University of Patras - Computer Engineering and Informatics Department

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Computational Biology and Bioinformatics Group

Publications

23.02.2015: ncRNAclass: A Web Platform for Non-Coding RNA Feature Calculation and MicroRNAs and Targets Prediction (Journal paper)

Karathanou,K., Theofilatos,K., Kleftogiannis,D., Alexakos,C., Likothanassis,S., Tsakalidis,A., & Mavroudi,S. (2015). ncRNAclass: A Web Platform for Non-Coding RNA Feature Calculation and MicroRNAs and Targets Prediction. International Journal on Artificial Intelligence Tools, 24(01), 1540002

19.02.2015: Predicting protein complexes from weighted protein–protein interaction graphs with a novel unsupervised methodology: Evolutionary enhanced Markov clustering (Journal paper)

Georgopoulos,E., & Mavroudi,S. (2015). Predicting protein complexes from weighted protein–protein interaction graphs with a novel unsupervised methodology: Evolutionary enhanced Markov clustering. Artificial intelligence in medicine, 63(3), 181-189

10.02.2015: Predicting human miRNA target genes using a novel computational intelligent framework (Journal paper)

Korfiati,A., Theofilatos,K., Kleftogiannis,D., Alexakos,C., Likothanassis,S., & Mavroudi,S. (2015). Predicting human miRNA target genes using a novel computational intelligent framework. Information Sciences ,294, 576-585

 

23.01.2015: YamiPred: A novel evolutionary method for predicting pre-miRNAs and selecting relevant features (Journal paper)

Kleftogiannis,D., Theofilatos,K., Likothanassis,S., & Mavroudi,S. (2015). YamiPred: A novel evolutionary method for predicting pre-miRNAs and selecting relevant features. Computational Biology and Bioinformatics, IEEE/ACM Transactions on , vol.12, no.5, pp.1183-1192

17.10.2014: The Human Interactome Knowledge Base (HINT-KB): an integrative human protein interaction database enriched with predicted protein–protein interaction scores using a novel hybrid technique (Journal paper)

Theofilatos,K., Dimitrakopoulos,C., Likothanassis,S., Kleftogiannis,D., Moschopoulos,C., Alexakos,C., & Mavroudi,S. (2014). The Human Interactome Knowledge Base (HINT-KB): an integrative human protein interaction database enriched with predicted protein–protein interaction scores using a novel hybrid technique. Artificial Intelligence Review, 42(3), 427-443

 

20.09.2014: A New Framework for Bridging the Gap from Protein-Protein Interactions to Biological Process Interactions (Conference paper)

Dimitrakopoulos,C., Vlantis,A.D., Theofilatos,K., Likothanassis,S., & Mavroudi,S. (2014). A New Framework for Bridging the Gap from Protein-Protein Interactions to Biological Process Interactions. In Artificial Intelligence Applications and Innovations (pp.196-204). SpringerBerlinHeidelberg

15.08.2014: Ensemble GASVR: a novel ensemble method for classifying missense single nucleotide polymorphisms (Journal paper)

Rapakoulia,T., Theofilatos,K., Kleftogiannis,D., Likothanasis,S., Tsakalidis,A., & Mavroudi,S. (2014). Ensemble GASVR: a novel ensemble method for classifying missense single nucleotide polymorphisms. Bioinformatics, 30(16), 2324-2333

12.07.2013: The Human Interactome Knowledge Base (HINT-KB): an integrative human protein interaction database enriched with predicted protein–protein interaction scores using a novel hybrid technique (Journal paper)

K Theofilatos, C. Dimitrakopoulos, S. Likothanassis, D. Kleftogiannis, C.Moschopoulos, C. Alexakos, S. Papadimitriou, S. Mavroudi,

 

03.07.2013: Where we stand, where we are moving: Surveying computational techniques for identifying miRNA genes and uncovering their regulatory role (Journal paper)

Dimitrios, K., Aigli, K., Konstantinos, T., Spiros, L., Athanasios, T., Seferina, M., Where we stand, where we are moving: Surveying computational techniques for identifying miRNA genes and uncovering their regulatory role, Journal of biomedical informatics, 2013

 

Key Points:

Surveying computational techniques for identifying miRNA genes and uncovering their regulatory role.

Updating the methodologies list and emphasizing on the computational issues that arise from the miRNA data analysis.

The various miRNA data analysis steps are treated as an integrated procedure whose aims and scope is to uncover

the regulatory role and mechanisms of the miRNA genes.

04.04.2013: Analyzing Human Proteome: From Protein-Protein Interaction Prediction To Protein Complex Prediction And Function Characterization Of Proteins (Conference paper)

K. Theofilatos, S. Likothanassis and S. Mavroudi

Analyzing Human Proteome: From Protein-Protein Interaction Prediction To Protein Complex Prediction And Function Characterization Of Proteins, ELEVIT Cconference, 2013 (BEST STUDENT PAPER AWARD)

 

Key Points:

Α ecomputational framework for the analysis of Human Proteome. Combination of a novel computational method

for the prediction and scoring of PPIs in human with a novel protein complex prediction method.

27.11.2012: HINT-KB: The Human Interactome Knowledge Base (Conference paper)

K. Theofilatos, C. Dimitrakopoulos, D. Kleftogiannis, C. Moschopoulos, S. Papadimitriou, S. Likothanassis and S. Mavroudi, HINT-KB: The Human Interactome Knowledge Base, AIAI 2012, Chalkidiki, Greece, 27-30 September 2012 (IFIP International Federation for Information Processing, pp. 612-621, 2012)

27.11.2012: ncRNA-Class Web Tool: Non-coding RNA Feature Extraction and Pre-miRNA Classification Web Tool (Conference paper)

D. Kleftogiannis, K. Theofilatos, S. Papadimitriou, A. Tsakalidis, S. Likothanassis and S. Mavroudi, ncRNA-Class Web Tool:  Non-coding RNA Feature Extraction and Pre-miRNA Classification Web Tool, AIAI 2012, Chalkidiki, Greece, 27-30 September 2012 (IFIP International Federation for Information Processing 2012, pp. 632-641, 2012).