000Research.1096169.1  0.352
2013 Macmanes MD, Eisen MB. Improving transcriptome assembly through error correction of high-throughput sequence reads. Peerj. 1: e113. PMID 23904992 DOI: 10.7717/Peerj.113  0.305
2013 Bradnam KR, Fass JN, Alexandrov A, Baranay P, Bechner M, Birol I, Boisvert S, Chapman JA, Chapuis G, Chikhi R, Chitsaz H, Chou WC, Corbeil J, Del Fabbro C, Docking TR, ... ... Macmanes MD, et al. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. Gigascience. 2: 10. PMID 23870653 DOI: 10.1186/2047-217X-2-10  0.381
2013 Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, Bowden J, Couger MB, Eccles D, Li B, Lieber M, Macmanes MD, Ott M, Orvis J, Pochet N, Strozzi F, et al. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nature Protocols. 8: 1494-512. PMID 23845962 DOI: 10.1038/Nprot.2013.084  0.368
2012 MacManes MD, Lacey EA. The social brain: transcriptome assembly and characterization of the hippocampus from a social subterranean rodent, the colonial tuco-tuco (Ctenomys sociabilis). Plos One. 7: e45524. PMID 23049809 DOI: 10.1371/Journal.Pone.0045524  0.557
2012 MacManes MD, Lacey EA. Is promiscuity associated with enhanced selection on MHC-DQα in mice (genus Peromyscus)? Plos One. 7: e37562. PMID 22649541 DOI: 10.1371/Journal.Pone.0037562  0.548
2011 MacManes MD. Promiscuity in mice is associated with increased vaginal bacterial diversity. Die Naturwissenschaften. 98: 951-60. PMID 21964973 DOI: 10.1007/S00114-011-0848-2  0.346
2011 Rowe KC, Singhal S, Macmanes MD, Ayroles JF, Morelli TL, Rubidge EM, Bi K, Moritz CC. Museum genomics: low-cost and high-accuracy genetic data from historical specimens. Molecular Ecology Resources. 11: 1082-92. PMID 21791033 DOI: 10.1111/J.1755-0998.2011.03052.X  0.371
2010 Benedict L, Bowie RCK, Fuchs J, Macmanes M. 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. 152: 223-225. DOI: 10.1111/J.1474-919X.2010.01015.X  0.532
2009 Quan YF, Macmanes MD, Ebensperger LA, Lacey EA, Hayes LD. Isolation and characterization of polymorphic microsatellite loci from Octodon degus. Molecular Ecology Resources. 9: 999-1001. PMID 21564818 DOI: 10.1111/J.1755-0998.2009.02536.X  0.523
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