BioJava: an open-source framework for bioinformatics in 2012. - Andreas Prlic; Andrew D. Yates; Spencer Bliven; Peter W. Rose; Julius O. B. Jacobsen; Peter V. Troshin; Mark Chapman; Jianjiong Gao; Chuan Hock Koh; Sylvain Foisy; Richard C. G. Holland; Gediminas Rimsa; et al. (Bioinform., 2012)

The EBI enzyme portal. - Rafael Alcántara; Joseph Onwubiko; Hong Cao; Paula de Matos; Jennifer A. Cham; Julius O. B. Jacobsen; Gemma L. Holliday; Julia D. Fischer; Syed Asad Rahman; Bijay Jassal; Mickael Goujon; Francis Rowland; et al. (Nucleic Acids Res., 2013)

SIFTS: Structure Integration with Function, Taxonomy and Sequences resource. - Sameer Velankar; Jose M. Dana; Julius O. B. Jacobsen; Glen van Ginkel; Paul J. Gane; Jie Luo; Thomas J. Oldfield; Claire O'Donovan; Maria Jesus Martin; Gerard J. Kleywegt (Nucleic Acids Res., 2013)

Using association rule mining to determine promising secondary phenotyping hypotheses. - Anika Oellrich; Julius O. B. Jacobsen; Irene Papatheodorou; Damian Smedley (Bioinform., 2014)

The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymes. - Nicholas Furnham; Gemma L. Holliday; Tjaart A. P. de Beer; Julius O. B. Jacobsen; William R. Pearson; Janet M. Thornton (Nucleic Acids Res., 2014)

Phenopolis: an open platform for harmonization and analysis of genetic and phenotypic data. - Nikolas Pontikos; Jing Yu 006; Ismail Moghul; Lucy Withington; Fiona Blanco-Kelly; Tom Vulliamy; Tsz Lun Ernest Wong; Cian Murphy; Valentina Cipriani; Alessia Fiorentino; Gavin Arno; Daniel Greene; et al. (Bioinform., 2017)

The Human Phenotype Ontology in 2017. - Sebastian Köhler 001; Nicole A. Vasilevsky; Mark Engelstad; Erin Foster; Julie A. McMurry; Ségolène Aymé; Gareth Baynam; Susan M. Bello; Cornelius F. Boerkoel; Kym M. Boycott; Michael Brudno; Orion J. Buske; et al. (Nucleic Acids Res., 2017)

The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species. - Christopher J. Mungall; Julie A. McMurry; Sebastian Köhler 001; James P. Balhoff; Charles D. Borromeo; Matthew H. Brush; Seth Carbon; Tom Conlin; Nathan A. Dunn; Mark Engelstad; Erin Foster; Jean-Philippe F. Gourdine; et al. (Nucleic Acids Res., 2017)

Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources. - Sebastian Köhler 001; Leigh Carmody; Nicole A. Vasilevsky; Julius O. B. Jacobsen; Daniel Danis; Jean-Philippe F. Gourdine; Michael A. Gargano; Nomi L. Harris; Nicolas Matentzoglu; Julie A. McMurry; David Osumi-Sutherland; Valentina Cipriani; et al. (Nucleic Acids Res., 2019)

The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species. - Kent A. Shefchek; Nomi L. Harris; Michael A. Gargano; Nicolas Matentzoglu; Deepak R. Unni; Matthew H. Brush; Dan Keith; Tom Conlin; Nicole A. Vasilevsky; Xingmin Aaron Zhang; James P. Balhoff; Larry Babb; et al. (Nucleic Acids Res., 2020)

Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases. - Julius O. B. Jacobsen; Catherine Kelly; Valentina Cipriani; Peter N. Robinson; Damian Smedley (Briefings Bioinform., 2022)

Learning from conect4children: A Collaborative Approach towards Standardisation of Disease-Specific Paediatric Research Data. - Anando Sen; Victoria Hedley; Eva Degraeuwe; Steven Hirschfeld; Ronald Cornet; Ramona Walls; John Owen; Peter N. Robinson; Edward G. Neilan; Thomas Liener; Giovanni Nisato; Neena Modi; et al. (Data, 2024)

Towards a standard benchmark for phenotype-driven variant and gene prioritisation algorithms: PhEval - Phenotypic inference Evaluation framework. - Yasemin Bridges; Vinicius de Souza; Katherina G. Cortes; Melissa A. Haendel; Nomi L. Harris; Daniel R. Korn; Nikolaos M. Marinakis; Nicolas Matentzoglu; James A. McLaughlin; Christopher J. Mungall; Aaron Odell; David Osumi-Sutherland; et al. (BMC Bioinform., 2025)