Software
AMOUNTAIN: Active modules for multilayer weighted gene co-expression networks
Dong Li developed a novel algorithm to identify active modules from multilayer weighted gene co-expression networks based on a convex optimization approach. You can download the source code from our Github or the R package from the R Bioconductor page
MODA: Module differential analysis for weighted gene co-expression network
Dong Li developed a R package to conduct module differential analysis for weighted gene co-expression networks based on WGCNA, a popular algorithm for weighted co-expression network analysis. You can download the source code from our Github or the R package from the R Bioconductor page
DiME: A Scalable Disease Module Extraction Algorithm
Yunpeng Liu developed a disease module extracted algorithm for biological networks. We have applied the algorithm to Glima progression gene expression dataset and discovered several new potential regulators. The paper was published in PLOS ONE. You can download the source code and R package from the software webpage, where you can also find a comprehensive user guide and a sample dataset.
Robust twin boosting for feature selection
We developed a feature selection algorithm called robust twin boosting algorithm for extracting features from noisy omics data. The paper was published in Information Science (PDF available here). The Matlab source of the algorithm and sample datasets are available at here.
Cooperative Co-evolutionary Module Identification (CoCoMI)
We developed a module identification algorithm based on a cooperative co-evolutionary algorithm. The paper was published in IEEE Transactions on Evolutionary Computation (PDF available here). The Matlab source of the algorithm and sample datasets are available at here.
Multi-platform Unbiased optimisation of Spectrometry via Closed Loop Experimentation (MUSCLE)
Together with Prof. Mark Viant, Dr Rick Dunn, Prof. Joshua Knowles and Prof. Goodacre, James Bradbury developed a software package that can automatically optimise the control parameters of mass spectormeters, a widely used analytical instruments in biosciences. Our paper was published in Bioionformatics. You can download the software and read the detailed instruction at the project webpage.