Software

The CA1 Pyramidal Cell Model

NEURON code for the experiments described in:

1. Poirazi, P. Brannon, T. and Mel, B.W. Arithmetic of Subthreshold Synaptic Summation in a Model CA1 Pyramidal Cell.
Neuron, vol 37, pg. 977-987, March 2003. [Abstract] [PDF]

2. Poirazi, P. Brannon, T. and Mel, B.W. Pyramidal Neuron as 2-Layer Neural Network.
Neuron, vol 37, pg. 989-999, March 2003. [Abstract] [PDF]

3. Poirazi, P. Brannon, T. and Mel, B.W. About the Model (online supplement)
Neuron, vol 37, pg. 988, March 2003. [PDF]

The CER classifier: a Feature Selection/Classification Tool

Code for the feature selection and classification method described in:

Pavlidis P. and Poirazi P.
Individualized markers optimize class prediction of microarray data.
BMC Bioinformatics, 2006, 7:345 (14Jul2006)
[Abstract] [PDF]

ANN models for Growth Rate Prediction of Streptococcus macedonicus ACA-DC 198

Matlab code for the ANN models used in:

Poirazi, P., Leroy, F., Georgalaki, M.D., Aktypis, A., De Vuyst, L., and Tsakalidou, E.
Use of artificial neural networks and a gamma-concept-based approach to model growth of and bacteriocin production by Streptococcus macedonicus ACA-DC 198 under conditions simulating Kasseri cheese technology.
Appl. Environ. Microbiol. 2007, Feb;73(3):768-76.
[Abstract] [PDF]

Expression Profiling Suite 2.1: Compilation of Methods for Microarray Data Analysis

The Expression Profiling Suite of tools used in:

Petalidis, L.P., Oulas, A.,Wayland, M.T., Liu, L., Plant, K., Happerfield, L., Renault-Mihara , F., Freeman, T.C., Poirazi, P., & Collins, P.V.
Grading of human astrocytic brain tumours by artificial neural network analysis of gene expression microarray data.
Molecular Cancer Therapeutics, vol. 7, No 5, pg. 1013-24, May 2008 (Cover feature).
[Abstract] [PDF]

Note: If you need more information about this software please contact oulas at imbb.forth.gr

SSCprofiler: a Web-based tool for computational identification of novel miRNA precursors

The SSCprofiler tool used in:

Oulas, A. Boutla, A. Gkirtzou, K. Reczko, M. Kalantidis, K. and Poirazi, P.
Prediction of novel microRNA genes in cancer associated genomic regions: a combined computational and experimental approach
Nucleic Acid Research, doi: 10.1093/nar/gkp120, March 2009.
[Abstract] [PDF]

Note: If you want to download the source code for this software please contact oulas at imbb.forth.gr

Mature Bayes: a Web-based tool for the computational identification of mature miRNAs

The Mature Bayes tool used in:

Gkirtzou K, Tsamardinos I, Tsakalides P, Poirazi P.
MatureBayes: a probabilistic algorithm for identifying the mature miRNA within novel precursors.
PLoS One, 5(8). pii: e11843 , Aug. 2010.
[Abstract] [PDF]