Visual Data Mining of Biological Networks: One Size Does Not Fit All. - Chiara Pastrello; David Otasek; Kristen Fortney; Giuseppe Agapito; Mario Cannataro; Elize Shirdel; Igor Jurisica (PLoS Comput. Biol., 2013)

Visual Data Mining: Effective Exploration of the Biological Universe. - David Otasek; Chiara Pastrello; Andreas Holzinger; Igor Jurisica (Interactive Knowledge Discovery and Data Mining in Biomedical Informatics, 2014)

Prioritizing Therapeutics for Lung Cancer: An Integrative Meta-analysis of Cancer Gene Signatures and Chemogenomic Data. - Kristen Fortney; Joshua Griesman; Max Kotlyar; Chiara Pastrello; Marc Angeli; Ming-Sound Tsao; Igor Jurisica (PLoS Comput. Biol., 2015)

Robust quantitative scratch assay. - Andrea Vargas; Marc Angeli; Chiara Pastrello; Rosanne McQuaid; Han Li; Andrea Jurisicova; Igor Jurisica (Bioinform., 2016)

Integrated interactions database: tissue-specific view of the human and model organism interactomes. - Max Kotlyar; Chiara Pastrello; Nicholas Sheahan; Igor Jurisica (Nucleic Acids Res., 2016)

pathDIP: an annotated resource for known and predicted human gene-pathway associations and pathway enrichment analysis. - Sara Rahmati; Mark Abovsky; Chiara Pastrello; Igor Jurisica (Nucleic Acids Res., 2017)

SDREGION: Fast Spotting of Changing Communities in Biological Networks. - Serene W. H. Wong; Chiara Pastrello; Max Kotlyar; Christos Faloutsos; Igor Jurisica (KDD, 2018)

mirDIP 4.1 - integrative database of human microRNA target predictions. - Tomás Tokár; Chiara Pastrello; Andrea E. M. Rossos; Mark Abovsky; Anne-Christin Hauschild; Mike Tsay; Richard Lu; Igor Jurisica (Nucleic Acids Res., 2018)

IID 2018 update: context-specific physical protein-protein interactions in human, model organisms and domesticated species. - Max Kotlyar; Chiara Pastrello; Zara Malik; Igor Jurisica (Nucleic Acids Res., 2019)

Visualization of Biomedical Networks. - Anne-Christin Hauschild; Chiara Pastrello; Andrea E. M. Rossos; Igor Jurisica (Encyclopedia of Bioinformatics and Computational Biology (1), 2019)

Protein-Protein Interaction Databases. - Max Kotlyar; Chiara Pastrello; Andrea E. M. Rossos; Igor Jurisica (Encyclopedia of Bioinformatics and Computational Biology (1), 2019)

Two Decades of Biological Pathway Databases: Results and Challenges. - Sara Rahmati; Chiara Pastrello; Andrea E. M. Rossos; Igor Jurisica (Encyclopedia of Bioinformatics and Computational Biology (1), 2019)

The IMEx coronavirus interactome: an evolving map of Coronaviridae-host molecular interactions. - Livia Perfetto; Chiara Pastrello; Noemi del-Toro; Margaret J. Duesbury; Marta Iannuccelli; Max Kotlyar; Luana Licata; Birgit Meldal; Kalpana Panneerselvam; Simona Panni; N. Rahimzadeh; Sylvie Ricard-Blum; et al. (Database J. Biol. Databases Curation, 2020)

BioPAX-Parser: parsing and enrichment analysis of BioPAX pathways. - Giuseppe Agapito; Chiara Pastrello; Pietro Hiram Guzzi; Igor Jurisica; Mario Cannataro (Bioinform., 2020)

GSOAP: a tool for visualization of gene set over-representation analysis. - Tomás Tokár; Chiara Pastrello; Igor Jurisica (Bioinform., 2020)

pathDIP 4: an extended pathway annotations and enrichment analysis resource for human, model organisms and domesticated species. - Sara Rahmati; Mark Abovsky; Chiara Pastrello; Max Kotlyar; Richard Lu; Christian A. Cumbaa; Proton Rahman; Vinod Chandran; Igor Jurisica (Nucleic Acids Res., 2020)

Informed Use of Protein-Protein Interaction Data: A Focus on the Integrated Interactions Database (IID). - Chiara Pastrello; Max Kotlyar; Igor Jurisica (Protein-Protein Interaction Networks, 2020)

Comprehensive pathway enrichment analysis workflows: COVID-19 case study. - Giuseppe Agapito; Chiara Pastrello; Igor Jurisica (Briefings Bioinform., 2021)

Pathway integration and annotation: building a puzzle with non-matching pieces and no reference picture. - Giuseppe Agapito; Chiara Pastrello; Yun Niu; Igor Jurisica (Briefings Bioinform., 2022)

miRAnno - network-based functional microRNA annotation. - Tomás Tokár; Chiara Pastrello; Mark Abovsky; Sara Rahmati; Igor Jurisica (Bioinform., 2022)

IID 2021: towards context-specific protein interaction analyses by increased coverage, enhanced annotation and enrichment analysis. - Max Kotlyar; Chiara Pastrello; Zuhaib Ahmed; Justin Chee; Zofia Varyova; Igor Jurisica (Nucleic Acids Res., 2022)

MirDIP 5.2: tissue context annotation and novel microRNA curation. - Anne-Christin Hauschild; Chiara Pastrello; Gitta Kirana Anindya Ekaputeri; Dylan Bethune-Waddell; Mark Abovsky; Zuhaib Ahmed; Max Kotlyar; Richard Lu; Igor Jurisica (Nucleic Acids Res., 2023)

USNAP: fast unique dense region detection and its application to lung cancer. - Serene W. H. Wong; Chiara Pastrello; Max Kotlyar; Christos Faloutsos; Igor Jurisica (Bioinform., 2023)