Matthew MacManes
Matthew MacManes
Verified email at unh.edu - Homepage
TitleCited byYear
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, 2013
31622013
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), 10, 2013
5162013
On the optimal trimming of high-throughput mRNA sequence data
MD MacManes
Frontiers in Genetics 5, 13, 2014
1082014
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
792011
Comparative genomics explains the evolutionary success of reef-forming corals
D Bhattacharya, S Agrawal, M Aranda, S Baumgarten, M Belcaid, ...
eLife, 2016
782016
Improving transcriptome assembly through error correction of high-throughput sequence reads
MD MacManes, MB Eisen
PeerJ 1, e113, 2013
332013
Evaluation of tools for long read RNA-seq splice-aware alignment
K Križanović, A Echchiki, J Roux, M Šikić
Bioinformatics 34 (5), 748-754, 2017
232017
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
232014
Establishing evidenced-based best practice for the de novo assembly and evaluation of transcriptomes from non-model organisms
MD MacManes
BioRxiv, 035642, 2016
19*2016
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
192012
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
192009
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, 45125, 2017
152017
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
142017
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
142017
Is promiscuity associated with enhanced selection on MHC-DQα in mice (genus Peromyscus)?
MD MacManes, EA Lacey
PloS one 7 (5), e37562, 2012
142012
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
132016
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
122018
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
12*2017
Promiscuity in mice is associated with increased vaginal bacterial diversity
MD MacManes
Naturwissenschaften, 1-10, 2011
122011
The Oyster River Protocol: a multi-assembler and kmer approach for de novo transcriptome assembly
MD MacManes
PeerJ 6, e5428, 2018
102018
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Articles 1–20