Laura L. Elo

This study shows that disrupting the CIP2A gene reduces T cell-driven inflammation in experimental autoimmune encephalomyelitis.

ROTS 2.0 improves statistical modeling in omics studies by optimizing reproducibility across various experimental designs and provides open-source implementations in R and Python.

The paper shows that fetal testosterone deficiency reduces adult male kidney size in mice by affecting growth pathways.

Coralysis improves integration of imbalanced cell types and states in single-cell data by multi-level integration, outperforming existing methods in such scenarios.

This study benchmarks eight de novo peptide sequencing models on proteomics datasets to evaluate their performance and identify limitations in resolving sequence ambiguity.

The paper identifies unconjugated bilirubin as a protective metabolite against malaria by inhibiting parasite proliferation and hemozoin formation.

The paper introduces a new pathway analysis method for longitudinal data, demonstrating its application in early type 1 diabetes studies with subtle biological signals.

The paper evaluates deconvolution methods for inferring immune infiltration from bulk gene expression using a DREAM Challenge, finding that some community-contributed methods, especially deep learning-based ones, perform well.

VarSCAT annotates genomic variant sequence contexts, revealing that over 75% of human indels have breakpoint ambiguities and over 80% of STR region variants are indels.

Totem is an R package that automates tree-shaped trajectory inference from single-cell data by generating and evaluating multiple clustering results.

This study benchmarks 18 methods for detecting differential states in multi-subject scRNA-seq data, finding that pseudo-bulk and mixed models outperform naive single-cell approaches by reducing false positives.

The paper evaluates variant calling tools for indel detection across different NGS datasets, showing tool and sequencing setting impacts on accuracy.

scShaper is a fast and accurate linear trajectory inference method for single-cell RNA-seq data, outperforming existing methods in accuracy and generalizability.

PhosPiR automates phospho-proteomic analysis by integrating multiple R packages to provide data cleaning, statistical testing, enrichment analysis, and visualization for high-dimensional mass spectrometry data.

The paper introduces RolDE, a new differential expression method for longitudinal proteomics data, which outperforms existing methods in handling missing values and reproducibility.

The paper introduces a DIA-only metaproteomics approach that improves peptide yields and reduces data requirements compared to DDA-assisted methods.

ILoReg improves cell population identification in single-cell RNA-seq by using probabilistic feature extraction before clustering.

This study shows that LRRK2 activity suppresses protein synthesis in Parkinson's disease, with inhibition restoring normal translation in patient fibroblasts.

The paper characterizes the CIP2A interactome in Th17 cells using affinity-purification mass spectrometry and validates key interactions, revealing associations with RNA processing and other cellular processes.

The paper identifies DNA methylation differences in peripheral blood of Alzheimer’s disease discordant twin pairs, linking these to brain gene expression and neuronal functions.

The paper introduces MICTI, a feature extraction method for identifying cell-type-specific markers in single-cell RNA-seq data, validated on simulated and real datasets.

This paper presents a crowdsourced challenge to predict early discontinuation of docetaxel in mCRPC patients using clinical data from multiple trials, finding that ensemble models outperform individual models.