Terence P. Speed
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View article: Antigen reactivity defines tissue-resident memory and exhausted T cells in tumors
Antigen reactivity defines tissue-resident memory and exhausted T cells in tumors Open
CD8 + T cells are an important weapon in the therapeutic armamentarium against cancer. While CD8 + CD103 + T cells with a tissue-resident memory T (T RM ) cell phenotype are associated with favorable prognoses, the tumor microenvironment a…
View article: CMDdemux: an efficient single cell demultiplexing method
CMDdemux: an efficient single cell demultiplexing method Open
Multiplexing technologies label cells with molecular tags, allowing cells from different donors to be pooled together for sequencing. Although this approach enhances cell throughput, eliminates batch effects, and enables doublet detection,…
View article: The current landscape and emerging challenges of benchmarking single-cell methods
The current landscape and emerging challenges of benchmarking single-cell methods Open
With the rapid development of computational methods for single-cell sequencing data, benchmarking serves as a valuable resource. As the number of benchmarking studies surges, it is timely to assess the current state of the field. We conduc…
View article: Antigen reactivity defines tissue-resident memory and exhausted T cells in tumours
Antigen reactivity defines tissue-resident memory and exhausted T cells in tumours Open
CD8 + T cells are a key weapon in the therapeutic armamentarium against cancer. While CD8 + CD103 + T cells with a tissue-resident memory T (T RM ) cell phenotype have been favourably correlated with patient prognoses 1–6 , the tumour micr…
View article: Peripheral immune cell abundance differences link blood mitochondrial DNA copy number and Parkinson’s disease
Peripheral immune cell abundance differences link blood mitochondrial DNA copy number and Parkinson’s disease Open
Mitochondrial dysfunction plays an important role in Parkinson’s disease (PD), with mitochondrial DNA copy number (mtDNA-CN) emerging as a potential marker for mitochondrial health. We investigated the links between blood mtDNA-CN and PD s…
View article: Venetoclax dose escalation rapidly activates a BAFF/BCL-2 survival axis in chronic lymphocytic leukemia
Venetoclax dose escalation rapidly activates a BAFF/BCL-2 survival axis in chronic lymphocytic leukemia Open
Venetoclax, a first-in-class BH3 mimetic drug that targets B-cell lymphoma-2 (BCL-2), has improved the outcomes of patients with chronic lymphocytic leukemia (CLL). Early measurements of the depth of the venetoclax treatment response, asse…
View article: TNF⍰-mediated myeloid-instructed CD14<sup>+</sup>CD4<sup>+</sup>T cells within the tumor microenvironment are associated with poor survival in non-small cell lung cancer
TNF⍰-mediated myeloid-instructed CD14<sup>+</sup>CD4<sup>+</sup>T cells within the tumor microenvironment are associated with poor survival in non-small cell lung cancer Open
The tumor microenvironment (TME) harbors a diverse array of innate and adaptive immune cells that can either support anti-tumor immunity or facilitate tumor progression. Among these, myeloid cells are key drivers of immunosuppression, yet …
View article: Unveiling Peripheral Immune Dysfunction in Parkinson’s Disease through Analysis of Blood-based Mitochondrial DNA Copy Number
Unveiling Peripheral Immune Dysfunction in Parkinson’s Disease through Analysis of Blood-based Mitochondrial DNA Copy Number Open
Mitochondrial dysfunction plays an important role in Parkinson’s disease (PD), with mitochondrial DNA copy number (mtDNA-CN) emerging as a potential marker for mitochondrial health. Our study aimed to assess the association between blood m…
View article: GLMsim: a GLM-based single cell RNA-seq simulator incorporating batch and biological effects
GLMsim: a GLM-based single cell RNA-seq simulator incorporating batch and biological effects Open
With development of the single cell RNA-seq technologies, large numbers of cells can now be routinely sequenced by different platforms. This requires us to choose an efficient integration tool to merge those cells, and computational simula…
View article: Early cytokine-driven adaptation of survival pathways in lymphoid cells during targeted therapies
Early cytokine-driven adaptation of survival pathways in lymphoid cells during targeted therapies Open
Venetoclax, a first-in-class BH3 mimetic drug targeting BCL-2, has improved outcomes for patients with chronic lymphocytic leukemia (CLL). Early measurements of the depth of the venetoclax treatment response, assessed by minimal residual d…
View article: MAssively-Parallel Flow cytometry Xplorer (MAPFX): A Toolbox for Analysing Data from the Massively-Parallel Cytometry Experiments
MAssively-Parallel Flow cytometry Xplorer (MAPFX): A Toolbox for Analysing Data from the Massively-Parallel Cytometry Experiments Open
Massively-Parallel Cytometry (MPC) experiments allow cost-effective quantification of more than 200 surface proteins at single-cell resolution. The Infinity Flow (Inflow) analysis protocol was developed to measure highly informative protei…
View article: Full 16S and 23S rRNA gene-based,strain-level resolution of the microbiota of a mock bacterial microbiome using ONT nanopore sequencing
Full 16S and 23S rRNA gene-based,strain-level resolution of the microbiota of a mock bacterial microbiome using ONT nanopore sequencing Open
Purpose The feasibility of achieving near-strain taxonomic resolution and reliable microbiota strain-level abundance estimation using amplicon-based nanopore sequencing was investigated. Methods Denoising was applied to separate 16S and 23…
View article: From urn models to box models: Making Neyman's (1923) insights accessible
From urn models to box models: Making Neyman's (1923) insights accessible Open
Neyman’s 1923 paper introduced the potential outcomes framework and the foundations of randomization-based inference. We discuss the influence of Neyman’s paper on four introductory to intermediate-level textbooks by Berkeley faculty membe…
View article: The current landscape and emerging challenges of benchmarking single-cell methods
The current landscape and emerging challenges of benchmarking single-cell methods Open
With the rapid development of computational methods for single-cell sequencing data, benchmarking serves as a valuable resource. As the number of benchmarking studies surges, it is timely to assess the current state of the field. We conduc…
View article: Divergent molecular networks program functionally distinct CD8<sup>+</sup>skin-resident memory T cells
Divergent molecular networks program functionally distinct CD8<sup>+</sup>skin-resident memory T cells Open
Skin-resident CD8 + T cells include distinct interferon-γ–producing [tissue-resident memory T type 1 (T RM 1)] and interleukin-17 (IL-17)–producing (T RM 17) subsets that differentially contribute to immune responses. However, whether thes…
View article: Building A Theoretical Foundation for Combining Negative Controls and Replicates
Building A Theoretical Foundation for Combining Negative Controls and Replicates Open
Studies using assays to quantify the expression of thousands of genes on tens to thousands of cell samples have been carried out for over 20 years. Such assays are based on microarrays, DNA sequencing or other molecular technologies. All s…
View article: Establishing the Link between X-Chromosome Aberrations and TP53 Status, with Breast Cancer Patient Outcomes
Establishing the Link between X-Chromosome Aberrations and TP53 Status, with Breast Cancer Patient Outcomes Open
Ubiquitous to normal female human somatic cells, X-chromosome inactivation (XCI) tightly regulates the transcriptional silencing of a single X chromosome from each pair. Some genes escape XCI, including crucial tumour suppressors. Cancer s…
View article: sccomp: Robust differential composition and variability analysis for single-cell data
sccomp: Robust differential composition and variability analysis for single-cell data Open
Cellular omics such as single-cell genomics, proteomics, and microbiomics allow the characterization of tissue and microbial community composition, which can be compared between conditions to identify biological drivers. This strategy has …
View article: An open protocol for modeling T Cell Clonotype repertoires using TCRβ CDR3 sequences
An open protocol for modeling T Cell Clonotype repertoires using TCRβ CDR3 sequences Open
T cell receptor repertoires can be profiled using next generation sequencing (NGS) to measure and monitor adaptive dynamical changes in response to disease and other perturbations. Genomic DNA-based bulk sequencing is cost-effective but ne…
View article: Spatial analysis with SPIAT and spaSim to characterize and simulate tissue microenvironments
Spatial analysis with SPIAT and spaSim to characterize and simulate tissue microenvironments Open
Spatial proteomics technologies have revealed an underappreciated link between the location of cells in tissue microenvironments and the underlying biology and clinical features, but there is significant lag in the development of downstrea…
View article: Supplementary Tables S4-S10 from The Ratio of Exhausted to Resident Infiltrating Lymphocytes Is Prognostic for Colorectal Cancer Patient Outcome
Supplementary Tables S4-S10 from The Ratio of Exhausted to Resident Infiltrating Lymphocytes Is Prognostic for Colorectal Cancer Patient Outcome Open
An excel file with several sheets, representing supp. tables S4-S10 in the paper.
View article: Supplementary Tables S2 and S3 from The Ratio of Exhausted to Resident Infiltrating Lymphocytes Is Prognostic for Colorectal Cancer Patient Outcome
Supplementary Tables S2 and S3 from The Ratio of Exhausted to Resident Infiltrating Lymphocytes Is Prognostic for Colorectal Cancer Patient Outcome Open
Table S2 is the list of studies identifying genes associated with Exh/Res programs. Table S3 is a list of signatures used for scoring tumour data and performing survival analysis
View article: Supplementary Tables S2 and S3 from The Ratio of Exhausted to Resident Infiltrating Lymphocytes Is Prognostic for Colorectal Cancer Patient Outcome
Supplementary Tables S2 and S3 from The Ratio of Exhausted to Resident Infiltrating Lymphocytes Is Prognostic for Colorectal Cancer Patient Outcome Open
Table S2 is the list of studies identifying genes associated with Exh/Res programs. Table S3 is a list of signatures used for scoring tumour data and performing survival analysis
View article: Supplementary Figures from The Ratio of Exhausted to Resident Infiltrating Lymphocytes Is Prognostic for Colorectal Cancer Patient Outcome
Supplementary Figures from The Ratio of Exhausted to Resident Infiltrating Lymphocytes Is Prognostic for Colorectal Cancer Patient Outcome Open
Supplementary data containing 25 Supp. figures that support the results of the paper.
View article: Supplementary Tables S4-S10 from The Ratio of Exhausted to Resident Infiltrating Lymphocytes Is Prognostic for Colorectal Cancer Patient Outcome
Supplementary Tables S4-S10 from The Ratio of Exhausted to Resident Infiltrating Lymphocytes Is Prognostic for Colorectal Cancer Patient Outcome Open
An excel file with several sheets, representing supp. tables S4-S10 in the paper.
View article: Data from The Ratio of Exhausted to Resident Infiltrating Lymphocytes Is Prognostic for Colorectal Cancer Patient Outcome
Data from The Ratio of Exhausted to Resident Infiltrating Lymphocytes Is Prognostic for Colorectal Cancer Patient Outcome Open
Immunotherapy success in colorectal cancer is mainly limited to patients whose tumors exhibit high microsatellite instability (MSI). However, there is variability in treatment outcomes within this group, which is in part driven by the freq…
View article: Data from The Ratio of Exhausted to Resident Infiltrating Lymphocytes Is Prognostic for Colorectal Cancer Patient Outcome
Data from The Ratio of Exhausted to Resident Infiltrating Lymphocytes Is Prognostic for Colorectal Cancer Patient Outcome Open
Immunotherapy success in colorectal cancer is mainly limited to patients whose tumors exhibit high microsatellite instability (MSI). However, there is variability in treatment outcomes within this group, which is in part driven by the freq…
View article: Supplementary Table S1 from The Ratio of Exhausted to Resident Infiltrating Lymphocytes Is Prognostic for Colorectal Cancer Patient Outcome
Supplementary Table S1 from The Ratio of Exhausted to Resident Infiltrating Lymphocytes Is Prognostic for Colorectal Cancer Patient Outcome Open
List of the tools and packages used in the manuscript