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 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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

Collaborators

  • Quang M Trinh
  • Jason A Sprowl
  • Xin Feng
  • Todd W Harris
  • Liya Wang
  • Martin G Reese
  • Kar Ming Chu
  • Peter Ruzanov
  • Sergio Contrino
  • Ziru Zhou
  • Fei Yang Arthur Jen
  • Marc D Perry
  • Ellen T Kephart
  • Baoqing Guo
  • Irina Kalatskaya
  • Stephen R Armstrong
  • Kerry Reed
  • Amadeo M Parissenti
  • Carita Lanner
  • Stacey L Hembruff
  • Adam Tam
  • Robert Grossman
  • Norie De La Cruz
  • Arun Rangarajan
  • Philip Ozersky
  • Ranjana Kishore
  • Paul Davis
  • Mark Yandell
  • Raymond Lee
  • Hans Michael Muller
  • Gabor T Marth
  • Gary Williams
  • Barry Moore
  • Jolene Fernandes
  • Colin Batchelor
  • Paul Flicek
  • Fiona Cunningham
  • Juancarlos Chan
  • Kimberly Van Auken
  • Tamberlyn Bieri
  • Andrei Petcherski
  • Michael Han
  • Xiaodong Wang
  • Anthony Rogers
  • Richard Durbin
  • Paul W Sternberg
  • Cecilia Nakamura
  • Mary Ann Tuli
  • Igor Antoshechkin
  • Karen Yook
  • Wen J Chen
  • Margaret Duesbury
  • Ruihua Fang
  • Gary Schindelman
  • Karen Eilbeck
  • John Spieth
  • Daniel Wang
  • Fidel Salas
  • Erich M Schwarz
  • Darin Blasiar

Detail Information

Publications9

  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 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...
  3. 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...
  4. 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...
  5. 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
    ....
  6. 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...
  7. 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...
  8. 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...
  9. 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...