Matthew MacManes

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Manfred GrabherrAssociate Professor, Inland Norway University of Applied SciencesVerified email at inn.no
Alexie PapanicolaouAssociate Professor, Hawkesbury Institute for the Environment, Western SydneyVerified email at westernsydney.edu.au
Richard LeDucBioinformatics Platform Director, Children's Hospital Research Institute of ManitobaVerified email at chrim.ca
Brian HaasBroad InstituteVerified email at broadinstitute.org
Moran YassourThe Hebrew University of JerusalemVerified email at mail.huji.ac.il
Joshua OrvisInstitute for Genome Sciences & Johns HopkinsVerified email at som.umaryland.edu
Nir FriedmanProfessor of Computer Science and Medicine, Hebrew UniversityVerified email at mail.huji.ac.il
Bo LiPrincipal Scientist, Cell and Tissue Genomics, GenentechVerified email at gene.com
David Andrew EcclesBioinformatics Research Analyst, Gringene BioinformaticsVerified email at gringene.org
Colin DeweyProfessor of Biostatistics and Medical Informatics, University of Wisconsin-MadisonVerified email at biostat.wisc.edu
Francesco StrozziiTeos TherapeuticsVerified email at iteostherapeutics.com
Matthew Brian CougerBrigham and Women's Hospital / Harvard Medical SchoolVerified email at bwh.harvard.edu
Joshua C BowdenCSIROVerified email at csiro.au
Robert HenschelIndiana University, Technische Universität Dresden, Technical University Dresden, Dresden University of TechnologyVerified email at iu.edu
Nathalie PochetAssistant Professor, BWH/HMS/BroadVerified email at broadinstitute.org
Rebecca M. CalisiAssistant Professor of Neurobiology, Physiology and Behavior, University of California, DavisVerified email at ucdavis.edu
Suzanne H. AustinOregon State UniversityVerified email at oregonstate.edu
Kyle SummersEast Carolina UniversityVerified email at ecu.edu
Tyler LinderothUniversity of CambridgeVerified email at cam.ac.uk
David PlachetzkiUniversity of New HamphsireVerified email at unh.edu

Matthew MacManes

University of New Hampshire

Verified email at unh.edu - Homepage

Evolutionary Physiology and Genomics


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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	7343	2013
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	772	2013
On the optimal trimming of high-throughput mRNA sequence data MD MacManes Frontiers in genetics 5, 13, 2014	223	2014
Comparative genomics explains the evolutionary success of reef-forming corals D Bhattacharya, S Agrawal, M Aranda, S Baumgarten, M Belcaid, ... eLife, 2016	184	2016
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	147	2011
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	107	2019
The Oyster River Protocol: a multi-assembler and kmer approach for de novo transcriptome assembly MD MacManes PeerJ 6, e5428, 2018	98	2018
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	65	2018
Improving transcriptome assembly through error correction of high-throughput sequence reads MD MacManes, MB Eisen PeerJ 1, e113, 2013	52	2013
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	51	2017
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	47	2020
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	41	2017
Establishing evidenced-based best practice for the de novo assembly and evaluation of transcriptomes from non-model organisms MD MacManes BioRxiv, 035642, 2015	37*	2015
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	36	2017
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	36	2014
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), 1-15, 2019	35	2019
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	34	2020
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	32	2016
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	31	2009
Sex-biased transcriptomic response of the reproductive axis to stress RM Calisi, SH Austin, AS Lang, MD MacManes Hormones and behavior 100, 56-68, 2018	26	2018

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