Software

Software tools and packages under active development and maintanance

BEclear - Batch Effect Detection and Adjustment in DNA Methylation Data. - PLoS One (2016)

DACO - A novel transcription factor complex prediction algorithm. - Bioinformatics (2014)

MCDS (Heuristic solution) - MCDS is a Cytoscape app that allows users to find an approximate MCDS solution in a directed graph. - BMC Systems Biology (2016)

MDS and MCDS (Optimal solutions) - Implementation of the ILP formulations for MDS and MCDS problems in the Sage software system using the glpk solver underlying gene regulatory networks. - BMC Systems Biology (2016)

Mebitoo - Mebitoo is a bioinformatics tool to embrace computational analysis methods with a uniform graphical user interface. Moreover, the software enables persistent storage with an incorporated database engine, which supports XML files for customized data structures. - BICoB (2015)

MolTPC - MolTPC provides a solution for fully automatic tautomer enumeration. - Journal of Computational Chemistry (2013)

PPICompare - PPICompare detects rewiring events in protein interaction networks. 

PPIXpress - PPIXpress constructs spicing-specific protein interaction networks from transcript expression data. - Bioinformatics (2015)

PreTIS - PreTIS is a web service to predict non-canonical translational start sites in the 5' UTR from the mRNA sequence. - PLoS Computational Biology (2016)

TFmiR - TFmiR is a web service that builds a TF and miRNA co-regulatory network based on user parameters set and generate general and disease-specific co-regulatory networks. - Nucleic Acid Research (2015)

Software no longer in active development

Brownmove - A many-particle Brownian-Dynamics simulation package.

CESIP (cellular simulation package) in C++

EPOSBP - Ensemble of Pockets on Protein Surfaces with BALLPass.

PROPORES (PROtein PORE identification toolS) - “PROPORES” is a novel toolkit for identifying pockets, cavities and channels of protein structures. - Proteins: Structure, Function, and Bioinformatics (2012)

QVADIS Java3D program package to characterize proton transfer pathways in biomolecules accounting for side chain flexibility and transfer kinetics.

TopoView

SnvDMiR - Associating the genomic  proximity of genetic variants with deregulated miRNAs and differentially methylated regions.  (R code)

Vesimulus - A molecular stochastic simulations of metabolic or signaling systems. - PLoS One (2010)