Crispin J. Miller

发表

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

Martino Barenco, E. Papouli, Sonia H. Shah, 2009, Bioinform..

Exon level integration of proteomics and microarray data

Michal J. Okoniewski, Crispin J. Miller, Danny A. Bitton, 2008, BMC Bioinformatics.

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

Michal J. Okoniewski, Crispin J. Miller, Tim Yates, 2007, Nucleic Acids Res..

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

Michal J. Okoniewski, Crispin J. Miller, M. Okoniewski, 2006, BMC Bioinformatics.

Comprehensive Analysis of Affymetrix Exon Arrays Using BioConductor

Michal J. Okoniewski, Crispin J. Miller, M. Okoniewski, 2008, PLoS Comput. Biol..

Bioinformatics goes back to the future

Teresa K. Attwood, Crispin J. Miller, T. Attwood, 2003, Nature Reviews Molecular Cell Biology.

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

Mahmood Ayub, Caroline Dive, Ged Brady, 2017, Bioinform..

Genome Analysis in a Dynamically Scaled Hybrid Cloud

Hong Linh Truong, Georgiana Copil, Wei Xing, 2015, 2015 IEEE 11th International Conference on e-Science.

GIMS-a data warehouse for storage and analysis of genome sequence and functional data

Shengli Wu, Carole A. Goble, Norman W. Paton, 2001, Proceedings 2nd Annual IEEE International Symposium on Bioinformatics and Bioengineering (BIBE 2001).

A cost-effective approach to improving performance of big genomic data analyses in clouds

Marios D. Dikaiakos, George Pallis, Wei Xing, 2017, Future Gener. Comput. Syst..

Exploiting sample variability to enhance multivariate analysis of microarray data

Crispin J. Miller, Carla S. Möller-Levet, Catharine M. West, 2007, Bioinform..

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

Crispin J. Miller, Claire L. Wilson, 2005, Bioinform..

Analysing Cancer Genomics in the Elastic Cloud

Marios D. Dikaiakos, George Pallis, Wei Xing, 2015, 2015 15th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing.

Datamining the NOAO NVO Portal: Automated Image Classification

Ryan Christopher Smith, Crispin J. Miller, Irene Barg, 2006 .

Exon Array Analysis of Head and Neck Cancers Identifies a Hypoxia Related Splice Variant of LAMA3 Associated with a Poor Prognosis

Crispin J. Miller, Carla S. Möller-Levet, Adrian L. Harris, 2009, PLoS Comput. Biol..

PSST... the probabilistic sequence search tool

Terri K. Attwood, Crispin J. Miller, T. Attwood, 2001, Proceedings 2nd Annual IEEE International Symposium on Bioinformatics and Bioengineering (BIBE 2001).

rHVDM – a fast and user-friendly R package to predict transcription factor targets from microarray time series data

Martino Barenco, Sonia H. Shah, Daniel Brewer, 2007, BMC Systems Biology.

A RAPID algorithm for sequence database comparisons: application to the identification of vector contamination in the EMBL databases

Andy Brass, John R. Gurd, Crispin J. Miller, 1999, Bioinform..

CADRE: the Central Aspergillus Data REpository

Norman W. Paton, Erich Bornberg-Bauer, Terri K. Attwood, 2004, Nucleic Acids Res..

SCAN: A Smart Application Platform for Empowering Parallelizations of Big Genomic Data Analysis in Clouds

Wei Jie, Wei Xing, Crispin J. Miller, 2015, 2015 44th International Conference on Parallel Processing.

Wrapping and Interoperating Bioinformatics Resources Using CORBA

Robert Stevens, Crispin J. Miller, R. Stevens, 2000, Briefings Bioinform..

ADAPT: a database of affymetrix probesets and transcripts

Hui Sun Leong, Crispin J. Miller, Tim Yates, 2005, Bioinform..

Cell Culture

Crispin J. Miller, Claire L. Wilson, Stuart D. Pepper, 2010, Cell.

The NOAO NVO Portal: Client-Side VO

Erika Fuentes, Crispin J. Miller, David Gasson, 2007 .

The NOAO NVO Portal

Erika Fuentes, Crispin J. Miller, David Gasson, 2007 .

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

Crispin J. Miller, Tim Yates, Simon J. Furney, 2014, Source Code for Biology and Medicine.

Mycoplasma infection significantly alters microarray gene expression profiles.

Crispin J. Miller, H. Kassem, S. Pepper, 2003, BioTechniques.

Mutation pattern analysis reveals polygenic mini-drivers associated with relapse after surgery in lung adenocarcinoma

Crispin J. Miller, Christopher Smowton, Laura Bennett, 2018, Scientific Reports.

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

Crispin J. Miller, J. Bradford, Yaoyong Li, 2010, BMC Genomics.

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

Crispin J. Miller, Yaoyong Li, T. Somervaille, 2012, Cancer cell.

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

Crispin J. Miller, M. Okoniewski, A. Howell, 2008, BMC Medical Genomics.

Eight-channel iTRAQ Enables Comparison of the Activity of Six Leukemogenic Tyrosine Kinases*S

Crispin J. Miller, Danny A. Bitton, M. Okoniewski, 2008, Molecular & Cellular Proteomics.

Relation of a hypoxia metagene derived from head and neck cancer to prognosis of multiple cancers.

Crispin J. Miller, A. Harris, H. Turley, 2007, Cancer research.

A 26-Gene Hypoxia Signature Predicts Benefit from Hypoxia-Modifying Therapy in Laryngeal Cancer but Not Bladder Cancer

Crispin J. Miller, A. Harris, P. Span, 2013, Clinical Cancer Research.

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

Bohdan Waszkowycz, Crispin J. Miller, Yaoyong Li, 2013, Proceedings of the National Academy of Sciences.

Cancer-Associated Protein Kinase C Mutations Reveal Kinase’s Role as Tumor Suppressor

Emily Kang, Crispin J. Miller, Christopher Wirth, 2015, Cell.

An Integrated Mass-Spectrometry Pipeline Identifies Novel Protein Coding-Regions in the Human Genome

Crispin J. Miller, Danny A. Bitton, Yvonne Connolly, 2010, PloS one.

A model of k-mer surprisal to quantify local sequence information content surrounding splice regions

Crispin J. Miller, M. Rattray, C. Dive, 2020, PeerJ.

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

Hui Sun Leong, Crispin J. Miller, Yvonne Connolly, 2014, Nature Communications.

1628O Development of the Manchester Cancer Research Centre Molecular Tumour Board for matching patients to clinical trials based on tumour and ctDNA genetic profiling.

Mahmood Ayub, Caroline Dive, Ged Brady, 2017 .

Investigation of Radiosensitivity Gene Signatures in Cancer Cell Lines

Crispin J. Miller, Lucile Armenoult, P. Stern, 2014, PloS one.

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

Crispin J. Miller, J. Erler, I. Stratford, 2004, Molecular and Cellular Biology.

CADRE: the Central Aspergillus Data REpository.

Norman W. Paton, Erich Bornberg-Bauer, David W. Denning, 2004 .

Utility of ctDNA to support patient selection for early phase clinical trials: the TARGET study

Crispin J. Miller, S. Gulati, R. Marais, 2019, Nature Medicine.

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

Crispin J. Miller, N. Clarke, N. Dhomen, 2019, European urology oncology.

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

Crispin J. Miller, N. Clarke, N. Dhomen, 2018 .

In silico prediction of housekeeping long intergenic non-coding RNAs reveals HKlincR1 as an essential player in lung cancer cell survival

Crispin J. Miller, D. Memon, Jing Bi, 2019, Scientific Reports.

Gene expression Exploiting sample variability to enhance multivariate analysis of microarray data

Crispin J. Miller, C. Möller-Levet, C. West, 2007 .

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

Crispin J. Miller, A. Harris, S. Pepper, 2013, European journal of cancer.

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

Crispin J. Miller, Suzanne M Johnson, Yaoyong Li, 2015, Oncotarget.

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

Crispin J. Miller, J. Brognard, S. Furney, 2018, Science Signaling.

Truncation and Motif Based Pan-Cancer Analysis Highlights Novel Tumor Suppressing Kinases

Crispin J. Miller, J. Brognard, S. Furney, 2018, bioRxiv.

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

Crispin J. Miller, Christopher Smowton, Yaoyong Li, 2016, Nature Medicine.

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

Crispin J. Miller, V. Kouskoff, Yaoyong Li, 2014, Blood.

Mouse RUNX1C regulates Pre-Megakaryocytic/Erythroid output and maintains survival of Megakaryocyte Progenitors Short title: RUNX1C’s critical role in megakaryopoiesis

Crispin J. Miller, V. Kouskoff, M. Z. Fadlullah, 2017 .

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

Crispin J. Miller, V. Kouskoff, M. Z. Fadlullah, 2017, Blood.

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

Crispin J. Miller, V. Kouskoff, M. Z. Fadlullah, 2016, PLoS genetics.

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

Crispin J. Miller, Claire L. Wilson, S. Baldwin, 2013 .

Pulmonary venous circulating tumor cell dissemination before tumor resection and disease relapse

Crispin J. Miller, Nicolai J. Birkbak, Angela E. Leek, 2019, Nature Medicine.

Vasculogenic mimicry in small cell lung cancer

Crispin J. Miller, M. Hendrix, E. Seftor, 2016, Nature Communications.

Gastrointestinal differentiation marker Cytokeratin 20 is regulated by homeobox gene CDX1

Ying Liu, Crispin J. Miller, David Bicknell, 2009, Proceedings of the National Academy of Sciences.

PYCR1-dependent proline synthesis in cancer-associated fibroblasts is required for the deposition of pro-tumorigenic extracellular matrix

Crispin J. Miller, J. Saez-Rodriguez, K. Kirschner, 2020, bioRxiv.

Metabolic control of tumour extracellular matrix production in cancer-associated fibroblasts

Crispin J. Miller, J. Saez-Rodriguez, K. Blyth, 2020 .

Oncogenic KRAS Regulates Tumor Cell Signaling via Stromal Reciprocation

Crispin J. Miller, D. Lauffenburger, C. Jørgensen, 2016, Cell.

High correspondence between Affymetrix exon and standard expression arrays.

Crispin J. Miller, M. Okoniewski, S. Pepper, 2007, BioTechniques.

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

Crispin J. Miller, B. Göttgens, Victoria Moignard, 2015, Nature Cell Biology.

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

Mahmood Ayub, Dominic G Rothwell, Caroline Dive, 2014, Nature Medicine.

CXCR4 Mediated Chemotaxis Is Regulated by 5T4 Oncofetal Glycoprotein in Mouse Embryonic Cells

Crispin J. Miller, G. Marinov, P. Stern, 2010, PloS one.

Quantitative Proteomics Analysis Demonstrates Post-transcriptional Regulation of Embryonic Stem Cell Differentiation to Hematopoiesis*S

Crispin Miller, Crispin J. Miller, Lee Lancashire, 2008, Molecular & Cellular Proteomics.

Epithelial and Stromal MicroRNA Signatures of Columnar Cell Hyperplasia Linking Let-7c to Precancerous and Cancerous Breast Cancer Cell Proliferation

Crispin J. Miller, A. Howell, H. Olsson, 2014, PloS one.

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

Crispin J. Miller, Danny A. Bitton, P. Stern, 2011, Blood.

AEP , and ICAM 1 expression are associated with CNS disease in a

Crispin J. Miller, Danny A. Bitton, P. Stern, 2011 .

RAC 2 , AEP , and ICAM 1 expression are associated with CNS disease in a mouse model of pre-B childhood acute lymphoblastic leukemia *

Crispin J. Miller, Danny A. Bitton, P. Stern, 2011 .

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

Crispin J. Miller, Andrew Pierce, Claire L. Wilson, 2006, Blood.

Ly6C defines a subset of memory-like CD27+ γδ T cells with inducible cancer-killing function

Crispin J. Miller, K. Kirschner, K. Blyth, 2020, bioRxiv.

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

Marek Dynowski, Caroline Dive, Ged Brady, 2017, Molecular Cancer Research.

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

Crispin J. Miller, T. Hunter, Yaoyong Li, 2016, Cancer research.

Cancer-associated fibroblasts require proline synthesis by PYCR1 for the deposition of pro-tumorigenic extracellular matrix

Crispin J. Miller, J. Saez-Rodriguez, K. Kirschner, 2022, Nature Metabolism.

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

Crispin J. Miller, Yaoyong Li, S. Pepper, 2014, BMC Genomics.

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

Crispin J. Miller, Yaoyong Li, C. Dive, 2015, Molecular oncology.

Methods comparison for high-resolution transcriptional analysis of archival material on Affymetrix Plus 2.0 and Exon 1.0 microarrays.

Crispin J. Miller, J. Radford, A. Freemont, 2009, BioTechniques.

Ex vivo culture of cells derived from circulating tumour cell xenograft to support small cell lung cancer research and experimental therapeutics

Crispin J. Miller, S. Gulati, T. Helleday, 2018, British journal of pharmacology.

Profiling of Circulating Free DNA Using Targeted and Genome-wide Sequencing in Patients with SCLC

Crispin J. Miller, C. Faivre-Finn, C. Dive, 2020, Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer.

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

Crispin J. Miller, R. Marais, J. Brognard, 2018, npj Genomic Medicine.

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

Crispin J. Miller, Christopher Wirth, J. Brognard, 2015, Pharmacogenomics.

Which Craft Is Best in Bioinformatics?

Crispin J. Miller, T. K. Attwood, C. J. Miller, 2001, Comput. Chem..

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

Crispin J. Miller, Christopher Smowton, C. Dive, 2016, npj Genomic Medicine.

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

Crispin J. Miller, Danny A. Bitton, J. Bradford, 2011, Molecular Systems Biology.

Amplification protocols introduce systematic but reproducible errors into gene expression studies.

Crispin J. Miller, Claire L. Wilson, S. Pepper, 2004, BioTechniques.

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

Reinhard Ullmann, Crispin Miller, Crispin J. Miller, 2007, Genes, chromosomes & cancer.

The Combination of the PARP Inhibitor Olaparib and the WEE1 Inhibitor AZD1775 as a New Therapeutic Option for Small Cell Lung Cancer

Crispin J. Miller, S. Gulati, M. O’Connor, 2018, Clinical Cancer Research.

Single-cell analysis uncovers differential regulation of lung γδ T cell subsets by the co-inhibitory molecules, PD-1 and TIM-3

Crispin J. Miller, N. Batada, K. Kirschner, 2021, bioRxiv.

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

Crispin Miller, Gerard Brady, Crispin J. Miller, 2007, Blood.

Mzt1/Tam4, a fission yeast MOZART1 homologue, is an essential component of the γ-tubulin complex and directly interacts with GCP3Alp6

Crispin J. Miller, Danny A. Bitton, J. Schwabe, 2013, Molecular biology of the cell.

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

Crispin J. Miller, J. Hoyland, E. Sakhinia, 2013 .

Brain microenvironment-driven resistance to immune and targeted therapies in acral melanoma

Crispin J. Miller, N. Carragher, P. Mundra, 2020, ESMO Open.

Discrepancies in cancer genomic sequencing highlight opportunities for driver mutation discovery.

Crispin J. Miller, Tim Yates, Phil Chapman, 2014, Cancer research.

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

Crispin J. Miller, A. Harris, C. Möller-Levet, 2013, European journal of cancer.

Oncogenic KRAS Regulates Tumor Cell Signaling via Stromal Reciprocation

Crispin J. Miller, D. Lauffenburger, C. Jørgensen, 2016, Cell.

Augmented Annotation of the Schizosaccharomyces pombe Genome Reveals Additional Genes Required for Growth and Viability

Crispin J. Miller, Danny A. Bitton, V. Wood, 2011, Genetics.

In silico error correction improves cfDNA mutation calling

Chang Sik Kim, Sumitra Mohan, Mahmood Ayub, 2018, Bioinform..

Utility of ctDNA to support patient selection for early phase clinical trials: the TARGET study

Crispin J. Miller, S. Gulati, R. Marais, 2019, Nature Medicine.

Serum Proteomics and Plasma Fibulin-3 in Differentiation of Mesothelioma From Asbestos-Exposed Controls and Patients With Other Pleural Diseases

Crispin J. Miller, Matthew P. Neilson, M. Munavvar, 2021, Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer.

The TARGET trial: Molecular profiling of circulating tumour DNA to stratify patients to early phase clinical trials

Crispin J. Miller, S. Gulati, R. Marais, 2016 .

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

Crispin J. Miller, S. de Sanjosé, P. Stern, 2013, International journal of radiation oncology, biology, physics.

Cancer Hypoxia-Modifying Therapy in Laryngeal Cancer but Not Bladder A 26-Gene Hypoxia Signature Predicts Benefit from

Crispin J. Miller, A. Harris, P. Span, 2013 .

Predictive Biomarkers and Personalized Medicine A 26-Gene Hypoxia Signature Predicts Bene fi t fromHypoxia-Modifying Therapy in Laryngeal Cancer but Not Bladder Cancer

Crispin J. Miller, A. Harris, P. Span, 2013 .

An annotation infrastructure for the analysis and interpretation of Affymetrix exon array data

Crispin J. Miller, Tim Yates, M. Okoniewski, 2007, Genome Biology.

Description of simpleaffy: easy analysis routines for Affymetrix data

Crispin J. Miller, 2006 .