Terence Paul Speed

Strain resolution and wide relative abundance quantification of bacterial microbiomes with nanopore sequencing of the ribosomal RNA operon

This paper demonstrates strain-level resolution and quantification of bacterial microbiomes using nanopore sequencing of the ribosomal RNA operon, showing accurate relative abundance quantification over multiple orders of magnitude.

CMDdemux: an efficient single cell demultiplexing method

CMDdemux improves single-cell demultiplexing accuracy by integrating hashing and mRNA data, outperforming existing methods on both high- and low-quality datasets.

TNF-mediated myeloid-instructed CD14+CD4+ T cells within the tumor microenvironment are associated with poor survival in non-small cell lung cancer.

The paper identifies CD14+CD4+ T cells in NSCLC tumor microenvironment driven by TNF, linked to poor patient survival.

Fast, accurate and scalable normalization for RNA sequencing data with the RUVprps software package

The paper introduces RUVprps, a software package for normalizing RNA-seq data by removing unwanted variation, offering improved performance and features for analysis.

The current landscape and emerging challenges of benchmarking single-cell methods

This paper benchmarks single-cell methods by analyzing 282 papers, highlighting challenges in combining benchmarking studies and preventing fatigue.

Antigen reactivity defines tissue-resident memory and exhausted T cells in tumours

This study distinguishes tissue-resident memory (TRM) and exhausted T (TEX) cells in tumors by analyzing their antigen reactivity, clonality, and functional outcomes.

Unveiling Peripheral Immune Dysfunction in Parkinson's Disease through Analysis of Blood-based Mitochondrial DNA Copy Number

This study investigates the association between blood mitochondrial DNA copy number and Parkinson's disease, finding that peripheral immune dysfunction, not mitochondrial dysfunction, underlies the observed associations.

Early cytokine-driven adaptation of survival pathways in lymphoid cells during targeted therapies

This study shows that CLL cells rapidly adapt to venetoclax by upregulating pro-survival proteins and cytokines, suggesting combination therapies targeting these pathways could improve treatment outcomes.

GLMsim: a GLM-based single cell RNA-seq simulator incorporating batch and biological effects

GLMsim simulates single cell RNA-seq data incorporating library size, biology, and batch effects, enabling benchmarking of integration methods.

MAssively-Parallel Flow cytometry Xplorer (MAPFX): A Toolbox for Analysing Data from the Massively-Parallel Cytometry Experiments

MAPFX improves analysis of massively-parallel cytometry data by preprocessing, background correction, and imputing missing markers to enhance biological signal preservation and reduce technical variation.

Full 16S and 23S rRNA gene-based,strain-level resolution of the microbiota of a mock bacterial microbiome using ONT nanopore sequencing

The paper investigates using nanopore sequencing and denoising to achieve strain-level resolution and abundance estimation in a mock microbiome.

An open protocol for modeling T Cell Clonotype repertoires using TCRβ CDR3 sequences

The paper presents a cost-effective, non-commercial protocol for normalizing TCRβ CDR3 sequencing data to correct amplification bias in bulk TCR repertoire profiling.

Removing unwanted variation from large-scale cancer RNA-sequencing data

This paper identifies major sources of unwanted variation in cancer RNA-seq data and proposes a novel method to remove them using pseudo-replicates of pseudo-samples.

RUV-III-NB: Normalization of single cell RNA-seq Data

RUV-III-NB normalizes scRNA-seq data by removing unwanted variation from both cell embeddings and gene-level counts, improving differential expression and clustering results across multiple datasets.

Robust differential composition and variability analysis for multisample cell omics

The paper introduces sccomp, a method for differential composition and variability analysis in cell omics data, showing improved performance over existing methods and identifying novel biological insights in breast cancer.

A species-specific retrotransposon drives a conserved Cdk2ap1 isoform essential for preimplantation development

The paper identifies a species-specific retrotransposon promoter that generates a conserved Cdk2ap1 isoform essential for preimplantation development across mammals.

hRUV: Hierarchical approach to removal of unwanted variation for large-scale metabolomics data

The paper introduces hRUV, a hierarchical method to remove unwanted variation in large-scale metabolomics data, showing improved preservation of biological signals.

Finding a suitable library size to call variants in RNA-seq

The paper evaluates the impact of library size on variant detection sensitivity in RNA-seq, finding that 30M-40M fragments are needed to recover 90%-95% of variants in recurrently mutated myeloid genes.

Strain-level sample characterisation using long reads and MAPQ scores

The paper presents a method for strain-level microbial sample characterization using long reads and MAPQ scores, achieving better strain differentiation than existing tools.

Tumor cell total mRNA expression shapes the molecular and clinical phenotype of cancer

The paper quantifies tumor-specific total mRNA expression from bulk data and shows its association with clinical outcomes across 15 cancer types.

CytofRUV: Removing unwanted variation to integrate multiple CyTOF datasets

CytofRUV integrates multiple CyTOF datasets by correcting batch effects to compare cellular changes across patients and conditions.

scClassify: hierarchical classification of cells

scClassify improves cell type classification in scRNA-seq data by using ensemble learning, achieving more accurate and fine-grained results than original publications.

Evaluating stably expressed genes in single cells

This study evaluates stably expressed genes (SEGs) in single cells using a computational framework and finds they are more stable than traditional housekeeping genes across species.

DECENT: Differential Expression with Capture Efficiency AdjustmeNT for Single-Cell RNA-seq Data

DECENT improves differential expression analysis in scRNA-seq by modeling dropout, outperforming existing methods on simulated and real data without requiring spike-ins.

A new normalization for the Nanostring nCounter gene expression assay

The paper introduces a new normalization method, RUV-III, for Nanostring nCounter gene expression data and evaluates its effectiveness across multiple datasets.

scMerge: Integration of multiple single-cell transcriptomics datasets leveraging stable expression and pseudo-replication

scMerge integrates multiple scRNA-Seq datasets by removing unwanted variation through stably expressed genes and pseudo-replicates, enhancing biological discovery.

Ferrous-glutathione coupling mediates ferroptosis and frailty in Caenorhabditis elegans

This study shows that ferrous-glutathione coupling promotes ferroptosis and frailty in C. elegans, and blocking ferroptosis extends lifespan and healthspan.

Using long-read sequencing to detect imprinted DNA methylation

The paper uses long-read nanopore sequencing to detect imprinted DNA methylation and identifies known and novel differentially methylated regions.

Maps of variability in cell lineage trees

The paper introduces lineage variability maps to quantify variation in cell lineage trees, showing how phenotype is determined by founder cells and how cell fate becomes more restricted over generations.

MSCypher: an integrated database searching and machine learning workflow for multiplexed proteomics.

MSCypher improves proteomics analysis by integrating database searching with machine learning to enhance identification rates and handle multiplexed spectra.