Samuel Aparicio

发表

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

Alexandre Bouchard-Côté, Samuel Aparicio, Andrew Roth, 2017, Genome Biology.

Divergent modes of clonal spread and intraperitoneal mixing in high-grade serous ovarian cancer

Ali Bashashati, Alexandre Bouchard-Côté, Richard A. Moore, 2016, Nature Genetics.

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

Alexandre Bouchard-Côté, Damian Yap, Adrian Wan, 2016, Nature Methods.

Resource: Scalable whole genome sequencing of 40,000 single cells identifies stochastic aneuploidies, genome replication states and clonal repertoires

Richard A. Moore, C. Steidl, M. Marra, 2018, bioRxiv.

Dissociation of solid tumor tissues with cold active protease for single-cell RNA-seq minimizes conserved collagenase-associated stress responses

Kieran R. Campbell, Richard A. Moore, Allen W. Zhang, 2019, Genome Biology.

Dissociation of solid tumour tissues with cold active protease for single-cell RNA-seq minimizes conserved collagenase-associated stress responses

Kieran R. Campbell, Richard A. Moore, Allen W. Zhang, 2019, bioRxiv.

Clonal Decomposition and DNA Replication States Defined by Scaled Single-Cell Genome Sequencing

Richard A. Moore, Khanh N. Dinh, S. Tavaré, 2019, Cell.

The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discovery

Steven J. M. Jones, Marcel H. Schulz, Richard A. Moore, 2016, Cell.

Eleven grand challenges in single-cell data science

Alexey M. Kozlov, Benjamin J. Raphael, Kieran R. Campbell, 2020, Genome Biology.

Columnar cell lesions, mammographic density and breast cancer risk

N. Boyd, Lisa J. Martin, G. Turashvili, 2009, Breast Cancer Research and Treatment.

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

Gary D Bader, A. Condon, A. Bashashati, 2015, Nature Communications.

CDK12 regulates alternative last exon mRNA splicing and promotes breast cancer cell invasion

Christopher S. Hughes, A. Bashashati, S. Shah, 2017, Nucleic acids research.

High-throughput microfluidic single-cell RT-qPCR

Samuel Aparicio, Michael VanInsberghe, Carl L Hansen, 2011, Proceedings of the National Academy of Sciences.

Scalable whole-genome single-cell library preparation without preamplification

Samuel Aparicio, Emma Laks, Sohrab P Shah, 2017, Nature Methods.

Method iReckon : Simultaneous isoform discovery and abundance estimation from RNA-seq data

Orion J. Buske, Derek Y. Chiang, Eric J. M. Smith, 2013 .

Are columnar cell lesions the earliest histologically detectable non-obligate precursor of breast cancer?

G. Turashvili, B. Gilks, P. Watson, 2008, Virchows Archiv.

clonealign: statistical integration of independent single-cell RNA & DNA-seq from human cancers

Kieran R. Campbell, A. Bouchard-Côté, S. Shah, 2018, bioRxiv.

Interfaces of Malignant and Immunologic Clonal Dynamics in Ovarian Cancer

Wyeth W. Wasserman, Sohrab P. Shah, Ali Bashashati, 2018, Cell.

clonealign: statistical integration of independent single-cell RNA and DNA sequencing data from human cancers

Kieran R. Campbell, A. Bouchard-Côté, S. Shah, 2019, Genome Biology.

Epiclomal: Probabilistic clustering of sparse single-cell DNA methylation data

Richard A. Moore, Mirela Andronescu, M. Hirst, 2018, bioRxiv.

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

H. G. Schulze, M. Blades, R. Turner, 2011, Analytical chemistry.

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

A. Bashashati, M. Marra, S. Shah, 2014 .

ReMixT: clone-specific genomic structure estimation in cancer

S. C. Sahinalp, A. Bouchard-Côté, S. Shah, 2017, Genome Biology.

ReMixT: clone-specific genomic structure estimation in cancer

S. C. Sahinalp, A. Bouchard-Côté, S. Shah, 2017, Genome Biology.

The clonal and mutational evolution spectrum of primary triple-negative breast cancers

Irmtraud M. Meyer, A. Bashashati, I. Birol, 2012, Nature.

Mutation Discovery in Regions of Segmental Cancer Genome Amplifications with CoNAn-SNV: A Mixture Model for Next Generation Sequencing of Tumors

Allen D. Delaney, M. Marra, M. Hirst, 2012, PloS one.

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

Sohrab P. Shah, Ali Bashashati, Marco A. Marra, 2014, Genome research.

Genomic consequences of aberrant DNA repair mechanisms stratify ovarian cancer histotypes

Ali Bashashati, Richard A. Moore, Gavin Ha, 2017, Nature Genetics.

Integrative analysis of genome-wide loss of heterozygosity and monoallelic expression at nucleotide resolution reveals disrupted pathways in triple-negative breast cancer

A. Bashashati, M. Marra, M. Hirst, 2012, Genome research.

A Multifunctional Anchor for Multimodal Expansion Microscopy

Kristina E. Kitko, E. Boyden, Gaojie Yang, 2022, bioRxiv.

Accurate determination of CRISPR-mediated gene fitness in transplantable tumours

Mirela Andronescu, A. Bouchard-Côté, S. McKinney, 2022, Nature Communications.

Correction to: ReMixT: clone-specific genomic structure estimation in cancer

S. C. Sahinalp, A. Bouchard-Côté, S. Shah, 2017, Genome Biology.

Single-cell genomic variation induced by mutational processes in cancer

Allen W. Zhang, Nicole Rusk, A. McPherson, 2022, Nature.

Cancer phylogenetic tree inference at scale from 1000s of single cell genomes

Kieran R. Campbell, Marc J. Williams, Mirela Andronescu, 2020, bioRxiv.

In vivo radioimaging of bradykinin receptor b1, a widely overexpressed molecule in human cancer.

G. Turashvili, F. Bénard, Jinhe Pan, 2015, Cancer research.

ISMB 2009 Special Interest Group on Short Read Sequencing List of Talks

Michael Brudno, Sohrab P. Shah, Quaid Morris, 2009 .

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

Ali Bashashati, Martin Hirst, Kaston Leung, 2016, Proceedings of the National Academy of Sciences.

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

G. Turashvili, D. Huntsman, S. McKinney, 2012, Experimental and molecular pathology.

Results of the phase I CCTG IND.231 trial of CX-5461 in patients with advanced solid tumors enriched for DNA-repair deficiencies

Bingshu E. Chen, A. Tinker, H. Feilotter, 2022, Nature Communications.

CX-5461 is a DNA G-quadruplex stabilizer with selective lethality in BRCA1/2 deficient tumours

Jian Xian, Anni Zhang, Carlos Caldas, 2017, Nature Communications.

SNVMix: predicting single nucleotide variants from next-generation sequencing of tumors

Kevin P. Murphy, Sohrab P. Shah, Ryan D. Morin, 2010, Bioinform..

Mutation of FOXL2 in granulosa-cell tumors of the ovary.

Ryan D. Morin, A. deFazio, D. Bowtell, 2009, The New England journal of medicine.

DriverNet: uncovering the impact of somatic driver mutations on transcriptional networks in cancer

A. Bashashati, S. Shah, S. Aparicio, 2012, Genome Biology.

Dissociation of solid tumor tissues with cold active protease for single-cell RNA-seq minimizes conserved collagenase-associated stress responses

Kieran R. Campbell, Allen W. Zhang, S. Shah, 2019, Genome Biology.

A Scalable Strand-Specific Protocol Enabling Full-Length Total RNA Sequencing From Single Cells

Steven J. M. Jones, Richard A. Moore, I. Birol, 2021, Frontiers in Genetics.

Eleven grand challenges in single-cell data science

Alexey M. Kozlov, Benjamin J. Raphael, Kieran R. Campbell, 2020, Genome Biology.

GeneVector: Identification of transcriptional programs using dense vector representations defined by mutual information

Nicole Rusk, A. McPherson, N. Ceglia, 2023, bioRxiv.

Probabilistic cell-type assignment of single-cell RNA-seq for tumor microenvironment profiling

Kieran R. Campbell, Christian Steidl, Daniel Lai, 2019, Nature Methods.

Loss of CIC promotes mitotic dysregulation and chromosome segregation defects

M. Marra, J. Cairncross, G. Morin, 2019 .

Patterns of somatic structural variation in human cancer genomes

Nuno A. Fonseca, Gary D Bader, Benjamin J. Raphael, 2020, Nature.

Probabilistic cell type assignment of single-cell transcriptomic data reveals spatiotemporal microenvironment dynamics in human cancers

Kieran R. Campbell, Andrew P. Weng, Timothy A. Chan, 2019, bioRxiv.

Clonal fitness inferred from time-series modelling of single-cell cancer genomes

Kieran R. Campbell, Marc J. Williams, Richard A. Moore, 2021, Nature.

clonealign: statistical integration of independent single-cell RNA and DNA sequencing data from human cancers

Kieran R. Campbell, A. Bouchard-Côté, S. Shah, 2019, Genome Biology.

Retinoblastoma-binding proteins 4 and 9 are important for human pluripotent stem cell maintenance.

Elizabeth D. Wederell, Allen D. Delaney, M. Marra, 2011, Experimental hematology.

Kisspeptin and GPR54 immunoreactivity in a cohort of 518 patients defines favourable prognosis and clear cell subtype in ovarian carcinoma

D. Huntsman, S. McKinney, M. Köbel, 2007, BMC medicine.

Recurrent somatic DICER1 mutations in nonepithelial ovarian cancers.

Steven J. M. Jones, Anthony P. Fejes, P. Sorensen, 2012, The New England journal of medicine.

JointSNVMix: a probabilistic model for accurate detection of somatic mutations in normal/tumour paired next-generation sequencing data

Sohrab P. Shah, Ali Bashashati, Ryan D. Morin, 2012, Bioinform..

The Imaging and Molecular Annotation of Xenografts and Tumours (IMAXT) High Throughput Data and Analysis Infrastructure

S. Tavaré, E. Boyden, S. Shah, 2021, bioRxiv.

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

C. Caldas, S. McKinney, L. Prentice, 2015, Breast Cancer Research.

Evolutionary tracking of cancer haplotypes at single-cell resolution

Marc J. Williams, Nicole Rusk, S. Shah, 2021, bioRxiv.

The impact of mutational processes on structural genomic plasticity in cancer cells

Marc J. Williams, Richard A. Moore, Allen W. Zhang, 2021, bioRxiv.

The interface of malignant and immunologic clonal dynamics in high-grade serous ovarian cancer

Richard A. Moore, Yi Kan Wang, Scott D. Brown, 2017, bioRxiv.

Single cell fitness landscapes induced by genetic and pharmacologic perturbations in cancer

Kieran R. Campbell, Marc J. Williams, Richard A. Moore, 2020, bioRxiv.

Reconstructing clonal tree for phylo-phenotypic characterization of cancer using single-cell transcriptomics

Jeff E. Mold, R. Sandberg, J. Hartman, 2023, Nature Communications.

PhylEx: Accurate reconstruction of clonal structure via integrated analysis of bulk DNA-seq and single cell RNA-seq data

Jeff E. Mold, R. Sandberg, J. Hartman, 2021, bioRxiv.

Efficient Bayesian inference of phylogenetic trees from large scale, low-depth genome-wide single-cell data

Kieran R. Campbell, Marc J. Williams, Sohrab Salehi, 2020 .

Feature-based classifiers for somatic mutation detection in tumour–normal paired sequencing data

Gholamreza Haffari, Anne Condon, Sohrab P. Shah, 2011, Bioinform..

P-cadherin expression as a prognostic biomarker in a 3992 case tissue microarray series of breast cancer

Karen A Gelmon, Paul A Rejto, David G Huntsman, 2011, Modern Pathology.

Correction to: ReMixT: clone-specific genomic structure estimation in cancer

S. C. Sahinalp, A. Bouchard-Côté, A. McPherson, 2017, Genome Biology.

The testosterone-dependent and independent transcriptional networks in the hypothalamus of Gpr54 and Kiss1 knockout male mice are not fully equivalent

G. Turashvili, D. Huntsman, S. McKinney, 2011, BMC Genomics.

Chemogenomic profiling of breast cancer patient-derived xenografts reveals targetable vulnerabilities for difficult-to-treat tumors

A. Wan, N. Bertos, P. Siegel, 2020, Communications Biology.

Engineered in-vitro cell line mixtures and robust evaluation of computational methods for clonal decomposition and longitudinal dynamics in cancer

Anne-Marie Mes-Masson, Hossein Farahani, Camila P E de Souza, 2017, Scientific Reports.

Cancer phylogenetic tree inference at scale from 1000s of single cell genomes

Kieran R. Campbell, Marc J. Williams, Mirela Andronescu, 2020, bioRxiv.

CLK-dependent exon recognition and conjoined gene formation revealed with a novel small molecule inhibitor

Christopher S. Hughes, Jamie Rosner, S. McKinney, 2017, Nature Communications.

HIGH-THROUGHPUT MICROFLUIDIC RT-QPCR OF SINGLE CELLS

C. Hansen, M. VanInsberghe, M. Hamidi, 2011 .

12 Grand Challenges in Single-Cell Data Science

Alexander Zelikovsky, Fabian J. Theis, Marcel J. T. Reinders, 2019, PeerJ Prepr..

iReckon: Simultaneous isoform discovery and abundance estimation from RNA-seq data

Orion J. Buske, Derek Y. Chiang, Eric J. M. Smith, 2013, Genome research.

Comprehensive molecular characterization of mitochondrial genomes in human cancers

Nuno A. Fonseca, Gary D Bader, Benjamin J. Raphael, 2017, bioRxiv.

Evolutionary concepts in biobanking - the BC BioLibrary

Adrian Png, Samuel Aparicio, Rebecca O Barnes, 2009, Journal of Translational Medicine.

Intensity calibration and automated cell cycle gating for high‐throughput image‐based siRNA screens of mammalian cells

Steven McKinney, Darren N Saunders, S. Aparicio, 2008, Cytometry. Part A : the journal of the International Society for Analytical Cytology.

Multi-Omic Analysis of CIC’s Functional Networks Reveals Novel Interaction Partners and a Potential Role in Mitotic Fidelity

Christopher S. Hughes, M. Marra, J. Cairncross, 2023, bioRxiv.

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

Carlos Caldas, Damian Yap, Adrian Wan, 2015, Breast Cancer Research.

Cancer phylogenetic tree inference at scale from 1000s of single cell genomes

Kieran R. Campbell, Marc J. Williams, Mirela Andronescu, 2020, bioRxiv.

Raman Microscopy of Human Embryonic Stem Cells Exposed to Heat and Cold Stress

H. Georg Schulze, Michael W. Blades, Robin F. B. Turner, 2011 .

Kisspeptin and GPR54 immunoreactivity in a cohort of 518 patients defines favourable prognosis and clear cell subtype in ovarian carcinoma.

D. Huntsman, S. McKinney, M. Köbel, 2007, BMC medicine.

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

M. Hirst, Yongjun Zhao, Thomas Zeng, 2014, Cell stem cell.

A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns

Nuno A. Fonseca, Benjamin J. Raphael, Allison P. Heath, 2020, Nature Communications.

clonealign: statistical integration of independent single-cell RNA & DNA-seq from human cancers

Kieran R. Campbell, A. Bouchard-Côté, A. McPherson, 2018, bioRxiv.

Identification of transcriptional programs using dense vector representations defined by mutual information with GeneVector

Nicole Rusk, A. McPherson, B. Greenbaum, 2023, Nature Communications.

Eleven grand challenges in single-cell data science

Alexey M. Kozlov, Benjamin J. Raphael, Kieran R. Campbell, 2020, Genome Biology.

Homologous recombination deficiency and host anti-tumor immunity in triple-negative breast cancer

E. Winer, S. Loi, L. Newman, 2018, Breast Cancer Research and Treatment.

Divergent modes of clonal spread and intraperitoneal mixing in high-grade serous ovarian cancer

Richard A. Moore, Allen W. Zhang, A. Bashashati, 2016, Nature Genetics.

Eleven grand challenges in single-cell data science

Alexey M. Kozlov, Benjamin J. Raphael, Kieran R. Campbell, 2020, Genome Biology.

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

A. Bashashati, M. Marra, A. McPherson, 2014, Genome research.

Integrative analysis of genome-wide loss of heterozygosity and mono-allelic expression at nucleotide resolution reveals disrupted pathways in triple negative breast cancer Supplemental Material

A. Bashashati, M. Marra, M. Hirst, 2012 .

Kisspeptin and GPR54 immunoreactivity in a cohort of 518 patients defines favourable prognosis and clear cell subtype in ovarian carcinoma

D. Huntsman, S. McKinney, Erika Mehl, 2007, BMC medicine.