GeneQuiz: A Workbench for Sequence Analysis. - Michael Scharf; Reinhard Schneider 002; Georg Casari; Peer Bork; Alfonso Valencia; Christos A. Ouzounis; Chris Sander (ISMB, 1994)

The Functional Composition of Living Machines as a Design Principle for Artificial Organisms. - Christos A. Ouzounis; Alfonso Valencia; Javier Tamames; Peer Bork; Chris Sander (ECAL, 1995)

HinCyc: A Knowledge Base of the Complete Genome and Metabolic Pathways of H. influenzae. - Peter D. Karp; Christos A. Ouzounis; Suzanne M. Paley (ISMB, 1996)

Prediction of Enzyme Classification from Protein Sequence without the Use of Sequence Similarity. - Marie desJardins; Peter D. Karp; Markus Krummenacker; Thomas J. Lee; Christos A. Ouzounis (ISMB, 1997)

Sequence analysis of the Methanococcus jannaschii genome and the prediction of protein function. - Miguel A. Andrade; Georg Casari; Antoine de Daruvar; Chris Sander; Reinhard Schneider 002; Javier Tamames; Alfonso Valencia; Christos A. Ouzounis (Comput. Appl. Biosci., 1997)

EUCLID: automatic classification of proteins in functional classes by their database annotations. - Javier Tamames; Christos A. Ouzounis; Georg Casari; Chris Sander; Alfonso Valencia (Bioinform., 1998)

Automatic Extraction of Biological Information from Scientific Text: Protein-Protein Interactions. - Christian Blaschke; Miguel A. Andrade; Christos A. Ouzounis; Alfonso Valencia (ISMB, 1999)

Automated genome sequence analysis and annotation. - Miguel A. Andrade; Nigel P. Brown; Christophe Leroy; S. Hörsch; Antoine de Daruvar; C. Reich; Angelo Franchini; Javier Tamames; Alfonso Valencia; Christos A. Ouzounis; Chris Sander (Bioinform., 1999)

A Million Annotations for the Molecular Biologist. - Christos A. Ouzounis (German Conference on Bioinformatics, 2000)

GeneRAGE: a robust algorithm for sequence clustering and domain detection. - Anton J. Enright; Christos A. Ouzounis (Bioinform., 2000)

Two or three myths about bioinformatics. - Christos A. Ouzounis (Bioinform., 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)

TEXTQUEST: Document Clustering of MEDLINE Abstracts For Concept Discovery In Molecular Biology. - Ioannis Iliopoulos; Anton J. Enright; Christos A. Ouzounis (Pacific Symposium on Biocomputing, 2001)

Transcription-associated protein families are primarily taxon-specific. - Richard M. R. Coulson; Anton J. Enright; Christos A. Ouzounis (Bioinform., 2001)

BioLayout-an automatic graph layout algorithm for similarity visualization. - Anton J. Enright; Christos A. Ouzounis (Bioinform., 2001)

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)

Bioinformatics and the theoretical foundations of molecular biology. - 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)

COmplete GENome Tracking (COGENT): A Flexible Data Environment for Computational Genomics. - Paul J. Janssen; Anton J. Enright; Benjamin Audit; Ildefonso Cases; Leon Goldovsky; Nicola Harte; Victor Kunin; Christos A. Ouzounis (Bioinform., 2003)

Comparison of sequence masking algorithms and the detection of biased protein sequence regions. - David P. Kreil; Christos A. Ouzounis (Bioinform., 2003)

GeneTRACE - Reconstruction of Gene Content of Ancestral Species. - Victor Kunin; Christos A. Ouzounis (Bioinform., 2003)

Early bioinformatics: the birth of a discipline - a personal view. - Christos A. Ouzounis; Alfonso Valencia (Bioinform., 2003)

PseuRECA: genome annotation and gene context analysis for Pseudomonas aeruginosa PAO1. - Christian Weinel; Maria D. Ermolaeva; Christos A. Ouzounis (Bioinform., 2003)

Properties of Genes involved in Human Genetic Disease. - Núria López-Bigas; Christos A. Ouzounis (Spanish Bioinformatics Conference, 2004)

Robustness of Metabolic Map Reconstruction. - Dag G. Ahrén; Christos A. Ouzounis (J. Bioinform. Comput. Biol., 2004)

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)

The properties of protein family space depend on experimental design. - Victor Kunin; Sarah A. Teichmann; Martijn A. Huynen; Christos A. Ouzounis (Bioinform., 2005)

MagicMatch - cross-referencing sequence identifiers across databases. - Mike Smith 001; Victor Kunin; Leon Goldovsky; Anton J. Enright; Christos A. Ouzounis (Bioinform., 2005)

Clustering the annotation space of proteins. - Victor Kunin; Christos A. Ouzounis (BMC Bioinform., 2005)

Probabilistic annotation of protein sequences based on functional classifications. - Emmanuel D. Levy; Christos A. Ouzounis; Walter R. Gilks; Benjamin Audit (BMC Bioinform., 2005)

Highly consistent patterns for inherited human diseases at the molecular level. - Núria López-Bigas; Benjamin J. Blencowe; Christos A. Ouzounis (Bioinform., 2006)

CORRIE: enzyme sequence annotation with confidence estimates. - Benjamin Audit; Emmanuel D. Levy; Walter R. Gilks; Leon Goldovsky; Christos A. Ouzounis (BMC Bioinform., 2007)

PuReD-MCL: a graph-based PubMed document clustering methodology. - Theodosios Theodosiou; Nikos Darzentas; Lefteris Angelis; Christos A. Ouzounis (Bioinform., 2008)

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)

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)

BioTextQuest: a web-based biomedical text mining suite for concept discovery. - Nikolas Papanikolaou; Evangelos Pafilis; Stavros Nikolaou; Christos A. Ouzounis; Ioannis Iliopoulos; Vasilis J. Promponas (Bioinform., 2011)

Keynote lectures. - Metin Akay; Yuan-Ting Zhang; Konstantina S. Nikita; Miguel A. Andrade; Christos A. Ouzounis (BIBE, 2012)

Multi-genome Core Pathway Identification through Gene Clustering. - Dimitrios M. Vitsios; Fotis E. Psomopoulos; Pericles A. Mitkas; Christos A. Ouzounis (AIAI (2), 2012)

Rise and Demise of Bioinformatics? Promise and Progress. - Christos A. Ouzounis (PLoS Comput. Biol., 2012)

Experimental evidence validating the computational inference of functional associations from gene fusion events: a critical survey. - Vasilis J. Promponas; Christos A. Ouzounis; Ioannis Iliopoulos (Briefings Bioinform., 2014)

BioTextQuest+: a knowledge integration platform for literature mining and concept discovery. - Nikolas Papanikolaou; Georgios A. Pavlopoulos; Evangelos Pafilis; Theodosios Theodosiou; Reinhard Schneider 002; Venkata P. Satagopam; Christos A. Ouzounis; Aristides G. Eliopoulos; Vasilis J. Promponas; Ioannis Iliopoulos (Bioinform., 2014)

Using Personalized Finger Gestures for Navigating Virtual Characters. - Christos A. Ouzounis; Christos Mousas; Christos-Nikolaos Anagnostopoulos; Paul Newbury (VRIPHYS, 2015)

BioTextQuest+: a knowledge integration platform for literature mining and concept discovery. - Nikolas Papanikolaou; Georgios A. Pavlopoulos; Evangelos Pafilis; Theodosios Theodosiou; Reinhard Schneider 002; Venkata P. Satagopam; Christos A. Ouzounis; Aristides G. Eliopoulos; Vasilis J. Promponas; Ioannis Iliopoulos (Bioinform., 2015)

Inference of Pathway Decomposition Across Multiple Species Through Gene Clustering. - Dimitrios M. Vitsios; Fotis E. Psomopoulos; Pericles A. Mitkas; Christos A. Ouzounis (Int. J. Artif. Intell. Tools, 2015)

Brain Radiation Information Data Exchange (BRIDE): integration of experimental data from low-dose ionising radiation research for pathway discovery. - Christos Karapiperis; Stefan J. Kempf; Roel Quintens; Omid Azimzadeh; Victoria Linares Vidal; Simonetta Pazzaglia; Dimitry Bazyka; Pier G. Mastroberardino; Zacharias G. Scouras; Soile Tapio; Mohammed Abderrafi Benotmane; Christos A. Ouzounis (BMC Bioinform., 2016)

Kernel Projection of Latent Structures Regression for Facial Animation Retargeting. - Christos A. Ouzounis; Alex Kilias; Christos Mousas (VRIPHYS, 2017)

BioPAXViz: a cytoscape application for the visual exploration of metabolic pathway evolution. - Fotis E. Psomopoulos; Dimitrios M. Vitsios; Shakuntala Baichoo; Christos A. Ouzounis (Bioinform., 2017)

Computational complexity of algorithms for sequence comparison, short-read assembly and genome alignment. - Shakuntala Baichoo; Christos A. Ouzounis (Biosyst., 2017)

Establishment of computational biology in Greece and Cyprus: Past, present, and future. - Anastasia Chasapi; Michalis Aivaliotis; Lefteris Angelis; Anastasios Chanalaris; Ioannis Iliopoulos; Ilias Kappas; Christos Karapiperis; Nikos Kyrpides; Evangelos Pafilis; Eleftherios Panteris; Pantelis Topalis; George Tsiamis; et al. (PLoS Comput. Biol., 2019)

Disentangling the complexity of low complexity proteins. - Pablo Mier; Lisanna Paladin; Stella Tamana; Sophia Petrosian; Borbála Hajdu-Soltész; Annika Urbanek; Aleksandra Gruca; Dariusz Plewczynski; Marcin Grynberg; Pau Bernadó; Zoltán Gáspári; Christos A. Ouzounis; et al. (Briefings Bioinform., 2020)

The bioinformatics wealth of nations. - Anastasia Chasapi; Vasilis J. Promponas; Christos A. Ouzounis (Bioinform., 2020)

DisProt: intrinsic protein disorder annotation in 2020. - András Hatos; Borbála Hajdu-Soltész; Alexander Miguel Monzon; Nicolas Palopoli; Lucía Álvarez; Burcu Aykaç Fas; Claudio Bassot; Guillermo I. Benítez; Martina Bevilacqua; Anastasia Chasapi; Lucía B. Chemes; Norman E. Davey; et al. (Nucleic Acids Res., 2020)

The Coming of Age for Big Data in Systems Radiobiology, an Engineering Perspective. - Christos Karapiperis; Anastasia Chasapi; Lefteris Angelis; Zacharias G. Scouras; Pier G. Mastroberardino; Soile Tapio; Michael Atkinson; Christos A. Ouzounis (Big Data, 2021)

DisProt in 2022: improved quality and accessibility of protein intrinsic disorder annotation. - Federica Quaglia; Bálint Mészáros; Edoardo Salladini; András Hatos; Rita Pancsa; Lucía B. Chemes; Mátyás Pajkos; Tamas Lazar; Samuel Peña-Díaz; Jaime Santos; Veronika Ács; Nazanin Farahi; et al. (Nucleic Acids Res., 2022)

Bio-Electrical Nanonetworks: A New Paradigm of Biological Nanocommunication based on Living Cable Bacteria Filaments. - Konstantinos F. Kantelis; Vassilios Asteriou; Aliki Papadimitriou; Anthi Petrou; Christos A. Ouzounis; Lefteris Angelis; Ioannis S. Vizirianakis; Petros Nicopolitidis; Georgios I. Papadimitriou (NANOCOM, 2023)

CGG toolkit: Software components for computational genomics. - Dimitrios Vasileiou; Christos Karapiperis; Ismini Baltsavia; Anastasia Chasapi; Dag G. Ahrén; Paul J. Janssen; Ioannis Iliopoulos; Vasilis J. Promponas; Anton J. Enright; Christos A. Ouzounis (PLoS Comput. Biol., 2023)

The Net of Life, a short story: Intricate patterns of gene flows across hundreds of extant genomes, all the way to LUCA. - Christos A. Ouzounis (Biosyst., 2024)