P. Robinson

John M. Hancock, Chris Mungall, Georgios V. Gkoutos, 2009, 2009 Annual International Conference of the IEEE Engineering in Medicine and Biology Society.

Phenotypic overlap in the contribution of individual genes to CNV pathogenicity revealed by cross-species computational analysis of single-gene mutations in humans, mice and zebrafish

Damian Smedley, Paul N. Schofield, Sebastian Bauer, 2012, Disease Models & Mechanisms.

RD-Connect: An Integrated Platform Connecting Databases, Registries, Biobanks and Clinical Bioinformatics for Rare Disease Research

P. Robinson, I. Gut, K. Zatloukal, 2014, Journal of General Internal Medicine.

Finding Our Way through Phenotypes

Laura M. Jackson, Paula M. Mabee, Carolyn J. Lawrence, 2015, PLoS biology.

Modelling kidney disease using ontology: insights from the Kidney Precision Medicine Project

Lucy Lu Wang, A. Diehl, C. Mungall, 2020, Nature Reviews Nephrology.

Deletions of chromosomal regulatory boundaries are associated with congenital disease

S. Lewis, M. Hurles, D. Smedley, 2014, Genome Biology.

How many rare diseases are there?

Tudor I. Oprea, Peter N. Robinson, S. Köhler, 2019, Nature Reviews Drug Discovery.

Towards a European consensus for reporting incidental findings during clinical NGS testing

Gabrielle M. Christenhusz, Peter N. Robinson, J. Hehir-Kwa, 2015, European Journal of Human Genetics.

Construction and accessibility of a cross-species phenotype ontology along with gene annotations for biomedical research

Damian Smedley, Sebastian Bauer, Monte Westerfield, 2013, F1000Research.

Minimum Information about a Genotyping Experiment (MIGEN)

R. Scheuermann, A. Pertsemlidis, P. Robinson, 2010, Standards in genomic sciences.

Computing Minimal Boolean Models of Gene Regulatory Networks

Guy Karlebach, P. Robinson, 2021, bioRxiv.

Variant relevance prediction in extremely imbalanced training sets

Giorgio Valentini, Matteo Re, Max Schubach, 2017 .

MouseFinder: Candidate disease genes from mouse phenotype data

Damian Smedley, Monte Westerfield, Sebastian Köhler, 2012, Human mutation.

Clinical interpretation of CNVs with cross-species phenotype data

Damian Smedley, Sebastian Köhler, Johanna Christina Czeschik, 2014, Journal of Medical Genetics.

Phenotype Ontologies and Cross-Species Analysis for Translational Research

Caleb Webber, Peter N. Robinson, C. Webber, 2014, PLoS genetics.

Navigating the phenotype frontier: The Monarch Initiative

Julius O. B. Jacobsen, Matthew H. Brush, S. Lewis, 2016, bioRxiv.

A systematic, large-scale comparison of transcription factor binding site models

Jana Marie Schwarz, Peter N. Robinson, D. Seelow, 2016, BMC Genomics.

Computing Minimal Boolean Models of Gene Regulatory Networks

Guy Karlebach, P. Robinson, 2021, bioRxiv.

Finding Our Way Through Phenotypes

Laura M. Jackson, Paula M. Mabee, Katja C. Seltmann, 2019 .

Perspective Finding Our Way through Phenotypes

Laura M. Jackson, Paula M. Mabee, Katja C. Seltmann, 2014 .

Parameters tuning boosts hyperSMURF predictions of rare deleterious non-coding genetic variants

Giorgio Valentini, Giuliano Grossi, Marco Mesiti, 2017 .

The GA4GH Variation Representation Specification (VRS): a Computational Framework for the Precise Representation and Federated Identification of Molecular Variation

Alex H. Wagner, Matthew H. Brush, Andrew D. Yates, 2021, bioRxiv.

Mondo Disease Ontology: Harmonizing Disease Concepts Across the World (short paper)

C. Mungall, N. Harris, P. Robinson, 2020, ICBO/ODLS.

Characterizing Long COVID: Deep Phenotype of a Complex Condition

S. Köhler, G. Stein, C. Chute, 2021, EBioMedicine.

Tools for exploring mouse models of human disease

S. Lewis, D. Smedley, C. Mungall, 2016 .

Reclassification of Infectious Disease in the Mondo Disease Ontology

C. Mungall, P. Robinson, M. Haendel, 2021, ICBO.

The influence of disease categories on gene candidate predictions from model organism phenotypes

Damian Smedley, Peter N. Robinson, Chris Mungall, 2014, Journal of Biomedical Semantics.

Walking the interactome for candidate prioritization in exome sequencing studies of Mendelian diseases

Damian Smedley, Peter N. Robinson, Sebastian Köhler, 2014, Bioinform..

The impact of biological sex on alternative splicing

Tudor I. Oprea, Xingmin Aaron Zhang, Jeremy J. Yang, 2018, bioRxiv.

Review The case for open science: rare diseases

Esther van Enckevort, C. Nellåker, N. Harris, 2020 .

Investigation of heart proteome of different consomic mouse strains. Testing the effect of polymorphisms on the proteome-wide trans-variation of proteins

S. Köhler, V. Regitz-Zagrosek, H. Lehrach, 2015 .

Accurate and simultaneous identification of differential expression and splicing using hierarchical Bayesian analysis

Peter N. Robinson, Guy Karlebach, P. Robinson, 2019, bioRxiv.

Short ultraconserved promoter regions delineate a class of preferentially expressed alternatively spliced transcripts.

Marcel H. Schulz, S. Köhler, Sebastian Bauer, 2009, Genomics.

The 100,000 Genomes Pilot on Rare Disease Diagnosis in Healthcare − A Preliminary Report

Julius O. B. Jacobsen, Robert W. Taylor, Eleanor F. Dewhurst, 2021, The New England journal of medicine.

A CRISPR-Cas9–engineered mouse model for GPI-anchor deficiency mirrors human phenotypes and exhibits hippocampal synaptic dysfunctions

D. Horn, S. Mundlos, A. Becker, 2020, Proceedings of the National Academy of Sciences.

NSAID use and clinical outcomes in COVID-19 patients: A 38-center retrospective cohort study

Andrew E. Williams, C. Mungall, J. Singh, 2021, medRxiv.

Curation and expansion of Human Phenotype Ontology for defined groups of inborn errors of immunity

E. Hoppenreijs, C. Wouters, M. van der Burg, 2021, The Journal of allergy and clinical immunology.

GraPE: fast and scalable Graph Processing and Embedding

C. Mungall, G. Valentini, P. Robinson, 2021, ArXiv.

Computing Minimal Boolean Models of Gene Regulatory Networks

P. Robinson, G. Karlebach, 2021, bioRxiv.

Computing Minimal Boolean Models of Gene Regulatory Networks

Guy Karlebach, P. Robinson, G. Karlebach, 2021, bioRxiv.

Building Population Phenotypic Journeys from Laboratory Tests in Electronic Health Records for Translational Research

G. Stolovitzky, P. Robinson, L. Jin, 2022, medRxiv.

Computing Minimal Boolean Models of Gene Regulatory Networks

Guy Karlebach, P. Robinson, G. Karlebach, 2021, bioRxiv.

The Clinical Variant Analysis Tool: Analyzing the evidence supporting reported genomic variation in clinical practice.

Julius O. B. Jacobsen, D. Smedley, L. Prentice, 2022, Genetics in medicine : official journal of the American College of Medical Genetics.

Ontologizing health systems data at scale: making translational discovery a reality

Sanya Bathla Taneja, Adrianne L. Stefanski, Andrew E. Williams, 2022, NPJ digital medicine.

Assessment of Bones Deficient in Fibrillin-1 Microfibrils Reveals Pronounced Sex Differences

P. Robinson, U. Kornak, B. Wildemann, 2019, International journal of molecular sciences.

Phenotype Ontologies Traversing All The Organisms (POTATO) workshop aims to reconcile logical definitions across species. Workshop Report

Melissa Haendel, Anne E. Thessen, James P. Balhoff, 2018 .

Phenotype-aware prioritisation of rare Mendelian disease variants

D. Smedley, P. Robinson, N. Pontikos, 2022, Trends in genetics : TIG.

Enhancing the Human Phenotype Ontology for Use by the Layperson

Peter N. Robinson, Chris Mungall, Melissa Haendel, 2016, ICBO/BioCreative.

Low budget analysis of Direct-To-Consumer genomic testing familial data

Gustavo Glusman, J. Bhak, P. Robinson, 2012, F1000Research.

Disease insights through cross-species phenotype comparisons

Julius O. B. Jacobsen, Matthew H. Brush, S. Lewis, 2015, Mammalian Genome.

Clinical phenotype-based gene prioritization: an initial study using semantic similarity and the human phenotype ontology

Jeffrey W. Pennington, I. Krantz, N. Spinner, 2014, BMC Bioinformatics.

Defining Disease, Diagnosis, and Translational Medicine within a Homeostatic Perturbation Paradigm: The National Institutes of Health Undiagnosed Diseases Program Experience

Damian Smedley, Cheng-Kang Hsieh, Karen Xu, 2017, Front. Med..

Computational Prediction of Position Effects of Apparently Balanced Human Chromosomal Rearrangements.

Fowzan S Alkuraya, Michael E Talkowski, Karen W Gripp, 2017, American journal of human genetics.

A Whole-Genome Analysis Framework for Effective Identification of Pathogenic Regulatory Variants in Mendelian Disease.

Giorgio Valentini, Tudor Groza, Harry Hochheiser, 2016, American journal of human genetics.

Deletions of chromosomal regulatory boundaries are associated with congenital disease

Peter N. Robinson, S. Lewis, M. Hurles, 2014, Genome Biology.

The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data

Damian Smedley, Paul N. Schofield, Peter N. Robinson, 2014, Nucleic Acids Res..

Construction and accessibility of a cross-species phenotype ontology along with gene annotations for biomedical research.

Damian Smedley, Sebastian Bauer, Monte Westerfield, 2013, F1000Research.

Introduction to Bio-Ontologies

Peter N. Robinson, Sebastian Bauer, Sebastian Bauer, 2011 .

Representing glycophenotypes: semantic unification of glycobiology resources for disease discovery

Jean-Philippe F Gourdine, Matthew H Brush, Nicole A Vasilevsky, 2019, Database J. Biol. Databases Curation.

The National COVID Cohort Collaborative (N3C): Rationale, design, infrastructure, and deployment

Philip R. O. Payne, Jeffrey G. Klann, Haendel Melissa, 2020, J. Am. Medical Informatics Assoc..

The Human Phenotype Ontology in 2021

Christopher G Chute, Damian Smedley, Yongqun He, 2020, Nucleic Acids Res..

parSMURF, a high-performance computing tool for the genome-wide detection of pathogenic variants

Giuliano Grossi, Marco Mesiti, Alessandro Petrini, 2020, bioRxiv.

Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources

Tudor Groza, Damian Smedley, Peter N. Robinson, 2018, Nucleic Acids Res..

PhenoDigm: analyzing curated annotations to associate animal models with human diseases

Damian Smedley, Peter N. Robinson, Chris Mungall, 2013, Database J. Biol. Databases Curation.

PEDIA: prioritization of exome data by image analysis

Borut Peterlin, Sebastian Köhler, Na Zhu, 2018, Genetics in Medicine.

Erratum to: A systematic, large-scale comparison of transcription factor binding site models

Jana Marie Schwarz, D. Seelow, P. Robinson, 2016, BMC Genomics.

The GA4GH Phenopacket schema: A computable representation of clinical data for precision medicine

Julius O. B. Jacobsen, Michael A. Gargano, J. Beckmann, 2021, medRxiv.

KG-COVID-19: A Framework to Produce Customized Knowledge Graphs for COVID-19 Response

Peter N. Robinson, Seth Carbon, Tiffany J. Callahan, 2020, bioRxiv.

SvAnna: efficient and accurate pathogenicity prediction of coding and regulatory structural variants in long-read genome sequencing

Julius O. B. Jacobsen, D. Smedley, C. Mungall, 2021, Genome Medicine.

Bioinformatics for Human Genetics: Promises and Challenges

P. Robinson, P. Robinson, A. Lindblom, 2011, Human mutation.

Response to Biesecker et al.

C. Bult, J. Lupski, R. Gibbs, 2021, American journal of human genetics.

The Human Phenotype Ontology in 2017

Tudor Groza, Damian Smedley, Peter N. Robinson, 2016, Nucleic Acids Res..

HBA-DEALS: accurate and simultaneous identification of differential expression and splicing using hierarchical Bayesian analysis

Guy Karlebach, P. Robinson, Olga Anczuków, 2020, Genome Biology.

The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species

Tudor Groza, Harry Hochheiser, Damian Smedley, 2016, bioRxiv.

Improving ontologies by automatic reasoning and evaluation of logical definitions

Paul N. Schofield, Sebastian Bauer, Peter N. Robinson, 2011, BMC Bioinformatics.

The GA4GH Variation Representation Specification: A computational framework for variation representation and federated identification

Matthew H. Brush, Andrew D. Yates, David A. Kreda, 2021, Cell genomics.

GA4GH: International policies and standards for data sharing across genomic research and healthcare

Grant M. Wood, James A. Eddy, Julius O. B. Jacobsen, 2021, Cell genomics.

Betacoronavirus-specific alternate splicing

Amanda M. Saravia-Butler, Deanne M. Taylor, Peter N. Robinson, 2021, bioRxiv.

Interpretable Clinical Genomics with a Likelihood Ratio Paradigm.

Damian Smedley, Julius O. B. Jacobsen, Xingmin Aaron Zhang, 2020, American journal of human genetics.

Phenotyping: Targeting genotype's rich cousin for diagnosis

Tudor Groza, Michael Brudno, Peter Claes, 2014, Journal of paediatrics and child health.

Deep phenotyping for precision medicine

Peter N. Robinson, P. Robinson, P. Robinson, 2012, Human mutation.

Alternate-locus aware variant calling in whole genome sequencing

K. Reinert, D. Church, P. Robinson, 2016, Genome Medicine.

Supervised learning with word embeddings derived from PubMed captures latent knowledge about protein kinases and cancer

Tudor I. Oprea, C. Bult, C. Mungall, 2021, bioRxiv.

Interpretable prioritization of splice variants in diagnostic next-generation sequencing

Julius O. B. Jacobsen, Michael A. Gargano, Peter N. Robinson, 2021, bioRxiv.

Encoding Clinical Data with the Human Phenotype Ontology for Computational Differential Diagnostics

Tudor Groza, Damian Smedley, Peter N. Robinson, 2019, Current protocols in human genetics.

Phenotype-driven strategies for exome prioritization of human Mendelian disease genes

D. Smedley, P. Robinson, 2015, Genome Medicine.

Bayesian ontology querying for accurate and noise-tolerant semantic searches

Marcel H. Schulz, Sebastian Bauer, Peter N. Robinson, 2012, Bioinform..

Exact score distribution computation for ontological similarity searches

Marcel H. Schulz, Sebastian Bauer, Peter N. Robinson, 2011, BMC Bioinformatics.

Clinical phenotype-based gene prioritization: an initial study using semantic similarity and the human phenotype ontology

Peter N. Robinson, Jeffrey W. Pennington, Aaron J. Masino, 2014, BMC Bioinformatics.

The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species

Tudor Groza, Damian Smedley, Simon Jupp, 2019, Nucleic Acids Res..

Ontological phenotype standards for neurogenetics

Sebastian Köhler, Ana Rath, Ségolène Aymé, 2012, Human mutation.

Genomic data sharing for translational research and diagnostics

Peter N Robinson, P. Robinson, 2014, Genome Medicine.

The influence of disease categories on gene candidate predictions from model organism phenotypes

S. Lewis, D. Smedley, S. Köhler, 2014, J. Biomed. Semant..

An expanded evaluation of protein function prediction methods shows an improvement in accuracy

Tapio Salakoski, Paolo Fontana, Silvio C. E. Tosatto, 2016, Genome Biology.

The Ontology of Biological Attributes (OBA) - Computational Traits for the Life Sciences

David O. Walton, Laura W. Harris, D. Smedley, 2023, bioRxiv.

Automatic concept recognition using the Human Phenotype Ontology reference and test suite corpora

Nigel Collier, Tudor Groza, Damian Smedley, 2015, Database J. Biol. Databases Curation.

Navigating the Phenotype Frontier: The Monarch Initiative

Tudor Groza, Harry Hochheiser, Damian Smedley, 2016, Genetics.

Summarizing Phenotype Evolution Patterns from Report Cases

Belén Pilo, Diego Martínez, María Taboada, 2012, Journal of Medical Systems.

Het-node2vec: second order random walk sampling for heterogeneous multigraphs embedding pdf

Peter Robinson, Elena Casiraghi, Giorgio Valentini, 2021, ArXiv.

Improved detection of overrepresentation of Gene-Ontology annotations with parent-child analysis

Martin Vingron, Sebastian Bauer, Peter N. Robinson, 2007, Bioinform..

Repository of mutations from Oman: The entry point to a national mutation database

P. Robinson, Nishath Hamza, B. Mons, 2015, F1000Research.

PhenoMiner: from text to a database of phenotypes associated with OMIM diseases

Dietrich Rebholz-Schuhmann, Nigel Collier, Tudor Groza, 2015, Database J. Biol. Databases Curation.

Integrative analysis of genomic, functional and protein interaction data predicts long-range enhancer-target gene interactions

Marcel H. Schulz, Sebastian Bauer, Sebastian Köhler, 2010, Nucleic acids research.

KG-COVID-19: A Framework to Produce Customized Knowledge Graphs for COVID-19 Response

Peter N. Robinson, Benjamin M. Good, James P. Balhoff, 2020, Patterns.

Ontologizing gene-expression microarray data: characterizing clusters with Gene Ontology

Peter N. Robinson, Ulrike Böhme, Bradley J. Beattie, 2004, Bioinform..

Abdominal Computed Tomography Imaging Findings in Hospitalized COVID-19 Patients: A Year-Long Experience and Associations Revealed by Explainable Artificial Intelligence

G. Valentini, P. Robinson, E. Casiraghi, 2021, J. Imaging.

Prediction of Human Phenotype Ontology terms by means of hierarchical ensemble methods

G. Valentini, P. Robinson, M. Schubach, 2017, BMC Bioinformatics.

PHENOstruct: Prediction of human phenotype ontology terms using heterogeneous data sources

Karin M. Verspoor, Karin Verspoor, Indika Kahanda, 2015, F1000Research.

Phenotate: crowdsourcing phenotype annotations as exercises in undergraduate classes

Willie H. Chang, Alexander X. Lozano, M. Brudno, 2020, Genetics in Medicine.

Open Peer Review Repository of Mutations from Oman: the Entry Point to a National Mutation Database [version 1; Referees: 2 Approved] Referee Status

P. Robinson, Nishath Hamza, B. Mons, 2022 .

k-BOOM: A Bayesian approach to ontology structure inference, with applications in disease ontology construction

Christopher J. Mungall, Melissa Haendel, Sebastian Koehler, 2016, bioRxiv.

Explainable Machine Learning for Early Assessment of COVID-19 Risk Prediction in Emergency Departments

Dario Malchiodi, Alessandro Rizzi, Peter N. Robinson, 2020, IEEE Access.

PEDIA: prioritization of exome data by image analysis

M. Nöthen, O. Bar, S. Köhler, 2018, Genetics in Medicine.

Cyclooxygenase inhibitor use is associated with increased COVID-19 severity

Andrew E. Williams, Guy Karlebach, C. Mungall, 2021, medRxiv.

Binary State Pattern Clustering: A Digital Paradigm for Class and Biomarker Discovery in Gene Microarray Studies of Cancer

Peter N. Robinson, Bradley J. Beattie, Peter N. Robinson, 2006, J. Comput. Biol..

Semantic integration of clinical laboratory tests from electronic health records for deep phenotyping and biomarker discovery

Daniel J. Vreeman, Christopher G. Chute, Clement J. McDonald, 2019, bioRxiv.

Plain-language medical vocabulary for precision diagnosis

Tudor Groza, Michael Bamshad, Chris Mungall, 2018, Nature Genetics.

An Improved Statistic for Detecting Over-Represented Gene Ontology Annotations in Gene Sets

Martin Vingron, Sebastian Bauer, Peter N. Robinson, 2006, RECOMB.

GraPE: fast and scalable Graph Processing and Embedding pdf

Giorgio Valentini, Elena Casiraghi, Chris Mungall, 2021, ArXiv.

Imbalance-Aware Machine Learning for Predicting Rare and Common Disease-Associated Non-Coding Variants

G. Valentini, P. Robinson, M. Schubach, 2017, Scientific Reports.

Ontologies, Knowledge Representation, and Machine Learning for Translational Research: Recent Contributions

Peter N Robinson, Melissa A Haendel, P. Robinson, 2020, Yearbook of Medical Informatics.

Supplementation of the ESID registry working definitions for the clinical diagnosis of inborn errors of immunity with encoded human phenotype ontology (HPO) terms.

P. Robinson, K. Boztug, M. Seidel, 2020, The journal of allergy and clinical immunology. In practice.

Model-based gene set analysis for Bioconductor

Sebastian Bauer, Peter N. Robinson, Julien Gagneur, 2011, Bioinform..

Linked Registries: Connecting Rare Diseases Patient Registries through a Semantic Web Layer

Núria Queralt-Rosinach, José Luís Oliveira, Rajaram Kaliyaperumal, 2017, BioMed research international.

An ontological foundation for ocular phenotypes and rare eye diseases

Rachel Thompson, Peter N Robinson, Annie Olry, 2019, Orphanet Journal of Rare Diseases.

Clinical Data: Sources and Types, Regulatory Constraints, Applications

Christopher G Chute, Casey Overby Taylor, Chunhua Weng, 2019, Clinical and translational science.

Ensembling Descendant Term Classifiers to Improve Gene - Abnormal Phenotype Predictions

Giorgio Valentini, Peter N. Robinson, Marco Mesiti, 2017, CIBB.

PhenoTagger: A Hybrid Method for Phenotype Concept Recognition using Human Phenotype Ontology

Andrew J. Oler, Peter N. Robinson, Zhiyong Lu, 2020, Bioinform..

HEMDAG: a family of modular and scalable hierarchical ensemble methods to improve Gene Ontology term prediction

Giorgio Valentini, Elena Casiraghi, Alessandro Petrini, 2021, Bioinform..

Crowdsourced direct-to-consumer genomic analysis of a family quartet

Fiona G. G. Nielsen, A. Harrison, P. Robinson, 2015, BMC Genomics.

Characterization of glycosylphosphatidylinositol biosynthesis defects by clinical features, flow cytometry, and automated image analysis

Peter N. Robinson, N. Brown, S. Köhler, 2017, Genome Medicine.

Bayesian Networks for Modeling and Inferring Gene Regulatory Networks

Sebastian Bauer, Peter N. Robinson, Sebastian Bauer, 2010 .

PhenoRerank: A re-ranking model for phenotypic concept recognition pre-trained on human phenotype ontology

Andrew J. Oler, Zhiyong Lu, P. Robinson, 2022, J. Biomed. Informatics.

Integrating the Human Phenotype Ontology into HeTOP Terminology-Ontology Server

Jean Charlet, Lina Fatima Soualmia, Stéfan Jacques Darmoni, 2013, MedInfo.

Classification, Ontology, and Precision Medicine.

C. Chute, P. Robinson, M. Haendel, 2018, The New England journal of medicine.

User testing of a diagnostic decision support system with machine-assisted chart review to facilitate clinical genomic diagnosis

Michael M. Segal, Nephi A. Walton, Marc S. Williams, 2021, BMJ Health & Care Informatics.

User testing of a Diagnostic Decision Support System with Automated Chart Review to Facilitate Clinical Genomic Diagnosis

Michael M. Segal, N. A. Walton, Nephi A. Walton, 2020, medRxiv.

Exact Score Distribution Computation for Similarity Searches in Ontologies

Martin Vingron, Marcel H. Schulz, Sebastian Bauer, 2009, WABI.

Ontological phenotype standards for neurogenetics

P. Robinson, A. Rath, S. Doelken, 2012, Human mutation.

uPheno 2: Framework for standardised representation of phenotypes across species

Yvonne M. Bradford, Christian A. Grove, Sofia M. C. Robb, 2019 .