List of works - Suzanna Lewis

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

scientific article published on 25 August 2016

A high throughput screen to identify secreted and transmembrane proteins involved in Drosophila embryogenesis

scientific article

A knowledge based approach to matching human neurodegenerative disease and animal models

scientific article published on 14 May 2013

A short study on the success of the Gene Ontology

2004 article

Anatomy of BioJS, an open source community for the life sciences

scientific article

Annotation of the Drosophila melanogaster euchromatic genome: a systematic review

scientific article

Apollo: Democratizing genome annotation

scientific article from PLOS Computational Biology

Apollo: a community resource for genome annotation editing

scientific article

Assessing the effectiveness of knowledge-based interventions in increasing skin cancer awareness, knowledge, and protective behaviors in skin of color populations

scientific article published in October 2017

Assessment of genome-wide protein function classification for Drosophila melanogaster

scientific article published on September 2003

Best Practice Data Life Cycle Approaches for the Life Sciences

scholarly article

Best practice data life cycle approaches for the life sciences

article

BioJS: an open source standard for biological visualisation - its status in 2014

scientific article

Calling on a million minds for community annotation in WikiProteins

scientific article

Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster

scientific article (publication date: 4 October 2002)

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

Correction: Reactome: a knowledge base of biologic pathways and processes.

scientific article published on 4 February 2009

Coxsackie eruption arising in areas of epidermolytic ichthyosis

scientific article published on 17 March 2015

Deletions of chromosomal regulatory boundaries are associated with congenital disease

scientific article

Disease insights through cross-species phenotype comparisons

scientific article

EGASP: the human ENCODE Genome Annotation Assessment Project

scientific article

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

scientific article

Emerging semantics to link phenotype and environment

scientific article

Entity/quality-based logical definitions for the human skeletal phenome using PATO

scientific article

Finding our way through phenotypes

scientific article

Gearing up to handle the mosaic nature of life in the quest for orthologs

scientific article published on 30 August 2017

Gene Ontology Causal Activity Modeling (GO-CAM) moves beyond GO annotations to structured descriptions of biological functions and systems

scientific article published on 01 October 2019

Gene Ontology: looking backwards and forwards

scientific article

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

scientific article

Integrating phenotype ontologies across multiple species

scientific article

Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project

scientific article

Invariance (?) of Mutational Parameters for Relative Fitness Over 400 Generations of Mutation Accumulation inCaenorhabditis elegans ⬇️

scientific article published on December 1, 2012

JBrowse: a dynamic web platform for genome visualization and analysis

scientific article published on 12 April 2016

Joining forces in the quest for orthologs

scientific article published on 29 September 2009

Large-scale inference of gene function through phylogenetic annotation of Gene Ontology terms: case study of the apoptosis and autophagy cellular processes

scientific article published on 26 December 2016

Large-scale trends in the evolution of gene structures within 11 animal genomes

scientific article

Linking human diseases to animal models using ontology-based phenotype annotation

scientific article

MSAViewer: interactive JavaScript visualization of multiple sequence alignments

scientific article published on 13 July 2016

Model organism data evolving in support of translational medicine

scientific article published on 17 September 2018

Modelling data across labs, genomes, space and time

scientific article

MouseFinder: Candidate disease genes from mouse phenotype data

scientific article

National Center for Biomedical Ontology: advancing biomedicine through structured organization of scientific knowledge

scientific article

Navigating the Phenotype Frontier: The Monarch Initiative

scientific article

Navigating the phenotype frontier: The Monarch Initiative

Novel sequence feature variant type analysis of the HLA genetic association in systemic sclerosis

scientific article

OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies

scientific article published on 13 October 2021

OBO-Edit--an ontology editor for biologists

scientific article

On ontologies for biologists: the Gene Ontology--untangling the web.

scientific article

On the Use of Gene Ontology Annotations to Assess Functional Similarity among Orthologs and Paralogs: A Short Report

scientific article

Ontology annotation: mapping genomic regions to biological function

scientific article published on 5 January 2007

PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium

scientific article

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

scientific article published on 9 May 2013

Phenotype Ontology Research Coordination Network meeting report: creating a community network for comparing and leveraging phenotype-genotype knowledge across species

scientific article published on 20 July 2012

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

Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium

scientific article

Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project

scientific article (publication date: August 2008)

Quest for Orthologs Entails Quest for Tree of Life: In Search of the Gene Stream

scientific article published in July 2015

Reactome knowledgebase of human biological pathways and processes

scientific article (publication date: 2009)

Reactome: a knowledge base of biologic pathways and processes

scientific article

Sequence ontology annotation guide

scientific article published on January 2004

Standardized benchmarking in the quest for orthologs

scientific article (publication date: 4 April 2016)

Standardized description of scientific evidence using the Evidence Ontology (ECO)

scientific article

Survey-based naming conventions for use in OBO Foundry ontology development

scientific article (publication date: 27 April 2009)

Systematic determination of patterns of gene expression during Drosophila embryogenesis

scientific article

The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations

scientific article

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

scientific article (publication date: 2014)

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: 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 OBO Foundry: coordinated evolution of ontologies to support biomedical data integration

scientific article published in November 2007

The RNA Ontology Consortium: an open invitation to the RNA community

scientific article published on 16 February 2006

The Sequence Ontology: a tool for the unification of genome annotations

scientific article published in 2005

The Vision and Challenges of the Gene Ontology

scientific article published on January 2017

The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation

scientific article

The environment ontology: contextualising biological and biomedical entities

article

The generic genome browser: a building block for a model organism system database

scientific article

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

scientific article

The minimum information about a genome sequence (MIGS) specification

scientific article

The modENCODE Data Coordination Center: lessons in harvesting comprehensive experimental details

scientific article (publication date: 2011)

The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective

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)

Uberon, an integrative multi-species anatomy ontology

scientific article

Uberon: towards a comprehensive multi-species anatomy ontology

Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon

scientific article

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 ontologies to define the relation between neurodegenerative disease and associated animal model phenotypes

Web Apollo: a web-based genomic annotation editing platform

scientific article (publication date: 30 August 2013)

Wrestling with SUMO and bio-ontologies

scientific article published on January 2006

modMine: flexible access to modENCODE data

scientific article

List of works by Suzanna Lewis

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

A high throughput screen to identify secreted and transmembrane proteins involved in Drosophila embryogenesis

A knowledge based approach to matching human neurodegenerative disease and animal models

A short study on the success of the Gene Ontology

Anatomy of BioJS, an open source community for the life sciences

Annotation of the Drosophila melanogaster euchromatic genome: a systematic review

Apollo: Democratizing genome annotation

Apollo: Democratizing genome annotation

Apollo: a community resource for genome annotation editing

Assessing the effectiveness of knowledge-based interventions in increasing skin cancer awareness, knowledge, and protective behaviors in skin of color populations

Assessment of genome-wide protein function classification for Drosophila melanogaster

Best Practice Data Life Cycle Approaches for the Life Sciences

Best practice data life cycle approaches for the life sciences

BioJS: an open source standard for biological visualisation - its status in 2014

Calling on a million minds for community annotation in WikiProteins

Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster

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

Correction: Reactome: a knowledge base of biologic pathways and processes.

Coxsackie eruption arising in areas of epidermolytic ichthyosis

Deletions of chromosomal regulatory boundaries are associated with congenital disease

Disease insights through cross-species phenotype comparisons

EGASP: the human ENCODE Genome Annotation Assessment Project

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

Emerging semantics to link phenotype and environment

Entity/quality-based logical definitions for the human skeletal phenome using PATO

Finding our way through phenotypes

Gearing up to handle the mosaic nature of life in the quest for orthologs

Gene Ontology Causal Activity Modeling (GO-CAM) moves beyond GO annotations to structured descriptions of biological functions and systems

Gene Ontology: looking backwards and forwards

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

Integrating phenotype ontologies across multiple species

Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project

Invariance (?) of Mutational Parameters for Relative Fitness Over 400 Generations of Mutation Accumulation inCaenorhabditis elegans ⬇️

JBrowse: a dynamic web platform for genome visualization and analysis

Joining forces in the quest for orthologs

Large-scale inference of gene function through phylogenetic annotation of Gene Ontology terms: case study of the apoptosis and autophagy cellular processes

Large-scale trends in the evolution of gene structures within 11 animal genomes

Linking human diseases to animal models using ontology-based phenotype annotation

MSAViewer: interactive JavaScript visualization of multiple sequence alignments

Model organism data evolving in support of translational medicine

Modelling data across labs, genomes, space and time

MouseFinder: Candidate disease genes from mouse phenotype data

National Center for Biomedical Ontology: advancing biomedicine through structured organization of scientific knowledge

Navigating the Phenotype Frontier: The Monarch Initiative

Navigating the phenotype frontier: The Monarch Initiative

Novel sequence feature variant type analysis of the HLA genetic association in systemic sclerosis

OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies

OBO-Edit--an ontology editor for biologists

On ontologies for biologists: the Gene Ontology--untangling the web.

On the Use of Gene Ontology Annotations to Assess Functional Similarity among Orthologs and Paralogs: A Short Report

Ontology annotation: mapping genomic regions to biological function

PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium

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

Phenotype Ontology Research Coordination Network meeting report: creating a community network for comparing and leveraging phenotype-genotype knowledge across species

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

Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium

Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project

Quest for Orthologs Entails Quest for Tree of Life: In Search of the Gene Stream

Reactome knowledgebase of human biological pathways and processes

Reactome: a knowledge base of biologic pathways and processes

Sequence ontology annotation guide

Standardized benchmarking in the quest for orthologs

Standardized description of scientific evidence using the Evidence Ontology (ECO)

Survey-based naming conventions for use in OBO Foundry ontology development

Systematic determination of patterns of gene expression during Drosophila embryogenesis

The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations

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

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

The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration

The RNA Ontology Consortium: an open invitation to the RNA community

The Sequence Ontology: a tool for the unification of genome annotations

The Vision and Challenges of the Gene Ontology

The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation

The environment ontology: contextualising biological and biomedical entities

The generic genome browser: a building block for a model organism system database

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