De novo transcriptome assembly: A comprehensive cross-species comparison of short-read RNA-Seq assemblers
Background In recent years, massively parallel complementary DNA sequencing (RNA
sequencing [RNA-Seq]) has emerged as a fast, cost-effective, and robust technology to …
sequencing [RNA-Seq]) has emerged as a fast, cost-effective, and robust technology to …
[HTML][HTML] Assembly, Assessment, and Availability of De novo Generated Eukaryotic Transcriptomes
J Moreton, A Izquierdo, RD Emes - Frontiers in genetics, 2016 - frontiersin.org
De novo assembly of a complete transcriptome without the need for a guiding reference
genome is attractive, particularly where the cost and complexity of generating a eukaryote …
genome is attractive, particularly where the cost and complexity of generating a eukaryote …
[HTML][HTML] Bioinformatics for marine products: An overview of resources, bottlenecks, and perspectives
The sea represents a major source of biodiversity. It exhibits many different ecosystems in a
huge variety of environmental conditions where marine organisms have evolved with …
huge variety of environmental conditions where marine organisms have evolved with …
[HTML][HTML] Evaluation of de novo transcriptome assemblies from RNA-Seq data
B Li, N Fillmore, Y Bai, M Collins, JA Thomson… - Genome biology, 2014 - Springer
De novo RNA-Seq assembly facilitates the study of transcriptomes for species without
sequenced genomes, but it is challenging to select the most accurate assembly in this …
sequenced genomes, but it is challenging to select the most accurate assembly in this …
[HTML][HTML] De novo transcriptome assembly, annotation and comparison of four ecological and evolutionary model salmonid fish species
Background Salmonid fishes exhibit high levels of phenotypic and ecological variation and
are thus ideal model systems for studying evolutionary processes of adaptive divergence …
are thus ideal model systems for studying evolutionary processes of adaptive divergence …
StrainXpress: strain aware metagenome assembly from short reads
X Kang, X Luo, A Schönhuth - Nucleic Acids Research, 2022 - academic.oup.com
Next-generation sequencing–based metagenomics has enabled to identify microorganisms
in characteristic habitats without the need for lengthy cultivation. Importantly, clinically …
in characteristic habitats without the need for lengthy cultivation. Importantly, clinically …
[HTML][HTML] Construction of a public CHO cell line transcript database using versatile bioinformatics analysis pipelines
Chinese hamster ovary (CHO) cell lines represent the most commonly used mammalian
expression system for the production of therapeutic proteins. In this context, detailed …
expression system for the production of therapeutic proteins. In this context, detailed …
Evaluation of potential candidate genes involved in salinity tolerance in striped catfish (Pangasianodon hypophthalmus) using an RNA-Seq approach
Increasing salinity levels in freshwater and coastal environments caused by sea level rise
linked to climate change is now recognized to be a major factor that can impact fish growth …
linked to climate change is now recognized to be a major factor that can impact fish growth …
[HTML][HTML] Performance and scaling behavior of bioinformatic applications in virtualization environments to create awareness for the efficient use of compute resources
The large amount of biological data available in the current times, makes it necessary to use
tools and applications based on sophisticated and efficient algorithms, developed in the …
tools and applications based on sophisticated and efficient algorithms, developed in the …
Differential expression analysis of RNA-seq reads: overview, taxonomy, and tools
HA Chowdhury, DK Bhattacharyya… - IEEE/ACM transactions …, 2018 - ieeexplore.ieee.org
Analysis of RNA-sequence (RNA-seq) data is widely used in transcriptomic studies and it
has many applications. We review RNA-seq data analysis from RNA-seq reads to the results …
has many applications. We review RNA-seq data analysis from RNA-seq reads to the results …