Ontologizing gene-expression microarray data: characterizing clusters with Gene Ontology - Peter N. Robinson; Andreas Wollstein; Ulrike Böhme; Bradley J. Beattie (Bioinform., 2004)

An Improved Statistic for Detecting Over-Represented Gene Ontology Annotations in Gene Sets. - Steffen Grossmann; Sebastian Bauer 002; Peter N. Robinson; Martin Vingron (RECOMB, 2006)

HotSwap for bioinformatics: A STRAP tutorial. - Christoph Gille; Peter N. Robinson (BMC Bioinform., 2006)

Binary State Pattern Clustering: A Digital Paradigm for Class and Biomarker Discovery in Gene Microarray Studies of Cancer. - Bradley J. Beattie; Peter N. Robinson (J. Comput. Biol., 2006)

Improved detection of overrepresentation of Gene-Ontology annotations with parent-child analysis. - Steffen Grossmann; Sebastian Bauer 002; Peter N. Robinson; Martin Vingron (Bioinform., 2007)

Ontologizer 2.0 - a multifunctional tool for GO term enrichment analysis and data exploration. - Sebastian Bauer 002; Steffen Grossmann; Martin Vingron; Peter N. Robinson (Bioinform., 2008)

The generalised k-Truncated Suffix Tree for time-and space-efficient searches in multiple DNA or protein sequences. - Marcel H. Schulz; Sebastian Bauer 002; Peter N. Robinson (Int. J. Bioinform. Res. Appl., 2008)

Exact Score Distribution Computation for Similarity Searches in Ontologies. - Marcel H. Schulz; Sebastian Köhler 001; Sebastian Bauer 002; Martin Vingron; Peter N. Robinson (WABI, 2009)

Microindel detection in short-read sequence data. - Peter M. Krawitz; Christian Rödelsperger; Marten Jäger; Luke Jostins; Sebastian Bauer 002; Peter N. Robinson (Bioinform., 2010)

Model-based gene set analysis for Bioconductor. - Sebastian Bauer 002; Peter N. Robinson; Julien Gagneur (Bioinform., 2011)

Identity-by-descent filtering of exome sequence data for disease-gene identification in autosomal recessive disorders. - Christian Rödelsperger; Peter M. Krawitz; Sebastian Bauer 002; Jochen Hecht; Abigail W. Bigham; Michael Bamshad; Birgit Jonske de Condor; Michal R. Schweiger; Peter N. Robinson (Bioinform., 2011)

Improving ontologies by automatic reasoning and evaluation of logical definitions. - Sebastian Köhler 001; Sebastian Bauer 002; Chris Mungall; Gabriele Carletti; Cynthia L. Smith; Paul N. Schofield; Georgios V. Gkoutos; Peter N. Robinson (BMC Bioinform., 2011)

Exact score distribution computation for ontological similarity searches. - Marcel H. Schulz; Sebastian Köhler 001; Sebastian Bauer 002; Peter N. Robinson (BMC Bioinform., 2011)

Bayesian ontology querying for accurate and noise-tolerant semantic searches. - Sebastian Bauer 002; Sebastian Köhler 001; Marcel H. Schulz; Peter N. Robinson (Bioinform., 2012)

Querying phenotype-genotype relationships on patient datasets using semantic web technology: the example of cerebrotendinous xanthomatosis. - Maria Taboada; Diego Martínez Hernández; Belén Pilo; Adriano Jiménez-Escrig; Peter N. Robinson; María Jesús Sobrido (BMC Medical Informatics Decis. Mak., 2012)

Integrating the Human Phenotype Ontology into HeTOP Terminology-Ontology Server. - Julien Grosjean; Tayeb Merabti; Lina Fatima Soualmia; Catherine Letord; Jean Charlet; Peter N. Robinson; Stéfan Jacques Darmoni (MedInfo, 2013)

PhenoDigm: analyzing curated annotations to associate animal models with human diseases. - Damian Smedley; Anika Oellrich; Sebastian Köhler 001; Barbara J. Ruef; Monte Westerfield; Peter N. Robinson; Suzanna Lewis; Christopher J. Mungall (Database J. Biol. Databases Curation, 2013)

Walking the interactome for candidate prioritization in exome sequencing studies of Mendelian diseases. - Damian Smedley; Sebastian Köhler 001; Johanna Christina Czeschik; Joanna S. Amberger; Carol A. Bocchini; Ada Hamosh; Julian Veldboer; Tomasz Zemojtel; Peter N. Robinson (Bioinform., 2014)

The influence of disease categories on gene candidate predictions from model organism phenotypes. - Anika Oellrich; Sebastian Köhler 001; Nicole L. Washington; Chris Mungall; Suzanna Lewis; Melissa A. Haendel; Peter N. Robinson; Damian Smedley (J. Biomed. Semant., 2014)

Clinical phenotype-based gene prioritization: an initial study using semantic similarity and the human phenotype ontology. - Aaron J. Masino; Elizabeth T. Dechene; Matthew C. Dulik; Alisha Wilkens; Nancy B. Spinner; Ian D. Krantz; Jeffrey W. Pennington; Peter N. Robinson; Peter S. White (BMC Bioinform., 2014)

The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data. - Sebastian Köhler 001; Sandra C. Doelken; Christopher J. Mungall; Sebastian Bauer 002; Helen V. Firth; Isabelle Bailleul-Forestier; Graeme C. M. Black; Danielle L. Brown; Michael Brudno; Jennifer Campbell; David R. FitzPatrick; Janan T. Eppig; et al. (Nucleic Acids Res., 2014)

Prediction of Human Gene - Phenotype Associations by Exploiting the Hierarchical Structure of the Human Phenotype Ontology. - Giorgio Valentini; Sebastian Köhler 001; Matteo Ré; Marco Notaro; Peter N. Robinson (IWBBIO (1), 2015)

A Hierarchical Ensemble Method for DAG-Structured Taxonomies. - Peter N. Robinson; Marco Frasca 001; Sebastian Köhler 001; Marco Notaro; Matteo Re; Giorgio Valentini (MCS, 2015)

PhenoMiner: from text to a database of phenotypes associated with OMIM diseases. - Nigel Collier; Tudor Groza; Damian Smedley; Peter N. Robinson; Anika Oellrich; Dietrich Rebholz-Schuhmann (Database J. Biol. Databases Curation, 2015)

Automatic concept recognition using the Human Phenotype Ontology reference and test suite corpora. - Tudor Groza; Sebastian Köhler 001; Sandra C. Doelken; Nigel Collier; Anika Oellrich; Damian Smedley; Francisco M. Couto; Gareth Baynam; Andreas Zankl; Peter N. Robinson (Database J. Biol. Databases Curation, 2015)

IMSEQ - a fast and error aware approach to immunogenetic sequence analysis. - Léon Kuchenbecker; Mikalai Nienen; Jochen Hecht; Avidan U. Neumann; Nina Babel; Knut Reinert; Peter N. Robinson (Bioinform., 2015)

Strategies to improve the performance of rare variant association studies by optimizing the selection of controls. - Na Zhu; Verena Heinrich; Thorsten Dickhaus; Jochen Hecht; Peter N. Robinson; Stefan Mundlos; Tom Kamphans; Peter M. Krawitz (Bioinform., 2015)

Capturing domain knowledge from multiple sources: the rare bone disorders use case. - Tudor Groza; Tania Tudorache; Peter N. Robinson; Andreas Zankl (J. Biomed. Semant., 2015)

Enhancing the Human Phenotype Ontology for Use by the Layperson. - Nicole A. Vasilevsky; Mark Engelstad; Erin Foster; Chris Mungall; Peter N. Robinson; Sebastian Köhler 001; Melissa A. Haendel (ICBO/BioCreative, 2016)

The digital revolution in phenotyping. - Anika Oellrich; Nigel Collier; Tudor Groza; Dietrich Rebholz-Schuhmann; Nigam Shah; Olivier Bodenreider; Mary Regina Boland; Ivo I. Georgiev; Hongfang Liu; Kevin M. Livingston; Augustin Luna; Ann-Marie Mallon; et al. (Briefings Bioinform., 2016)

Ensembling Descendant Term Classifiers to Improve Gene - Abnormal Phenotype Predictions. - Marco Notaro; Max Schubach; Marco Frasca 001; Marco Mesiti; Peter N. Robinson; Giorgio Valentini (CIBB, 2017)

Aligning the Human Phenotype and Mammalian Phenotype Ontology using Dead Simple Ontology Design Patterns. - Nicole A. Vasilevsky; James P. Balhoff; Christopher J. Mungall; David Osumi-Sutherland; Sebastian Köhler 001; Susan M. Bello; Cynthia L. Smith; Peter N. Robinson; Melissa A. Haendel (ICBO, 2017)

A likelihood ratio-based method to predict exact pedigrees for complex families from next-generation sequencing data. - Verena Heinrich; Tom Kamphans; Stefan Mundlos; Peter N. Robinson; Peter M. Krawitz (Bioinform., 2017)

Prediction of Human Phenotype Ontology terms by means of hierarchical ensemble methods. - Marco Notaro; Max Schubach; Peter N. Robinson; Giorgio Valentini (BMC 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)

L1Base 2: more retrotransposition-active LINE-1s, more mammalian genomes. - Tobias Penzkofer; Marten Jäger; Marek Figlerowicz; Richard Badge; Stefan Mundlos; Peter N. Robinson; Tomasz Zemojtel (Nucleic Acids Res., 2017)

Medical Action Ontology (MAxO). - Leigh C. Carmody; Xingmin Aaron Zhang; Nicole A. Vasilevsky; Christopher J. Mungall; Nicolas Matentzoglu; Peter N. Robinson (ICBO, 2019)

Representing glycophenotypes: semantic unification of glycobiology resources for disease discovery. - Jean-Philippe F. Gourdine; Matthew H. Brush; Nicole A. Vasilevsky; Kent A. Shefchek; Sebastian Köhler 001; Nicolas Matentzoglu; Monica C. Munoz-Torres; Julie A. McMurry; Xingmin Aaron Zhang; Peter N. Robinson; Melissa A. Haendel (Database J. Biol. Databases Curation, 2019)

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)

Semantic integration of clinical laboratory tests from electronic health records for deep phenotyping and biomarker discovery. - Xingmin Aaron Zhang; Amy Yates; Nicole A. Vasilevsky; Jean-Philippe F. Gourdine; Tiffany J. Callahan; Leigh C. Carmody; Daniel Danis; Marcin P. Joachimiak; Vida Ravanmehr; Emily R. Pfaff; James Champion; Kimberly Robasky; et al. (npj Digit. Medicine, 2019)

Mondo Disease Ontology: Harmonizing Disease Concepts Across the World (short paper). - Nicole A. Vasilevsky; Shahim Essaid; Nicolas Matentzoglu; Nomi L. Harris; Melissa A. Haendel; Peter N. Robinson; Christopher J. Mungall (ICBO/ODLS, 2020)

Explainable Machine Learning for Early Assessment of COVID-19 Risk Prediction in Emergency Departments. - Elena Casiraghi; Dario Malchiodi; Gabriella Trucco; Marco Frasca 001; Luca Cappelletti; Tommaso Fontana; Alessandro Andrea Esposito; Emanuele Avola; Alessandro Jachetti; Justin T. Reese; Alessandro Rizzi; Peter N. Robinson; et al. (IEEE Access, 2020)

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)

COVID-19 Mortality Prediction among Patients with Cancer Using a Large National Cohort. - Feifan Liu; Noha Sharafeldin; Vithal Madhira; Katie R. Bradwell; Qianqian Song; Benjamin Bates; Yu R. Shao; Jing Su 003; Alfred Anzalone; Timothym Bergquist; Sarah Cutrona; Ben S. Gerber; et al. (AMIA, 2021)

Reclassification of Infectious Disease in the Mondo Disease Ontology. - Nicole A. Vasilevsky; Sabrina Toro; Nicolas Matentzoglu; Dazhi Jiao; Melissa A. Haendel; Peter N. Robinson; Christopher J. Mungall (ICBO, 2021)

PhenoTagger: a hybrid method for phenotype concept recognition using human phenotype ontology. - Ling Luo 001; Shankai Yan; Po-Ting Lai; Daniel Veltri; Andrew J. Oler; Sandhya Xirasagar; Rajarshi Ghosh; Morgan Similuk; Peter N. Robinson; Zhiyong Lu (Bioinform., 2021)

HEMDAG: a family of modular and scalable hierarchical ensemble methods to improve Gene Ontology term prediction. - Marco Notaro; Marco Frasca 001; Alessandro Petrini; Jessica Gliozzo; Elena Casiraghi; Peter N. Robinson; Giorgio Valentini (Bioinform., 2021)

Het-node2vec: second order random walk sampling for heterogeneous multigraphs embedding. - Giorgio Valentini; Elena Casiraghi; Luca Cappelletti; Vida Ravanmehr; Tommaso Fontana; Justin T. Reese; Peter N. Robinson (CoRR, 2021)

GraPE: fast and scalable Graph Processing and Embedding. - Luca Cappelletti; Tommaso Fontana; Elena Casiraghi; Vida Ravanmehr; Tiffany J. Callahan; Marcin P. Joachimiak; Christopher J. Mungall; Peter N. Robinson; Justin T. Reese; Giorgio Valentini (CoRR, 2021)

The National COVID Cohort Collaborative (N3C): Rationale, design, infrastructure, and deployment. - Melissa A. Haendel; Christopher G. Chute; Tellen D. Bennett; David A. Eichmann; Justin Guinney; Warren A. Kibbe; Philip R. O. Payne; Emily R. Pfaff; Peter N. Robinson; Joel H. Saltz; Heidi Spratt; Christine Suver; et al. (J. Am. Medical Informatics Assoc., 2021)

Abdominal Computed Tomography Imaging Findings in Hospitalized COVID-19 Patients: A Year-Long Experience and Associations Revealed by Explainable Artificial Intelligence. - Alice Scarabelli; Massimo Zilocchi; Elena Casiraghi; Pierangelo Fasani; Guido Giovanni Plensich; Alessandro Andrea Esposito; Elvira Stellato; Alessandro Petrini; Justin T. Reese; Peter N. Robinson; Giorgio Valentini; Gianpaolo Carrafiello (J. Imaging, 2021)

The Human Phenotype Ontology in 2021. - Sebastian Köhler 001; Michael A. Gargano; Nicolas Matentzoglu; Leigh Carmody; David Lewis-Smith; Nicole A. Vasilevsky; Daniel Danis; Ganna Balagura; Gareth Baynam; Amy M. Brower; Tiffany J. Callahan; Christopher G. Chute; et al. (Nucleic Acids Res., 2021)

KG-COVID-19: A Framework to Produce Customized Knowledge Graphs for COVID-19 Response. - Justin T. Reese; Deepak R. Unni; Tiffany J. Callahan; Luca Cappelletti; Vida Ravanmehr; Seth Carbon; Kent A. Shefchek; Benjamin M. Good; James P. Balhoff; Tommaso Fontana; Hannah Blau; Nicolas Matentzoglu; et al. (Patterns, 2021)

ParSMURF-NG: A Machine Learning High Performance Computing System for the Analysis of Imbalanced Big Omics Data. - Alessandro Petrini; Marco Notaro; Jessica Gliozzo; Tiziana Castrignanò; Peter N. Robinson; Elena Casiraghi; Giorgio Valentini (AIAI (Workshops), 2022)

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)

Tell Bennet, Christopher Chute, Peter DeWitt, Kenneth Gersing, Andrew Girvin, Melissa Haendel, Jeremy Harper, Janos Hajagos, Stephanie Hong, Emily Pfaff, Jane Reusch, Corneliu Antoniescu, Kimberly Robaski: A Methodological Framework for the Comparative Evaluation of Multiple Imputation Methods: Multiple Imputation of Race, Ethnicity and Body Mass Index in the U.S. National COVID Cohort Collaborative. - Elena Casiraghi; Rachel Wong; Margaret Hall; Ben D. Coleman; Marco Notaro; Michael D. Evans; Jena S. Tronieri; Hannah Blau; Bryan Laraway; Tiffany J. Callahan; Lauren E. Chan; Carolyn T. Bramante; et al. (CoRR, 2022)

Ontologizing Health Systems Data at Scale: Making Translational Discovery a Reality. - Tiffany J. Callahan; Adrianne L. Stefanski; Jordan M. Wyrwa; Chenjie Zeng; Anna Ostropolets; Juan M. Banda; William A. Baumgartner Jr.; Richard D. Boyce; Elena Casiraghi; Ben D. Coleman; Janine H. Collins; Sara J. Deakyne Davies; et al. (CoRR, 2022)

Demonstrating an approach for evaluating synthetic geospatial and temporal epidemiologic data utility: results from analyzing >1.8 million SARS-CoV-2 tests in the United States National COVID Cohort Collaborative (N3C). - Jason A. Thomas; Randi E. Foraker; Noa Zamstein; Jon D. Morrow; Philip R. O. Payne; Adam B. Wilcox; Melissa A. Haendel; Christopher G. Chute; Kenneth R. Gersing; Anita Walden; Tellen D. Bennett; David A. Eichmann; et al. (J. Am. Medical Informatics Assoc., 2022)

PhenoRerank: A re-ranking model for phenotypic concept recognition pre-trained on human phenotype ontology. - Shankai Yan; Ling Luo 001; Po-Ting Lai; Daniel Veltri; Andrew J. Oler; Sandhya Xirasagar; Rajarshi Ghosh; Morgan Similuk; Peter N. Robinson; Zhiyong Lu (J. Biomed. Informatics, 2022)

Deep phenotyping: symptom annotation made simple with SAMS. - Robin Steinhaus; Sebastian Proft; Evelyn Seelow; Tobias Schalau; Peter N. Robinson; Dominik Seelow (Nucleic Acids Res., 2022)

FABIAN-variant: predicting the effects of DNA variants on transcription factor binding. - Robin Steinhaus; Peter N. Robinson; Dominik Seelow (Nucleic Acids Res., 2022)

Degree-Normalization Improves Random-Walk-Based Embedding Accuracy in PPI Graphs. - Luca Cappelletti; Stefano Taverni; Tommaso Fontana; Marcin P. Joachimiak; Justin T. Reese; Peter N. Robinson; Elena Casiraghi; Giorgio Valentini (IWBBIO (2), 2023)

KG-Hub - Building and Exchanging Biological Knowledge Graphs. - J. Harry Caufield; Tim E. Putman; Kevin Schaper; Deepak R. Unni; Harshad Hegde; Tiffany J. Callahan; Luca Cappelletti; Sierra A. T. Moxon; Vida Ravanmehr; Seth Carbon; Lauren E. Chan; Katherina Cortes; et al. (CoRR, 2023)

An Open-Source Knowledge Graph Ecosystem for the Life Sciences. - Tiffany J. Callahan; Ignacio J. Tripodi; Adrianne L. Stefanski; Luca Cappelletti; Sanya Bathla Taneja; Jordan M. Wyrwa; Elena Casiraghi; Nicolas A. Matentzoglu; Justin T. Reese; Jonathan C. Silverstein; Charles Tapley Hoyt; Richard D. Boyce; et al. (CoRR, 2023)

RNA-KG: An ontology-based knowledge graph for representing interactions involving RNA molecules. - Emanuele Cavalleri; Alberto Cabri; Mauricio Soto Gomez; Sara Bonfitto; Paolo Perlasca; Jessica Gliozzo; Tiffany J. Callahan; Justin T. Reese; Peter N. Robinson; Elena Casiraghi; Giorgio Valentini; Marco Mesiti (CoRR, 2023)

GRAPE for fast and scalable graph processing and random-walk-based embedding. - Luca Cappelletti; Tommaso Fontana; Elena Casiraghi; Vida Ravanmehr; Tiffany J. Callahan; Carlos Cano; Marcin P. Joachimiak; Christopher J. Mungall; Peter N. Robinson; Justin T. Reese; Giorgio Valentini (Nat. Comput. Sci., 2023)

Ontologizing health systems data at scale: making translational discovery a reality. - Tiffany J. Callahan; Adrianne L. Stefanski; Jordan M. Wyrwa; Chenjie Zeng; Anna Ostropolets; Juan M. Banda; William A. Baumgartner Jr.; Richard D. Boyce; Elena Casiraghi; Ben D. Coleman; Janine H. Collins; Sara J. Deakyne Davies; et al. (npj Digit. Medicine, 2023)

A method for comparing multiple imputation techniques: A case study on the U.S. national COVID cohort collaborative. - Elena Casiraghi; Rachel Wong; Margaret Hall; Ben D. Coleman; Marco Notaro; Michael D. Evans; Jena S. Tronieri; Hannah Blau; Bryan Laraway; Tiffany J. Callahan; Lauren E. Chan; Carolyn T. Bramante; et al. (J. Biomed. Informatics, 2023)

An expectation-maximization framework for comprehensive prediction of isoform-specific functions. - Guy Karlebach; Leigh Carmody; Jagadish Chandrabose Sundaramurthi; Elena Casiraghi; Peter Hansen; Justin T. Reese; Christopher J. Mungall; Giorgio Valentini; Peter N. Robinson (Bioinform., 2023)

The promises of large language models for protein design and modeling. - Giorgio Valentini; Dario Malchiodi; Jessica Gliozzo; Marco Mesiti; Mauricio Soto Gomez; Alberto Cabri; Justin T. Reese; Elena Casiraghi; Peter N. Robinson (Frontiers Bioinform., 2023)

Term-BLAST-like alignment tool for concept recognition in noisy clinical texts. - Tudor Groza; Honghan Wu; Marcel E. Dinger; Daniel Danis; Coleman Hilton; Anita Bagley; Jon R. Davids; Ling Luo 001; Zhiyong Lu; Peter N. Robinson (Bioinform., 2023)

The Environmental Conditions, Treatments, and Exposures Ontology (ECTO): connecting toxicology and exposure to human health and beyond. - Lauren E. Chan; Anne E. Thessen; William D. Duncan; Nicolas Matentzoglu; Charles Schmitt; Cynthia J. Grondin; Nicole A. Vasilevsky; Julie A. McMurry; Peter N. Robinson; Christopher J. Mungall; Melissa A. Haendel (J. Biomed. Semant., 2023)

Fine-Tuning of Conditional Transformers Improves the Generation of Functionally Characterized Proteins. - Marco Nicolini; Dario Malchiodi; Alberto Cabri; Emanuele Cavalleri; Marco Mesiti; Alberto Paccanaro; Peter N. Robinson; Justin T. Reese; Elena Casiraghi; Giorgio Valentini (BIOSTEC (1), 2024)

Initial achievements in relation extraction from RNA-focused scientific papers. - Emanuele Cavalleri; Mauricio Soto Gomez; Ali Pashaeibarough; Dario Malchiodi; J. Harry Caufield; Justin T. Reese; Christopher J. Mungall; Peter N. Robinson; Elena Casiraghi; Giorgio Valentini; Marco Mesiti (SEBD, 2024)

SPIREX: Improving LLM-based relation extraction from RNA-focused scientific literature using graph machine learning. - Emanuele Cavalleri; Mauricio Soto Gomez; Ali Pashaeibarough; Dario Malchiodi; J. Harry Caufield; Justin T. Reese; Chris Mungall; Peter N. Robinson; Elena Casiraghi; Giorgio Valentini; Marco Mesiti (VLDB Workshops, 2024)

CurateGPT: A flexible language-model assisted biocuration tool. - J. Harry Caufield; Carlo Kroll; Shawn T. O'Neil; Justin T. Reese; Marcin P. Joachimiak; Harshad Hegde; Nomi L. Harris; Madan Krishnamurthy; James A. McLaughlin; Damian Smedley; Melissa A. Haendel; Peter N. Robinson; et al. (CoRR, 2024)

Predicting nutrition and environmental factors associated with female reproductive disorders using a knowledge graph and random forests. - Lauren E. Chan; Elena Casiraghi; Justin T. Reese; Quaker E. Harmon; Kevin Schaper; Harshad Hegde; Giorgio Valentini; Charles Schmitt; Alison A. Motsinger-Reif; Janet E. Hall; Christopher J. Mungall; Peter N. Robinson; et al. (Int. J. Medical Informatics, 2024)

Computing Minimal Boolean Models of Gene Regulatory Networks. - Guy Karlebach; Peter N. Robinson (J. Comput. Biol., 2024)

Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES): a method for populating knowledge bases using zero-shot learning. - J. Harry Caufield; Harshad Hegde; Vincent Emonet; Nomi L. Harris; Marcin P. Joachimiak; Nicolas Matentzoglu; Hyeongsik Kim 001; Sierra A. T. Moxon; Justin T. Reese; Melissa A. Haendel; Peter N. Robinson; Christopher J. Mungall (Bioinform., 2024)

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)

An evaluation of GPT models for phenotype concept recognition. - Tudor Groza; J. Harry Caufield; Dylan Gration; Gareth Baynam; Melissa A. Haendel; Peter N. Robinson; Christopher J. Mungall; Justin T. Reese (BMC Medical Informatics Decis. Mak., 2024)

Intrinsic-dimension analysis for guiding dimensionality reduction and data fusion in multi-omics data processing. - Jessica Gliozzo; Mauricio Soto Gomez; Valentina Guarino; Arturo Bonometti; Alberto Cabri; Emanuele Cavalleri; Justin T. Reese; Peter N. Robinson; Marco Mesiti; Giorgio Valentini; Elena Casiraghi (Artif. Intell. Medicine, 2025)

National COVID Cohort Collaborative data enhancements: a path for expanding common data models. - Kellie M. Walters; Marshall Clark; Sofia Dard; Stephanie S. Hong; Elizabeth Kelly; Kristin Kostka; Adam M. Lee; Robert T. Miller; Michele Morris; Matvey B. Palchuk; Emily R. Pfaff; Adam B. Wilcox; et al. (J. Am. Medical Informatics Assoc., 2025)

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)