Lincoln D Stein

Summary

Publications

  1. pmc Bioinformatics: alive and kicking
    Lincoln D Stein
    Ontario Institute for Cancer Research, Toronto, ON, M5G 0A3, Canada
    Genome Biol 9:114. 2008
  2. pmc The Reactome BioMart
    Robin A Haw
    Ontario Institute for Cancer Research, Toronto, ON, M5G0A3, Canada
    Database (Oxford) 2011:bar031. 2011
  3. pmc The modENCODE Data Coordination Center: lessons in harvesting comprehensive experimental details
    Nicole L Washington
    Lawrence Berkeley National Laboratory, Genomics Division, 1 Cyclotron Road MS64 121, Berkeley, CA 94720, USA
    Database (Oxford) 2011:bar023. 2011
  4. pmc Reactome: a database of reactions, pathways and biological processes
    David Croft
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 39:D691-7. 2011
  5. pmc Alterations in tumor necrosis factor signaling pathways are associated with cytotoxicity and resistance to taxanes: a study in isogenic resistant tumor cells
    Jason A Sprowl
    Regional Cancer Program, Sudbury Regional Hospital, 41 Ramsey Lake Road, Sudbury ON P3E 5J1, Canada
    Breast Cancer Res 14:R2. 2012
  6. pmc Using GBrowse 2.0 to visualize and share next-generation sequence data
    Lincoln D Stein
    Ontario Institute for Cancer Research, 101 College Street, Suite 800, Toronto, Ontario, Canada
    Brief Bioinform 14:162-71. 2013
  7. pmc A standard variation file format for human genome sequences
    Martin G Reese
    Omicia, 2200 Powell Street, Suite 525, Emeryville, CA 94608, USA
    Genome Biol 11:R88. 2010
  8. pmc PeakRanger: a cloud-enabled peak caller for ChIP-seq data
    Xin Feng
    Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794, USA
    BMC Bioinformatics 12:139. 2011
  9. pmc Localizing triplet periodicity in DNA and cDNA sequences
    Liya Wang
    Cold Spring Harbor Laboratory, Williams 5, Cold Spring Harbor, NY 11724, USA
    BMC Bioinformatics 11:550. 2010
  10. pmc The case for cloud computing in genome informatics
    Lincoln D Stein
    Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada
    Genome Biol 11:207. 2010

Collaborators

Detail Information

Publications16

  1. pmc Bioinformatics: alive and kicking
    Lincoln D Stein
    Ontario Institute for Cancer Research, Toronto, ON, M5G 0A3, Canada
    Genome Biol 9:114. 2008
    ..Bioinformatics has become too central to biology to be left to specialist bioinformaticians. Biologists are all bioinformaticians now...
  2. pmc The Reactome BioMart
    Robin A Haw
    Ontario Institute for Cancer Research, Toronto, ON, M5G0A3, Canada
    Database (Oxford) 2011:bar031. 2011
    ..Database URL: http://www.reactome.org...
  3. pmc The modENCODE Data Coordination Center: lessons in harvesting comprehensive experimental details
    Nicole L Washington
    Lawrence Berkeley National Laboratory, Genomics Division, 1 Cyclotron Road MS64 121, Berkeley, CA 94720, USA
    Database (Oxford) 2011:bar023. 2011
    ..modENCODE data can be found at http://www.modencode.org...
  4. pmc Reactome: a database of reactions, pathways and biological processes
    David Croft
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 39:D691-7. 2011
    ..The resulting inferred pathway sets can be browsed and analyzed with our Species Comparison tool. Collaborations are also underway to create manually curated data sets on the Reactome framework for chicken, Drosophila and rice...
  5. pmc Alterations in tumor necrosis factor signaling pathways are associated with cytotoxicity and resistance to taxanes: a study in isogenic resistant tumor cells
    Jason A Sprowl
    Regional Cancer Program, Sudbury Regional Hospital, 41 Ramsey Lake Road, Sudbury ON P3E 5J1, Canada
    Breast Cancer Res 14:R2. 2012
    ..Our study aimed to correlate alterations in the TNF pathway with taxane cytotoxicity and the acquisition of taxane resistance...
  6. pmc Using GBrowse 2.0 to visualize and share next-generation sequence data
    Lincoln D Stein
    Ontario Institute for Cancer Research, 101 College Street, Suite 800, Toronto, Ontario, Canada
    Brief Bioinform 14:162-71. 2013
    ..SAM/BAM tracks provide semantic zooming and support both local and remote data sources. This article provides step-by-step instructions for configuring GBrowse to display NGS data...
  7. pmc A standard variation file format for human genome sequences
    Martin G Reese
    Omicia, 2200 Powell Street, Suite 525, Emeryville, CA 94608, USA
    Genome Biol 11:R88. 2010
    ....
  8. pmc PeakRanger: a cloud-enabled peak caller for ChIP-seq data
    Xin Feng
    Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794, USA
    BMC Bioinformatics 12:139. 2011
    ..Other algorithms are limited in their configurability, performance on large data sets, and ability to distinguish closely-spaced peaks...
  9. pmc Localizing triplet periodicity in DNA and cDNA sequences
    Liya Wang
    Cold Spring Harbor Laboratory, Williams 5, Cold Spring Harbor, NY 11724, USA
    BMC Bioinformatics 11:550. 2010
    ..Here, we report a technique that provides higher-resolution identification of these boundaries, and use the technique to explore the biological correlates of TP regions in the genome of the model organism C. elegans...
  10. pmc The case for cloud computing in genome informatics
    Lincoln D Stein
    Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada
    Genome Biol 11:207. 2010
    ..With DNA sequencing now getting cheaper more quickly than data storage or computation, the time may have come for genome informatics to migrate to the cloud...
  11. pmc WormBase: a comprehensive resource for nematode research
    Todd W Harris
    Ontario Institute for Cancer Research, Toronto, ON, Canada
    Nucleic Acids Res 38:D463-7. 2010
    ..Here, we describe new species and data types now available at WormBase. In addition, we detail enhancements to our curatorial pipeline and website infrastructure to accommodate new genomes and an extensive user base...
  12. pmc nGASP--the nematode genome annotation assessment project
    Avril Coghlan
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
    BMC Bioinformatics 9:549. 2008
    ..elegans genome. Predictions were compared to reference gene sets consisting of confirmed or manually curated gene models from WormBase...
  13. pmc JBrowse: a next-generation genome browser
    Mitchell E Skinner
    Department of Bioengineering, University of California at Berkeley, Berkeley, California 94720, USA
    Genome Res 19:1630-8. 2009
    ....
  14. doi request reprint An introduction to the informatics of "next-generation" sequencing
    Lincoln D Stein
    Ontario Institute for Cancer Research, Toronto, Ontario, Canada
    Curr Protoc Bioinformatics . 2011
    ..This unit surveys the software packages that are available for managing and analyzing NGS data...
  15. pmc Cloud-based uniform ChIP-Seq processing tools for modENCODE and ENCODE
    Quang M Trinh
    Ontario Institute for Cancer Research, MaRS Centre, South Tower, 101 College Street, Suite 800, Toronto, ON, M5G 0A3, Canada
    BMC Genomics 14:494. 2013
    ..Unfortunately this can be a time consuming and logistically challenging proposition...
  16. doi request reprint Feasibility of real time next generation sequencing of cancer genes linked to drug response: results from a clinical trial
    Ben Tran
    Department of Medical Oncology, Princess Margaret Hospital, University Health Network, University of Toronto, Toronto, Ontario, Canada
    Int J Cancer 132:1547-55. 2013
    ..Additionally, actionable mutations identified in this study were relatively stable between archival and biopsy samples, implying that cancer mutations that are good predictors of drug response may remain constant across clinical stages...