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
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
Richard LeDucBioinformatics Platform Director, Children's Hospital Research Institute of ManitobaVerified email at chrim.ca
Brian HaasBroad InstituteVerified email at broadinstitute.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
Rebecca M. CalisiAssistant Professor of Neurobiology, Physiology and Behavior, University of California, DavisVerified email at ucdavis.edu
Moran YassourThe Hebrew University of JerusalemVerified email at mail.huji.ac.il
Bo LiPrincipal Scientist, Biology Research | AI Development, gRED Computational Sciences, GenentechVerified email at gene.com
David Andrew EcclesBioinformatics Research Analyst, Gringene BioinformaticsVerified email at gringene.org
Suzanne H. AustinOregon State UniversityVerified email at oregonstate.edu
Kyle SummersEast Carolina UniversityVerified email at ecu.edu
Tyler LinderothMichigan State University, W.K. Kellogg Biological StationVerified email at msu.edu
Victoria FarrarNSF postdoctoral fellow, University of IllinoisVerified email at illinois.edu
Anna Tigano, Ph.D.Bioinformatics Biologist, Department of Fisheries and OceansVerified email at dfo-mpo.gc.ca

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	8024	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	810	2013
On the optimal trimming of high-throughput mRNA sequence data MD MacManes Frontiers in genetics 5, 13, 2014	236	2014
Comparative genomics explains the evolutionary success of reef-forming corals D Bhattacharya, S Agrawal, M Aranda, S Baumgarten, M Belcaid, ... eLife, 2016	191	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	157	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	139	2019
The Oyster River Protocol: a multi-assembler and kmer approach for de novo transcriptome assembly MD MacManes PeerJ 6, e5428, 2018	115	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	70	2018
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	64	2020
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	54	2017
Improving transcriptome assembly through error correction of high-throughput sequence reads MD MacManes, MB Eisen PeerJ 1, e113, 2013	52	2013
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	48	2017
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	43	2020
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	43	2019
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	43	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	41	2014
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
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	34	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	34	2009
RETRACTED: The genomics of mimicry: Gene expression throughout development provides insights into convergent and divergent phenotypes in a Müllerian mimicry system AMM Stuckert, M Chouteau, M McClure, TM LaPolice, T Linderoth, ... Molecular Ecology 30 (16), 4039-4061, 2021	32	2021

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