Pathway-based, reaction-specific annotation of disease variants for elucidation of molecular phenotypes.
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Database J. Biol. Databases Curation, January, 2024
FAIR Header Reference genome: a TRUSTworthy standard.
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Briefings Bioinform., 2024
JBrowse Jupyter: a Python interface to JBrowse 2.
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Bioinform., January, 2023
Fourteen quick tips for crowdsourcing geographically linked data for public health advocacy.
PLoS Comput. Biol., 2023
Evaluating the predictive accuracy of curated biological pathways in a public knowledgebase.
Database J. Biol. Databases Curation, 2022
The Dockstore: enhancing a community platform for sharing reproducible and accessible computational protocols.
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Nucleic Acids Res., 2021
JBrowseR: an R interface to the JBrowse 2 genome browser.
Bioinform., 2021
JBrowse Connect: A server API to connect JBrowse instances and users.
PLoS Comput. Biol., 2020
Whole genomes define concordance of matched primary, xenograft, and organoid models of pancreas cancer.
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PLoS Comput. Biol., 2019
Reactome and ORCID - fine-grained credit attribution for community curation.
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Database J. Biol. Databases Curation, 2019
Reactome graph database: Efficient access to complex pathway data.
PLoS Comput. Biol., 2018
Reactome diagram viewer: data structures and strategies to boost performance.
Bioinform., 2018
Plant Reactome: a resource for plant pathways and comparative analysis.
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Nucleic Acids Res., 2017
The Dockstore: enabling modular, community-focused sharing of Docker-based genomics tools and workflows.
F1000Research, 2017
Reactome pathway analysis: a high-performance in-memory approach.
BMC Bioinform., 2017
Data analysis: Create a cloud commons.
Nat., 2015
A genome-wide association study platform built on iPlant cyber-infrastructure.
Concurr. Comput. Pract. Exp., 2015
ReactomeFIViz: the Reactome FI Cytoscape app for pathway and network-based data analysis.
F1000Research, 2014
Reconstructing subclonal composition and evolution from whole genome sequencing of tumors.
CoRR, 2014
Inferring clonal evolution of tumors from single nucleotide somatic mutations.
BMC Bioinform., 2014
Using GBrowse 2.0 to visualize and share next-generation sequence data.
Briefings Bioinform., 2013
Modeling the Clonal Evolution of Cancer from Next Generation Sequencing Data
CoRR, 2012
PeakRanger: A cloud-enabled peak caller for ChIP-seq data.
BMC Bioinform., 2011
The modENCODE Data Coordination Center: lessons in harvesting comprehensive experimental details.
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Database J. Biol. Databases Curation, 2011
Database J. Biol. Databases Curation, 2011
Localizing triplet periodicity in DNA and cDNA sequences.
BMC Bioinform., 2010
The systematic annotation of the three main GPCR families in Reactome.
Database J. Biol. Databases Curation, 2010
Reactome knowledgebase of human biological pathways and processes.
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Nucleic Acids Res., 2009
CMap 1.01: a comparative mapping application for the Internet.
Bioinform., 2009
Gramene QTL database: development, content and applications.
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Database J. Biol. Databases Curation, 2009
<i>Gallus</i> GBrowse: a unified genomic database for the chicken.
Nucleic Acids Res., 2008
Panzea: an update on new content and features.
Nucleic Acids Res., 2008
The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations.
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Nucleic Acids Res., 2008
nGASP - the nematode genome annotation assessment project.
BMC Bioinform., 2008
WormBook: the online review of <i>Caenorhabditis elegans</i> biology.
Nucleic Acids Res., 2007
Reactome: An integrated expert model of human molecular processes and access toolkit.
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J. Integr. Bioinform., 2007
Panzea: a database and resource for molecular and functional diversity in the maize genome.
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Nucleic Acids Res., 2006
Look-Align: an interactive web-based multiple sequence alignment viewer with polymorphism analysis support.
Bioinform., 2006
Reactome - A Knowledgebase of Biological Pathways.
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Proceedings of the On the Move to Meaningful Internet Systems 2006: OTM 2006 Workshops, 2006
Reactome: a knowledgebase of biological pathways.
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Nucleic Acids Res., 2005
SynBrowse: a synteny browser for comparative sequence analysis.
Bioinform., 2005
Applying Semantic Web Services to Bioinformatics: Experiences Gained, Lessons Learnt.
Proceedings of the Semantic Web, 2004
Identifying MicroRNAs in Plant Genomes.
Proceedings of the 3rd International IEEE Computer Society Computational Systems Bioinformatics Conference, 2004
The SNP Consortium website: past, present and future.
Nucleic Acids Res., 2003
Gramene: a resource for comparative grass genomics.
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Nucleic Acids Res., 2002
WormBase: network access to the genome and biology of Caenorhabditis elegans.
Nucleic Acids Res., 2001
The Distributed Annotation System.
BMC Bioinform., 2001
AceDB: a genome database management system.
Comput. Sci. Eng., 1999
SBOX: Put CGI Scripts in a Box.
Proceedings of the 1999 USENIX Annual Technical Conference, 1999
Writing Apache modules with Perl and C - the Apache API and mod Perl.
O'Reilly, ISBN: 978-1-56592-567-0, 1999
The LabBase system for data management in large scale biology research laboratories.
Bioinform., 1998
The LabFlow System for Workflow Management in Large Scale Biology Research Laboratories.
Proceedings of the 6th International Conference on Intelligent Systems for Molecular Biology (ISMB-98), Montréal, Québec, Canada, June 28, 1998
The electronic medical record: promises and threats.
World Wide Web J., 1997
Building Human Genome Maps with Radiation Hybrids.
J. Comput. Biol., 1997
How to Set Up and Maintain a World Wide Web Site: The Guide for Information Providers.
Addison-Wesley, ISBN: 0-201-63389-2, 1995
Building a Laboratory Information System Around a C++-Based Object-Oriented DBMS.
Proceedings of the VLDB'94, 1994
Splicing UNIX into a Genome Mapping Laboratory.
Proceedings of the USENIX Summer 1994 Technical Conference, 1994
Constructing a Domain-Specific DBMS using a Persistent Object System.
Proceedings of the Persistent Object Systems, 1994
Requirements for a Deductive Query Language in the MapBase Genome-Mapping Database.
Proceedings of the Workshop on Programming with Logic Databases. In Conjunction with ILPS, 1993
Requirements for a Deductive Query Language in a Genome-Mapping Database.
Proceedings of the Applications of Logic Databases, 1993