List of works - Damian Smedley

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

scientific article published on 25 August 2016

A gene expression resource generated by genome-wide lacZ profiling in the mouse

scientific article

A large scale hearing loss screen reveals an extensive unexplored genetic landscape for auditory dysfunction.

scientific article published on 12 October 2017

A mouse informatics platform for phenotypic and translational discovery.

scientific article

An Improved Phenotype-Driven Tool for Rare Mendelian Variant Prioritization: Benchmarking Exomiser on Real Patient Whole-Exome Data

scientific article published on 23 April 2020

An overview of Ensembl

scientific article (publication date: May 2004)

Application of eVOC: controlled vocabularies for unifying gene expression data

scientific article

Applying the ARRIVE Guidelines to an In Vivo Database

scientific article

Association and haplotype analysis of the insulin-degrading enzyme (IDE) gene, a strong positional and biological candidate for type 2 diabetes susceptibility

scientific article published in May 2003

Automatic concept recognition using the human phenotype ontology reference and test suite corpora

scientific article

Beyond knockouts: cre resources for conditional mutagenesis

scientific article published on 29 August 2012

BioMart Central Portal--unified access to biological data

scientific article

BioMart Central Portal: an open database network for the biological community

scientific article

BioMart as an integration solution for the International Knockout Mouse Consortium

scientific article

BioMart--biological queries made easy

scientific article (publication date: 14 January 2009)

CASIMIR: Coordination and Sustainability of International Mouse Informatics Resources

Clinical interpretation of CNVs with cross-species phenotype data

scientific article

Computational evaluation of exome sequence data using human and model organism phenotypes improves diagnostic efficiency.

scientific article

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

scientific article published on February 2013

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

article

Cre recombinase resources for conditional mouse mutagenesis

scientific article published on 31 December 2010

CreZOO--the European virtual repository of Cre and other targeted conditional driver strains

scientific article published on 21 June 2012

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

scientific article

Deletions of chromosomal regulatory boundaries are associated with congenital disease

scientific article

Disease insights through cross-species phenotype comparisons

scientific article

Disease model discovery from 3,328 gene knockouts by The International Mouse Phenotyping Consortium.

scientific article published on 26 June 2017

Distributed Cognition and Process Management Enabling Individualized Translational Research: The NIH Undiagnosed Diseases Program Experience

scientific article published on 12 October 2016

EMMA--mouse mutant resources for the international scientific community

scientific article

Effective diagnosis of genetic disease by computational phenotype analysis of the disease-associated genome

scientific article

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

scientific article published on 01 September 2019

EnsMart: a generic system for fast and flexible access to biological data

scientific article (publication date: 2004)

Ensembl variation resources

scientific article published in 2010

Ensembl's 10th year

scientific article

Erratum: Author Correction: Identification of genes required for eye development by high-throughput screening of mouse knockouts

scientific article published on 07 March 2019

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

article by Sebastian Köhler et al published 8 January 2019 in Nucleic Acids Research

Finding and sharing: new approaches to registries of databases and services for the biomedical sciences

scientific article

GANESH: software for customized annotation of genome regions

scientific article published in September 2003

Generation of silver standard concept annotations from biomedical texts with special relevance to phenotypes

scientific article

Getting ready for the Human Phenome Project: the 2012 forum of the Human Variome Project

scientific article

High-throughput discovery of genetic determinants of circadian misalignment

scientific article published on 13 January 2020

High-throughput mouse phenomics for characterizing mammalian gene function

scientific article published on 6 April 2018

Human and mouse essentiality screens as a resource for disease gene discovery

scientific article published on 31 January 2020

Identification of UBAP1 mutations in juvenile hereditary spastic paraplegia in the 100,000 Genomes Project

scientific article published on 15 September 2020

Identification of genes required for eye development by high-throughput screening of mouse knockouts

scientific article published on 21 December 2018

Identifying genetic determinants of inflammatory pain in mice using a large-scale gene-targeted screen

scientific article published on 13 September 2021

Improved exome prioritization of disease genes through cross-species phenotype comparison

scientific article

Incremental data integration for tracking genotype-disease associations

scientific article published on 27 January 2020

Interpretable Clinical Genomics with a Likelihood Ratio Paradigm

scientific article published on 29 July 2020

Interpretable Clinical Genomics with a Likelihood Ratio Paradigm

scholarly article published 28 January 2020

Jannovar: a java library for exome annotation

scientific article

Linking gene expression to phenotypes via pathway information

scientific article published on 11 April 2015

Linking tissues to phenotypes using gene expression profiles

scientific article published on 13 March 2014

Models for financial sustainability of biological databases and resources

scientific article (publication date: 2009)

Mondo: Unifying diseases for the world, by the world

Mouse Resource Browser--a database of mouse databases

scientific article published on 06 July 2010

MouseFinder: Candidate disease genes from mouse phenotype data

scientific article

Navigating the Phenotype Frontier: The Monarch Initiative

scientific article

Navigating the phenotype frontier: The Monarch Initiative

New methods for finding disease-susceptibility genes: impact and potential

scientific article

New models for human disease from the International Mouse Phenotyping Consortium

scientific article published on 24 May 2019

Next-generation diagnostics and disease-gene discovery with the Exomiser

scientific article

OpenStats: A robust and scalable software package for reproducible analysis of high-throughput phenotypic data

scientific article published on 30 December 2020

PanelApp crowdsources expert knowledge to establish consensus diagnostic gene panels

scientific article published on 01 November 2019

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

scientific article published on 9 May 2013

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

scientific article

Phenotype-aware prioritisation of rare Mendelian disease variants

scientific article published in 2022

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

scientific article

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

scientific article published on 25 October 2012

Prevalence of sexual dimorphism in mammalian phenotypic traits

scientific article

Research funding. Sustaining the data and bioresource commons

scientific article

Soft windowing application to improve analysis of high-throughput phenotyping data

scientific article published on 01 March 2020

Solutions for data integration in functional genomics: a critical assessment and case study

scientific article

TRACER: a resource to study the regulatory architecture of the mouse genome

scientific article

The 100 000 Genomes Project: bringing whole genome sequencing to the NHS

scientific article published in the British Medical Journal

The BioMart community portal: an innovative alternative to large, centralized data repositories

scientific article (publication date: July 2015)

The Deep Genome Project

scientific article published on 03 February 2020

The Human Phenotype Ontology in 2017

scientific article (publication date: 28 November 2016)

The Human Phenotype Ontology in 2021

scientific article published on 02 December 2020

The Human Phenotype Ontology in 2024: phenotypes around the world

scientific article published in 2023

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

scientific article (publication date: 2014)

The IKMC web portal: a central point of entry to data and resources from the International Knockout Mouse Consortium

scientific article

The International Mouse Phenotyping Consortium (IMPC): a functional catalogue of the mammalian genome that informs conservation

scientific article published on 19 May 2018

The International Mouse Phenotyping Consortium Web Portal, a unified point of access for knockout mice and related phenotyping data

scientific article

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

scientific article published on 01 January 2020

The Monarch Initiative in 2024: an analytic platform integrating phenotypes, genes and diseases across species

The Monarch Initiative: Insights across species reveal human disease mechanisms

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

scientific article

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

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

scientific article

The mammalian gene function resource: the International Knockout Mouse Consortium

scientific article

Towards BioDBcore: a community-defined information specification for biological databases

scientific article

Towards BioDBcore: a community-defined information specification for biological databases

scientific article (publication date: 2011)

Towards dynamic database infrastructures for mouse genetics

article

Towards the integration of mouse databases - definition and implementation of solutions to two use-cases in mouse functional genomics

scientific article (publication date: 22 January 2010)

Unusual Breakpoint Distribution of 8p Abnormalities in T-Prolymphocytic Leukemia

Use of animal models for exome prioritization of rare disease genes

article

Use of model organism and disease databases to support matchmaking for human disease gene discovery

scientific article

Using association rule mining to determine promising secondary phenotyping hypotheses

scientific article

Variation at the IRF2 gene and susceptibility to psoriasis in chromosome 4q-linked families

scientific article

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

scientific article

XGAP: a uniform and extensible data model and software platform for genotype and phenotype experiments

scientific article

eVOC: a controlled vocabulary for unifying gene expression data

scientific article

matchbox: An open-source tool for patient matching via the Matchmaker Exchange

scientific article published on 03 October 2018

List of works by Damian Smedley

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

A gene expression resource generated by genome-wide lacZ profiling in the mouse

A large scale hearing loss screen reveals an extensive unexplored genetic landscape for auditory dysfunction.

A mouse informatics platform for phenotypic and translational discovery.

An Improved Phenotype-Driven Tool for Rare Mendelian Variant Prioritization: Benchmarking Exomiser on Real Patient Whole-Exome Data

An overview of Ensembl

Application of eVOC: controlled vocabularies for unifying gene expression data

Applying the ARRIVE Guidelines to an In Vivo Database

Association and haplotype analysis of the insulin-degrading enzyme (IDE) gene, a strong positional and biological candidate for type 2 diabetes susceptibility

Automatic concept recognition using the human phenotype ontology reference and test suite corpora

Beyond knockouts: cre resources for conditional mutagenesis

BioMart Central Portal--unified access to biological data

BioMart Central Portal: an open database network for the biological community

BioMart as an integration solution for the International Knockout Mouse Consortium

BioMart--biological queries made easy

CASIMIR: Coordination and Sustainability of International Mouse Informatics Resources

Clinical interpretation of CNVs with cross-species phenotype data

Computational evaluation of exome sequence data using human and model organism phenotypes improves diagnostic efficiency.

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

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

Cre recombinase resources for conditional mouse mutagenesis

CreZOO--the European virtual repository of Cre and other targeted conditional driver strains

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

Deletions of chromosomal regulatory boundaries are associated with congenital disease

Disease insights through cross-species phenotype comparisons

Disease model discovery from 3,328 gene knockouts by The International Mouse Phenotyping Consortium.

Distributed Cognition and Process Management Enabling Individualized Translational Research: The NIH Undiagnosed Diseases Program Experience

EMMA--mouse mutant resources for the international scientific community

Effective diagnosis of genetic disease by computational phenotype analysis of the disease-associated genome

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

EnsMart: a generic system for fast and flexible access to biological data

Ensembl variation resources

Ensembl's 10th year

Erratum: Author Correction: Identification of genes required for eye development by high-throughput screening of mouse knockouts

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

Finding and sharing: new approaches to registries of databases and services for the biomedical sciences

GANESH: software for customized annotation of genome regions

Generation of silver standard concept annotations from biomedical texts with special relevance to phenotypes

Getting ready for the Human Phenome Project: the 2012 forum of the Human Variome Project

High-throughput discovery of genetic determinants of circadian misalignment

High-throughput mouse phenomics for characterizing mammalian gene function

Human and mouse essentiality screens as a resource for disease gene discovery

Identification of UBAP1 mutations in juvenile hereditary spastic paraplegia in the 100,000 Genomes Project

Identification of genes required for eye development by high-throughput screening of mouse knockouts

Identifying genetic determinants of inflammatory pain in mice using a large-scale gene-targeted screen

Improved exome prioritization of disease genes through cross-species phenotype comparison

Incremental data integration for tracking genotype-disease associations

Interpretable Clinical Genomics with a Likelihood Ratio Paradigm

Interpretable Clinical Genomics with a Likelihood Ratio Paradigm

Jannovar: a java library for exome annotation

Linking gene expression to phenotypes via pathway information

Linking tissues to phenotypes using gene expression profiles

Models for financial sustainability of biological databases and resources

Mondo: Unifying diseases for the world, by the world

Mouse Resource Browser--a database of mouse databases

MouseFinder: Candidate disease genes from mouse phenotype data

Navigating the Phenotype Frontier: The Monarch Initiative

Navigating the phenotype frontier: The Monarch Initiative

New methods for finding disease-susceptibility genes: impact and potential

New models for human disease from the International Mouse Phenotyping Consortium

Next-generation diagnostics and disease-gene discovery with the Exomiser

OpenStats: A robust and scalable software package for reproducible analysis of high-throughput phenotypic data

PanelApp crowdsources expert knowledge to establish consensus diagnostic gene panels

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

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

Phenotype-aware prioritisation of rare Mendelian disease variants

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

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

Prevalence of sexual dimorphism in mammalian phenotypic traits

Research funding. Sustaining the data and bioresource commons

Soft windowing application to improve analysis of high-throughput phenotyping data

Solutions for data integration in functional genomics: a critical assessment and case study

TRACER: a resource to study the regulatory architecture of the mouse genome

The 100 000 Genomes Project: bringing whole genome sequencing to the NHS

The BioMart community portal: an innovative alternative to large, centralized data repositories

The Deep Genome Project

The Human Phenotype Ontology in 2017

The Human Phenotype Ontology in 2021

The Human Phenotype Ontology in 2024: phenotypes around the world