Matthew MacManes

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Moran YassourThe Hebrew University of JerusalemVerified email at mail.huji.ac.il
Alexie PapanicolaouSenior Lecturer/Assistant Professor, Hawkesbury Institute for the Environment, Western SydneyVerified email at westernsydney.edu.au
Manfred GrabherrSenior Researcher and Team Leader, Uppsala UniversityVerified email at imbim.uu.se
Joshua OrvisInstitute for Genome Sciences & Johns HopkinsVerified email at som.umaryland.edu
Nir FriedmanProfessor of Computer Science and Life Sciences, Hebrew UniversityVerified email at mail.huji.ac.il
Richard LeDucDirector of Computational Proteomics, Proteomics Center of Excellence, Northwestern UniversityVerified email at northwestern.edu
Bo LiAssistant Professor of Medicine, Harvard Medical SchoolVerified email at mgh.harvard.edu
David Andrew EcclesBioinformatics Research Analyst, Gringene BioinformaticsVerified email at gringene.org
Brian HaasBroad InstituteVerified email at broadinstitute.org
Colin DeweyProfessor of Biostatistics and Medical Informatics, University of Wisconsin-MadisonVerified email at biostat.wisc.edu
Francesco StrozziEnterome BioscienceVerified email at enterome.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
Anthony WestbrookUniversity of New HampshireVerified email at unh.edu
Tyler LinderothUniversity of CambridgeVerified email at cam.ac.uk

Matthew MacManes

University of New Hampshire

Verified email at unh.edu - Homepage

Evolutionary 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	5160	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	664	2013
On the optimal trimming of high-throughput mRNA sequence data MD MacManes Frontiers in genetics 5, 13, 2014	175	2014
Comparative genomics explains the evolutionary success of reef-forming corals D Bhattacharya, S Agrawal, M Aranda, S Baumgarten, M Belcaid, ... eLife, 2016	129	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	116	2011
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	45	2018
Improving transcriptome assembly through error correction of high-throughput sequence reads MD MacManes, MB Eisen PeerJ 1, e113, 2013	44	2013
The Oyster River Protocol: a multi-assembler and kmer approach for de novo transcriptome assembly MD MacManes PeerJ 6, e5428, 2018	41	2018
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	40	2019
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	40	2018
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	33	2017
Establishing evidenced-based best practice for the de novo assembly and evaluation of transcriptomes from non-model organisms MD MacManes BioRxiv, 035642, 2016	33	2016
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	30	2014
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	28	2017
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	26	2009
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 Public Library of Science 7 (9), e45524, 2012	25	2012
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	24	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	24	2016
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	23	2017
Promiscuity in mice is associated with increased vaginal bacterial diversity MD MacManes Naturwissenschaften, 1-10, 2011	20	2011

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