Lauren M. McIntyre

Sex and Alternative Splicing in Disease: a meta-analytic approach to identify interactions

The paper uses a meta-analytic approach to identify sex-dependent splicing interactions in type 1 diabetes, finding higher prevalence in CD4 T cells than CD8 T cells.

A framework for identifying transcript orthologs: the evolution of sex bias in alternative transcript structure in Drosophila

The paper develops a framework to identify transcript orthologs across Drosophila species, revealing conserved sex-biased alternative transcripts and their potential role in sexual conflict resolution.

Spatial transcriptomics from pancreas and local draining lymph node tissue reveals a lymphotoxin-β signature in human type 1 diabetes

This study uses spatial transcriptomics to identify inflammation signatures in pancreas and lymph node tissues of T1D patients, highlighting LTB and other genes involved in disease pathogenesis.

Multiparent Recombinant Inbred lines crossed to a tester provide novel insights into sources of cis and trans regulation of gene expression

The paper introduces a method using multi-parent RILs crossed to a tester to dissect cis and trans regulation of gene expression in Drosophila, finding environmental and genetic trans effects in 31% and 19% of loci respectively.

SQANTI-reads: a tool for the quality assessment of long read data in multi-sample lrRNA-seq experiments.

SQANTI-reads assesses long-read RNA-seq data quality using SQANTI3 metrics, identifying under-annotated genes and splicing site variation across samples.

High-resolution methylome analysis in the clonal Populus nigra cv. 'Italica' reveals environmentally sensitive hotspots and drought-responsive TE superfamilies

This study analyzes the methylome of Populus nigra cv. 'Italica' under various environmental stresses and identifies stress-specific and generic methylation responses.

SQANTI3: curation of long-read transcriptomes for accurate identification of known and novel isoforms

SQANTI3 extends long-read transcriptome quality control with transcript-end subcategories, a short-read TSS ratio, rules or random-forest filters and a rescue module, raising SIRV-benchmarked F-score stepwise.

The evolution of splicing: transcriptome complexity and transcript distances implemented in TranD

This paper introduces TranD, a tool for comparing transcriptome structures using nucleotide-level distance metrics to assess transcript complexity and structural differences between species or annotations.

Shifts in isoform usage underlie transcriptional differences in regulatory T cells in type 1 diabetes

The paper identifies shifts in isoform usage in Tregs associated with Type 1 Diabetes by comparing gene expression between cases and controls.

An anchored experimental design and meta-analysis approach to address batch effects in large-scale metabolomics

The paper introduces an experimental design with anchor strains to reduce batch effects in metabolomics, enabling integration of NMR and LC-MS data across studies.

Ozone sensitivity of diverse maize genotypes is associated with differences in gene regulation, not gene content

The paper examines how gene regulation, not gene content, contributes to maize genotypes' sensitivity to ozone stress by analyzing gene expression across diverse inbred lines.

Power Calculator for Detecting Allelic Imbalance Using Hierarchical Bayesian Model

The paper presents a power calculator using a hierarchical Bayesian model to estimate the required reads and replicates for detecting allelic imbalance with specified power and type I error control.

GAIT-GM integrative cross-omics analyses reveal cholinergic defects in a C. elegans model of Parkinson's disease

The paper introduces GAIT-GM, a Galaxy tool for multi-omics analysis, and finds a link between branched-chain amino acid metabolism and cholinergic neuron defects in a C. elegans Parkinson's disease model.

Testcrosses are an efficient strategy for identifying cis regulatory variation: Bayesian analysis of allele specific expression (BASE)

The paper introduces BASE, a Bayesian pipeline for analyzing allelic imbalance to identify cis regulatory variation, showing it validates ~75% of predicted differences between non-tester alleles.

GAIT-GM: Galaxy tools for modeling metabolite changes as a function of gene expression

GAIT-GM provides Galaxy tools for integrating gene expression and metabolomics data through pathway-based analysis and flexible modeling of metabolite changes.

tappAS: A comprehensive computational framework for the analysis of the functional impact of differential splicing

The paper introduces tappAS, a framework for analyzing the functional impact of differential splicing, showing AltTP plays a major role in neural development by altering protein function and regulation.

Experimental design for large scale omic studies

The paper discusses experimental design for large-scale omic studies, emphasizing the importance of balancing omics batches and accounting for experimental factors to improve statistical power.