MLST revisited: the gene-by-gene approach to bacterial genomics
MCJ Maiden, MJJ Van Rensburg, JE Bray… - Nature Reviews …, 2013 - nature.com
Multilocus sequence typing (MLST) was proposed in 1998 as a portable sequence-based
method for identifying clonal relationships among bacteria. Today, in the whole-genome era …
method for identifying clonal relationships among bacteria. Today, in the whole-genome era …
Quantitative and logic modelling of molecular and gene networks
N Le Novere - Nature Reviews Genetics, 2015 - nature.com
Behaviours of complex biomolecular systems are often irreducible to the elementary
properties of their individual components. Explanatory and predictive mathematical models …
properties of their individual components. Explanatory and predictive mathematical models …
[HTML][HTML] The NCATS BioPlanet–an integrated platform for exploring the universe of cellular signaling pathways for toxicology, systems biology, and chemical genomics
R Huang, I Grishagin, Y Wang, T Zhao… - Frontiers in …, 2019 - frontiersin.org
Chemical genomics aims to comprehensively define, and ultimately predict, the effects of
small molecule compounds on biological systems. Chemical activity profiling approaches …
small molecule compounds on biological systems. Chemical activity profiling approaches …
[HTML][HTML] Joint and individual variation explained (JIVE) for integrated analysis of multiple data types
Research in several fields now requires the analysis of datasets in which multiple high-
dimensional types of data are available for a common set of objects. In particular, The …
dimensional types of data are available for a common set of objects. In particular, The …
Mendelian randomization: new applications in the coming age of hypothesis-free causality
DM Evans, G Davey Smith - Annual review of genomics and …, 2015 - annualreviews.org
Mendelian randomization (MR) is an approach that uses genetic variants associated with a
modifiable exposure or biological intermediate to estimate the causal relationship between …
modifiable exposure or biological intermediate to estimate the causal relationship between …
[HTML][HTML] The iPlant collaborative: cyberinfrastructure for plant biology
The iPlant Collaborative (iPlant) is a United States National Science Foundation (NSF)
funded project that aims to create an innovative, comprehensive, and foundational …
funded project that aims to create an innovative, comprehensive, and foundational …
Web scraping technologies in an API world
D Glez-Peña, A Lourenço… - Briefings in …, 2014 - academic.oup.com
Web services are the de facto standard in biomedical data integration. However, there are
data integration scenarios that cannot be fully covered by Web services. A number of Web …
data integration scenarios that cannot be fully covered by Web services. A number of Web …
[HTML][HTML] Open PHACTS: semantic interoperability for drug discovery
Open PHACTS is a public–private partnership between academia, publishers, small and
medium sized enterprises and pharmaceutical companies. The goal of the project is to …
medium sized enterprises and pharmaceutical companies. The goal of the project is to …
[HTML][HTML] The human genome project: big science transforms biology and medicine
Abstract The Human Genome Project has transformed biology through its integrated big
science approach to deciphering a reference human genome sequence along with the …
science approach to deciphering a reference human genome sequence along with the …
[HTML][HTML] Comparing the normalization methods for the differential analysis of Illumina high-throughput RNA-Seq data
Background Recently, rapid improvements in technology and decrease in sequencing costs
have made RNA-Seq a widely used technique to quantify gene expression levels. Various …
have made RNA-Seq a widely used technique to quantify gene expression levels. Various …