[{TableOfContents}]

!!!List of Software
# [ADR]
# [CKSAAP-Palm]
# [DeterminePPI]
# [GNTInfer]
# [GRNInfer]
# [HMC]
# [InferPPI]
# [LOHCRP]
# [MCDGPA]
# [MDCInfer]
# [MNAligner]
# [ModularityOptimization]
# [NRWRH]
# [PPICPM]
# [PPINA]
# [PRNA]
# [PSN]
# [PTG]
# [PTMPred]
# [SABIC]
# [Samo]
# [SANA]
# [StruComp]

!!!Genome Analysis (6)

* [HMC]: Haplotype inference tool based on Markov Chain model
* [PTG]: Pasimonious tree-grow method for haplotype inference
* [LOHCRP]: LOH inference and segmentation tool based on conditional random field model
* [CKSAAP-Palm]: A tool for predicting palmitoylation sites from protein sequences
* [PTMPred]: A tool for predicting post-transcriptional modification sites from protein sequences
* [PRNA]: Prediction of protein-RNA binding sites by a random forest method with combined features

!!!Molecular Networks (9)

!!Gene Regulatory Networks Inference (2)

* [GNTInfer]: Gene network reconstruction tool with compound targets by integrating multiple microarray datasets and prior information 
* [GRNInfer]: Gene regulatory network inference tool from multiple microarray datasets 

!!PPI Networks Inference (3)

* [MDCInfer]: PPI prediction tool based on multiple domain cooperation analysis
* [DeterminePPI]: Inferring protein-protein interactions by parsimony principle 
* [InferPPI]: Predicting protein interactions based on parsimony tendency of domain interactions

!!Network Module Analysis (2)
* [PPICPM]: Identification of functional modules in PPI network by clique percolation clustering
* [ModularityOptimization]: Modularity optimization in community identification of complex networks

!!Network Alignment (2)
* [MNAligner]: Alignment of molecular networks by quadratic programming
* [PPINA]: Alignment of protein interaction networks by integer quadratic programming


!!!Structure Biology (5)

* [Samo]: Protein structure alignment tool based on multiple objective optimization
* [SANA]: Protein Structure Alignment by Neighborhood Alignment
* [SABIC]: protein Structure Alignment Based on Internal Coordinates
* [StruComp]: Evaluating protein similarity from coarse structures
* [PSN]: Protein pocket similarity networks

!!!Systems Biology (2)
* [ADR]: Detecting and analyzing differentially activated pathways in brain regions of Alzheimer's disease patients
* [MCDGPA]: Modularized Candidate Disease Genes Prioritization Algorithm
* [NRWRH]: Network-based Random Walk with Restart on the Heterogeneous network