Author details

Full Name

Terence P Speed

Affiliation

ORCID

Career Start Year

1974

Papers

238

H Index

Expertise

CM4AI Collaborator

PMID	Paper Title	Journal Title	Published Year
37188662	Spatial analysis with SPIAT and spaSim to characterize and simulate tissue microenvironments.	Nat Commun	2023
36109686	Removing unwanted variation from large-scale RNA sequencing data with PRPS.	Nature Biotechnology	2023
37549298	sccomp: Robust differential composition and variability analysis for single-cell data.	Proc Natl Acad Sci U S A	2023
36827978	Intratumoral CD8<sup>+</sup> TÂ cells with a tissue-resident memory phenotype mediate local immunity and immune checkpoint responses in breast cancer.	Cancer Cell	2023
36824803	An open protocol for modeling T Cell Clonotype repertoires using TCRÎ² CDR3 sequences.	Res Sq	2023
36709040	Genomic characterisation of hormone receptor-positive breast cancer arising in very young women.	Ann Oncol	2023
36641753	Stem cell plasticity, acetylation of H3K14, and de novo gene activation rely on KAT7.	Cell Rep	2023
35882933	Runx3 drives a CD8<sup>+</sup> T cell tissue residency program that is absent in CD4<sup>+</sup> T cells.	Nat Immunol	2022
35758618	RUV-III-NB: normalization of single cell RNA-seq data.	Nucleic Acids Research	2022
34426691	Discrete tissue microenvironments instruct diversity in resident memory T cell function and plasticity.	Nat Immunol	2021
32719399	Controlling technical variation amongst 6693 patient microarrays of the randomized MINDACT trial.	Commun Biol	2020
33026635	Correction to: Serum microRNA is a biomarker for post-operative monitoring in glioma.	J Neurooncol	2020
32915353	Serum microRNA is a biomarker for post-operative monitoring in glioma.	J Neurooncol	2020
32518073	Multiple sclerosis risk variants regulate gene expression in innate and adaptive immune cells.	Life Science Alliance	2020
30793194	Using long-read sequencing to detect imprinted DNA methylation.	Nucleic Acids Res	2019
31772231	Identification of cancer sex-disparity in the functional integrity of p53 and its X chromosome network.	Nat Commun	2019
30084929	Evaluation of cross-platform and interlaboratory concordance via consensus modelling of genomic measurements.		2019
30753182	Maps of variability in cell lineage trees.	PLoS Computational Biology	2019
29415752	Correction to: A statistical framework for analyzing deep mutational scanning data.	Genome Biol	2018
29862382	Accurate RNA Sequencing From Formalin-Fixed Cancer Tissue To Represent High-Quality Transcriptome From Frozen Tissue.	JCO Precis Oncol	2018
30045771	The healthy ageing gene expression signature for Alzheimer's disease diagnosis: a random sampling perspective.		2018
30135555	Publisher Correction: Single-cell profiling of breast cancer T cells reveals a tissue-resident memory subset associated with improved prognosis.	Nature Medicine	2018
29942092	Single-cell profiling of breast cancer T cells reveals a tissue-resident memory subset associated with improved prognosis.	Nature Medicine	2018
29401521	RLE plots: Visualizing unwanted variation in high dimensional data.	PLoS ONE	2018
29182143	Joint Modeling of Mixed <i>Plasmodium</i> Species Infections Using a Bivariate Poisson Lognormal Model.	Am J Trop Med Hyg	2018
28082412	Deficiency of microRNA <i>miR-34a</i> expands cell fate potential in pluripotent stem cells.	Science	2017
28430777	Correction: The Subclonal Architecture of Metastatic Breast Cancer: Results from a Prospective Community-Based Rapid Autopsy Program "CASCADE".	PLoS Med	2017
28784151	A statistical framework for analyzing deep mutational scanning data.	Genome Biol	2017
29097403	GRIDSS: sensitive and specific genomic rearrangement detection using positional de Bruijn graph assembly.	Genome Res	2017
28027312	The Subclonal Architecture of Metastatic Breast Cancer: Results from a Prospective Community-Based Rapid Autopsy Program "CASCADE".	PLoS Med	2016
27134182	Corrigendum to 'MicroRNAs in CD4 T cell subsets are markers of disease risk and T cell dysfunction in individuals at risk for type 1 diabetes' [J. Autoimmun. 68C (2016) 52-61].	Journal of Autoimmunity	2016
26786119	MicroRNAs in CD4(+) T cell subsets are markers of disease risk and T cell dysfunction in individuals at risk for type 1 diabetes.	Journal of Autoimmunity	2016
26950239	A molecular threshold for effector CD8(+) T cell differentiation controlled by transcription factors Blimp-1 and T-bet.	Nat Immunol	2016
27451143	Contextual fear conditioning induces differential alternative splicing.	Neurobiology of Learning and Memory	2016
26286812	Correcting gene expression data when neither the unwanted variation nor the factor of interest are observed.	Biostatistics	2016
27801296	Removal of unwanted variation reveals novel patterns of gene expression linked to sleep homeostasis in murine cortex.	BMC Genomics	2016
26452468	Assessment of DNA methylation profiling and copy number variation as indications of clonal relationship in ipsilateral and contralateral breast cancers to distinguish recurrent breast cancer from a second primary tumour.	BMC Cancer	2015
25692814	Statistical methods for handling unwanted variation in metabolomics data.	Analytical Chemistry	2015
25385008	Signatures of tumour immunity distinguish Asian and non-Asian gastric adenocarcinomas.	Gut	2015
26403471	Systematic noise degrades gene co-expression signals but can be corrected.	BMC Bioinformatics	2015
25990733	Removing unwanted variation in a differential methylation analysis of Illumina HumanMethylation450 array data.	Nucleic Acids Research	2015
26202970	How data analysis affects power, reproducibility and biological insight of RNA-seq studies in complex datasets.	Nucleic Acids Research	2015
24559675	Silencing of odorant receptor genes by G protein Î²Î³ signaling ensures the expression of one odorant receptor per olfactory sensory neuron.	Neuron	2014
25270265	Deciphering clonality in aneuploid breast tumors using SNP array and sequencing data.	Genome Biol	2014
25517617	Distinct epigenetic signatures delineate transcriptional programs during virus-specific CD8(+) T cell differentiation.	Immunity	2014
24489824	Investigating and correcting plasma DNA sequencing coverage bias to enhance aneuploidy discovery.	PLoS ONE	2014
25150836	Normalization of RNA-seq data using factor analysis of control genes or samples.	Nature Biotechnology	2014
24885750	Combining calls from multiple somatic mutation-callers.	BMC Bioinformatics	2014
24879464	Dating rare mutations from small samples with dense marker data.	Genetics	2014
23497823	Determining epithelial contribution to in vivo mesenchymal tumour expression signature using species-specific microarray profiling analysis of xenografts.	Genet Res (Camb)	2013