Software

Neuroscience

Relevant publication:
Basal tree complexity shapes functional pathways in the prefrontal cortex.
Papoutsi A, Kastellakis G., Poirazi P.
J Neurophysiol. 12 July 2017 | doi: 10.1152/jn.00099.2017
[Abstract][PDF]​

Relevant publication:
Dendrites of dentate gyrus granule cells contribute to pattern separation by controlling sparsity
Chavlis, S., Petrantonakis, C.P., Poirazi, P.
Hippocampus. 2016 Oct, DOI: http://dx.doi.org/10.1002/hipo.22675
[Abstract][PDF]

Relevant Publication:

Linking Memories across Time via Neuronal and Dendritic Overlaps in Model Neurons with Active Dendrites
George Kastellakis, Alcino J. Silva and Panayiota Poirazi
Cell Reports (2016) | http://dx.doi.org/10.1016/j.celrep.2016.10.015

[Abstract] [PDF]

Relevant publication:

REMOD: A Tool for Analyzing and Remodeling the Dendritic Architecture of Neural Cells
Bozelos P., Stefanos S.S., Bouloukakis G, Melachrinos C. and Poirazi P.
Front. Neuroanat., 06 January 2016 | http://dx.doi.org/10.3389/fnana.2015.00156

[Abstract][PDF]

Relevant publication:
Arithmetic of Subthreshold Synaptic Summation in a Model CA1 Pyramidal Cell.
Poirazi P, Brannon T, Mel BW.
Neuron. 2003 Mar 27;37(6):977-87.
[Abstract][PDF]

Relevant publication:
Distinguishing Linear vs. Non-Linear Integration in CA1 Radial Oblique Dendrites: It’s about Time.
Gómez González JF, Mel BW, Poirazi P.
Front Comput Neurosci. 2011 Nov 14;5:44. doi: 10.3389/fncom.2011.00044. eCollection 2011.
[Abstract][PDF]

Relevant publication:
Predictive Features of Persistent Activity Emergence in Regular Spiking and Intrinsic Bursting Model Neurons.
Sidiropoulou K, Poirazi P.
PLoS Comput Biol. 2012;8(4):e1002489. doi: 10.1371/journal.pcbi.1002489. Epub 2012 Apr 26.
[Abstract][PDF]

Relevant publication:
Dendritic Nonlinearities Reduce Network Size Requirements and Mediate ON and OFF States of Persistent Activity in a PFC Microcircuit Model.
Papoutsi A, Sidiropoulou K, Poirazi P.
PLoS Comput Biol. 2014 Jul 31;10(7):e1003764. doi: 10.1371/journal.pcbi.1003764. eCollection 2014.
[Abstract][PDF]

Relevant publication:
Modulatory effects of inhibition on persistent activity in a cortical microcircuit model.
Konstantoudaki X, Papoutsi A, Chalkiadaki K, Poirazi P, Sidiropoulou K.
Front Neural Circuits. 2014 Jan 31;8:7. doi: 10.3389/fncir.2014.00007. eCollection 2014.
[Abstract][PDF]

Relevant publication:
Towards predicting persistent activity of neurons by statistical and fractal dimension-based features.
Petrantonakis, P.C., Papoutsi, A., Poirazi, P.
The 2013 International Joint Conference on Neural Networks (IJCNN). Dallas, TX, 4-9 August, 2013
[PDF]

Relevant publication:
Dentate Gyrus Circuitry Features Improve Performance of Sparse Approximation Algorithms.
Panagiotis C. Petrantonakis and Panayiota Poirazi
PLoS One. 2015; 10(1): e0117023. Published online 2015 Jan 30. doi: 10.1371/journal.pone.0117023
[Abstract][PDF]

Relevant publication:
A computational study on how theta modulated inhibition can account for the long temporal windows in the entorhinal-hippocampal loop.
Cutsuridis V, Poirazi P
Neurobiol Learn Mem.2015 Apr;120:69-83. doi: 10.1016/j.nlm.2015.02.002. Epub 2015 Feb 24.
[Abstract][PDF]

Bioinformatics

Relevant publication: 

MiRduplexSVM: A High-Performing MiRNA-Duplex Prediction and Evaluation Methodology.
Karathanasis N, Tsamardinos I, Poirazi P.
PLoS One. 2015 May 11;10(5):e0126151. doi: 10.1371/journal.pone.0126151. eCollection 2015.

[Abstract][PDF]

Relevant publication:
Individualized markers optimize class prediction of microarray data.
Pavlidis P, Poirazi P.
BMC Bioinformatics. 2006 Jul 14;7:345.
[Abstract][PDF]

Relevant publication:
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.
Poirazi P, Leroy F, Georgalaki MD, Aktypis A, De Vuyst L, Tsakalidou E.
Appl Environ Microbiol. 2007 Feb;73(3):768-76. Epub 2006 Dec 8.
[Abstract][PDF]

Relevant publication:
Improved grading and survival prediction of human astrocytic brain tumors by artificial neural network analysis of gene expression microarray data.
Petalidis LP, Oulas A, Backlund M, Wayland MT, Liu L, Plant K, Happerfield L, Freeman TC, Poirazi P, Collins VP.
Mol Cancer Ther. 2008 May;7(5):1013-24. doi: 10.1158/1535-7163.MCT-07-0177. Epub 2008 Apr 29.
[Abstract][PDF] Note: If you need more information about this software please contact oulas at imbb.forth.gr

Relevant publication:
Prediction of novel microRNA genes in cancer-associated genomic regions–a combined computational and experimental approach.
Oulas A, Boutla A, Gkirtzou K, Reczko M, Kalantidis K, Poirazi P.
Nucleic Acids Res. 2009 Jun;37(10):3276-87. doi: 10.1093/nar/gkp120. Epub 2009 Mar 25.
[Abstract][PDF]

Relevant publication:
MatureBayes: a probabilistic algorithm for identifying the mature miRNA within novel precursors.
Gkirtzou K, Tsamardinos I, Tsakalides P, Poirazi P.
PLoS One. 2010 Aug 6;5(8):e11843. doi: 10.1371/journal.pone.0011843.
[Abstract][PDF]

Relevant publication:
A new microRNA target prediction tool identifies a novel interaction of a putative miRNA with CCND2.
Oulas A, Karathanasis N, Louloupi A, Iliopoulos I, Kalantidis K, Poirazi P.
RNA Biol. 2012 Sep;9(9):1196-207. doi: 10.4161/rna.21725. Epub 2012 Sep 1.
[Abstract][PDF]