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Osamu MARUYAMA

Dr. Sci., Associate Professor
Institute of Mathematics for Industry and Graduate School of Systems Life Sciences, Kyushu University
744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
E-Mail Address:
om at imi dot kyushu-u dot ac dot jp
Last modified: July 02, 2015


PPSampler2 tool for predicting protein complexes by sampling

 

   Version 2.3:

           readme.txt

           PPSampler2.exe

 

           Whatfs new? The following two options are available:

 

    --f1DenominatorExponent <exponent>

        set the exponent of the denominator of f1(c), where c is a cluster,

        to be <exponent>. The default is 0.5.

    --f2

        add the function, f2, into the whole scoring function, f. Without this

        option, f2 is not included in f. In the default, this option is not valid.

 

   Version 2.2:

readme.txt

PPSampler2.exe

 

Verify the MATLAB Compiler Runtime (MCR) is installed and ensure you have installed version 8.2 (R2013b).  

MCR will be found in http://www.mathworks.com/products/compiler/mcr/index.html.

 

Citation: Chasanah Kusumastuti Widita and Osamu Maruyama, PPSampler2: Predicting protein complexes more accurately and efficiently by sampling, BMC Systems Biology, 7(Suppl 6):S14, 2013.

 


PPSampler tool for predicting protein complexes by sampling

readme.txt

PPSamplerVer1.2.exe

Verify the MATLAB Compiler Runtime (MCR) is installed and ensure you have installed version 8.1 (R2013a).  

MCR will be found in http://www.mathworks.com/products/compiler/mcr/index.html.

 

Citation: Daisuke Tatsuke and Osamu Maruyama, Sampling strategy for protein complex prediction using cluster size frequency, Gene, 518(1), 152-158, 2012.

 


Naïve Bayes classifier for Heterodimeric protein complex prediction:

README.txt (updated at 07/08/2014)

The main program (jar file) is NBC-HD-PCP.jar. (updated at 07/08/2014)

features.txt specifies the names of features embedded into naïve Bayes classifiers.

Input data files can be found in data_files.zip.

 

Citation: Osamu Maruyama, Heterodimeric Protein Complex Identification by Naïve Bayes Classifiers, BMC Bioinformatics, 14:347, 2013.


NWE Node weighted expansion for predicting protein complexes by random walks with restarts

    NWE.zip

    Citation: Osamu Maruyama and Ayaka Chihara, NWE: Node-weighted expansion for protein complex prediction using random walk distances, Proteome Science, 9(Suppl 1):S14, 2011.

 


Softwares | Supporting Information | Links


List of Papers

 

Osamu Maruyama - Google Scholar Citations