List of works - Crispin J. Miller

<scp>PTEN</scp> deficiency exposes a requirement for an <scp>ARF GTPase</scp> module for integrin‐dependent invasion in ovarian cancer

scientific article published in 2023

A 26-gene hypoxia signature predicts benefit from hypoxia-modifying therapy in laryngeal cancer but not bladder cancer

scientific article published on 02 July 2013

A comparison of digital cameras.

scientific article published on January 1999

A comparison of massively parallel nucleotide sequencing with oligonucleotide microarrays for global transcription profiling

scientific article

A global non-coding RNA system modulates fission yeast protein levels in response to stress.

scientific article

ADAPT: a database of affymetrix probesets and transcripts

scientific article published on 03 March 2005

Acquisition of biologically relevant gene expression data by Affymetrix microarray analysis of archival formalin-fixed paraffin-embedded tumours

scientific article

Amplification and translocation of 3q26 with overexpression of EVI1 in Fanconi anemia-derived childhood acute myeloid leukemia with biallelic FANCD1/BRCA2 disruption

scientific article published on April 2007

An in vivo hypoxia metagene identifies the novel hypoxia inducible factor target gene SLCO1B3.

scientific article

An integrated mass-spectrometry pipeline identifies novel protein coding-regions in the human genome

scientific article

Augmented annotation of the Schizosaccharomyces pombe genome reveals additional genes required for growth and viability

scientific article

Bioinformatics goes back to the future

scientific article published on 01 February 2003

CXCR4 mediated chemotaxis is regulated by 5T4 oncofetal glycoprotein in mouse embryonic cells

scientific article

Cancer-associated protein kinase C mutations reveal kinase's role as tumor suppressor

scientific article

Clinical quantitation of diagnostic and predictive gene expression levels in follicular and diffuse large B-cell lymphoma by RT-PCR gene expression profiling

scientific article published on 25 January 2007

Comprehensive analysis of affymetrix exon arrays using BioConductor

scientific article

Discrepancies in cancer genomic sequencing highlight opportunities for driver mutation discovery

scientific article published on 25 September 2014

Effects of oestrogen on gene expression in epithelium and stroma of normal human breast tissue

scientific article published in June 2006

Eight-channel iTRAQ enables comparison of the activity of six leukemogenic tyrosine kinases

scientific article published on 21 October 2007

Enhanced stability of microRNA expression facilitates classification of FFPE tumour samples exhibiting near total mRNA degradation.

scientific article

Epithelial and stromal microRNA signatures of columnar cell hyperplasia linking Let-7c to precancerous and cancerous breast cancer cell proliferation

scientific article

Evaluation and validation of a robust single cell RNA-amplification protocol through transcriptional profiling of enriched lung cancer initiating cells.

scientific article

Exon array analysis of head and neck cancers identifies a hypoxia related splice variant of LAMA3 associated with a poor prognosis

scientific article

Exon level integration of proteomics and microarray data

scientific article

Exploiting sample variability to enhance multivariate analysis of microarray data

scientific article

GFI1 proteins orchestrate the emergence of haematopoietic stem cells through recruitment of LSD1.

scientific article

Gastrointestinal differentiation marker Cytokeratin 20 is regulated by homeobox gene CDX1

scientific article

Genetic profiling of tumours using both circulating free DNA and circulating tumour cells isolated from the same preserved whole blood sample.

scientific article published on 19 November 2015

Genomic Evaluation of Multiparametric Magnetic Resonance Imaging-visible and -nonvisible Lesions in Clinically Localised Prostate Cancer

scientific article published on 05 September 2018

High correspondence between Affymetrix exon and standard expression arrays.

scientific article published on February 2007

Hybridization interactions between probesets in short oligo microarrays lead to spurious correlations

scientific article

Hypoxia-driven splicing into noncoding isoforms regulates the DNA damage response

scientific article published on 20 July 2016

Hypoxia-mediated down-regulation of Bid and Bax in tumors occurs via hypoxia-inducible factor 1-dependent and -independent mechanisms and contributes to drug resistance

scientific article published on April 2004

In silico error correction improves cfDNA mutation calling

scientific article published on 01 July 2019

Investigation of radiosensitivity gene signatures in cancer cell lines.

scientific article published on 22 January 2014

Large meta-analysis of multiple cancers reveals a common, compact and highly prognostic hypoxia metagene

scientific article published on January 2010

Large meta-analysis of multiple cancers reveals a common, compact and highly prognostic hypoxia metagene.

scientific article published on 7 September 2010

Large meta-analysis of multiple cancers reveals a common, compact and highly prognostic hypoxia metagene.

scientific article published on 28 September 2010

Molecular analysis of circulating tumor cells identifies distinct copy-number profiles in patients with chemosensitive and chemorefractory small-cell lung cancer

scientific article

Mouse RUNX1C regulates premegakaryocytic/erythroid output and maintains survival of megakaryocyte progenitors

scientific article

Mzt1/Tam4, a fission yeast MOZART1 homologue, is an essential component of the γ-tubulin complex and directly interacts with GCP3(Alp6)

scientific article published on 04 September 2013

Next-Generation Sequencing Analysis and Algorithms for PDX and CDX Models

scientific article published on 25 April 2017

Onco-STS: a web-based laboratory information management system for sample and analysis tracking in oncogenomic experiments.

scientific article

Oncogenic KRAS Regulates Tumor Cell Signaling via Stromal Reciprocation. ⬇️

scientific article published on June 2016

Oncogenic KRAS Regulates Tumor Cell Signaling via Stromal Reciprocation.

scientific article published on 13 April 2016

Poor prognosis associated with human papillomavirus α7 genotypes in cervical carcinoma cannot be explained by intrinsic radiosensitivity.

scientific article published on 17 January 2013

Programmed fluctuations in sense/antisense transcript ratios drive sexual differentiation in S. pombe

scientific article published on 20 December 2011

Progress in bioinformatics and the importance of being earnest.

scientific article

Prospective technical validation and assessment of intra-tumour heterogeneity of a low density array hypoxia gene profile in head and neck squamous cell carcinoma.

scientific article

Quantitative proteomics analysis demonstrates post-transcriptional regulation of embryonic stem cell differentiation to hematopoiesis

scientific article

Quantitative proteomics reveals posttranslational control as a regulatory factor in primary hematopoietic stem cells

scientific article published on 28 February 2006

RAC2, AEP, and ICAM1 expression are associated with CNS disease in a mouse model of pre-B childhood acute lymphoblastic leukemia

scientific article published on 23 May 2011

RUNX1 positively regulates a cell adhesion and migration program in murine hemogenic endothelium prior to blood emergence.

scientific article

RUNX1B Expression Is Highly Heterogeneous and Distinguishes Megakaryocytic and Erythroid Lineage Fate in Adult Mouse Hematopoiesis

scientific article published on 25 January 2016

Recurrent MLK4 Loss-of-Function Mutations Suppress JNK Signaling to Promote Colon Tumorigenesis.

scientific article published on 4 December 2015

Relation of a Hypoxia Metagene Derived from Head and Neck Cancer to Prognosis of Multiple Cancers

article

Signaling pathway screening platforms are an efficient approach to identify therapeutic targets in cancers that lack known driver mutations: a case report for a cancer of unknown primary origin.

scientific article published on 20 June 2018

Simpleaffy: a BioConductor package for Affymetrix Quality Control and data analysis

scientific article

Stromal cell-mediated mitochondrial redox adaptation regulates drug resistance in childhood acute lymphoblastic leukemia

scientific article published on 13 October 2015

Targeted genetic dependency screen facilitates identification of actionable mutations in FGFR4, MAP3K9, and PAK5 in lung cancer

scientific article

The histone demethylase KDM1A sustains the oncogenic potential of MLL-AF9 leukemia stem cells

scientific article published on 29 March 2012

The removal of multiplicative, systematic bias allows integration of breast cancer gene expression datasets - improving meta-analysis and prediction of prognosis

scientific article

The utility of MAS5 expression summary and detection call algorithms

scientific article

Traject3d allows label-free identification of distinct co-occurring phenotypes within 3D culture by live imaging

scientific article published in 2022

Truncation- and motif-based pan-cancer analysis reveals tumor-suppressing kinases.

scientific article published on 17 April 2018

Tumorigenicity and genetic profiling of circulating tumor cells in small-cell lung cancer.

scientific article published in June 2014

Tumourigenic non-small-cell lung cancer mesenchymal circulating tumour cells: a clinical case study.

scientific article published on 24 March 2016

Using large-scale genomics data to identify driver mutations in lung cancer: methods and challenges

scientific article (publication date: 2015)

Vasculogenic mimicry in small cell lung cancer

scientific article

Which craft is best in bioinformatics?

scientific article

X:Map: annotation and visualization of genome structure for Affymetrix exon array analysis.

scientific article

rHVDM: an R package to predict the activity and targets of a transcription factor

scientific article published on 15 December 2008

twoddpcr: An R/Bioconductor package and Shiny app for Droplet Digital PCR analysis.

scientific article published on 5 May 2017

List of works by Crispin J. Miller

<scp>PTEN</scp> deficiency exposes a requirement for an <scp>ARF GTPase</scp> module for integrin‐dependent invasion in ovarian cancer

A 26-gene hypoxia signature predicts benefit from hypoxia-modifying therapy in laryngeal cancer but not bladder cancer

A comparison of digital cameras.

A comparison of massively parallel nucleotide sequencing with oligonucleotide microarrays for global transcription profiling

A global non-coding RNA system modulates fission yeast protein levels in response to stress.

ADAPT: a database of affymetrix probesets and transcripts

Acquisition of biologically relevant gene expression data by Affymetrix microarray analysis of archival formalin-fixed paraffin-embedded tumours

Amplification and translocation of 3q26 with overexpression of EVI1 in Fanconi anemia-derived childhood acute myeloid leukemia with biallelic FANCD1/BRCA2 disruption

An in vivo hypoxia metagene identifies the novel hypoxia inducible factor target gene SLCO1B3.

An integrated mass-spectrometry pipeline identifies novel protein coding-regions in the human genome

Augmented annotation of the Schizosaccharomyces pombe genome reveals additional genes required for growth and viability

Bioinformatics goes back to the future

CXCR4 mediated chemotaxis is regulated by 5T4 oncofetal glycoprotein in mouse embryonic cells

Cancer-associated protein kinase C mutations reveal kinase's role as tumor suppressor

Clinical quantitation of diagnostic and predictive gene expression levels in follicular and diffuse large B-cell lymphoma by RT-PCR gene expression profiling

Comprehensive analysis of affymetrix exon arrays using BioConductor

Discrepancies in cancer genomic sequencing highlight opportunities for driver mutation discovery

Effects of oestrogen on gene expression in epithelium and stroma of normal human breast tissue

Eight-channel iTRAQ enables comparison of the activity of six leukemogenic tyrosine kinases

Enhanced stability of microRNA expression facilitates classification of FFPE tumour samples exhibiting near total mRNA degradation.

Epithelial and stromal microRNA signatures of columnar cell hyperplasia linking Let-7c to precancerous and cancerous breast cancer cell proliferation

Evaluation and validation of a robust single cell RNA-amplification protocol through transcriptional profiling of enriched lung cancer initiating cells.

Exon array analysis of head and neck cancers identifies a hypoxia related splice variant of LAMA3 associated with a poor prognosis

Exon level integration of proteomics and microarray data

Exploiting sample variability to enhance multivariate analysis of microarray data

GFI1 proteins orchestrate the emergence of haematopoietic stem cells through recruitment of LSD1.

Gastrointestinal differentiation marker Cytokeratin 20 is regulated by homeobox gene CDX1

Genetic profiling of tumours using both circulating free DNA and circulating tumour cells isolated from the same preserved whole blood sample.

Genomic Evaluation of Multiparametric Magnetic Resonance Imaging-visible and -nonvisible Lesions in Clinically Localised Prostate Cancer

High correspondence between Affymetrix exon and standard expression arrays.

Hybridization interactions between probesets in short oligo microarrays lead to spurious correlations

Hypoxia-driven splicing into noncoding isoforms regulates the DNA damage response

Hypoxia-mediated down-regulation of Bid and Bax in tumors occurs via hypoxia-inducible factor 1-dependent and -independent mechanisms and contributes to drug resistance

In silico error correction improves cfDNA mutation calling

Investigation of radiosensitivity gene signatures in cancer cell lines.

Large meta-analysis of multiple cancers reveals a common, compact and highly prognostic hypoxia metagene

Large meta-analysis of multiple cancers reveals a common, compact and highly prognostic hypoxia metagene.

Large meta-analysis of multiple cancers reveals a common, compact and highly prognostic hypoxia metagene.

Molecular analysis of circulating tumor cells identifies distinct copy-number profiles in patients with chemosensitive and chemorefractory small-cell lung cancer

Mouse RUNX1C regulates premegakaryocytic/erythroid output and maintains survival of megakaryocyte progenitors

Mzt1/Tam4, a fission yeast MOZART1 homologue, is an essential component of the γ-tubulin complex and directly interacts with GCP3(Alp6)

Next-Generation Sequencing Analysis and Algorithms for PDX and CDX Models

Onco-STS: a web-based laboratory information management system for sample and analysis tracking in oncogenomic experiments.

Oncogenic KRAS Regulates Tumor Cell Signaling via Stromal Reciprocation. ⬇️

Oncogenic KRAS Regulates Tumor Cell Signaling via Stromal Reciprocation.

Poor prognosis associated with human papillomavirus α7 genotypes in cervical carcinoma cannot be explained by intrinsic radiosensitivity.

Programmed fluctuations in sense/antisense transcript ratios drive sexual differentiation in S. pombe

Progress in bioinformatics and the importance of being earnest.

Prospective technical validation and assessment of intra-tumour heterogeneity of a low density array hypoxia gene profile in head and neck squamous cell carcinoma.

Quantitative proteomics analysis demonstrates post-transcriptional regulation of embryonic stem cell differentiation to hematopoiesis

Quantitative proteomics reveals posttranslational control as a regulatory factor in primary hematopoietic stem cells

RAC2, AEP, and ICAM1 expression are associated with CNS disease in a mouse model of pre-B childhood acute lymphoblastic leukemia

RUNX1 positively regulates a cell adhesion and migration program in murine hemogenic endothelium prior to blood emergence.

RUNX1B Expression Is Highly Heterogeneous and Distinguishes Megakaryocytic and Erythroid Lineage Fate in Adult Mouse Hematopoiesis

Recurrent MLK4 Loss-of-Function Mutations Suppress JNK Signaling to Promote Colon Tumorigenesis.

Relation of a Hypoxia Metagene Derived from Head and Neck Cancer to Prognosis of Multiple Cancers

Signaling pathway screening platforms are an efficient approach to identify therapeutic targets in cancers that lack known driver mutations: a case report for a cancer of unknown primary origin.

Simpleaffy: a BioConductor package for Affymetrix Quality Control and data analysis

Stromal cell-mediated mitochondrial redox adaptation regulates drug resistance in childhood acute lymphoblastic leukemia

Targeted genetic dependency screen facilitates identification of actionable mutations in FGFR4, MAP3K9, and PAK5 in lung cancer

The histone demethylase KDM1A sustains the oncogenic potential of MLL-AF9 leukemia stem cells

The removal of multiplicative, systematic bias allows integration of breast cancer gene expression datasets - improving meta-analysis and prediction of prognosis

The utility of MAS5 expression summary and detection call algorithms

Traject3d allows label-free identification of distinct co-occurring phenotypes within 3D culture by live imaging

Truncation- and motif-based pan-cancer analysis reveals tumor-suppressing kinases.

Tumorigenicity and genetic profiling of circulating tumor cells in small-cell lung cancer.

Tumourigenic non-small-cell lung cancer mesenchymal circulating tumour cells: a clinical case study.

Using large-scale genomics data to identify driver mutations in lung cancer: methods and challenges

Vasculogenic mimicry in small cell lung cancer

Which craft is best in bioinformatics?

X:Map: annotation and visualization of genome structure for Affymetrix exon array analysis.

rHVDM: an R package to predict the activity and targets of a transcription factor

twoddpcr: An R/Bioconductor package and Shiny app for Droplet Digital PCR analysis.