World's Best Scientists 2026 revealed!

D-Index & Metrics

Computer Science

D-Index
34
Citations
8646
World Ranking
11926
National Ranking
4870

Overview

John H. Gennari is affiliated with the University of Washington in the United States. Their research focuses primarily on Biochemistry, Genetics, and Molecular Biology, with significant contributions to Molecular Biology, Information Systems and Management, Biophysics, Oncology, and Artificial Intelligence.

The main topics covered in their work include:

  • Gene Regulatory Network Analysis
  • Bioinformatics and Genomic Networks
  • Scientific Computing and Data Management
  • Microbial Metabolic Engineering and Bioproduction
  • Cell Image Analysis Techniques
  • Single-cell and Spatial Transcriptomics
  • Biomedical Text Mining and Ontologies

Some of the recent papers authored or co-authored by John H. Gennari include:

  • BioSimulators: a central registry of simulation engines and services for recommending specific tools, 2022, CU Scholar (University of Colorado Boulder)
  • Deep phenotyping of cardiac function in heart transplant patients using cardiovascular system models, 2020, The Journal of Physiology
  • Open modeling and exchange (OMEX) metadata specification version 1.0, 2020, Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics
  • OMEX metadata specification (version 1.2), 2021, Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics
  • libOmexMeta: enabling semantic annotation of models to support FAIR principles, 2021, Bioinformatics

Frequent co-authors who have collaborated with John H. Gennari include:

  • David Nickerson
  • Herbert M. Sauro
  • Joseph L. Hellerstein
  • Anand Rampadarath
  • Ion I. Moraru

The venues where John H. Gennari has published most frequently are:

  • bioRxiv (Cold Spring Harbor Laboratory)
  • Bioinformatics
  • Annals of Oncology
  • Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics
  • arXiv (Cornell University)

Best Publications

  • The evolution of Protégé: an environment for knowledge-based systems development

    John H. Gennari;Mark A. Musen;Ray W. Fergerson;William E. Grosso

  • Models of incremental concept formation

    John H. Gennari;Pat Langley;Doug Fisher

  • Models of incremental concept formation

    John H. Gennari;Pat Langley;Doug Fisher

  • The guideline interchange format: a model for representing guidelines.

    Lucila Ohno-Machado;John H. Gennari;Shawn N. Murphy;Nilesh L. Jain

  • Knowledge modeling at the millennium : The design and evolution of Protégé-2000

    William Grosso;Henrik Eriksson;Ray Fergerson;John Gennari

  • The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology

    Michal Galdzicki;Kevin P. Clancy;Ernst Oberortner;Matthew Pocock

  • Incorporating ideas from computer-supported cooperative work

    Wanda Pratt;Madhu C. Reddy;David W. McDonald;Peter Tarczy-Hornoch

  • Mapping domains to methods in support of reuse

    John H. Gennari;Samson W. Tu;Thomas E. Rothenfluh;Mark A. Musen

  • Ontology-based configuration of problem-solving methods and generation of knowledge-acquisition tools: application of PROTEGE-II to protocol-based decision support.

    Samson W Tu;Henrik Eriksson;John H Gennari;Yuval Shahar

  • PROTEGE-II: computer support for development of intelligent systems from libraries of components.

    Musen Ma;Gennari Jh;Eriksson H;Tu Sw

  • Evaluating clinical decision support systems: monitoring CPOE order check override rates in the Department of Veterans Affairs' Computerized Patient Record System.

    Ching Ping Lin;Thomas H. Payne;W. Paul Nichol;Patricia J. Hoey

  • Standard Biological Parts Knowledgebase

    Michal Galdzicki;Cesar Rodriguez;Deepak Chandran;Herbert M. Sauro

  • Asynchronous collaborative writing through annotations

    Chunhua Weng;John H. Gennari

  • Reusable ontologies, knowledge-acquisition tools, and performance systems: PROTE´GE´-II solutions to Sisyphus-2

    Thomas E. Rothenfluh;John H. Gennari;Henrik Eriksson;Angel R. Puerta

  • Sharing Structure and Function in Biological Design with SBOL 2.0.

    Nicholas Roehner;Jacob Beal;Kevin Clancy;Bryan Bartley

  • Making generic guidelines site-specific.

    D. B. Fridsma;J. H. Gennari;M. A. Musen

  • Integrating systems biology models and biomedical ontologies

    Robert Hoehndorf;Michel Dumontier;John H. Gennari;Sarala M. Wimalaratne

  • Beyond data models for automated user interface generation

    Angel R. Puerta;Henrik Eriksson;John H. Gennari;Mark A. Musen

  • Harmonizing semantic annotations for computational models in biology

    Maxwell Lewis Neal;Matthias König;David P. Nickerson;Goksel Misirli

  • Multiple ontologies in action: Composite annotations for biosimulation models

    John H. Gennari;Maxwell L. Neal;Michal Galdzicki;Daniel L. Cook

  • Participatory design of a collaborative clinical trial protocol writing system

    Chunhua Weng;David W. McDonald;Dana Sparks;Jason McCoy

Frequent Co-Authors

Mark A. Musen
Mark A. Musen Stanford University
Chris J. Myers
Chris J. Myers University of Colorado Boulder
Samson W. Tu
Samson W. Tu Stanford University
Herbert M. Sauro
Herbert M. Sauro University of Washington
Jacob Beal
Jacob Beal Raytheon (United States)
Chunhua Weng
Chunhua Weng Columbia University
David W. McDonald
David W. McDonald University of Washington
Peter Tarczy-Hornoch
Peter Tarczy-Hornoch University of Washington
Pat Langley
Pat Langley Stanford University
Guy-Bart Stan
Guy-Bart Stan Imperial College London

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