List of works - Melissa Haendel

A Census of Disease Ontologies

scientific article published on 09 May 2018

A Measure of Open Data: A Metric and Analysis of Reusable Data Practices in Biomedical Data Resources

scholarly article published 16 March 2018

A Simple Standard for Sharing Ontological Mappings (SSSOM)

preprint published on 15 December 2021

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

scientific article published on 25 August 2016

A harmonized meta-knowledgebase of clinical interpretations of somatic genomic variants in cancer

scientific article published on 03 April 2020

A phenome-wide association study of 26 mendelian genes reveals phenotypic expressivity of common and rare variants within the general population

scientific article published on 23 November 2020

A resource of lipidomics and metabolomics data from individuals with undiagnosed diseases

scientific article published on 21 April 2021

A sea of standards for omics data: sink or swim?

scientific article (publication date: 2014)

A unified anatomy ontology of the vertebrate skeletal system

scientific article (publication date: 2012)

Achieving human and machine accessibility of cited data in scholarly publications

scientific article

Achieving human and machine accessibility of cited data in scholarly publications

article published in 2015

An F-domain introduced by alternative splicing regulates activity of the zebrafish thyroid hormone receptor alpha

scientific article published on 27 April 2007

An analysis and metric of reusable data licensing practices for biomedical resources

An ontology-based method for secondary use of electronic dental record data

scientific article

An overview of the BioCreative 2012 Workshop Track III: interactive text mining task

scientific article published on 17 January 2013

Association Between COVID-19 and Mortality in Hip Fracture Surgery in the National COVID Cohort Collaborative (N3C): A Retrospective Cohort Study

scientific article published on 04 January 2022

Associations between HIV infection and clinical spectrum of COVID-19: a population level analysis based on US National COVID Cohort Collaborative (N3C) data

scientific article published on 13 October 2021

Barriers and Considerations for Diagnosing Rare Diseases in Indigenous Populations

scientific article published on 14 December 2020

Bedside Back to Bench: Building Bridges between Basic and Clinical Genomic Research

scientific article

Biolink Model: A Universal Schema for Knowledge Graphs in Clinical, Biomedical, and Translational Science ⬇️

scientific article

CARO – The Common Anatomy Reference Ontology

article

CLO: The cell line ontology

scientific article

Capturing phenotypes for precision medicine

scientific article

Characterizing Long COVID: Deep Phenotype of a Complex Condition

scientific article published on 25 November 2021

Classification, Ontology, and Precision Medicine

ClinGen advancing genomic data-sharing standards as a GA4GH driver project

scientific article published on 01 November 2018

Clinical interpretation of CNVs with cross-species phenotype data

scientific article

Community Approaches for Integrating Environmental Exposures into Human Models of Disease

scientific article published on 28 December 2020

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

scientific article

Connecting evolutionary morphology to genomics using ontologies: a case study from Cypriniformes including zebrafish

scientific article published in September 2007

Cytoskeletal changes during neurogenesis in cultures of avian neural crest cells

article

DSCAM: a novel member of the immunoglobulin superfamily maps in a Down syndrome region and is involved in the development of the nervous system

scientific article published in February 1998

Data-driven method to enhance craniofacial and oral phenotype vocabularies

scientific article published on 01 November 2019

Dealing with Data: A Case Study on Information and Data Management Literacy ⬇️

scientific article (publication date: 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

Developmental toxicity of the dithiocarbamate pesticide sodium metam in zebrafish

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

Drug repositioning candidates identified using in-silico quasi-quantum molecular simulation demonstrate reduced COVID-19 mortality in 1.5M patient records

scholarly article by Joy Alamgir published in 2021

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

scientific article

Enabling Global Clinical Collaborations on Identifiable Patient Data: The Minerva Initiative

scientific article published on 29 July 2019

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

scientific article published on 01 September 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

FAIRshake: Toolkit to Evaluate the FAIRness of Research Digital Resources

scientific article published on 30 October 2019

Finding our way through phenotypes

scientific article

From EHRs to Linked Data: representing and mining encounter data for clinical expertise evaluation

scientific article

From Reductionism to Reintegration: Solving society's most pressing problems requires building bridges between data types across the life sciences

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

scientific article published on 10 November 2021

Gold-standard ontology-based anatomical annotation in the CRAFT Corpus

article

How many rare diseases are there?

scientific article published on 01 February 2020

IRF2BPL Is Associated with Neurological Phenotypes

Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data

scientific article (publication date: 20 March 2017)

Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data

scientific article

Implementation of Zebrafish Ontologies for Toxicology Screening

scientific article published on 11 March 2022

Improved Diagnosis and Care for Rare Diseases through Implementation of Precision Public Health Framework

scientific article published in January 2017

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

scientific article

Integrating phenotype ontologies across multiple species

scientific article

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

Interpretable prioritization of splice variants in diagnostic next-generation sequencing

scientific article published on 21 July 2021

Is authorship sufficient for today's collaborative research? A call for contributor roles

scientific article published on 30 June 2020

KG-COVID-19: a framework to produce customized knowledge graphs for COVID-19 response

scientific article published on 9 November 2020

KG-Hub -- Building and Exchanging Biological Knowledge Graphs

preprint published in 2023

KG-Hub—building and exchanging biological knowledge graphs

scientific article published in 2023

Laying a Community-Based Foundation for Data-Driven Semantic Standards in Environmental Health Sciences

scientific article

Leukaemia inhibitory factor (LIF) is functionally linked to axotrophin and both LIF and axotrophin are linked to regulatory immune tolerance

scientific journal article

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

scientific article

Lost and found in behavioral informatics

scientific article published on January 2012

Matchmaker Exchange

scientific article

Meeting report: Identifying practical applications of ontologies for biodiversity informatics.

scientific article published on 17 May 2015

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

scientific article published on 16 September 2020

Modularization for the Cell Ontology

scientific article published on 12 December 2011

Mondo: Unifying diseases for the world, by the world

Muscle Logic: New Knowledge Resource for Anatomy Enables Comprehensive Searches of the Literature on the Feeding Muscles of Mammals

scientific article

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

scientific article published on 15 May 2022

Navigating the Phenotype Frontier: The Monarch Initiative

scientific article

Navigating the phenotype frontier: The Monarch Initiative

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

Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology

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 the reproducibility of science: unique identification of research resources in the biomedical literature

scientific article

One is the loneliest number: genotypic matchmaking using the electronic health record

scientific article published on 06 July 2021

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

scientific article published on 21 August 2020

Ontology Development Kit: a toolkit for building, maintaining, and standardising biomedical ontologies

preprint published on 06 July 2022

Ontology based molecular signatures for immune cell types via gene expression analysis

scientific article

OpenVIVO: Transparency in Scholarship

scientific article published on 30 September 2017

PDX-MI: Minimal Information for Patient-Derived Tumor Xenograft Models.

scientific article published in November 2017

PhenomeCentral: a portal for phenotypic and genotypic matchmaking of patients with rare genetic diseases

scientific article

Phenotype ontologies: the bridge between genomics and evolution

scientific article published on 09 April 2007

Plain-language medical vocabulary for precision diagnosis

scientific article published in April 2018

Preface

Prenatal phenotyping: A community effort to enhance the Human Phenotype Ontology

scientific article published in 2022

Proceedings of a Sickle Cell Disease Ontology workshop - Towards the first comprehensive ontology for Sickle Cell Disease

scientific article published on 15 March 2016

Representing glycophenotypes: semantic unification of glycobiology resources for disease discovery

scientific article published on 01 January 2019

Reproducibility and conflicts in immune epitope data

scientific article

Reproducible and reusable research: Are journal data sharing policies meeting the mark?

scientific article published on 12 November 2016

Reproducible and reusable research: are journal data sharing policies meeting the mark?

scientific article

Research resources: curating the new eagle-i discovery system ⬇️

scientific article (publication date: 2012)

Semantic Integration of Clinical Laboratory Tests from Electronic Health Records for Deep Phenotyping and Biomarker Discovery: Supplementary materials

article

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

article

Sharing Clinical and Genomic Data on Cancer - The Need for Global Solutions

scientific article

Sharing biological data: why, when, and how

scientific article published in 2021

Sleep and circadian informatics data harmonization: a workshop report from the Sleep Research Society and Sleep Research Network

scientific article published on 15 January 2022

Slow degeneration of zebrafish Rohon-Beard neurons during programmed cell death

scientific article

Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES): a method for populating knowledge bases using zero-shot learning

scientific article published on 21 February 2024

Structuring, reuse and analysis of electronic dental data using the Oral Health and Disease Ontology

scientific article published on 20 August 2020

Summarizing and visualizing structural changes during the evolution of biomedical ontologies using a Diff Abstraction Network

scientific article

TMOD-19. GABRIELLA MILLER KIDS FIRST DATA RESOURCE CENTER: LARGE-SCALE HARMONIZED CLINICAL AND GENOMIC DATA PLATFORM TO SUPPORT CHILDHOOD CANCER AND STRUCTURAL BIRTH DEFECT RESEARCH

scientific article published on 23 April 2019

Teaching data science fundamentals through realistic synthetic clinical cardiovascular data

scholarly article published 12 December 2017

Ten quick tips for biocuration

scientific article published on 02 May 2019

The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability

scientific article

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

scientific article published on 19 April 2022

The Data Use Ontology to streamline responsible access to human biomedical datasets

scientific article published on 10 November 2021

The Global academic research organization network: Data sharing to cure diseases and enable learning health systems

scientific article published on 03 December 2018

The Hearing Impairment Ontology: A Tool for Unifying Hearing Impairment Knowledge to Enhance Collaborative Research

scientific article published on 21 November 2019

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 Human Phenotype Ontology: Semantic Unification of Common and Rare Disease

scientific article

The IDeaS initiative: pilot study to assess the impact of rare diseases on patients and healthcare systems

scientific article published on 22 October 2021

The Matchmaker Exchange: a platform for rare disease gene discovery

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 for Biomedical Investigations

scientific article

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

The Pediatric Cell Atlas: Defining the Growth Phase of Human Development at Single-Cell Resolution

scientific article published on 28 March 2019

The Porifera Ontology (PORO): enhancing sponge systematics with an anatomy ontology

scientific article

The Resource Identification Initiative: A Cultural Shift in Publishing

scientific article from The Journal of Comparative Neurology

The Resource Identification Initiative: A Cultural Shift in Publishing

scientific article published on 20 November 2015 from Neuroinformatics

The Resource Identification Initiative: A cultural shift in publishing

scientific article (publication date: 2015) from F1000Research

The Resource Identification Initiative: a cultural shift in publishing

scientific article (publication date: 2016)

The Zebrafish Information Network: the zebrafish model organism database ⬇️

scientific article

The Zebrafish Information Network: the zebrafish model organism database provides expanded support for genotypes and phenotypes

scientific article

The case for open science: rare diseases

scientific article published on 12 September 2020

The health care and life sciences community profile for dataset descriptions

scientific article (publication date: 2016)

The health care and life sciences community profile for dataset descriptions

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

scientific article

The landscape of nutri-informatics: a review of current resources and challenges for integrative nutrition research

The teleost anatomy ontology: anatomical representation for the genomics age

scientific article

The zebrafish anatomy and stage ontologies: representing the anatomy and development of Danio rerio

scientific article published on 25 February 2014

Thematic series on biomedical ontologies in JBMS: challenges and new directions

scientific article

Tools for exploring mouse models of human disease

scientific article published on 30 August 2017

Transforming the study of organisms: Phenomic data models and knowledge bases

scientific article published on 24 November 2020

Uberon

ontology

Uberon, an integrative multi-species anatomy ontology

scientific article

Uberon: towards a comprehensive multi-species anatomy ontology

Underrepresentation of Phenotypic Variability of 16p13.11 Microduplication Syndrome Assessed With an Online Self-Phenotyping Tool (Phenotypr): Cohort Study

scientific article published on 16 March 2021

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

scientific article

Unifying the Identification of Biomedical Entities with the Bioregistry ⬇️

preprint published on 10 July 2022

Unifying the identification of biomedical entities with the Bioregistry ⬇️

scientific article published on 19 November 2022

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

What is an anatomy ontology?

scientific article

eagle-i: An Ontology-Driven Framework For Biomedical Resource Curation And Discovery

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

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

scientific article published on 03 October 2018

List of works by Melissa Haendel

A Census of Disease Ontologies

A Measure of Open Data: A Metric and Analysis of Reusable Data Practices in Biomedical Data Resources

A Simple Standard for Sharing Ontological Mappings (SSSOM)

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

A harmonized meta-knowledgebase of clinical interpretations of somatic genomic variants in cancer

A phenome-wide association study of 26 mendelian genes reveals phenotypic expressivity of common and rare variants within the general population

A resource of lipidomics and metabolomics data from individuals with undiagnosed diseases

A sea of standards for omics data: sink or swim?

A unified anatomy ontology of the vertebrate skeletal system

Achieving human and machine accessibility of cited data in scholarly publications

Achieving human and machine accessibility of cited data in scholarly publications

Achieving human and machine accessibility of cited data in scholarly publications

Achieving human and machine accessibility of cited data in scholarly publications

Achieving human and machine accessibility of cited data in scholarly publications

Achieving human and machine accessibility of cited data in scholarly publications

An F-domain introduced by alternative splicing regulates activity of the zebrafish thyroid hormone receptor alpha

An analysis and metric of reusable data licensing practices for biomedical resources

An ontology-based method for secondary use of electronic dental record data

An overview of the BioCreative 2012 Workshop Track III: interactive text mining task

Association Between COVID-19 and Mortality in Hip Fracture Surgery in the National COVID Cohort Collaborative (N3C): A Retrospective Cohort Study

Associations between HIV infection and clinical spectrum of COVID-19: a population level analysis based on US National COVID Cohort Collaborative (N3C) data

Barriers and Considerations for Diagnosing Rare Diseases in Indigenous Populations

Bedside Back to Bench: Building Bridges between Basic and Clinical Genomic Research

Biolink Model: A Universal Schema for Knowledge Graphs in Clinical, Biomedical, and Translational Science ⬇️

CARO – The Common Anatomy Reference Ontology

CLO: The cell line ontology

Capturing phenotypes for precision medicine

Characterizing Long COVID: Deep Phenotype of a Complex Condition

Classification, Ontology, and Precision Medicine

ClinGen advancing genomic data-sharing standards as a GA4GH driver project

Clinical interpretation of CNVs with cross-species phenotype data

Community Approaches for Integrating Environmental Exposures into Human Models of Disease

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

Connecting evolutionary morphology to genomics using ontologies: a case study from Cypriniformes including zebrafish

Cytoskeletal changes during neurogenesis in cultures of avian neural crest cells

DSCAM: a novel member of the immunoglobulin superfamily maps in a Down syndrome region and is involved in the development of the nervous system

Data-driven method to enhance craniofacial and oral phenotype vocabularies

Dealing with Data: A Case Study on Information and Data Management Literacy ⬇️

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

Developmental toxicity of the dithiocarbamate pesticide sodium metam in zebrafish

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

Drug repositioning candidates identified using in-silico quasi-quantum molecular simulation demonstrate reduced COVID-19 mortality in 1.5M patient records

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

Enabling Global Clinical Collaborations on Identifiable Patient Data: The Minerva Initiative

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

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

FAIRshake: Toolkit to Evaluate the FAIRness of Research Digital Resources

Finding our way through phenotypes

From EHRs to Linked Data: representing and mining encounter data for clinical expertise evaluation

From Reductionism to Reintegration: Solving society's most pressing problems requires building bridges between data types across the life sciences

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

Gold-standard ontology-based anatomical annotation in the CRAFT Corpus

How many rare diseases are there?

IRF2BPL Is Associated with Neurological Phenotypes

Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data

Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data

Implementation of Zebrafish Ontologies for Toxicology Screening

Improved Diagnosis and Care for Rare Diseases through Implementation of Precision Public Health Framework

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

Integrating phenotype ontologies across multiple species

Interpretable Clinical Genomics with a Likelihood Ratio Paradigm

Interpretable Clinical Genomics with a Likelihood Ratio Paradigm

Interpretable prioritization of splice variants in diagnostic next-generation sequencing

Is authorship sufficient for today's collaborative research? A call for contributor roles

KG-COVID-19: a framework to produce customized knowledge graphs for COVID-19 response

KG-Hub -- Building and Exchanging Biological Knowledge Graphs

KG-Hub—building and exchanging biological knowledge graphs

Laying a Community-Based Foundation for Data-Driven Semantic Standards in Environmental Health Sciences

Leukaemia inhibitory factor (LIF) is functionally linked to axotrophin and both LIF and axotrophin are linked to regulatory immune tolerance

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

Lost and found in behavioral informatics

Matchmaker Exchange

Meeting report: Identifying practical applications of ontologies for biodiversity informatics.

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

Modularization for the Cell Ontology

Modularization for the Cell Ontology