Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis
The recent technological advances in next generation sequencing have brought the field
closer to the goal of reconstructing all genomes within a community by presenting high …
closer to the goal of reconstructing all genomes within a community by presenting high …
Strains, functions and dynamics in the expanded Human Microbiome Project
The characterization of baseline microbial and functional diversity in the human microbiome
has enabled studies of microbiome-related disease, diversity, biogeography, and molecular …
has enabled studies of microbiome-related disease, diversity, biogeography, and molecular …
Big data in biology: the hope and present-day challenges in it
The wave of new technologies has opened up the opportunity for cost-effective generation of
high-throughput profiles of biological systems. This is generating tons of biological data. It is …
high-throughput profiles of biological systems. This is generating tons of biological data. It is …
Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database
Background Microbial inhabitants of soils are important to ecosystem and planetary
functions, yet there are large gaps in our knowledge of their diversity and ecology. The …
functions, yet there are large gaps in our knowledge of their diversity and ecology. The …
CloVR: a virtual machine for automated and portable sequence analysis from the desktop using cloud computing
SV Angiuoli, M Matalka, A Gussman, K Galens… - BMC …, 2011 - Springer
Background Next-generation sequencing technologies have decentralized sequence
acquisition, increasing the demand for new bioinformatics tools that are easy to use …
acquisition, increasing the demand for new bioinformatics tools that are easy to use …
VIROME: a standard operating procedure for analysis of viral metagenome sequences
KE Wommack, J Bhavsar, SW Polson, J Chen… - Standards in genomic …, 2012 - Springer
One consistent finding among studies using shotgun metagenomics to analyze whole viral
communities is that most viral sequences show no significant homology to known …
communities is that most viral sequences show no significant homology to known …
Large-scale data integration framework provides a comprehensive view on glioblastoma multiforme
Background Coordinated efforts to collect large-scale data sets provide a basis for systems
level understanding of complex diseases. In order to translate these fragmented and …
level understanding of complex diseases. In order to translate these fragmented and …
A comparative analysis of library prep approaches for sequencing low input translatome samples
Background Cell type-specific ribosome-pulldown has become an increasingly popular
method for analysis of gene expression. It allows for expression analysis from intact tissues …
method for analysis of gene expression. It allows for expression analysis from intact tissues …
The IGS standard operating procedure for automated prokaryotic annotation
K Galens, J Orvis, S Daugherty, HH Creasy… - Standards in genomic …, 2011 - Springer
Abstract The Institute for Genome Sciences (IGS) has developed a prokaryotic annotation
pipeline that is used for coding gene/RNA prediction and functional annotation of Bacteria …
pipeline that is used for coding gene/RNA prediction and functional annotation of Bacteria …
Genomic diversity of EPEC associated with clinical presentations of differing severity
TH Hazen, MS Donnenberg, S Panchalingam… - Nature …, 2016 - nature.com
Enteropathogenic Escherichia coli (EPEC) are diarrhoeagenic E. coli, and are a significant
cause of gastrointestinal illness among young children in developing countries. Typical …
cause of gastrointestinal illness among young children in developing countries. Typical …