Prediction of Cell Wall Sorting Signals in Gram-Positive bacteria with a Hidden Markov Model: Application to Complete genomes. - Zoi I. Litou; Pantelis G. Bagos; Konstantinos D. Tsirigos; Theodore D. Liakopoulos; Stavros J. Hamodrakas (J. Bioinform. Comput. Biol., 2008)

Combined prediction of Tat and Sec signal peptides with hidden Markov models. - Pantelis G. Bagos; Elisanthi P. Nikolaou; Theodore D. Liakopoulos; Konstantinos D. Tsirigos (Bioinform., 2010)

ExTopoDB: a database of experimentally derived topological models of transmembrane proteins. - Georgios N. Tsaousis; Konstantinos D. Tsirigos; Xanthi D. Andrianou; Theodore D. Liakopoulos; Pantelis G. Bagos; Stavros J. Hamodrakas (Bioinform., 2010)

OMPdb: a database of β-barrel outer membrane proteins from Gram-negative bacteria. - Konstantinos D. Tsirigos; Pantelis G. Bagos; Stavros J. Hamodrakas (Nucleic Acids Res., 2011)

CW-PRED: A HMM-Based Method for the Classification of Cell Wall-Anchored Proteins of Gram-Positive Bacteria. - Danai K. Fimereli; Konstantinos D. Tsirigos; Zoi I. Litou; Theodore D. Liakopoulos; Pantelis G. Bagos; Stavros J. Hamodrakas (SETN, 2012)

Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat. - Patricia C. Babbitt; Pantelis G. Bagos; Amos Bairoch; Alex Bateman; Arnaud Chatonnet; Mark Jinan Chen; David J. Craik; Robert D. Finn; David E. Gloriam; Daniel H. Haft; Bernard Henrissat; Gemma L. Holliday; et al. (Database J. Biol. Databases Curation, 2015)

The TOPCONS web server for consensus prediction of membrane protein topology and signal peptides. - Konstantinos D. Tsirigos; Christoph Peters; Nanjiang Shu; Lukas Käll; Arne Elofsson (Nucleic Acids Res., 2015)

Inclusion of dyad-repeat pattern improves topology prediction of transmembrane β-barrel proteins. - Sikander Hayat; Christoph Peters; Nanjiang Shu; Konstantinos D. Tsirigos; Arne Elofsson (Bioinform., 2016)

Improved topology prediction using the terminal hydrophobic helices rule. - Christoph Peters; Konstantinos D. Tsirigos; Nanjiang Shu; Arne Elofsson (Bioinform., 2016)

PRED-TMBB2: improved topology prediction and detection of beta-barrel outer membrane proteins. - Konstantinos D. Tsirigos; Arne Elofsson; Pantelis G. Bagos (Bioinform., 2016)

GWAR: robust analysis and meta-analysis of genome-wide association studies. - Niki L. Dimou; Konstantinos D. Tsirigos; Arne Elofsson; Pantelis G. Bagos (Bioinform., 2017)

DisProt 7.0: a major update of the database of disordered proteins. - Damiano Piovesan; Francesco Tabaro; Ivan Micetic; Marco Necci; Federica Quaglia; Christopher J. Oldfield; Maria Cristina Aspromonte; Norman E. Davey; Radoslav Davidovic; Zsuzsanna Dosztányi; Arne Elofsson; Alessandra Gasparini; et al. (Nucleic Acids Res., 2017)

Extending hidden Markov models to allow conditioning on previous observations. - Ioannis A. Tamposis; Margarita C. Theodoropoulou; Konstantinos D. Tsirigos; Pantelis G. Bagos (J. Bioinform. Comput. Biol., 2018)

Semi-supervised learning of Hidden Markov Models for biological sequence analysis. - Ioannis A. Tamposis; Konstantinos D. Tsirigos; Margarita C. Theodoropoulou; Panagiota I. Kontou; Pantelis G. Bagos (Bioinform., 2019)

JUCHMME: a Java Utility for Class Hidden Markov Models and Extensions for biological sequence analysis. - Ioannis A. Tamposis; Konstantinos D. Tsirigos; Margarita C. Theodoropoulou; Panagiota I. Kontou; Georgios N. Tsaousis; Dimitra Sarantopoulou; Zoi I. Litou; Pantelis G. Bagos (Bioinform., 2019)

OMPdb: A Global Hub of Beta-Barrel Outer Membrane Proteins. - Ahmed F. Roumia; Konstantinos D. Tsirigos; Margarita C. Theodoropoulou; Ioannis A. Tamposis; Stavros J. Hamodrakas; Pantelis G. Bagos (Frontiers Bioinform., 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)

The next-generation Open Targets Platform: reimagined, redesigned, rebuilt. - David Ochoa; Andrew Hercules; Miguel Carmona; Daniel Suveges; Jarrod Baker; Cinzia Malangone; Irene Lopez; Alfredo Miranda; Carlos Cruz-Castillo; Luca Fumis; Manuel Bernal Llinares; Kirill Tsukanov; et al. (Nucleic Acids Res., 2023)

CW-PRED: Prediction of C-terminal surface anchoring sorting signals in bacteria and Archaea. - Aikaterini G. Chatziargyri; Evangelia A. Stasi; Konstantinos D. Tsirigos; Zoi I. Litou; Vassiliki A. Iconomidou; Pantelis G. Bagos (J. Bioinform. Comput. Biol., 2024)