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On the optimal trimming of high-throughput mRNA sequence data

Frontiers in genetics, 2014, Vol.5, p.13-13

Macmanes, Matthew D

2014

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The Oyster River Protocol: a multi-assembler and kmer approach for de novo transcriptome assembly

PeerJ (San Francisco, CA), 2018-08, Vol.6, p.e5428-e5428, Article e5428

MacManes, Matthew D

2018

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De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

Nature protocols, 2013-08, Vol.8 (8), p.1494-1512

2013

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Dynamic pigmentary and structural coloration within cephalopod chromatophore organs

Nature communications, 2019-03, Vol.10 (1), p.1004-1004, Article 1004

2019

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Brain Transcriptional Profiles of Male Alternative Reproductive Tactics and Females in Bluegill Sunfish

PloS one, 2016-12, Vol.11 (12), p.e0167509-e0167509

2016

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Variation in pigmentation gene expression is associated with distinct aposematic color morphs in the poison frog Dendrobates auratus

BMC ecology and evolution, 2019-04, Vol.19 (1), p.85, Article 85

2019

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A total crapshoot? Evaluating bioinformatic decisions in animal diet metabarcoding analyses

Ecology and evolution, 2020-09, Vol.10 (18), p.9721-9739

2020

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Sex-biased transcriptomic response of the reproductive axis to stress

Hormones and behavior, 2018-04, Vol.100, p.56-68

2018

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A novel CRISPR/Cas9 associated technology for sequence-specific nucleic acid enrichment

PloS one, 2019-04, Vol.14 (4), p.e0215441-e0215441

2019

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Stress-mediated convergence of splicing landscapes in male and female rock doves

BMC genomics, 2020-03, Vol.21 (1), p.251-251, Article 251

2020

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Signal, bias, and the role of transcriptome assembly quality in phylogenomic inference

BMC ecology and evolution, 2021-03, Vol.21 (1), p.43-43, Article 43

2021

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Divergent selection and drift shape the genomes of two avian sister species spanning a saline–freshwater ecotone

Ecology and evolution, 2019-12, Vol.9 (23), p.13477-13494

2019

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The social brain: transcriptome assembly and characterization of the hippocampus from a social subterranean rodent, the colonial tuco-tuco (Ctenomys sociabilis)

PloS one, 2012-09, Vol.7 (9), p.e45524-e45524

2012

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Comparative and population genomics approaches reveal the basis of adaptation to deserts in a small rodent

Molecular ecology, 2020-04, Vol.29 (7), p.1300-1314

2020

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Comparative Genomics of Color Morphs In the Coral Montastraea cavernosa

Scientific reports, 2017-11, Vol.7 (1), p.16039-13, Article 16039

2017

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When the tap runs dry: the physiological effects of acute experimental dehydration in Peromyscus eremicus

Journal of experimental biology, 2023-12, Vol.226 (23)

2023

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White-nose syndrome restructures bat skin microbiomes

Microbiology spectrum, 2023-12, Vol.11 (6), p.e0271523-e0271523

2023

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Characterization of the transcriptome, nucleotide sequence polymorphism, and natural selection in the desert adapted mouse Peromyscus eremicus

PeerJ (San Francisco, CA), 2014-10, Vol.2, p.e642-e642

2014

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Improving transcriptome assembly through error correction of high-throughput sequence reads

PeerJ (San Francisco, CA), 2013-07, Vol.1, p.e113-e113

2013

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Is promiscuity associated with enhanced selection on MHC-DQα in mice (genus Peromyscus)?

PloS one, 2012-05, Vol.7 (5), p.e37562-e37562

2012

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Characterization of a male reproductive transcriptome for Peromyscus eremicus (Cactus mouse)

PeerJ (San Francisco, CA), 2016-10, Vol.4, p.e2617-e2617, Article e2617

2016

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A linked‐read approach to museomics: Higher quality de novo genome assemblies from degraded tissues

Molecular ecology resources, 2020-07, Vol.20 (4), p.856-870

2020

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High total water loss driven by low-fat diet in desert-adapted mice

Journal of mammalogy, 2024-09

2024

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Characterizing the adult and larval transcriptome of the multicolored Asian lady beetle, Harmonia axyridis

PeerJ (San Francisco, CA), 2016-06, Vol.4, p.e2098-e2098, Article e2098

2016

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Disentangling environmental drivers of circadian metabolism in desert-adapted mice

Journal of experimental biology, 2021-09, Vol.224 (18)

2021

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On the optimal trimming of high-throughput mRNA sequence data

The Oyster River Protocol: a multi-assembler and kmer approach for de novo transcriptome assembly

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

Dynamic pigmentary and structural coloration within cephalopod chromatophore organs

Brain Transcriptional Profiles of Male Alternative Reproductive Tactics and Females in Bluegill Sunfish

Variation in pigmentation gene expression is associated with distinct aposematic color morphs in the poison frog Dendrobates auratus

A total crapshoot? Evaluating bioinformatic decisions in animal diet metabarcoding analyses

Sex-biased transcriptomic response of the reproductive axis to stress

A novel CRISPR/Cas9 associated technology for sequence-specific nucleic acid enrichment

Stress-mediated convergence of splicing landscapes in male and female rock doves

Signal, bias, and the role of transcriptome assembly quality in phylogenomic inference

Divergent selection and drift shape the genomes of two avian sister species spanning a saline–freshwater ecotone

The social brain: transcriptome assembly and characterization of the hippocampus from a social subterranean rodent, the colonial tuco-tuco (Ctenomys sociabilis)

Comparative and population genomics approaches reveal the basis of adaptation to deserts in a small rodent

Comparative Genomics of Color Morphs In the Coral Montastraea cavernosa

When the tap runs dry: the physiological effects of acute experimental dehydration in Peromyscus eremicus

White-nose syndrome restructures bat skin microbiomes

Characterization of the transcriptome, nucleotide sequence polymorphism, and natural selection in the desert adapted mouse Peromyscus eremicus

Improving transcriptome assembly through error correction of high-throughput sequence reads

Is promiscuity associated with enhanced selection on MHC-DQα in mice (genus Peromyscus)?

Characterization of a male reproductive transcriptome for Peromyscus eremicus (Cactus mouse)

A linked‐read approach to museomics: Higher quality de novo genome assemblies from degraded tissues

High total water loss driven by low-fat diet in desert-adapted mice

Characterizing the adult and larval transcriptome of the multicolored Asian lady beetle, Harmonia axyridis

Disentangling environmental drivers of circadian metabolism in desert-adapted mice

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