Anthony T. Papenfuss

ICOS blockade alleviates immune suppression in breast tumor microenvironment

This study shows that blocking ICOS reduces immune suppression in breast tumors by altering Treg and CD8 T cell dynamics, enhancing anti-tumor immunity.

Dual plasmepsin IX and X inhibitors are refractory to development of resistance

This study evaluates resistance development to PMX-selective and dual PMIX/X inhibitors in Plasmodium falciparum, finding that dual inhibitors have a higher resistance barrier.

Genomic alterations enable BRCA1 methylation loss and promoter bypass to drive resistance in high-grade serous ovarian cancer

This study identifies genomic mechanisms enabling BRCA1 methylation loss and promoter bypass in ovarian cancer, leading to PARP inhibitor resistance.

cellNexus: Quality control, annotation, aggregation and analytical layers for the Human Cell Atlas data

cellNexus enhances Human Cell Atlas data by adding quality control, metadata, normalization, and analysis layers to enable multi-study analyses and large-scale biological discovery.

ProteinDJ: a high-performance and modular protein design pipeline

ProteinDJ is a high-performance protein design pipeline that enables efficient generation and testing of synthetic protein binders using HPC systems.

Improved marker detection for rare population in single-cell transcriptomics through text mining-inspired scoring approach

The paper introduces smartid, a method for accurately detecting markers in rare cell populations using a modified TF-IDF approach with Gaussian Mixture Model, improving cell type annotation in single-cell RNA-seq data.

Deconvolution of the on-target activity of plasmepsin V peptidomimetics in P. falciparum parasites

This study investigates the on-target activity of plasmepsin V peptidomimetics in Plasmodium falciparum by combining chemoproteomic methods and genetic validation.

The JNK and Hippo pathways control epithelial integrity and prevent tumour initiation by regulating an overlapping transcriptome

The paper identifies how JNK and Hippo pathways regulate epithelial integrity by controlling an overlapping transcriptome, preventing tumour initiation through shared gene repression.

The tidyomics ecosystem: Enhancing omic data analyses

The paper introduces tidyomics, an ecosystem bridging Bioconductor and tidy R to streamline omic analysis using data from the Human Cell Atlas.

Disruption of metazoan gene regulatory networks in cancer alters the balance of co-expression between genes of unicellular and multicellular origins

The paper shows cancer disrupts gene regulatory networks by altering co-expression between genes of unicellular and multicellular origins, with changes more pronounced in advanced tumors.

A Risk-reward Examination of Sample Multiplexing Reagents for Single Cell RNA-Seq

This study evaluates sample multiplexing reagents and protocols for scRNA-Seq, finding that workflow improvements and reagent choice impact data quality and cost-effectiveness.

Integrating deep mutational scanning and low-throughput mutagenesis data to predict the impact of amino acid variants

The paper improves variant impact prediction by integrating deep mutational scanning and low-throughput alanine scanning data across multiple proteins.

svaRetro and svaNUMT: modular packages for annotation of retrotransposed transcripts and nuclear integration of mitochondrial DNA in genome sequencing data

svaRetro and svaNUMT are R packages for annotating retrotransposed transcripts and nuclear mitochondrial DNA integration in genome sequencing data, evaluated using simulations and benchmarking datasets.

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.

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.

Interfacing Seurat with the R tidy universe

This paper introduces tidyseurat, an interface that integrates Seurat with the tidyverse ecosystem for more efficient single-cell RNA sequencing data analysis.

VIRUSBreakend: Viral Integration Recognition Using Single Breakends

VIRUSBreakend identifies viral DNA integration with high sensitivity and low false discovery rate using single breakend variant calling in cancer genomes.

GRIDSS2: comprehensive characterisation of somatic structural variation using single breakend variants and structural variant phasing

GRIDSS2 identifies somatic structural variants by analyzing single breakends and phasing, achieving a 3.1% false negative rate in metastatic cancers and uncovering a novel duplication signature.

A Bayesian inference tool for identifying artifactual calls from differential transcript abundance analyses

The paper introduces ppcseq, a Bayesian tool to detect artifactual calls in differential transcript abundance analyses by identifying outliers in negative binomial models.

An open-source platform to distribute and interpret data from multiplexed assays of variant effect

The paper introduces MaveDB, a public repository for MAVE data, and MaveVis, a tool to visualize and contextualize variant effect maps.

GRIDSS, PURPLE, LINX: Unscrambling the tumor genome via integrated analysis of structural variation and copy number

A three-tool chain calls somatic structural variants, purity, ploidy and copy number from paired tumour/normal whole genomes, then clusters breakpoints into derivative chromosome structures and gene fusions.

Whole genome optical mapping reveals multiple fusion events chained by large novel sequences in cancer

The paper uses whole genome optical mapping to reveal complex chained fusion events and novel sequences in cancer genomes that are not detected by short-read sequencing.

Influence of fecal collection conditions and 16S rRNA gene sequencing protocols at two centers on human gut microbiota analysis

This study evaluates how fecal collection conditions and 16S rRNA sequencing protocols affect gut microbiome analysis across two centers, finding that center-specific differences outweigh collection method variations.

GRIDSS: sensitive and specific genomic rearrangement detection using positional de Bruijn graph assembly

GRIDSS detects genomic rearrangements with high sensitivity and specificity using a positional de Bruijn graph assembler, outperforming existing methods on simulated and tumor data.

Enrich2: a statistical framework for analyzing deep mutational scanning data

Enrich2 provides a statistical framework for analyzing deep mutational scanning data, improving variant score accuracy and hypothesis testing.