Erica MacKenzie, Author at Cancer Research UK Cambridge Institute

Executive Assistant

Research Group Home Page:: Laboratory Management

Work address:: Cancer Research UK Cambridge Institute University of Cambridge Li Ka Shing Centre Robinson Way Cambridge CB2 0RE

Publications:: FrenchFISH: Poisson Models for Quantifying DNA Copy Number From Fluorescence In Situ Hybridization of Tissue Sections.

E-pub date: 01 Feb 2021; Ultrasound-guided targeted biopsies of CT-based radiomic tumour habitats: technical development and initial experience in metastatic ovarian cancer.

E-pub date: 30 Nov 2020; Intestinal region-specific Wnt signalling profiles reveal interrelation between cell identity and oncogenic pathway activity in cancer development.

E-pub date: 30 Nov 2020; Three-Dimensional Printed Molds for Image-Guided Surgical Biopsies: An Open Source Computational Platform.

E-pub date: 31 Aug 2020; Integrative radiogenomics for virtual biopsy and treatment monitoring in ovarian cancer.

E-pub date: 31 Jul 2020; Unraveling tumor-immune heterogeneity in advanced ovarian cancer uncovers immunogenic effect of chemotherapy.

E-pub date: 08 Jun 2020; Tissue-specific and interpretable sub-segmentation of whole tumour burden on CT images by unsupervised fuzzy clustering.

E-pub date: 01 May 2020; Allele-specific multi-sample copy number segmentation in ASCAT.

E-pub date: 30 Apr 2020; The evolutionary history of 2,658 cancers.

E-pub date: 01 Feb 2020; Inferring structural variant cancer cell fraction.

E-pub date: 31 Jan 2020; Data generation and network reconstruction strategies for single cell transcriptomic profiles of CRISPR-mediated gene perturbations.

E-pub date: 31 Oct 2019; ZMIZ1 — A novel Estrogen Receptor co-activator that enhances the growth of ER+ breast cancer

E-pub date: 30 Sep 2019; Estimating the predictability of cancer evolution.

E-pub date: 30 Jun 2019; Correction to: VULCAN integrates ChIP-seq with patient-derived co-expression networks to identify GRHL2 as a key co-regulator of ERa at enhancers in breast cancer.

E-pub date: 31 May 2019; 3D-printed moulds of renal tumours for image-guided tissue sampling in the clinical setting

E-pub date: 31 May 2019; Low perfusion compartments in glioblastoma quantified by advanced magnetic resonance imaging and correlated with patient survival.

E-pub date: 01 May 2019; VULCAN integrates ChIP-seq with patient-derived co-expression networks to identify GRHL2 as a key co-regulator of ERa at enhancers in breast cancer.

E-pub date: 30 Apr 2019; The Genomic and Immune Landscapes of Lethal Metastatic Breast Cancer.

E-pub date: 30 Apr 2019; Characterizing tumor invasiveness of glioblastoma using multiparametric magnetic resonance imaging.

E-pub date: 31 Mar 2019; Decoding the Interdependence of Multiparametric Magnetic Resonance Imaging to Reveal Patient Subgroups Correlated with Survivals.

E-pub date: 28 Feb 2019; Multi-parametric and multi-regional histogram analysis of MRI: modality integration reveals imaging phenotypes of glioblastoma.

E-pub date: 31 Jan 2019; Immuno-phenotypes of Pancreatic Ductal Adenocarcinoma: Meta-analysis of transcriptional subtypes.

E-pub date: 31 Jan 2019; Ccube: A fast and robust method for estimating cancer cell fractions

E-pub date: 30 Nov 2018; frenchFISH: Poisson models for quantifying DNA copy-number from fluorescence in situ hybridisation of tissue sections

E-pub date: 30 Nov 2018; Intratumor heterogeneity defines treatment-resistant HER2+ breast tumors.

E-pub date: 01 Nov 2018; Genome-wide Estrogen Receptor-α activation is sustained, not cyclical.

E-pub date: 31 Oct 2018; Neutral tumor evolution?

E-pub date: 30 Sep 2018; Intratumoral Heterogeneity of Glioblastoma Infiltration Revealed by Joint Histogram Analysis of Diffusion Tensor Imaging.

E-pub date: 31 Aug 2018; Refining cellular pathway models using an ensemble of heterogeneous data sources

E-pub date: 31 Aug 2018; KHS101 disrupts energy metabolism in human glioblastoma cells and reduces tumor growth in mice.

E-pub date: 31 Jul 2018; Copy number signatures and mutational processes in ovarian carcinoma.

E-pub date: 31 Jul 2018; Genome-wide Estrogen Receptor-α activation is sustained, not cyclical

E-pub date: 31 Jul 2018; The evolutionary history of 2,658 cancers

E-pub date: 01 Jul 2018; Pervasive intra-tumour heterogeneity and subclonal selection across cancer types

E-pub date: 01 Jul 2018; 11 The heterogeneous genomic and immune landscapes of lethal metastatic breast cancer

E-pub date: 01 Jul 2018; A quantitative mass spectrometry-based approach to monitor the dynamics of endogenous chromatin-associated protein complexes.

E-pub date: 13 Jun 2018; The integrated genomic and immune landscapes of lethal metastatic breast cancer (MBC)

E-pub date: 30 Apr 2018; Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes

E-pub date: 30 Apr 2018; Parallel factor ChIP provides essential internal control for quantitative differential ChIP-seq.

E-pub date: 17 Apr 2018; Intra-tumor heterogeneity defines treatment-resistant HER2+ breast tumors

E-pub date: 31 Mar 2018; Network analysis of ChIP-seq data by VULCAN identifies GRHL2 as a key co-regulator of ERa in luminal breast cancer

E-pub date: 31 Jan 2018; The small molecule KHS101 induces bioenergetic dysfunction in glioblastoma cells through inhibition of mitochondrial HSPD1

E-pub date: 30 Sep 2017; Immuno-phenotypes of Pancreatic Ductal Adenocarcinoma: Metaanalysis of transcriptional subtypes

E-pub date: 30 Sep 2017; Analysis of heterogeneity in T2-weighted MR images can differentiate pseudoprogression from progression in glioblastoma.

E-pub date: 31 Aug 2017; Novel Quantitative ChIP-seq Methods Measure Absolute Fold-Change in ER Binding Upon Fulvestrant Treatment

E-pub date: 31 Jul 2017; Copy-number signatures and mutational processes in ovarian carcinoma

E-pub date: 31 Jul 2017; The evolutionary history of 2,658 cancers

E-pub date: 30 Jun 2017; Allele-specific multi-sample copy number segmentation

E-pub date: 30 Jun 2017; Inferring modulators of genetic interactions with epistatic nested effects models.

E-pub date: 01 Apr 2017; All biology is computational biology.

E-pub date: 31 Mar 2017; BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes.

E-pub date: 24 Feb 2017; How Subclonal Modeling Is Changing the Metastatic Paradigm.

E-pub date: 01 Feb 2017; Master Regulators of Oncogenic KRAS Response in Pancreatic Cancer: An Integrative Network Biology Analysis.

E-pub date: 31 Jan 2017; Practical and Robust Identification of Molecular Subtypes in Colorectal Cancer by Immunohistochemistry.

E-pub date: 15 Jan 2017; Patterns of Immune Infiltration in Breast Cancer and Their Clinical Implications: A Gene-Expression-Based Retrospective Study.

E-pub date: 31 Dec 2016; A phylogenetic latent feature model for clonal deconvolution

E-pub date: 30 Nov 2016; BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes

E-pub date: 30 Nov 2016; A saltationist theory of cancer evolution.

E-pub date: 28 Sep 2016; Quantifying tumor heterogeneity in the microenvironment

E-pub date: 01 Jul 2016; OncoNEM: inferring tumor evolution from single-cell sequencing data.

E-pub date: 15 Apr 2016; Quantifying patterns of tumor evolution

E-pub date: 01 Apr 2016; Accumulated Metabolites of Hydroxybutyric Acid Serve as Diagnostic and Prognostic Biomarkers of Ovarian High-Grade Serous Carcinomas.

E-pub date: 15 Feb 2016; Regulators of genetic risk of breast cancer identified by integrative network analysis.

E-pub date: 31 Jan 2016; Five selfish reasons to work reproducibly.

E-pub date: 08 Dec 2015; You Are Not Working for Me; I Am Working with You.

E-pub date: 01 Sep 2015; Automated immunohistochemistry-based identification of molecular subtypes in colorectal cancer

E-pub date: 31 Jul 2015; BitPhylogeny: a probabilistic framework for reconstructing intra-tumor phylogenies.

E-pub date: 13 Feb 2015; Spatial and temporal heterogeneity in high-grade serous ovarian cancer: a phylogenetic analysis.

E-pub date: 01 Feb 2015; A tumor DNA complex aberration index is an independent predictor of survival in breast and ovarian cancer.

E-pub date: 31 Jan 2015; Cancer evolution: mathematical models and computational inference.

E-pub date: 31 Jan 2015; Joining the dots: Network analysis of gene perturbation data

E-pub date: 31 Dec 2014; Systems genetics: Linking genotypes and phenotypes

E-pub date: 31 Dec 2014; An introduction to systems genetics

E-pub date: 31 Dec 2014; Combined image and genomic analysis of high-grade serous ovarian cancer reveals PTEN loss as a common driver event and prognostic classifier.

E-pub date: 17 Dec 2014; Gene regulatory network approaches to interpreting breast cancer GWAS results

E-pub date: 30 Nov 2014; SANTA: quantifying the functional content of molecular networks.

E-pub date: 01 Sep 2014; GoIFISH: a system for the quantification of single cell heterogeneity from IFISH images.

E-pub date: 26 Aug 2014; Phylogenetic quantification of intra-tumour heterogeneity.

E-pub date: 01 Apr 2014; Reconstructing evolving signalling networks by hidden Markov nested effects models

E-pub date: 31 Dec 2013; Dissecting cancer heterogeneity–an unsupervised classification approach.

E-pub date: 01 Nov 2013; Master regulators of FGFR2 signalling and breast cancer risk.

E-pub date: 31 Aug 2013; Poor-prognosis colon cancer is defined by a molecularly distinct subtype and develops from serrated precursor lesions.

E-pub date: 31 May 2013; Quantitative image analysis of cellular heterogeneity in breast tumors complements genomic profiling (Science Translational Medicine (2012) 4, (161er6))

E-pub date: 31 Oct 2012; Quantitative image analysis of cellular heterogeneity in breast tumors complements genomic profiling.

E-pub date: 24 Oct 2012; Posterior association networks and functional modules inferred from rich phenotypes of gene perturbations.

E-pub date: 31 Aug 2012; A sparse regulatory network of copy-number driven gene expression reveals putative breast cancer oncogenes.

E-pub date: 31 Jul 2012; Diverse epigenetic strategies interact to control epidermal differentiation.

E-pub date: 24 Jun 2012; RedeR: R/Bioconductor package for representing modular structures, nested networks and multiple levels of hierarchical associations.

E-pub date: 24 Apr 2012; The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups.

E-pub date: 18 Apr 2012; Patient-specific data fusion defines prognostic cancer subtypes.

E-pub date: 31 Oct 2011; Penalized regression elucidates aberration hotspots mediating subtype-specific transcriptional responses in breast cancer.

E-pub date: 01 Oct 2011; Differential C3NET reveals disease networks of direct physical interactions.

E-pub date: 21 Jul 2011; Deregulation upon DNA damage revealed by joint analysis of context-specific perturbation data.

E-pub date: 21 Jun 2011; HTSanalyzeR: an R/Bioconductor package for integrated network analysis of high-throughput screens.

E-pub date: 15 Mar 2011; Evolutionary distances in the twilight zone–a rational kernel approach.

E-pub date: 31 Dec 2010; Mapping dynamic histone acetylation patterns to gene expression in nanog-depleted murine embryonic stem cells.

E-pub date: 16 Dec 2010; How to understand the cell by breaking it: network analysis of gene perturbation screens.

E-pub date: 26 Feb 2010; Systems-level dynamic analyses of fate change in murine embryonic stem cells.

E-pub date: 19 Nov 2009; Analyzing gene perturbation screens with nested effects models in R and bioconductor.

E-pub date: 01 Nov 2008; Computational diagnostics with gene expression profiles.

E-pub date: 31 Aug 2008; Structure learning in Nested Effects Models.

E-pub date: 31 Aug 2008; Inferring cellular networks–a review.

E-pub date: 27 Sep 2007; Computational identification of cellular networks and pathways.

E-pub date: 31 Jul 2007; Nested effects models for high-dimensional phenotyping screens.

E-pub date: 01 Jul 2007; Computational Diagnostics

E-pub date: 01 Jan 1970; Show all Hide all

Erica MacKenzie

Executive Assistant

FrenchFISH: Poisson Models for Quantifying DNA Copy Number From Fluorescence In Situ Hybridization of Tissue Sections.

Ultrasound-guided targeted biopsies of CT-based radiomic tumour habitats: technical development and initial experience in metastatic ovarian cancer.

Intestinal region-specific Wnt signalling profiles reveal interrelation between cell identity and oncogenic pathway activity in cancer development.

Three-Dimensional Printed Molds for Image-Guided Surgical Biopsies: An Open Source Computational Platform.

Integrative radiogenomics for virtual biopsy and treatment monitoring in ovarian cancer.

Unraveling tumor-immune heterogeneity in advanced ovarian cancer uncovers immunogenic effect of chemotherapy.

Tissue-specific and interpretable sub-segmentation of whole tumour burden on CT images by unsupervised fuzzy clustering.

Allele-specific multi-sample copy number segmentation in ASCAT.

The evolutionary history of 2,658 cancers.

Inferring structural variant cancer cell fraction.

Data generation and network reconstruction strategies for single cell transcriptomic profiles of CRISPR-mediated gene perturbations.

ZMIZ1 — A novel Estrogen Receptor co-activator that enhances the growth of ER+ breast cancer

Estimating the predictability of cancer evolution.

Correction to: VULCAN integrates ChIP-seq with patient-derived co-expression networks to identify GRHL2 as a key co-regulator of ERa at enhancers in breast cancer.

3D-printed moulds of renal tumours for image-guided tissue sampling in the clinical setting

Low perfusion compartments in glioblastoma quantified by advanced magnetic resonance imaging and correlated with patient survival.

VULCAN integrates ChIP-seq with patient-derived co-expression networks to identify GRHL2 as a key co-regulator of ERa at enhancers in breast cancer.

The Genomic and Immune Landscapes of Lethal Metastatic Breast Cancer.

Characterizing tumor invasiveness of glioblastoma using multiparametric magnetic resonance imaging.

Decoding the Interdependence of Multiparametric Magnetic Resonance Imaging to Reveal Patient Subgroups Correlated with Survivals.

Multi-parametric and multi-regional histogram analysis of MRI: modality integration reveals imaging phenotypes of glioblastoma.

Immuno-phenotypes of Pancreatic Ductal Adenocarcinoma: Meta-analysis of transcriptional subtypes.

Ccube: A fast and robust method for estimating cancer cell fractions

frenchFISH: Poisson models for quantifying DNA copy-number from fluorescence in situ hybridisation of tissue sections

Intratumor heterogeneity defines treatment-resistant HER2+ breast tumors.

Genome-wide Estrogen Receptor-α activation is sustained, not cyclical.

Neutral tumor evolution?

Intratumoral Heterogeneity of Glioblastoma Infiltration Revealed by Joint Histogram Analysis of Diffusion Tensor Imaging.

Refining cellular pathway models using an ensemble of heterogeneous data sources

KHS101 disrupts energy metabolism in human glioblastoma cells and reduces tumor growth in mice.

Copy number signatures and mutational processes in ovarian carcinoma.

Genome-wide Estrogen Receptor-α activation is sustained, not cyclical

The evolutionary history of 2,658 cancers

Pervasive intra-tumour heterogeneity and subclonal selection across cancer types

11 The heterogeneous genomic and immune landscapes of lethal metastatic breast cancer

A quantitative mass spectrometry-based approach to monitor the dynamics of endogenous chromatin-associated protein complexes.

The integrated genomic and immune landscapes of lethal metastatic breast cancer (MBC)

Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes

Parallel factor ChIP provides essential internal control for quantitative differential ChIP-seq.

Intra-tumor heterogeneity defines treatment-resistant HER2+ breast tumors

Network analysis of ChIP-seq data by VULCAN identifies GRHL2 as a key co-regulator of ERa in luminal breast cancer

The small molecule KHS101 induces bioenergetic dysfunction in glioblastoma cells through inhibition of mitochondrial HSPD1

Immuno-phenotypes of Pancreatic Ductal Adenocarcinoma: Metaanalysis of transcriptional subtypes

Analysis of heterogeneity in T2-weighted MR images can differentiate pseudoprogression from progression in glioblastoma.

Novel Quantitative ChIP-seq Methods Measure Absolute Fold-Change in ER Binding Upon Fulvestrant Treatment

Copy-number signatures and mutational processes in ovarian carcinoma

The evolutionary history of 2,658 cancers

Allele-specific multi-sample copy number segmentation

Inferring modulators of genetic interactions with epistatic nested effects models.

All biology is computational biology.

BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes.

How Subclonal Modeling Is Changing the Metastatic Paradigm.

Master Regulators of Oncogenic KRAS Response in Pancreatic Cancer: An Integrative Network Biology Analysis.

Practical and Robust Identification of Molecular Subtypes in Colorectal Cancer by Immunohistochemistry.

Patterns of Immune Infiltration in Breast Cancer and Their Clinical Implications: A Gene-Expression-Based Retrospective Study.

A phylogenetic latent feature model for clonal deconvolution

BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes

A saltationist theory of cancer evolution.

Quantifying tumor heterogeneity in the microenvironment

OncoNEM: inferring tumor evolution from single-cell sequencing data.

Quantifying patterns of tumor evolution

Accumulated Metabolites of Hydroxybutyric Acid Serve as Diagnostic and Prognostic Biomarkers of Ovarian High-Grade Serous Carcinomas.

Regulators of genetic risk of breast cancer identified by integrative network analysis.

Five selfish reasons to work reproducibly.

You Are Not Working for Me; I Am Working with You.

Automated immunohistochemistry-based identification of molecular subtypes in colorectal cancer

BitPhylogeny: a probabilistic framework for reconstructing intra-tumor phylogenies.

Spatial and temporal heterogeneity in high-grade serous ovarian cancer: a phylogenetic analysis.

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

Cancer evolution: mathematical models and computational inference.

Joining the dots: Network analysis of gene perturbation data

Systems genetics: Linking genotypes and phenotypes

An introduction to systems genetics

Combined image and genomic analysis of high-grade serous ovarian cancer reveals PTEN loss as a common driver event and prognostic classifier.

Gene regulatory network approaches to interpreting breast cancer GWAS results

SANTA: quantifying the functional content of molecular networks.

GoIFISH: a system for the quantification of single cell heterogeneity from IFISH images.

Phylogenetic quantification of intra-tumour heterogeneity.