Kristen W. Lynch

Nonsense-mediated decay controls a negative feedback loop in innate immune sensing

The paper shows that dsRNA sensing inhibits NMD, forming a negative feedback loop that limits dsRNA-mediated immune responses.

Integrative analysis of RNA binding proteins identifies DDX55 as a novel regulator of 3'UTR isoform diversity

The paper identifies DDX55 as a novel regulator of 3'UTR isoform diversity through integrative analysis of RNA binding protein depletion experiments.

Coordination of nuclear RNA processing by speckle-localized kinase TAOK2

This study identifies TAOK2 as a kinase that regulates splicing and export of both viral and cellular transcripts by phosphorylating SRRM1/2, maintaining nuclear speckle structure and function.

Alternate isoforms of IRF7 Differentially Regulate Interferon Expression to Tune Response to Viral Infection

This study identifies an alternative splicing mechanism in IRF7 that generates a protein isoform with enhanced transcriptional activity, leading to increased resistance to viral infection.

Machine learning-optimized targeted detection of alternative splicing

This paper introduces LSV-seq, a targeted RNA-seq method optimized with machine learning to detect alternative splicing with high sensitivity and low sequencing depth.

Alternative Splicing of Apoptosis Genes Promotes Human T Cell Survival

This study shows that CD28 costimulation enhances alternative splicing of apoptosis-related genes, promoting T cell survival through combinatorial effects on caspase-9, Bax, and Bim.

MOCCASIN: A method for correcting for known and unknown confounders in RNA splicing analysis

MOCCASIN corrects known and unknown confounders in RNA splicing analysis using synthetic and real data from TARGET and ENCODE.

Alternative splicing redefines landscape of commonly mutated genes in acute myeloid leukemia

The paper shows that alternative splicing contributes to gene disruption in AML, increasing the number of patients with functional gene loss beyond what is detected by mutations alone.

Viral-Induced Alternative Splicing of Host Genes Promotes Influenza Replication

Ancient antagonism between CELF and RBFOX families tunes mRNA splicing outcomes

The paper identifies antagonistic splicing regulation between CELF2 and RBFOX family proteins in human T cells and shows evolutionary conservation across species.