Clary B. Clish

The paper introduces the Proteomic Sex Index (PSI), a continuous measure of plasma proteome alignment with chromosomal sex, showing its association with health and disease traits.

ScreenDMT identifies metabolites consistently linked to sleep disorders across three human cohorts, revealing replicable associations with insomnia, sleep duration, and daytime sleepiness.

The paper identifies shared and distinct biochemical responses to different exercise modes through plasma proteomics, metabolomics, and transcriptomics in sedentary humans.

This study identifies FAR1 as a key regulator of peroxisome degradation under hypoxia, linking ether lipid metabolism to autophagy and cardioprotection.

TorchGWAS2 improves genome-wide association testing in related samples by using a deterministic variance-correction algorithm, achieving faster and more powerful results across large-scale omics data.

The paper identifies N-acyl putrescines, particularly NOP, as immunomodulatory metabolites produced by gut microbiota that suppress inflammation in IBD models.

The paper identifies genetic drivers of protein change over time using longitudinal proteomics data from MESA, UK Biobank, and CARDIA, finding that baseline adjustment improves replication but may introduce biases.

This study integrates CAD GWAS with transcriptomic data to identify genes and networks associated with CAD and subclinical atherosclerosis.

The paper identifies tissue-specific transcriptional regulatory programs in rats undergoing endurance exercise training by integrating chromatin accessibility, DNA methylation, and gene expression data.

This study investigates the association between mosaic loss of Y chromosome (mLOY) and lung function, emphysema, and epigenetic aging in men across multiple cohorts.

This study identifies Blautia wexlerae's role in converting dietary fats into bioactive metabolites that enhance gut hormone secretion and improve metabolic health in mice and humans.

This study shows that ODC1 suppresses age-associated B cell features in meningeal inflammation of MS and EAE, affecting disease severity.

This study uses intraoperative arteriovenous sampling to measure tumor metabolism in NSCLC patients, revealing distinct metabolic profiles between tumor and normal lung tissue.

This study shows that ether lipids in cancer cells regulate membrane properties to influence iron uptake, ferroptosis, and metastasis, offering a therapeutic target.

This study identifies two distinct molybdenum-dependent enzyme families that produce urolithin A from ellagic acid, linking gut bacterial metabolism to host inflammation in IBD.

The paper links lower plasma plasmalogen levels to increased risk of lymph node positive breast cancer in humans and mice, showing dietary PUFA depletion promotes cancer survival in lymph nodes.

The paper analyzes circulating metabolites using genome-wide association data from the TOPMed program, identifying 1,778 loci and highlighting sex-specific genetic contributions.

This study identifies PGAM as a negative regulator of Th17 pathogenicity using single-cell RNA-seq and metabolic flux analysis.

The paper introduces a deep learning model, ICEBERG, for structural elucidation using tandem mass spectrometry, achieving high accuracy in identifying molecular structures from complex mixtures.

Eclipse aligns multiple nontargeted LC-MS metabolomics datasets using a graph-based subalignment approach.

This study identifies AKAP11's role in regulating lipid metabolism and neuronal support in astrocytes, linking its dysfunction to schizophrenia and bipolar disorder risk.

This study shows that ANGPTL3 regulates SmarcAL1 translocation to peroxisomes, affecting lipid metabolism and TG storage in response to cell growth states.

This paper introduces GENN, a method for multi-omic interactome analysis that improves prediction of biomedical outcomes by learning salient associations in a low-dimensional space.

This study identifies branched chain α-ketoacids (BCKAs) as novel signaling metabolites that activate HIF1α signaling in normoxia and modulate vascular smooth muscle cell function in pulmonary vascular disease.

This paper shows that m-tirofiban, a non-partial agonist of IIbβ3, effectively inhibits venous thrombosis without increasing bleeding in a mouse model.

This study examines how endurance exercise training affects rat subcutaneous white adipose tissue, revealing sex-specific molecular responses and differences in adiposity and metabolism.

This study uses multi-omics analysis to show that chemical reprogramming reduces biological age in mouse fibroblasts by altering metabolism and mitochondrial function.

The paper identifies impactful rare variants by integrating multi-omic data from MESA, showing that combining expression and protein data increases the detection of rare stop and frameshift variants.

This paper introduces MCFA, an unsupervised integration method for multi-omic data, and applies it to five omics types across 614 samples to infer shared and private factors.