Genomes and Genes
Affiliation: British Columbia
- A physical map of the mouse genomeSimon G Gregory
The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
Nature 418:743-50. 2002..The human sequence may be used to facilitate construction of other mammalian genome maps using the same strategy...
- Visualizing Clonal Evolution in CancerMartin Krzywinski
Canada s Michael Smith Genome Sciences Centre, BC Cancer Research Center, 100 570 West 7th Ave, Vancouver, BC V5Z 4S6, Canada Electronic address
Mol Cell 62:652-6. 2016..Krzywinski discusses how to present clone evolution plots in order to visualize temporal, phylogenetic, and spatial aspects of a tumor in a single static image. ..
- Hive plots--rational approach to visualizing networksMartin Krzywinski
BC Cancer Research Center, Vancouver, Canada
Brief Bioinform 13:627-44. 2012..The method is computationally straightforward, scales well and is amenable to a plugin for existing tools...
- Circos: an information aesthetic for comparative genomicsMartin Krzywinski
Canada s Michael Smith Genome Sciences Center, Vancouver, British Columbia V5Z 4S6, Canada
Genome Res 19:1639-45. 2009....
- A BAC clone fingerprinting approach to the detection of human genome rearrangementsMartin Krzywinski
BC Cancer Agency Genome Sciences Centre, West 7th Avenue, Vancouver, British Columbia, Canada V5Z 4S6
Genome Biol 8:R224. 2007..Our method has compelling potential for use as a whole-genome method for the identification and characterization of human genome rearrangements...
- A set of BAC clones spanning the human genomeMartin Krzywinski
BC Cancer Agency Genome Sciences Center and BC Cancer Agency, Vancouver, BC V5Z 4E6, Canada
Nucleic Acids Res 32:3651-60. 2004..We have made the clone set publicly available, anticipating that it will generally facilitate FISH or array-CGH-based identification and characterization of chromosomal alterations relevant to disease...
- PICS: probabilistic inference for ChIP-seqXuekui Zhang
Department of Statistics, University of British Columbia, Vancouver, BC, Canada
Biometrics 67:151-63. 2011..We then use a simulation study to confirm that PICS compares favorably to these methods and is robust to model misspecification...
- Automated ordering of fingerprinted clonesStephane Flibotte
Genome Sciences Centre, British Columbia Cancer Research Centre, Vancouver, BC Canada, V5Z 4E6
Bioinformatics 20:1264-71. 2004..A considerable amount of human intervention is currently required to produce high-quality fingerprint-based physical maps for genomic studies...
- Physical map-assisted whole-genome shotgun sequence assembliesRene L Warren
British Columbia Cancer Agency, Genome Sciences Centre, Vancouver, British Columbia V5Z 4S6, Canada
Genome Res 16:768-75. 2006..A 6.5-fold coverage draft DNA sequence of the Pan troglodytes (chimpanzee) genome was assembled using map-derived constraints and resulted in a 26.1% increase in scaffold contiguity...
- Oligonucleotide microarray analysis of genomic imbalance in children with mental retardationJ M Friedman
Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
Am J Hum Genet 79:500-13. 2006..This technology can detect at least twice as many potentially pathogenic de novo copy-number variants as conventional cytogenetic analysis can in people with mental retardation...
- Frequent mutation of histone-modifying genes in non-Hodgkin lymphomaRyan D Morin
Canada s Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
Nature 476:298-303. 2011..Our analysis suggests a previously unappreciated disruption of chromatin biology in lymphomagenesis...
- Sequence variant discovery in DNA repair genes from radiosensitive and radiotolerant prostate brachytherapy patientsTrevor J Pugh
Genome Sciences Centre, Provincial Prostate Brachytherapy Program, and Medical Biophysics, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
Clin Cancer Res 15:5008-16. 2009..We investigated whether variants in genes responsible for detecting and repairing DNA damage independently contribute to toxicity following prostate brachytherapy...
- SnapShot: Epigenomic AssaysMartin Krzywinski
Canada s Michael Smith Genome Sciences Centre, BC Cancer Agency Research Centre, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada
Cell 167:1430-1430.e1. 2016..This SnapShot depicts key sequencing-based methods used in the analysis of epigenomes, including (1)bisulfite sequencing, (2) chromatin immunoprecipiation sequencing, (3) determination of open chromatin, and (4) 3D chromatin capture...
- Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencingRyan Morin
Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
Biotechniques 45:81-94. 2008..Analysis of these variants, and previously unannotated splicing events in the HeLa S3 cell line, reveals an overrepresentation of gene categories including those previously implicated in cancer...
- Fusobacterium nucleatum infection is prevalent in human colorectal carcinomaMauro Castellarin
BC Cancer Agency, Michael Smith Genome Sciences Centre, Vancouver, British Columbia V5Z 1L3, Canada
Genome Res 22:299-306. 2012..5 × 10(-6)), and we observed a positive association with lymph node metastasis...
- Genome-wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor bindingA Gordon Robertson
BC Cancer Agency Genome Sciences Centre, Vancouver, Canada
Genome Res 18:1906-17. 2008....
- A physical map of the chicken genomeJohn W Wallis
Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA
Nature 432:761-4. 2004..This map represents approximately 91% of the chicken genome and enables identification of chicken clones aligned to positions in other sequenced genomes...
- Integrated and sequence-ordered BAC- and YAC-based physical maps for the rat genomeMartin Krzywinski
Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, Canada V5Z 4E6
Genome Res 14:766-79. 2004..The fingerprint map is a high-resolution integrative data resource that provides genome-ordered associations among BAC, YAC, and PAC clones and the assembled sequence of the rat genome...
- Genome sequence of the Brown Norway rat yields insights into mammalian evolutionRichard A Gibbs
Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, Texas 77030, USA lt http www hgsc bcm tmc edu
Nature 428:493-521. 2004....