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
29432013
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
4982013
On the optimal trimming of high-throughput mRNA sequence data
MD MacManes
Frontiers in Genetics 5, 13, 2014
942014
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
742016
Improving transcriptome assembly through error correction of high-throughput sequence reads
MD MacManes, MB Eisen
PeerJ 1, e113, 2013
312013
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
212014
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
212009
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
Establishing evidenced-based best practice for the de novo assembly and evaluation of transcriptomes from non-model organisms
MD MacManes
BioRxiv, 035642, 2016
17*2016
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
152017
Is promiscuity associated with enhanced selection on MHC-DQα in mice (genus Peromyscus)?
MD MacManes, EA Lacey
PloS one 7 (5), e37562, 2012
142012
Promiscuity in mice is associated with increased vaginal bacterial diversity
MD MacManes
Naturwissenschaften, 1-10, 2011
122011
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
112017
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
112017
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), 2017
11*2017
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
112016
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
102017
The Oyster River Protocol: a multi-assembler and kmer approach for de novo transcriptome assembly
MD MacManes
PeerJ 6, e5428, 2018
72018
De novo genome assembly of Geosmithia morbida, the causal agent of thousand cankers disease
TA Schuelke, A Westbrook, K Broders, K Woeste, MD MacManes
PeerJ 4, e1952, 2016
72016
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Articles 1–20