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Author Details

Samuel Aparicio
University of British Columbia
1993
193
82
Trey Ideker (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
36813776Reconstructing clonal tree for phylo-phenotypic characterization of cancer using single-cell transcriptomics.Nat Commun2023
37479706Obesity-associated changes in molecular biology of primary breast cancer.Nat Commun2023
37611092A MYCN-independent mechanism mediating secretome reprogramming and metastasis in <i>MYCN</i>-amplified neuroblastoma.Sci Adv2023
37729182Expansion microscopy using a single anchor molecule for high-yield multiplexed imaging of proteins and RNAs.PLoS One2023
37090647Single-cell DNA replication dynamics in genomically unstable cancers.bioRxiv2023
37345142Multi-Omic Analysis of CIC's Functional Networks Reveals Novel Interaction Partners and a Potential Role in Mitotic Fidelity.Cancers (Basel)2023
37474509Identification of transcriptional programs using dense vector representations defined by mutual information with GeneVector.Nat Commun2023
36289342Single-cell genomic variation induced by mutational processes in cancer.Nature2022
35437329Breast tumor microenvironment structures are associated with genomic features and clinical outcome.Nat Genet2022
35750695Results of the phase I CCTG IND.231 trial of CX-5461 in patients with advanced solid tumors enriched for DNA-repair deficiencies.Nat Commun2022
35927228Accurate determination of CRISPR-mediated gene fitness in transplantable tumours.Nat Commun2022
34163070Clonal fitness inferred from time-series modelling of single-cell cancer genomes.Nature2021
34856941Gene regulatory network analysis defines transcriptome landscape with alternative splicing of human umbilical vein endothelial cells during replicative senescence.BMC Genomics2021
34518533DNA methylation landscapes of 1538 breast cancers reveal a replication-linked clock, epigenomic instability and cis-regulation.Nat Commun2021
33963218Ubiquitin-mediated DNA damage response is synthetic lethal with G-quadruplex stabilizer CX-5461.Sci Rep2021
34149808A Scalable Strand-Specific Protocol Enabling Full-Length Total RNA Sequencing From Single Cells.Front Genet2021
32546838Chemogenomic profiling of breast cancer patient-derived xenografts reveals targetable vulnerabilities for difficult-to-treat tumors.Commun Biol2020
35121983Age-correlated protein and transcript expression in breast cancer and normal breast tissues is dominated by host endocrine effects.Nat Cancer2020
32033589Eleven grand challenges in single-cell data science.Genome Biol2020
31954521Identification of a selective DDX3X inhibitor with newly developed quantitative high-throughput RNA helicase assays.Biochem Biophys Res Commun2020
32910476Higher serum PD-L1 level predicts increased overall survival with lapatinib versus trastuzumab in the CCTG MA.31 phase 3 trial.Cancer2020
30867590Dynamics of breast-cancer relapse reveal late-recurring ER-positive genomic subgroups.Nature2019
31501550Probabilistic cell-type assignment of single-cell RNA-seq for tumor microenvironment profiling.Nat Methods2019
31623682Dissociation of solid tumor tissues with cold active protease for single-cell RNA-seq minimizes conserved collagenase-associated stress responses.Genome Biol2019
29532008Associations between genomic stratification of breast cancer and centrally reviewed tumour pathology in the METABRIC cohort.NPJ Breast Cancer2018
30078558High-Resolution Single-Cell DNA Methylation Measurements Reveal Epigenetically Distinct Hematopoietic Stem Cell Subpopulations.Stem Cell Reports2018
30067358Discovery of 3-Benzyl-1-( trans-4-((5-cyanopyridin-2-yl)amino)cyclohexyl)-1-arylurea Derivatives as Novel and Selective Cyclin-Dependent Kinase 12 (CDK12) Inhibitors.J Med Chem2018
30293940Decoding Transcriptome Dynamics of Genome-Encoded Polyadenylation and Autoregulation with Small-Molecule Modulators of Alternative Polyadenylation.Cell Chem Biol2018
29754820Interfaces of Malignant and Immunologic Clonal Dynamics in Ovarian Cancer.Cell2018
29736741Homologous recombination deficiency and host anti-tumor immunity in triple-negative breast cancer.Breast Cancer Res Treat2018
28068316Scalable whole-genome single-cell library preparation without preamplification.Nat Methods2017
35172494Homologous Recombination Deficiency in Breast Cancer: A Clinical Review.JCO Precis Oncol2017
28440616Discovery and Characterization of a Eukaryotic Initiation Factor 4A-3-Selective Inhibitor That Suppresses Nonsense-Mediated mRNA Decay.ACS Chem Biol2017
28283335Discovery of selective ATP-competitive eIF4A3 inhibitors.Bioorg Med Chem2017
28232751CLK-dependent exon recognition and conjoined gene formation revealed with a novel small molecule inhibitor.Nat Commun2017
28436987Genomic consequences of aberrant DNA repair mechanisms stratify ovarian cancer histotypes.Nat Genet2017
28484925Impact of serum HER2, TIMP-1, and CAIX on outcome for HER2+ metastatic breast cancer patients: CCTG MA.31 (lapatinib vs. trastuzumab).Breast Cancer Res Treat2017
28334900CDK12 regulates alternative last exon mRNA splicing and promotes breast cancer cell invasion.Nucleic Acids Res2017
28358513Discovery of Novel 1,4-Diacylpiperazines as Selective and Cell-Active eIF4A3 Inhibitors.J Med Chem2017
28249593ddClone: joint statistical inference of clonal populations from single cell and bulk tumour sequencing data.Genome Biol2017
28327288Atrophin controls developmental signaling pathways via interactions with Trithorax-like.Elife2017
28211448CX-5461 is a DNA G-quadruplex stabilizer with selective lethality in BRCA1/2 deficient tumours.Nat Commun2017
28183333Erratum to: Genome co-amplification upregulates a mitotic gene network activity that predicts outcome and response to mitotic protein inhibitors in breast cancer.Breast Cancer Res2017
28985744Correction to: ReMixT: clone-specific genomic structure estimation in cancer.Genome Biol2017
29044127Engineered in-vitro cell line mixtures and robust evaluation of computational methods for clonal decomposition and longitudinal dynamics in cancer.Sci Rep2017
28750660ReMixT: clone-specific genomic structure estimation in cancer.Genome Biol2017
28025139The RNA helicase DDX39B and its paralog DDX39A regulate androgen receptor splice variant AR-V7 generation.Biochem Biophys Res Commun2017
26938915Combined Use of Gene Expression Modeling and siRNA Screening Identifies Genes and Pathways Which Enhance the Activity of Cisplatin When Added at No Effect Levels to Non-Small Cell Lung Cancer Cells In Vitro.PLoS One2016
27851968Analysis of Normal Human Mammary Epigenomes Reveals Cell-Specific Active Enhancer States and Associated Transcription Factor Networks.Cell Rep2016
27641504A Biobank of Breast Cancer Explants with Preserved Intra-tumor Heterogeneity to Screen Anticancer Compounds.Cell2016
  • 1 - 50 of 193

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Edison T Liu
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David J Adams
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Paul C Boutros
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Collaborators

Carlos Caldas
Cancer Research UK Cambridge Institute, University of Cambridge
Co-authored papers 52
Sohrab P Shah
Memorial Sloan Kettering Cancer Center
Co-authored papers 42
David G Huntsman
University of British Columbia
Co-authored papers 27
Marco A Marra
University of British Columbia
Co-authored papers 27
Martin Hirst
University of British Columbia
Co-authored papers 22
Oscar M Rueda
University of Cambridge
Co-authored papers 18
Andrew McPherson
Memorial Sloan Kettering Cancer Center
Co-authored papers 17
Anne-Lise B??rresen-Dale
Institute for Cancer Research, Oslo University Hospital
Co-authored papers 15
Ali Bashashati
University of British Columbia
Co-authored papers 14
Christina Curtis
Stanford University School of Medicine
Co-authored papers 13
Richard A Moore
Co-authored papers 13
Leah M Prentice
British Columbia Women's Hospital and Health Centre
Co-authored papers 12
Cyril B Gilks
University of British Columbia
Co-authored papers 12
Andrew J Mungall
Co-authored papers 11
Steven J M Jones
University of British Columbia
Co-authored papers 10
Yongjun Zhao
Canada British Columbia Cancer Research Centre, University of British Columbia
Co-authored papers 10
James D Brenton
CRUK Cambridge Institute, University of Cambridge
Co-authored papers 9
Serena Nik-Zainal
Early Cancer Institute, University of Cambridge
Co-authored papers 8
Janine Senz
University of British Columbia
Co-authored papers 8
Ryan D Morin
Simon Fraser University
Co-authored papers 8
Andrea L Richardson
Co-authored papers 8
Jamie Rosner
University of British Columbia
Co-authored papers 7
Gilles Thomas
Co-authored papers 7
Patrick S Tarpey
Wellcome Trust Sanger Institute
Co-authored papers 7
Michael R Stratton
Wellcome Sanger Institute
Co-authored papers 7
Peter J Campbell
Wellcome Sanger Institute
Co-authored papers 7
Hans Kristian Moen Vollan
F Hoffmann-La Roche Ltd
Co-authored papers 6
Stephen-John Sammut
Co-authored papers 6
Manasa Ramakrishna
Co-authored papers 6
Mark J Dunning
The Medical School, The University of Sheffield
Co-authored papers 6
Release 1.2