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De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis
De novo assembly of RNA-seq data enables researchers to study transcriptomes without the need for a genome sequence; this approach can be usefully applied, for instance, in research on 'non-modelExpand
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De novo transcript sequence reconstruction from RNA-Seq: reference generation and analysis with Trinity
De novo assembly of RNA-Seq data allows us to study transcriptomes without the need for a genome sequence, such as in non-model organisms of ecological and evolutionary importance, cancer samples, orExpand
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A Tissue-Mapped Axolotl De Novo Transcriptome Enables Identification of Limb Regeneration Factors.
Mammals have extremely limited regenerative capabilities; however, axolotls are profoundly regenerative and can replace entire limbs. The mechanisms underlying limb regeneration remain poorlyExpand
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Genome Analysis of Staphylococcus agnetis, an Agent of Lameness in Broiler Chickens
Lameness in broiler chickens is a significant animal welfare and financial issue. Lameness can be enhanced by rearing young broilers on wire flooring. We have identified Staphylococcus agnetis asExpand
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Genome Sequences of the Lignin-Degrading Pseudomonas sp. Strain YS-1p and Rhizobium sp. Strain YS-1r Isolated from Decaying Wood
ABSTRACT Pseudomonas sp. strain YS-1p and Rhizobium sp. strain YS-1r were isolated from a lignin-degrading enrichment culture. The isolates degraded lignin-derived monomers, dimers, alkali lignin,Expand
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Penicillium echinulatum secretome analysis reveals the fungi potential for degradation of lignocellulosic biomass
BackgroundThe enzymatic degradation of lignocellulosic materials by fungal enzyme systems has been extensively studied due to its effectiveness in the liberation of fermentable sugars for bioethanolExpand
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Enabling large-scale next-generation sequence assembly with Blacklight
TLDR
A variety of extremely challenging biological sequence analyses were conducted on the XSEDE large shared memory resource Blacklight, using current bioinformatics tools and encompassing a wide range of scientific applications. Expand
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Research Resource: The Dexamethasone Transcriptome in Hypothalamic Embryonic Neural Stem Cells.
Exposure to excess glucocorticoids during fetal development has long-lasting physiological and behavioral consequences, although the mechanisms are poorly understood. The impact of prenatalExpand
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Nanopore ultra-long read sequencing technology for antimicrobial resistance detection in Mannheimia haemolytica.
Disruptive innovations in long-range, cost-effective direct template nucleic acid sequencing are transforming clinical and diagnostic medicine. A multidrug resistant strain and a pan-susceptibleExpand
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Enabling large‐scale next‐generation sequence assembly with Blacklight
TLDR
A variety of extremely challenging biological sequence analyses were conducted on the XSEDE large shared memory resource Blacklight, using current bioinformatics tools and encompassing a wide range of scientific applications. Expand
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