Lincoln Stein

Orcid: 0000-0002-1983-4588

Affiliations:
  • Ontario Institute for Cancer Research, Toronto, Canada


According to our database1, Lincoln Stein authored at least 91 papers between 1993 and 2024.

Collaborative distances:

Timeline

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Bibliography

2024
Pathway-based, reaction-specific annotation of disease variants for elucidation of molecular phenotypes.
Database J. Biol. Databases Curation, January, 2024

FAIR Header Reference genome: a TRUSTworthy standard.
Briefings Bioinform., 2024

2023
JBrowse Jupyter: a Python interface to JBrowse 2.
Bioinform., January, 2023

Fourteen quick tips for crowdsourcing geographically linked data for public health advocacy.
PLoS Comput. Biol., 2023

2022
The reactome pathway knowledgebase 2022.
Nucleic Acids Res., 2022

Evaluating the predictive accuracy of curated biological pathways in a public knowledgebase.
Database J. Biol. Databases Curation, 2022

2021
The Dockstore: enhancing a community platform for sharing reproducible and accessible computational protocols.
Nucleic Acids Res., 2021

Gramene 2021: harnessing the power of comparative genomics and pathways for plant research.
Nucleic Acids Res., 2021

The Gene Ontology resource: enriching a GOld mine.
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Nucleic Acids Res., 2021

JBrowseR: an R interface to the JBrowse 2 genome browser.
Bioinform., 2021

2020
JBrowse Connect: A server API to connect JBrowse instances and users.
PLoS Comput. Biol., 2020

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes.
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Nat., 2020

The evolutionary history of 2,658 cancers.
Nat., 2020

Plant Reactome: a knowledgebase and resource for comparative pathway analysis.
Nucleic Acids Res., 2020

The reactome pathway knowledgebase.
Nucleic Acids Res., 2020

WormBase: a modern Model Organism Information Resource.
Nucleic Acids Res., 2020

2019
Whole genomes define concordance of matched primary, xenograft, and organoid models of pancreas cancer.
PLoS Comput. Biol., 2019

Reactome and ORCID - fine-grained credit attribution for community curation.
Database J. Biol. Databases Curation, 2019

2018
Reactome graph database: Efficient access to complex pathway data.
PLoS Comput. Biol., 2018

Gramene 2018: unifying comparative genomics and pathway resources for plant research.
Nucleic Acids Res., 2018

WormBase 2017: molting into a new stage.
Nucleic Acids Res., 2018

The Reactome Pathway Knowledgebase.
Nucleic Acids Res., 2018

Reactome diagram viewer: data structures and strategies to boost performance.
Bioinform., 2018

2017
Plant Reactome: a resource for plant pathways and comparative analysis.
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

Reactome enhanced pathway visualization.
Bioinform., 2017

2016
Gramene 2016: comparative plant genomics and pathway resources.
Nucleic Acids Res., 2016

WormBase 2016: expanding to enable helminth genomic research.
Nucleic Acids Res., 2016

The Reactome pathway Knowledgebase.
Nucleic Acids Res., 2016

2015
Data analysis: Create a cloud commons.
Nat., 2015

A genome-wide association study platform built on iPlant cyber-infrastructure.
Concurr. Comput. Pract. Exp., 2015

2014
Gramene 2013: comparative plant genomics resources.
Nucleic Acids Res., 2014

WormBase 2014: new views of curated biology.
Nucleic Acids Res., 2014

The Reactome pathway knowledgebase.
Nucleic Acids Res., 2014

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

2013
Using GBrowse 2.0 to visualize and share next-generation sequence data.
Briefings Bioinform., 2013

2012
WormBase 2012: more genomes, more data, new website.
Nucleic Acids Res., 2012

modMine: flexible access to modENCODE data.
Nucleic Acids Res., 2012

Modeling the Clonal Evolution of Cancer from Next Generation Sequencing Data
CoRR, 2012

2011
Reactome: a database of reactions, pathways and biological processes.
Nucleic Acids Res., 2011

PeakRanger: A cloud-enabled peak caller for ChIP-seq data.
BMC Bioinform., 2011

The modENCODE Data Coordination Center: lessons in harvesting comprehensive experimental details.
Database J. Biol. Databases Curation, 2011

The Reactome BioMart.
Database J. Biol. Databases Curation, 2011

2010
WormBase: a comprehensive resource for nematode research.
Nucleic Acids Res., 2010

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

2009
Reactome knowledgebase of human biological pathways and processes.
Nucleic Acids Res., 2009

CMap 1.01: a comparative mapping application for the Internet.
Bioinform., 2009

Gramene QTL database: development, content and applications.
Database J. Biol. Databases Curation, 2009

2008
<i>Gallus</i> GBrowse: a unified genomic database for the chicken.
Nucleic Acids Res., 2008

WormBase 2007.
Nucleic Acids Res., 2008

Gramene: a growing plant comparative genomics resource.
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.
Nucleic Acids Res., 2008

nGASP - the nematode genome annotation assessment project.
BMC Bioinform., 2008

2007
WormBook: the online review of <i>Caenorhabditis elegans</i> biology.
Nucleic Acids Res., 2007

WormBase: new content and better access.
Nucleic Acids Res., 2007

Reactome: An integrated expert model of human molecular processes and access toolkit.
J. Integr. Bioinform., 2007

2006
Panzea: a database and resource for molecular and functional diversity in the maize genome.
Nucleic Acids Res., 2006

WormBase: better software, richer content.
Nucleic Acids Res., 2006

Gramene: a bird's eye view of cereal genomes.
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.
Proceedings of the On the Move to Meaningful Internet Systems 2006: OTM 2006 Workshops, 2006

2005
Reactome: a knowledgebase of biological pathways.
Nucleic Acids Res., 2005

WormBase: a comprehensive data resource for <i>Caenorhabditis</i> biology and genomics.
Nucleic Acids Res., 2005

SynBrowse: a synteny browser for comparative sequence analysis.
Bioinform., 2005

2004
WormBase: a multi-species resource for nematode biology and genomics.
Nucleic Acids Res., 2004

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

2003
The SNP Consortium website: past, present and future.
Nucleic Acids Res., 2003

WormBase: a cross-species database for comparative genomics.
Nucleic Acids Res., 2003

2002
Gramene: a resource for comparative grass genomics.
Nucleic Acids Res., 2002

2001
WormBase: network access to the genome and biology of Caenorhabditis elegans.
Nucleic Acids Res., 2001

The Distributed Annotation System.
BMC Bioinform., 2001

1999
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

1998
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

1997
The electronic medical record: promises and threats.
World Wide Web J., 1997

Exploring CGI with Perl.
World Wide Web J., 1997

Building Human Genome Maps with Radiation Hybrids.
J. Comput. Biol., 1997

1995
How to Set Up and Maintain a World Wide Web Site: The Guide for Information Providers.
Addison-Wesley, ISBN: 0-201-63389-2, 1995

1994
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

1993
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


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