Olga V. Tsoy

Detection of alternative splicing: deep sequencing or deep learning?

This study evaluates whether sequence-based tools can detect alternative splicing from low-depth RNA-seq data, showing promise for hypothesis generation but limitations in de novo detection.

AlterNet: Alternative splicing-aware gene regulatory network inference

AlterNet infers transcript-level gene regulatory networks by considering alternative splicing, revealing novel regulatory interactions not detectable at the gene-level in heart tissue data.

Aberrant splicing in human cancer has a large-scale functional impact on transcription factors

The paper identifies 2,118 aberrant splicing events affecting 718 transcription factors across 14 cancer types, showing functional perturbations in TFs due to cancer-specific alternative splicing.

Regulation of the transcriptome, miRNAs, and alternative splicing in a FSGS zebrafish injury model

This study investigates alternative splicing and miRNA regulation in a zebrafish FSGS model, identifying key splicing events and miRNAs associated with disease progression.

Comprehensive benchmark of differential transcript usage analysis for static and dynamic conditions

The paper benchmarks differential transcript usage analysis tools across static and dynamic conditions, finding optimal tools for different data types and experimental settings.

Alternative splicing in mechanically stretched podocytes as a model of glomerular hypertension

The paper investigates alternative splicing in mechanically stretched podocytes, identifying splicing events in Shroom3 and Myl6 that may contribute to hypertensive nephropathy.

Systematic Evaluation of Normalization Approaches in Tandem Mass Tag and Label-Free Protein Quantification Data Using PRONE

The paper evaluates normalization methods in proteomics data, finding that some methods perform better than others and develops a tool to assess their impact.

DREAMER: Exploring Common Mechanisms of Adverse Drug Reactions and Disease Phenotypes through Network-Based Analysis

DREAMER identifies molecular mechanisms of adverse drug reactions and disease phenotypes using network-based analysis, revealing key proteins and pathways involved in various conditions.

RNA sequencing depth guidelines for the study of alternative splicing

The paper provides sequencing depth guidelines for comprehensive alternative splicing analysis across tissues, showing that current depths are insufficient and recommending deeper sequencing or long-read technologies.

Network medicine-based epistasis detection in complex diseases: ready for quantum computing

The paper introduces NeEDL, a network medicine-based method for detecting higher-order epistatic interactions in complex diseases, showing improved statistical significance and applicability across eight diseases.

Convergent gene pairs restrict chromatin looping in Dictyostelium discoideum, acting as directional barriers for extrusion

The paper investigates chromatin looping in Dictyostelium discoideum, finding that convergent gene pairs act as directional barriers for chromatin extrusion during development.

The power and limits of predicting exon-exon interactions using protein 3D structures

The paper evaluates existing computational methods for predicting exon-exon interactions using protein structures and finds they can achieve moderate accuracy for this task.

Alternative splicing impacts microRNA regulation within coding regions

The paper investigates how alternative splicing affects miRNA regulation by analyzing six TCGA cancer datasets, finding that transcripts with miRNA target sites in coding regions better predict miRNA expression.

Systematic analysis of alternative splicing in time course data using Spycone

Spycone analyzes alternative splicing in time course data to detect isoform switches and provides downstream analysis tools.

Alternative splicing analysis benchmark with DICAST

DICAST benchmarks alternative splicing analysis tools, showing STAR and HISAT2 perform best, and proposes a reporting standard for event detection.

Florigen revisited: proteins of the FT/CETS/PEBP/PKIP/YbhB family may be the enzymes of small molecule metabolism

The paper revisits the florigen hypothesis, proposing that FT/CETS/PEBP/PKIP/YbhB family proteins may function as enzymes involved in small molecule metabolism rather than as hormone-like signaling molecules.

Functional enrichment of alternative splicing events with NEASE reveals insights into tissue identity and diseases

The paper introduces NEASE, a tool for functional analysis of alternative splicing events, showing its ability to identify pathways related to tissue identity and cell type development, and highlight splicing-related biomarkers.