Thomas D. Otto

Single-cell transcriptomics reveals life cycle and cell cycle gene expression dynamics during in vitro growth of two Leishmania species

This study uses single-cell transcriptomics to analyze life cycle and cell cycle gene expression dynamics in two Leishmania species during in vitro growth, revealing developmental endpoints and cell cycle-related gene expression patterns.

The genome of the avian malaria parasite Haemoproteus majoris (lineage WW2) and its relationship to other Plasmodium species

The paper presents the first assembled genome of Haemoproteus majoris, a common avian malaria parasite, and discusses its genomic features and evolutionary significance.

BLASE: Bulk Linkage Analysis for Single Cell Experiments - Teasing Out the Secrets of Bulk Transcriptomics with Trajectory Analysis

BLASE uses scRNA-seq references to analyze bulk RNA-seq data, identifying trajectory progress and correcting developmental differences in differential expression analysis.

Human Fibroblast-Myeloid cell tissue atlas across lung, synovium, skin and heart

The paper analyzes scRNAseq data from multiple tissues to identify shared and tissue-specific myeloid and stromal cell populations in health and disease.

The Trypanosoma cruzi cell atlas; a single-cell resource for understanding parasite population heterogeneity and differentiation.

This paper creates a single-cell atlas of Trypanosoma cruzi, revealing life cycle genes, cell heterogeneity, and transcriptomic changes during differentiation.

Autoimmune-like CD8⁺ T Cell Responses Drive Atherosclerotic Plaque Instability and Predict Cardiovascular Events

This study identifies autoimmune-like CD8⁺ T cell responses as drivers of atherosclerotic plaque instability and predictors of cardiovascular events in humans and mice.

Cell DiffErential Expression by Pooling (CellDEEP) highlights issues in differential gene expression in scRNA-seq

CellDEEP improves differential gene expression analysis in scRNA-seq by aggregating cells into metacells, reducing false positives and increasing true positives compared to single-cell and pseudobulk methods.

A partition-based spatial entropy for co-occurrence analysis with broad application.

The paper introduces a new spatial entropy measure, RCE, to analyze categorical co-occurrences in spatial data across various fields, identifying environment-dependent interactions.

Synovial lining expressed mechanosensor PIEZO1 drives inflammation-permissive macrophage phenotypes and joint inflammation

This study identifies PIEZO1 as a mechanosensor driving inflammation-permissive macrophage phenotypes in synovial tissue, contributing to joint inflammation in RA.

RNAcare: Integrating Clinical Data with Transcriptomic Evidence using Rheumatoid Arthritis as a Case Study

RNAcare integrates clinical and transcriptomic data for bulk RNA-Seq analysis, enabling hypothesis generation about gene expression-clinical symptom relationships in rheumatoid arthritis.

upsAI: A high-accuracy machine learning classifier for predicting Plasmodium falciparum var gene upstream groups

The paper introduces upsAI, a machine learning classifier that accurately predicts Plasmodium falciparum var gene upstream groups from partial sequences, achieving high accuracy compared to existing tools.

The dynamic transcriptome of Plasmodium malariae in the mosquito

This study analyzes the transcriptome of Plasmodium malariae during mosquito transmission, identifying developmentally regulated genes and unique transcription factor patterns.

Seasonal transcriptional profiling of malaria parasites using a new single-cell atlas of a Malian Plasmodium falciparum isolate

This study uses single-cell RNA-seq to profile seasonal changes in Plasmodium falciparum parasites, showing older parasites circulate in the dry season and transcriptional changes in exported proteins affecting cytoadhesion.

TrAGEDy: Trajectory Alignment of Gene Expression Dynamics

TrAGEDy aligns gene expression trajectories from different biological processes without integration, improving detection of biologically relevant genes in T cells and Trypanosoma brucei.

paraCell: A novel software tool for the interactive analysis and visualization of standard and dual host-parasite single cell RNA-Seq data

paraCell provides an interactive tool for analyzing and visualizing host-parasite single-cell RNA-Seq data without requiring programming skills.

Identification of novel PfEMP1 variants containing domain cassettes 11, 15 and 8 that mediate the Plasmodium falciparum virulence-associated rosetting phenotype

The paper identifies novel PfEMP1 variants associated with rosetting in Plasmodium falciparum, expanding the known types of PfEMP1 that mediate this phenotype.

PROS1 released by human lung basal cells upon SARS-CoV-2 infection facilitates epithelial cell repair and limits inflammation.

This study shows that PROS1 released by lung basal cells during SARS-CoV-2 infection reduces inflammation, promotes epithelial repair, and enhances antigen presentation.

Distinct tissue-niche localization and function of synovial tissue myeloid DC subsets in health, and in active and remission Rheumatoid Arthritis

This study identifies distinct myeloid DC subsets in synovial tissue across health and RA states, showing their roles in inflammation and tolerance.

Annotation and visualisation of parasite, fungi and arthropod genomes with Companion

The paper introduces an updated version of the Companion web server for genome annotation, improving efficiency and expanding reference genomes to include fungi and arthropods.

Spatial transcriptomics reveals recasting of signalling networks in the small intestine following tissue invasion by the helminth parasite Heligmosomoides polygyrus

This study uses spatial transcriptomics to analyze gene expression changes in the small intestine of H. polygyrus-infected mice, identifying altered signaling pathways and cell interactions during infection.

MalariaSED: a deep learning framework to decipher the regulatory contributions of noncoding variants in malaria parasites

MalariaSED predicts chromatin profiles in malaria parasites and identifies noncoding variants linked to invasion and drug resistance.

From contigs towards chromosomes: automatic Improvement of Long Read Assemblies (ILRA)

The paper introduces ILRA, a tool that improves long read assemblies by correcting homopolymer errors and merging contigs, resulting in higher-quality genome assemblies.

A novel computational pipeline for var gene expression augments the discovery of changes in the Plasmodium falciparum transcriptome during transition from in vivo to short-term in vitro culture

The paper introduces a new computational pipeline for var gene expression analysis, showing changes in var gene expression and core transcriptome during in vitro culture of Plasmodium falciparum.

peaks2utr: a robust Python tool for the annotation of 3' UTRs

peaks2utr annotates 3' UTRs using UTR enrichment from single-cell technologies to improve transcriptomic analysis.

Using topic modeling to detect cellular crosstalk in scRNA-seq

The paper introduces a topic modeling method using LDA to detect gene expression changes in interacting cells from scRNA-seq data, applied to synthetic and real datasets.

The apicoplast link to fever-survival and artemisinin-resistance in the malaria parasite

The paper identifies genes in Plasmodium falciparum that enable survival at febrile temperatures and links these to artemisinin resistance through apicoplast-related pathways.

Gene expression profiling of malaria parasites reveals common virulence gene expression in adult first-time infected patients and severecases

The paper identifies PfEMP1 variants associated with severe malaria in first-time infected adults and non-severe cases using RNA-seq and var gene analysis.

Varia: Prediction, analysis and visualisation of variable genes

Varia predicts var gene sequences and domain compositions from short sequence tags, enabling analysis of var gene expression in Plasmodium falciparum.

Refining the transcriptome of the human malaria parasite Plasmodium falciparum using amplification-free RNA-seq

This study develops DAFT-seq, an amplification-free RNA-seq protocol for P. falciparum, refining the transcriptome by improving coverage of AT-rich regions and identifying new transcriptional features.

Integrated pathogen load and dual transcriptome analysis of systemic host-pathogen interactions in severe malaria

This study uses dual transcriptome analysis to identify host and parasite gene expression associated with severe malaria in Gambian children, showing parasite load explains most human gene expression differences but only a third of parasite gene differences.