Sophia Tsoka

According to our database, Sophia Tsoka authored at least 29 papers between 2000 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2024

Optimisation-based modelling for explainable lead discovery in malaria.

Yutong Li, Jonathan Cardoso-Silva, John M. Kelly, Michael J. Delves, Nicholas Furnham, Lazaros G. Papageorgiou, Sophia Tsoka

Artif. Intell. Medicine, January, 2024

2023

Drug repurposing and prediction of multiple interaction types via graph embedding.

E. Amiri Souri, A. Chenoweth, S. N. Karagiannis, Sophia Tsoka

BMC Bioinform., December, 2023

Incorporating Prior Knowledge in Deep Learning Models via Pathway Activity Autoencoders.

Pedro Henrique da Costa Avelar, Min Wu, Sophia Tsoka

CoRR, 2023

2022

Novel drug-target interactions via link prediction and network embedding.

E. Amiri Souri, Roman Laddach, S. N. Karagiannis, Lazaros G. Papageorgiou, Sophia Tsoka

BMC Bioinform., 2022

A Matrix Factorization-Based Drug-Virus Link Prediction Method for SARS-CoV-2 Drug Prioritization.

Yutong Li, Xiaorui Xu, Sophia Tsoka

Proceedings of the Machine Learning, Optimization, and Data Science, 2022

Multi-omic Data Integration and Feature Selection for Survival-Based Patient Stratification via Supervised Concrete Autoencoders.

Pedro Henrique da Costa Avelar, Roman Laddach, Sophia Karagiannis, Min Wu, Sophia Tsoka

Proceedings of the Machine Learning, Optimization, and Data Science, 2022

2020

Identification of Important Biological Pathways for Ischemic Stroke Prediction through a Mathematical Programming Optimisation Model-DIGS.

Yongnan Chen, Konstantinos Theofilatos, Lazaros G. Papageorgiou, Sophia Tsoka

Proceedings of the 12th International Conference on Bioinformatics and Biomedical Technology, 2020

2019

Network-based piecewise linear regression for QSAR modelling.

Jonathan Cardoso-Silva, Lazaros G. Papageorgiou, Sophia Tsoka

J. Comput. Aided Mol. Des., 2019

2018

Reactome Pengine: a web-logic API to the Homo sapiens reactome.

Samuel R. Neaves, Sophia Tsoka, Louise A. C. Millard

Bioinform., 2018

2017

A regression tree approach using mathematical programming.

Lingjian Yang, Songsong Liu, Sophia Tsoka, Lazaros G. Papageorgiou

Expert Syst. Appl., 2017

2016

Mathematical programming for piecewise linear regression analysis.

Lingjian Yang, Songsong Liu, Sophia Tsoka, Lazaros G. Papageorgiou

Expert Syst. Appl., 2016

Organizational principles of the Reactome human BioPAX model using graph theory methods.

Aristotelis Kittas, Laura Bennett, Henning Hermjakob, Sophia Tsoka

J. Complex Networks, 2016

Community Structure Detection for Directed Networks through Modularity Optimisation.

Lingjian Yang, Jonathan Cardoso-Silva, Lazaros G. Papageorgiou, Sophia Tsoka

Algorithms, 2016

2015

Link Prediction Methods and Their Accuracy for Different Social Networks and Network Metrics.

Fei Gao, Katarzyna Musial, Colin Cooper, Sophia Tsoka

Sci. Program., 2015

Sample re-weighting hyper box classifier for multi-class data classification.

Lingjian Yang, Songsong Liu, Sophia Tsoka, Lazaros G. Papageorgiou

Comput. Ind. Eng., 2015

CytoASP: a Cytoscape app for qualitative consistency reasoning, prediction and repair in biological networks.

Aristotelis Kittas, Amélie Barozet, Jekaterina Sereshti, Niels Grabe, Sophia Tsoka

BMC Syst. Biol., 2015

Using ILP to Identify Pathway Activation Patterns in Systems Biology.

Samuel R. Neaves, Louise A. C. Millard, Sophia Tsoka

Proceedings of the Inductive Logic Programming - 25th International Conference, 2015

2014

Pathway activity inference for multiclass disease classification through a mathematical programming optimisation framework.

Lingjian Yang, Chrysanthi Ainali, Sophia Tsoka, Lazaros G. Papageorgiou

BMC Bioinform., 2014

2012

Detection of Disjoint and Overlapping Modules in Weighted Complex Networks.

Laura Bennett, Songsong Liu, Lazaros G. Papageorgiou, Sophia Tsoka

Adv. Complex Syst., 2012

Detection of Multi-clustered Genes and Community Structure for the Plant Pathogenic Fungus Fusarium graminearum.

Laura Bennett, Artem Lysenko, Lazaros G. Papageorgiou, Martin Urban, Kim E. Hammond-Kosack, Christopher J. Rawlings, Mansoor A. S. Saqi, Sophia Tsoka

Proceedings of the Computational Methods in Systems Biology, 2012

2010

A Systems Model for Immune Cell Interactions Unravels the Mechanism of Inflammation in Human Skin.

Najl V. Valeyev, Christian Hundhausen, Yoshinori Umezawa, Nikolai V. Kotov, Gareth Williams, Alex Clop, Crysanthi Ainali, Christos A. Ouzounis, Sophia Tsoka, Frank O. Nestle

PLoS Comput. Biol., 2010

Promoter Complexity and Tissue-Specific Expression of Stress Response Components in <i>Mytilus galloprovincialis</i>, a Sessile Marine Invertebrate Species.

Chrysa Pantzartzi, Elena Drosopoulou, Minas Yiangou, Ignat Drozdov, Sophia Tsoka, Christos A. Ouzounis, Zacharias G. Scouras

PLoS Comput. Biol., 2010

Module detection in complex networks using integer optimisation.

Gang Xu, Laura Bennett, Lazaros G. Papageorgiou, Sophia Tsoka

Algorithms Mol. Biol., 2010

2009

Stratification of co-evolving genomic groups using ranked phylogenetic profiles.

Shiri Freilich, Leon Goldovsky, Assaf Gottlieb, Eric Blanc, Sophia Tsoka, Christos A. Ouzounis

BMC Bioinform., 2009

2007

Computational methodologies for genome evolution and functional association.

Sophia Tsoka

Comput. Chem. Eng., 2007

2005

CoGenT++: an extensive and extensible data environment for computational genomics.

Leon Goldovsky, Paul J. Janssen, Dag G. Ahrén, Benjamin Audit, Ildefonso Cases, Nikos Darzentas, Anton J. Enright, Núria López-Bigas, José M. Peregrín-Alvarez, Mike Smith, Sophia Tsoka, Victor Kunin, Christos A. Ouzounis

Bioinform., 2005

2003

Evaluation of annotation strategies using an entire genome sequence.

Ioannis Iliopoulos, Sophia Tsoka, Miguel A. Andrade, Anton J. Enright, Mark Carroll, Patrick Poullet, Vasilis J. Promponas, Theodore Liakopoulos, Giorgos Palaios, Claude Pasquier, Stavros J. Hamodrakas, Javier Tamames, Asutosh T. Yagnik, Anna Tramontano, Damien Devos, Christian Blaschke, Alfonso Valencia, David Brett, David M. A. Martin, Christophe Leroy, Isidore Rigoutsos, Chris Sander, Christos A. Ouzounis

Bioinform., 2003

2002

Modeling the percolation of annotation errors in a database of protein sequences.

Walter R. Gilks, Benjamin Audit, Daniela De Angelis, Sophia Tsoka, Christos A. Ouzounis

Bioinform., 2002

2000

CAST: an iterative algorithm for the complexity analysis of sequence tracts.

Vasilis J. Promponas, Anton J. Enright, Sophia Tsoka, David P. Kreil, Christophe Leroy, Stavros J. Hamodrakas, Chris Sander, Christos A. Ouzounis

Bioinform., 2000