Matthew MacManes
Matthew MacManes
Verified email at unh.edu - Homepage
Title
Cited by
Cited by
Year
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
50852013
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
6522013
On the optimal trimming of high-throughput mRNA sequence data
MD MacManes
Frontiers in genetics 5, 13, 2014
1712014
Comparative genomics explains the evolutionary success of reef-forming corals
D Bhattacharya, S Agrawal, M Aranda, S Baumgarten, M Belcaid, ...
eLife, 2016
1272016
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
1162011
Improving transcriptome assembly through error correction of high-throughput sequence reads
MD MacManes, MB Eisen
PeerJ 1, e113, 2013
432013
Evaluation of tools for long read RNA-seq splice-aware alignment
K Križanović, A Echchiki, J Roux, M Šikić
Bioinformatics 34 (5), 748-754, 2018
422018
The Oyster River Protocol: a multi-assembler and kmer approach for de novo transcriptome assembly
MD MacManes
PeerJ 6, e5428, 2018
382018
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
352018
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), 1-15, 2019
332019
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), 1-13, 2017
332017
Establishing evidenced-based best practice for the de novo assembly and evaluation of transcriptomes from non-model organisms
MD MacManes
BioRxiv, 035642, 2016
332016
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
302014
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
272017
The social brain: transcriptome assembly and characterization of the hippocampus from a social subterranean rodent, the colonial tuco-tuco (Ctenomys sociabilis)
MD MacManes, EA Lacey
PloS one 7 (9), e45524, 2012
252012
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
252009
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
232017
Physiological and biochemical changes associated with acute experimental dehydration in the desert adapted mouse, Peromyscus eremicus
L Kordonowy, KD Lombardo, HL Green, MD Dawson, EA Bolton, ...
Physiological Reports 5 (6), e13218, 2017
232017
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
232016
Promiscuity in mice is associated with increased vaginal bacterial diversity
MD MacManes
Naturwissenschaften, 1-10, 2011
212011
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Articles 1–20