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Matthew MacManes
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De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis
BJ Haas, A Papanicolaou, M Yassour, M Grabherr, PD Blood, J Bowden, ...
Nature protocols 8 (8), 1494-1512, 2013
76162013
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
KR Bradnam, JN Fass, A Alexandrov, P Baranay, M Bechner, I Birol, ...
Gigascience 2 (1), 2047-217X-2-10, 2013
7932013
On the optimal trimming of high-throughput mRNA sequence data
MD MacManes
Frontiers in genetics 5, 75274, 2014
2262014
Comparative genomics explains the evolutionary success of reef-forming corals
D Bhattacharya, S Agrawal, M Aranda, S Baumgarten, M Belcaid, ...
eLife, 2016
1842016
Museum genomics: low‐cost and high‐accuracy genetic data from historical specimens
KC Rowe, S Singhal, MD Macmanes, JF Ayroles, TL Morelli, EM Rubidge, ...
Molecular Ecology Resources 11 (6), 1082-1092, 2011
1522011
Dynamic pigmentary and structural coloration within cephalopod chromatophore organs
TL Williams, SL Senft, J Yeo, FJ Martín-Martínez, AM Kuzirian, CA Martin, ...
Nature communications 10 (1), 1004, 2019
1222019
The Oyster River Protocol: a multi-assembler and kmer approach for de novo transcriptome assembly
MD MacManes
PeerJ 6, e5428, 2018
1052018
Reference generation and analysis with trinity
BJ Haas, A Papanicolaou, M Yassour, M Grabherr, D Philip, J Bowden, ...
Nat Protoc 8 (8), 1-43, 2014
912014
Genomic takeover by transposable elements in the strawberry poison frog
RL Rogers, L Zhou, C Chu, R Márquez, A Corl, T Linderoth, L Freeborn, ...
Molecular Biology and Evolution 35 (12), 2913-2927, 2018
682018
A total crapshoot? Evaluating bioinformatic decisions in animal diet metabarcoding analyses
DR O'Rourke, NA Bokulich, MA Jusino, MD MacManes, JT Foster
Ecology and Evolution 10 (18), 9721-9739, 2020
552020
Widespread patterns of sexually dimorphic gene expression in an avian hypothalamic–pituitary–gonadal (HPG) axis
MD MacManes, SH Austin, AS Lang, A Booth, V Farrar, RM Calisi
Scientific reports 7 (1), 45125, 2017
532017
Improving transcriptome assembly through error correction of high-throughput sequence reads
MD MacManes, MB Eisen
PeerJ 1, e113, 2013
522013
PALADIN: protein alignment for functional profiling whole metagenome shotgun data
A Westbrook, J Ramsdell, T Schuelke, L Normington, RD Bergeron, ...
Bioinformatics 33 (10), 1473-1478, 2017
442017
Characterization of the transcriptome, nucleotide sequence polymorphism, and natural selection in the desert adapted mouse Peromyscus eremicus
MD MacManes, MB Eisen
PeerJ 2, e642, 2014
392014
Severe acute dehydration in a desert rodent elicits a transcriptional response that effectively prevents kidney injury
MD MacManes
American Journal of Physiology-Renal Physiology 313 (2), F262-F272, 2017
382017
Establishing evidenced-based best practice for the de novo assembly and evaluation of transcriptomes from non-model organisms
MD MacManes
BioRxiv, 035642, 2015
38*2015
Comparative and population genomics approaches reveal the basis of adaptation to deserts in a small rodent
A Tigano, JP Colella, MD MacManes
Molecular Ecology 29 (7), 1300-1314, 2020
362020
Variation in pigmentation gene expression is associated with distinct aposematic color morphs in the poison frog Dendrobates auratus
AMM Stuckert, E Moore, KP Coyle, I Davison, MD MacManes, R Roberts, ...
BMC Evolutionary Biology 19, 1-15, 2019
362019
Brain transcriptional profiles of male alternative reproductive tactics and females in bluegill sunfish
CG Partridge, MD MacManes, R Knapp, BD Neff
PLoS One 11 (12), e0167509, 2016
332016
Isolation and characterization of polymorphic microsatellite loci from Octodon degus
YF Quan, MD Macmanes, LA Ebensperger, EA Lacey, LD Hayes
Molecular Ecology Resources 9 (3), 999-1001, 2009
312009
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Articles 1–20