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)

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)

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; et al. (Bioinform., 2003)

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 001; Sophia Tsoka; Victor Kunin; et al. (Bioinform., 2005)

Computational methodologies for genome evolution and functional association. - Sophia Tsoka (Comput. Chem. Eng., 2007)

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)

Module detection in complex networks using integer optimisation. - Gang Xu 005; Laura Bennett; Lazaros G. Papageorgiou; Sophia Tsoka (Algorithms Mol. Biol., 2010)

Promoter Complexity and Tissue-Specific Expression of Stress Response Components in Mytilus galloprovincialis, 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)

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)

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 (CMSB, 2012)

Detection of Disjoint and Overlapping Modules in Weighted Complex Networks. - Laura Bennett; Songsong Liu; Lazaros G. Papageorgiou; Sophia Tsoka (Adv. Complex Syst., 2012)

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)

Using ILP to Identify Pathway Activation Patterns in Systems Biology. - Samuel R. Neaves; Louise A. C. Millard; Sophia Tsoka (ILP, 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)

Sample re-weighting hyper box classifier for multi-class data classification. - Lingjian Yang; Songsong Liu; Sophia Tsoka; Lazaros G. Papageorgiou (Comput. Ind. Eng., 2015)

Link Prediction Methods and Their Accuracy for Different Social Networks and Network Metrics. - Fei Gao 009; Katarzyna Musial; Colin Cooper; Sophia Tsoka (Sci. Program., 2015)

Community Structure Detection for Directed Networks through Modularity Optimisation. - Lingjian Yang; Jonathan Cardoso-Silva; Lazaros G. Papageorgiou; Sophia Tsoka (Algorithms, 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)

Mathematical programming for piecewise linear regression analysis. - Lingjian Yang; Songsong Liu; Sophia Tsoka; Lazaros G. Papageorgiou (Expert Syst. Appl., 2016)

A regression tree approach using mathematical programming. - Lingjian Yang; Songsong Liu; Sophia Tsoka; Lazaros G. Papageorgiou (Expert Syst. Appl., 2017)

Reactome Pengine: a web-logic API to the Homo sapiens reactome. - Samuel R. Neaves; Sophia Tsoka; Louise A. C. Millard (Bioinform., 2018)

Network-based piecewise linear regression for QSAR modelling. - Jonathan Cardoso-Silva; Lazaros G. Papageorgiou; Sophia Tsoka (J. Comput. Aided Mol. Des., 2019)

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 (ICBBT, 2020)

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 008; Sophia Tsoka (LOD (2), 2022)

A Matrix Factorization-Based Drug-Virus Link Prediction Method for SARS-CoV-2 Drug Prioritization. - Yutong Li 006; Xiaorui Xu; Sophia Tsoka (LOD (1), 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)

Incorporating Prior Knowledge in Deep Learning Models via Pathway Activity Autoencoders. - Pedro Henrique da Costa Avelar; Min Wu 008; Sophia Tsoka (CoRR, 2023)

Drug repurposing and prediction of multiple interaction types via graph embedding. - E. Amiri Souri; A. Chenoweth; S. N. Karagiannis; Sophia Tsoka (BMC Bioinform., 2023)

Pathway Activity Autoencoders for Enhanced Omics Analysis and Clinical Interpretability. - Pedro Henrique da Costa Avelar; Le Ou-Yang; Min Wu 008; Sophia Tsoka (BIBM, 2024)

CLigOpt: controllable ligand design through target-specific optimization. - Yutong Li 006; Pedro Henrique da Costa Avelar; Xinyue Chen; Li Zhang; Min Wu 008; Sophia Tsoka (Bioinform., 2024)

Optimisation-based modelling for explainable lead discovery in malaria. - Yutong Li 006; Jonathan Cardoso-Silva; John M. Kelly; Michael J. Delves; Nicholas Furnham; Lazaros G. Papageorgiou; Sophia Tsoka (Artif. Intell. Medicine, 2024)

Enhancing Generalized Few-Shot Semantic Segmentation via Effective Knowledge Transfer. - Xinyue Chen; Miaojing Shi; Zijian Zhou 002; Lianghua He; Sophia Tsoka (AAAI, 2025)

Surg-3M: A Dataset and Foundation Model for Perception in Surgical Settings. - Chengan Che; Chao Wang; Tom Vercauteren; Sophia Tsoka; Luis C. García-Peraza-Herrera (CoRR, 2025)

Interpretable optimisation-based approach for hyper-box classification. - Georgios I. Liapis; Sophia Tsoka; Lazaros G. Papageorgiou (Mach. Learn., 2025)

Subset-Contrastive Multi-Omics Network Embedding. - Pedro Henrique da Costa Avelar; Min Wu 008; Sophia Tsoka (CoRR, 2025)