Thomas D. Otto

scReady - an automated and accessible pipeline for single-cell RNA-Seq preprocessing: Empowering novice bioinformaticians

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

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

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

Supersaturation mutagenesis reveals adaptive rewiring of essential genes among malaria parasites.

TrAGEDy-trajectory alignment of gene expression dynamics.

Spatial transcriptomics elucidates localized immune responses in atherosclerotic coronary artery.

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

Exploring homology detection via k-means clustering of proteins embedded with a large language model.

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

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

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

Annotation and visualization of parasite, fungi and arthropod genomes with Companion.

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

The <i>Trypanosoma cruzi</i> cell atlas; a single-cell resource for understanding parasite population heterogeneity and differentiation

Spatially resolved single-cell atlas unveils a distinct cellular signature of fatal lung COVID-19 in a Malawian population.

Sterile protection against <i>P. vivax</i> malaria by repeated blood stage infection in the <i>Aotus</i> monkey model.

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

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

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

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

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

Profiling the bloodstream form and procyclic form &lt;i&gt;Trypanosoma brucei&lt;/i&gt; cell cycle using single-cell transcriptomics.

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

From contigs towards chromosomes: automatic improvement of long read assemblies (ILRA).

Sterile protection against<i>P. vivax</i>malaria by repeated blood stage infection in the<i>Aotus</i>monkey model

Profiling the bloodstream form and procyclic form <i>Trypanosoma brucei</i> cell cycle using single cell transcriptomics

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

Author Response: 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

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