Publications by authors named "Samuel Aparicio"

100Publications

Identification of a selective DDX3X inhibitor with newly developed quantitative high-throughput RNA helicase assays.

Biochem Biophys Res Commun 2020 03 15;523(3):795-801. Epub 2020 Jan 15.

Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa, 251-8555, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.bbrc.2019.12.094DOI Listing
March 2020

Pharmacological systems analysis defines EIF4A3 functions in cell-cycle and RNA stress granule formation.

Commun Biol 2019 3;2:165. Epub 2019 May 3.

1Department of Molecular Oncology, BC Cancer, part of the Provincial Health Services Authority, 675 West 10th Avenue, Vancouver, BC V5Z 1L3 Canada.

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http://dx.doi.org/10.1038/s42003-019-0391-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6499833PMC
April 2020

Decoding Transcriptome Dynamics of Genome-Encoded Polyadenylation and Autoregulation with Small-Molecule Modulators of Alternative Polyadenylation.

Cell Chem Biol 2018 12 4;25(12):1470-1484.e5. Epub 2018 Oct 4.

Molecular Oncology, BC Cancer Agency, 675 W 10th Avenue, Vancouver, BC V5Z 1L3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S24519456183030
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http://dx.doi.org/10.1016/j.chembiol.2018.09.006DOI Listing
December 2018

High-Resolution Single-Cell DNA Methylation Measurements Reveal Epigenetically Distinct Hematopoietic Stem Cell Subpopulations.

Stem Cell Reports 2018 08 2;11(2):578-592. Epub 2018 Aug 2.

Department of Microbiology and Immunology and Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 1L3, Canada. Electronic address:

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http://dx.doi.org/10.1016/j.stemcr.2018.07.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6093082PMC
August 2018

Discovery of Novel 1,4-Diacylpiperazines as Selective and Cell-Active eIF4A3 Inhibitors.

J Med Chem 2017 04 11;60(8):3335-3351. Epub 2017 Apr 11.

Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited , 26-1, Muraoka-Higashi 2-Chome, Fujisawa, Kanagawa 251-8555, Japan.

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http://dx.doi.org/10.1021/acs.jmedchem.6b01904DOI Listing
April 2017

Discovery of selective ATP-competitive eIF4A3 inhibitors.

Bioorg Med Chem 2017 04 20;25(7):2200-2209. Epub 2017 Feb 20.

Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.bmc.2017.02.035DOI Listing
April 2017

ddClone: joint statistical inference of clonal populations from single cell and bulk tumour sequencing data.

Genome Biol 2017 03 1;18(1):44. Epub 2017 Mar 1.

Bioinformatics Graduate Program, University of British Columbia, 570 West 7th Avenue, Vancouver, V5Z 4S6, BC, Canada.

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http://dx.doi.org/10.1186/s13059-017-1169-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5333399PMC
March 2017

Scalable whole-genome single-cell library preparation without preamplification.

Nat Methods 2017 02 9;14(2):167-173. Epub 2017 Jan 9.

Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada.

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http://www.nature.com/articles/nmeth.4140
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http://dx.doi.org/10.1038/nmeth.4140DOI Listing
February 2017

The RNA helicase DDX39B and its paralog DDX39A regulate androgen receptor splice variant AR-V7 generation.

Biochem Biophys Res Commun 2017 01 23;483(1):271-276. Epub 2016 Dec 23.

Shonan Incubation Laboratories, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa, 251-8555, Japan; Integrated Technology Research Laboratories, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa, 251-8555, Japan. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S0006291X163221
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http://dx.doi.org/10.1016/j.bbrc.2016.12.153DOI Listing
January 2017

A Biobank of Breast Cancer Explants with Preserved Intra-tumor Heterogeneity to Screen Anticancer Compounds.

Cell 2016 09 15;167(1):260-274.e22. Epub 2016 Sep 15.

Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, UK; Cambridge Breast Unit, NIHR Cambridge Biomedical Research Centre and Cambridge Experimental Cancer Medicine Centre at Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 2QQ, UK. Electronic address:

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5037319PMC
http://dx.doi.org/10.1016/j.cell.2016.08.041DOI Listing
September 2016

Robust high-performance nanoliter-volume single-cell multiple displacement amplification on planar substrates.

Proc Natl Acad Sci U S A 2016 07 13;113(30):8484-9. Epub 2016 Jul 13.

Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada V6T 1Z4; Department of Physics and Astronomy, University of British Columbia, Vancouver, BC, Canada V6T 1Z4

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http://dx.doi.org/10.1073/pnas.1520964113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4968760PMC
July 2016

Bimolecular complementation affinity purification (BiCAP) reveals dimer-specific protein interactions for ERBB2 dimers.

Sci Signal 2016 07 12;9(436):ra69. Epub 2016 Jul 12.

The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia. School of Medical Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia.

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http://stke.sciencemag.org/lookup/doi/10.1126/scisignal.aaf0
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http://dx.doi.org/10.1126/scisignal.aaf0793DOI Listing
July 2016

Clonal genotype and population structure inference from single-cell tumor sequencing.

Nat Methods 2016 07 16;13(7):573-6. Epub 2016 May 16.

Department of Molecular Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada.

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http://dx.doi.org/10.1038/nmeth.3867DOI Listing
July 2016

Systematic analysis of somatic mutations impacting gene expression in 12 tumour types.

Nat Commun 2015 Oct 5;6:8554. Epub 2015 Oct 5.

Department of Molecular Oncology, BC Cancer Agency, 675 West 10th Avenue, Vancouver, British Columbia, Canada V5Z 1L3.

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http://dx.doi.org/10.1038/ncomms9554DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4600750PMC
October 2015

Examining the utility of patient-derived xenograft mouse models.

Nat Rev Cancer 2015 05;15(5):311-6

Department of Pediatrics, Columbia University Medical Center, New York, New York 10032, USA.

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http://www.nature.com/articles/nrc3944
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http://dx.doi.org/10.1038/nrc3944DOI Listing
May 2015

Lapatinib or Trastuzumab Plus Taxane Therapy for Human Epidermal Growth Factor Receptor 2-Positive Advanced Breast Cancer: Final Results of NCIC CTG MA.31.

J Clin Oncol 2015 May 16;33(14):1574-83. Epub 2015 Mar 16.

Karen A. Gelmon, David G. Huntsman, and Samuel Aparicio, British Columbia Cancer Agency, Vancouver Cancer Centre, Vancouver; Susan L. Ellard, British Columbia Cancer Agency, Cancer Centre for the Southern Interior, Kelowna, British Columbia; Julie Lemieux, Centre Hospitalier Affilié Hopital Du St Sacrement, Quebec City, Quebec; Lois E. Shepherd, Dora Nomikos, Judith-Anne W. Chapman, and Wendy R. Parulekar, NCIC Clinical Trials Group, Queen's University, Kingston; Susan Dent, Ottawa Health Research Institute, Ottawa; Kathleen I. Pritchard, Odette Cancer Centre, Sunnybrook Health Sciences Centre, Toronto; Timothy J. Whelan, Juravinski Cancer Centre at Hamilton Health Sciences, Hamilton, Ontario; Katia Tonkin, Cross Cancer Institute, Edmonton, Alberta, Canada; Frances M. Boyle, Patricia Ritchie Centre for Cancer Care and Research, Mater Hospital, North Sydney, New South Wales, Australia; Bella Kaufman, Sheba Medical Centre, Tel Hashomer; Shulamith Rizel, Rabin Medical Center, Petach Tikva, Israel; Alexey Manikhas, City Clinical Oncological Dispensery, St Petersburg; Sergei Tjulandin, Russian Cancer Research Center, Moscow; Rustem Khasanov, Clinical Oncology Dispensary, Kazan, Russia; Angelo Di Leo, Sandro Pitgliani Medical Oncology Unit, Prato, Italy; Miguel Martin, Servicio Oncologia Hospital Gregorio Marañon, Madrid, Spain; Lee S. Schwartzberg, West Clinic, Memphis, TN; Arnd Nusch, Praxis, Velbert, Germany; Robert E. Coleman, Weston Park Hospital, Cancer Research Centre, Sheffield, United Kingdom; Hirofumi Mukai, National Cancer Center Hospital East, Kashiwa-shi, Japan; Anne P. Connor, GlaxoSmithKline, Collegeville, PA; and Sergio L. Santillana, GlaxoSmithKline, Rio de Janeiro, Brazil.

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http://jco.ascopubs.org/content/33/14/1574.full.pdf
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http://jco.ascopubs.org/cgi/doi/10.1200/JCO.2014.56.9590
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http://dx.doi.org/10.1200/JCO.2014.56.9590DOI Listing
May 2015

A co-culture genome-wide RNAi screen with mammary epithelial cells reveals transmembrane signals required for growth and differentiation.

Breast Cancer Res 2015 Jan 9;17. Epub 2015 Jan 9.

Department of Pathology and Laboratory Medicine, University of British Columbia, and BC Cancer Agency, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada.

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http://dx.doi.org/10.1186/s13058-014-0510-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4322558PMC
January 2015

Dynamics of genomic clones in breast cancer patient xenografts at single-cell resolution.

Nature 2015 Feb 26;518(7539):422-6. Epub 2014 Nov 26.

1] Department of Molecular Oncology, BC Cancer Agency, 675 West 10th Avenue, Vancouver, British Columbia V5Z 1L3, Canada [2] Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia V6T 2B5, Canada [3] Michael Smith Genome Sciences Centre, Vancouver, British Columbia V5Z 1L3, Canada [4] Centre for Translational and Applied Genomics, BC Cancer Agency, 600 West 10th Avenue, Vancouver, British Columbia V5Z 4E6, Canada.

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http://dx.doi.org/10.1038/nature13952DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4864027PMC
February 2015

A tumor DNA complex aberration index is an independent predictor of survival in breast and ovarian cancer.

Mol Oncol 2015 Jan 8;9(1):115-27. Epub 2014 Aug 8.

Cancer Research UK, Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK; Department of Oncology, University of Cambridge, Hills Road, Cambridge CB2 2XZ, UK; Cambridge Experimental Cancer Medicine Centre, Cambridge CB2 0RE, UK; Cambridge Breast Unit, Addenbrooke's Hospital, Cambridge University Hospital NHS Foundation Trust and NIHR Cambridge Biomedical Research Centre, Cambridge CB2 2QQ, UK. Electronic address:

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http://dx.doi.org/10.1016/j.molonc.2014.07.019DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4286124PMC
January 2015

TITAN: inference of copy number architectures in clonal cell populations from tumor whole-genome sequence data.

Genome Res 2014 Nov 24;24(11):1881-93. Epub 2014 Jul 24.

Department of Molecular Oncology, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada; Department of Computer Science, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada;

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http://dx.doi.org/10.1101/gr.180281.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4216928PMC
November 2014

Up-regulation of the interferon-related genes in BRCA2 knockout epithelial cells.

J Pathol 2014 Nov 28;234(3):386-97. Epub 2014 Aug 28.

Department of Molecular Oncology, British Columbia Cancer Agency, Vancouver, BC, Canada.

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http://dx.doi.org/10.1002/path.4404DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4882165PMC
November 2014

Insulin-like peptide 5 is an orexigenic gastrointestinal hormone.

Proc Natl Acad Sci U S A 2014 Jul 15;111(30):11133-8. Epub 2014 Jul 15.

Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, United Kingdom;Metabolic Research Laboratories and MRC Metabolic Diseases Unit, Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, United Kingdom;

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http://dx.doi.org/10.1073/pnas.1411413111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4121845PMC
July 2014

TP53 mutation spectrum in breast cancer is subtype specific and has distinct prognostic relevance.

Clin Cancer Res 2014 Jul 6;20(13):3569-80. Epub 2014 May 6.

Authors' Affiliations: Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet; The K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine;

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http://dx.doi.org/10.1158/1078-0432.CCR-13-2943DOI Listing
July 2014

PyClone: statistical inference of clonal population structure in cancer.

Nat Methods 2014 Apr 16;11(4):396-8. Epub 2014 Mar 16.

1] Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada. [2] Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.

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http://dx.doi.org/10.1038/nmeth.2883DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4864026PMC
April 2014

The breast cancer oncogene EMSY represses transcription of antimetastatic microRNA miR-31.

Mol Cell 2014 Mar 27;53(5):806-18. Epub 2014 Feb 27.

Gurdon Institute and Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2014.01.029DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3988886PMC
March 2014

Clonal analysis via barcoding reveals diverse growth and differentiation of transplanted mouse and human mammary stem cells.

Cell Stem Cell 2014 Feb 16;14(2):253-63. Epub 2014 Jan 16.

Department of Microbiology and Immunology, Centre for High-Throughput Biology, University of British Columbia, 2125 East Mall, Vancouver, BC V6T 1Z4, Canada; Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, 675 West 10(th) Avenue, Vancouver, BC V5Z 1L3, Canada. Electronic address:

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http://dx.doi.org/10.1016/j.stem.2013.12.011DOI Listing
February 2014

The omics of triple-negative breast cancers.

Clin Chem 2014 Jan 2;60(1):122-33. Epub 2013 Dec 2.

Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC;

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http://dx.doi.org/10.1373/clinchem.2013.207167DOI Listing
January 2014

Solution NMR structure and histone binding of the PHD domain of human MLL5.

PLoS One 2013 9;8(10):e77020. Epub 2013 Oct 9.

Northeast Structural Genomics Consortium and Ontario Cancer Institute, University Health Network, Toronto, Ontario, Canada.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0077020PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3793974PMC
June 2014

Signatures of mutational processes in human cancer.

Nature 2013 Aug 14;500(7463):415-21. Epub 2013 Aug 14.

Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.

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http://dx.doi.org/10.1038/nature12477DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3776390PMC
August 2013

[Oncocytic tumors of the adrenal gland].

Acta Med Port 2013 Jan-Feb;26(1):61-6. Epub 2013 Apr 24.

Serviço de Oncologia Médica, Centro Hospitalar de São João, EPE, Porto, Portugal.

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April 2014

The implications of clonal genome evolution for cancer medicine.

N Engl J Med 2013 Feb;368(9):842-51

Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, Canada.

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http://www.nejm.org/doi/10.1056/NEJMra1204892
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http://dx.doi.org/10.1056/NEJMra1204892DOI Listing
February 2013

A new genome-driven integrated classification of breast cancer and its implications.

EMBO J 2013 Mar 8;32(5):617-28. Epub 2013 Feb 8.

Cancer Research UK, Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, UK.

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http://dx.doi.org/10.1038/emboj.2013.19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3590990PMC
March 2013

Quiz page June 2012: kidney failure in an HIV-positive patient.

Am J Kidney Dis 2012 Jun;59(6):A27-30

Department of Nephrology, Hospital Fernando Fonseca, Lisbon, Portugal.

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http://dx.doi.org/10.1053/j.ajkd.2012.03.005DOI Listing
June 2012

Opening Pandora's Box--the new biology of driver mutations and clonal evolution in cancer as revealed by next generation sequencing.

Curr Opin Genet Dev 2012 Feb 1;22(1):3-9. Epub 2012 Mar 1.

Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada.

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http://dx.doi.org/10.1016/j.gde.2012.01.008DOI Listing
February 2012

Molecular alterations between the primary breast cancer and the subsequent locoregional/metastatic tumor.

Oncologist 2012 20;17(2):172-8. Epub 2012 Jan 20.

Department of Medical Oncology, British Columbia Cancer Agency, University of British Columbia, 600 West 10th Avenue, Vancouver, British Columbia, Canada, V5Z 4E6.

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http://dx.doi.org/10.1634/theoncologist.2011-0127DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3286165PMC
June 2012

Nucleic acid quantity and quality from paraffin blocks: defining optimal fixation, processing and DNA/RNA extraction techniques.

Exp Mol Pathol 2012 Feb 21;92(1):33-43. Epub 2011 Sep 21.

The Centre of Translation and Applied Genomics, BC Cancer Agency, Provincial Health Services Authority, Vancouver, BC, Canada V5Z 4E6.

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http://dx.doi.org/10.1016/j.yexmp.2011.09.013DOI Listing
February 2012

Raman microscopy-based cytochemical investigations of potential niche-forming inhomogeneities present in human embryonic stem cell colonies.

Appl Spectrosc 2011 Sep;65(9):1009-16

Michael Smith Laboratories, The University of British Columbia, 2185 East Mall, Vancouver, BC, Canada, V6T 1Z4.

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http://dx.doi.org/10.1366/11-06312DOI Listing
September 2011

High-throughput microfluidic single-cell RT-qPCR.

Proc Natl Acad Sci U S A 2011 Aug 1;108(34):13999-4004. Epub 2011 Aug 1.

Centre for High-Throughput Biology, University of British Columbia, Vancouver, BC, Canada V6T 1Z4.

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http://dx.doi.org/10.1073/pnas.1019446108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3161570PMC
August 2011

Absolute quantification of intracellular glycogen content in human embryonic stem cells with Raman microspectroscopy.

Anal Chem 2011 Aug 21;83(16):6254-8. Epub 2011 Jul 21.

Michael Smith Laboratories, The University of British Columbia, Vancouver, British Columbia, Canada.

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http://dx.doi.org/10.1021/ac201581eDOI Listing
August 2011