J
Joshua C. Bowden
Researcher at Commonwealth Scientific and Industrial Research Organisation
Publications - 16
Citations - 7114
Joshua C. Bowden is an academic researcher from Commonwealth Scientific and Industrial Research Organisation. The author has contributed to research in topics: Diffusion MRI & Cartilage. The author has an hindex of 8, co-authored 15 publications receiving 5730 citations. Previous affiliations of Joshua C. Bowden include French Institute for Research in Computer Science and Automation & Flinders University.
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Journal ArticleDOI
De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis
Brian J. Haas,Alexie Papanicolaou,Moran Yassour,Moran Yassour,Manfred Grabherr,Philip D. Blood,Joshua C. Bowden,M. B. Couger,David Eccles,Bo Li,Matthias Lieber,Matthew D. MacManes,Michael Ott,Joshua Orvis,Nathalie Pochet,Nathalie Pochet,Francesco Strozzi,Nathan T. Weeks,Rick Westerman,Thomas William,Colin N. Dewey,Robert Henschel,Richard D. LeDuc,Nir Friedman,Aviv Regev +24 more
TL;DR: This protocol provides a workflow for genome-independent transcriptome analysis leveraging the Trinity platform and presents Trinity-supported companion utilities for downstream applications, including RSEM for transcript abundance estimation, R/Bioconductor packages for identifying differentially expressed transcripts across samples and approaches to identify protein-coding genes.
De novo transcript sequence reconstruction from RNA-Seq: reference generation and analysis with Trinity
Brian J. Haas,Alexie Papanicolaou,Moran Yassour,Manfred Grabherr,Philip D. Blood,Joshua C. Bowden,M. B. Couger,David Eccles,Bo Li,Matthias Lieber,Matthew D. MacManes,Michael Ott,Joshua Orvis,Nathalie Pochet,Francesco Strozzi,Nathan T. Weeks,Rick Westerman,Thomas William,Colin N. Dewey,Robert Henschel,Richard D. LeDuc,Nir Friedman,Aviv Regev +22 more
TL;DR: This protocol describes the use of the Trinity platform for de novo transcriptome assembly from RNA-Seq data in non-model organisms and presents Trinity’s supported companion utilities for downstream applications, including RSEM for transcript abundance estimation and R/Bioconductor packages for identifying differentially expressed transcripts across samples.
Journal ArticleDOI
Anisotropy of collagen fibre alignment in bovine cartilage: comparison of polarised light microscopy and spatially resolved diffusion-tensor measurements
S.K. de Visser,Joshua C. Bowden,Edeline Wentrup-Byrne,Llew Rintoul,Thor E. Bostrom,James M. Pope,Konstantin I. Momot +6 more
TL;DR: In this article, the authors compared the alignment angles obtained from DTI and diffusion tensor imaging in bovine articular cartilage using T2-weighted, diffusion-tensor, and PLM images.
Journal ArticleDOI
Diffusion tensor imaging of articular cartilage as a measure of tissue microstructure
TL;DR: In this paper, the authors used diffusion tensor MR micro-imaging to observe differences in magnitude and anisotropy of water diffusion between healthy cartilage and cartilage enzymatically degraded to simulate arthritic damage.
Journal ArticleDOI
Risk-conscious correction of batch effects: maximising information extraction from high-throughput genomic datasets
Yalchin Oytam,Fariborz Sobhanmanesh,Konsta Duesing,Joshua C. Bowden,Megan J. Osmond-McLeod,Jason P. Ross +5 more
TL;DR: Harman’s ability to better remove batch noise, and better preserve biologically meaningful signal simultaneously within a single study, and maintain the user-set trade-off between batch noise rejection and signal preservation across different studies makes it an effective alternative method to deal with batch effects in high-throughput genomic datasets.