- 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...
- Reactome: a database of reactions, pathways and biological processes
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...
- 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...
- 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...
- 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...
- 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
- PeakRanger: a cloud-enabled peak caller for ChIP-seq data
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...
- Localizing triplet periodicity in DNA and cDNA sequences
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...
- 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...
- nGASP--the nematode genome annotation assessment project
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...
- 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
- 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...
- 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...
- 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...
- 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...
- Feasibility of real time next generation sequencing of cancer genes linked to drug response: results from a clinical trial
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...