Clary B. Clish
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View article: Supplementary Figures S1-S7 from Effectors Enabling Adaptation to Mitochondrial Complex I Loss in Hürthle Cell Carcinoma
Supplementary Figures S1-S7 from Effectors Enabling Adaptation to Mitochondrial Complex I Loss in Hürthle Cell Carcinoma Open
Supplementary Figure 1: Mitochondrial and nuclear DNA alterations in an HCC cohort. Related to Figure 1. Supplementary Figure 2: Transcriptomic landscape of HCC. Related to Figure 2. Supplementary Figure 3: Metabolic signatures of HCC. Rel…
View article: Supplementary_Table2 from Effectors Enabling Adaptation to Mitochondrial Complex I Loss in Hürthle Cell Carcinoma
Supplementary_Table2 from Effectors Enabling Adaptation to Mitochondrial Complex I Loss in Hürthle Cell Carcinoma Open
Supplementary Table 2 provides the mtDNA and LOH analyses
View article: Supplementary_Table3 from Effectors Enabling Adaptation to Mitochondrial Complex I Loss in Hürthle Cell Carcinoma
Supplementary_Table3 from Effectors Enabling Adaptation to Mitochondrial Complex I Loss in Hürthle Cell Carcinoma Open
Supplementary Table3 provides the RNAseq analysis
View article: Supplementary_Table4 from Effectors Enabling Adaptation to Mitochondrial Complex I Loss in Hürthle Cell Carcinoma
Supplementary_Table4 from Effectors Enabling Adaptation to Mitochondrial Complex I Loss in Hürthle Cell Carcinoma Open
Supplementary Table4 provides the metabolomics analysis
View article: Supplementary_Table1 from Effectors Enabling Adaptation to Mitochondrial Complex I Loss in Hürthle Cell Carcinoma
Supplementary_Table1 from Effectors Enabling Adaptation to Mitochondrial Complex I Loss in Hürthle Cell Carcinoma Open
Supplementary Table 1 describes the HCC clinical cohort
View article: Supplementary_Table5 from Effectors Enabling Adaptation to Mitochondrial Complex I Loss in Hürthle Cell Carcinoma
Supplementary_Table5 from Effectors Enabling Adaptation to Mitochondrial Complex I Loss in Hürthle Cell Carcinoma Open
Supplementary Table5 provides the CRISPR screen results
View article: Data from Plasma Metabolomics and Breast Cancer Risk over 20 Years of Follow-up among Postmenopausal Women in the Nurses' Health Study
Data from Plasma Metabolomics and Breast Cancer Risk over 20 Years of Follow-up among Postmenopausal Women in the Nurses' Health Study Open
Background:Metabolite profiles provide insight into biologic mechanisms contributing to breast cancer development. We explored the association between prediagnostic plasma metabolites (N = 307) and invasive breast cancer among postm…
View article: Inhibiting ferroptosis enhances ex vivo expansion of human haematopoietic stem cells
Inhibiting ferroptosis enhances ex vivo expansion of human haematopoietic stem cells Open
Improved ex vivo expansion of human haematopoietic stem cells (HSCs) would considerably advance transplantation and genome-engineered therapies, yet existing culture methods still allow substantial HSC loss. Here we show that this attritio…
View article: Machine learning‐based clustering identifies obesity subgroups with differential multi‐omics profiles and metabolic patterns
Machine learning‐based clustering identifies obesity subgroups with differential multi‐omics profiles and metabolic patterns Open
OBJECTIVE: Individuals living with obesity are differentially susceptible to cardiometabolic diseases. We hypothesized that an integrative multi-omics approach might improve identification of subgroups of individuals with obesity who have …
View article: Circulating metabolites associated with protection against Mycobacterium tuberculosis infection and inhibition of mycobacterial growth
Circulating metabolites associated with protection against Mycobacterium tuberculosis infection and inhibition of mycobacterial growth Open
A significant proportion of individuals who are heavily exposed to infectious tuberculosis patients do not acquire Mycobacterium tuberculosis (Mtb) infection, as detected by an interferon gamma release assay (IGRA). We examined circulating…
View article: A machine learning framework for classifying lipids in untargeted metabolomics using mass-to-charge ratios and retention times
A machine learning framework for classifying lipids in untargeted metabolomics using mass-to-charge ratios and retention times Open
Introduction The identification of unknown metabolites remains a major challenge in untargeted metabolomics using liquid chromatography-mass spectrometry (LC–MS). This process typically depends on comparing mass spectral or chromatographic…
View article: Distinguishing diet- and microbe-derived metabolites in the human gut
Distinguishing diet- and microbe-derived metabolites in the human gut Open
View article: A Metabolomics Approach to Identify Metabolites Associated with Uremic Symptoms in Patients Receiving Maintenance Hemodialysis
A Metabolomics Approach to Identify Metabolites Associated with Uremic Symptoms in Patients Receiving Maintenance Hemodialysis Open
Background: The specific toxins causing uremic symptoms (nausea, vomiting, pruritus, fatigue, difficulty concentrating and pain) in kidney failure remain unknown. We used untargeted metabolomics to identify plasma metabolites associated wi…
View article: ODC1 restricts meningeal B cell age-associated-like phenotype and function in multiple sclerosis: a human and experimental study
ODC1 restricts meningeal B cell age-associated-like phenotype and function in multiple sclerosis: a human and experimental study Open
Meningeal inflammation, as a clinical feature of multiple sclerosis (MS), is associated with worse clinical disease outcomes. In both relapsing and secondary progressive MS and the experimental autoimmune encephalomyelitis (EAE) MS model, …
View article: Prospective study of circulating metabolomic profiles and breast cancer incidence among predominantly premenopausal women
Prospective study of circulating metabolomic profiles and breast cancer incidence among predominantly premenopausal women Open
View article: Baseline metabolomic profile as potential biomarker for weight change after Roux-en-Y gastric bypass (RYGB) surgery
Baseline metabolomic profile as potential biomarker for weight change after Roux-en-Y gastric bypass (RYGB) surgery Open
Metabolic and bariatric surgery (MBS) is the most effective intervention for sustained weight loss and cardiometabolic improvement in individuals with severe obesity. However, long-term outcomes vary, with many patients experiencing weight…
View article: Metabolomic signatures of hypocaloric dietary interventions associate with breast cancer risk in the Nurses’ Health Study II
Metabolomic signatures of hypocaloric dietary interventions associate with breast cancer risk in the Nurses’ Health Study II Open
Background An individual’s metabolic state plays a critical role in breast cancer (BC) risk, influenced by factors such as obesity and insulin signaling. Hypocaloric diets induce metabolic changes that influence these metabolic factors, th…
View article: Steroid hormone biosynthesis and dietary related metabolites associated with excessive daytime sleepiness
Steroid hormone biosynthesis and dietary related metabolites associated with excessive daytime sleepiness Open
Details regarding funding supporting this work and all studies involved are provided in the acknowledgements section.
View article: Association of the HDL lipidome with HDL traits before and after exercise training: HERITAGE family study
Association of the HDL lipidome with HDL traits before and after exercise training: HERITAGE family study Open
View article: Dietary Patterns, Circulating Metabolome, and Risk of Type 2 Diabetes
Dietary Patterns, Circulating Metabolome, and Risk of Type 2 Diabetes Open
Circulating metabolites may reflect biological homeostasis and have been linked to dietary intakes and human health, and may hold the promises to facilitate objective assessments of intakes and metabolic response to diets. Here, we integra…
View article: Plasma Metabolomics Profiles in Prodromal and Clinical Parkinson's Disease
Plasma Metabolomics Profiles in Prodromal and Clinical Parkinson's Disease Open
Background The long prodromal phase of Parkinson's disease (PD) and the link the disease has with metabolic factors suggest that metabolomics could help identify affected individuals at early stages. Objective The goal was to examine wheth…
View article: Inflammatory dietary potential and gut microbiota in older adults with overweight or obesity and metabolic syndrome
Inflammatory dietary potential and gut microbiota in older adults with overweight or obesity and metabolic syndrome Open
View article: Intraoperative arteriovenous patient sampling to assess <i>in situ</i> non-small cell lung cancer metabolism
Intraoperative arteriovenous patient sampling to assess <i>in situ</i> non-small cell lung cancer metabolism Open
We performed intraoperative arteriovenous sampling in participants undergoing surgical resection for non-small cell lung cancer (NSCLC) to characterize in situ tumor metabolism, directly measuring metabolite consumption and secretion in tu…
View article: Corrigendum to “The Dietary Biomarkers Development Consortium: An Initiative for Discovery and Validation of Dietary Biomarkers for Precision Nutrition. [Current Developments in Nutrition, Volume 9, Issue 5, May 2025, 107435]”
Corrigendum to “The Dietary Biomarkers Development Consortium: An Initiative for Discovery and Validation of Dietary Biomarkers for Precision Nutrition. [Current Developments in Nutrition, Volume 9, Issue 5, May 2025, 107435]” Open
[This corrects the article DOI: 10.1016/j.cdnut.2025.107435.].
View article: Dietary metabolic signatures and cardiometabolic risk
Dietary metabolic signatures and cardiometabolic risk Open
AIMS: Observational studies of diet in cardiometabolic-cardiovascular disease (CM-CVD) focus on self-reported consumption of food or dietary pattern, with limited information on individual metabolic responses to dietary intake linked to CM…
View article: Metabolic reprogramming of the neovascular niche promotes regenerative angiogenesis in proliferative retinopathy
Metabolic reprogramming of the neovascular niche promotes regenerative angiogenesis in proliferative retinopathy Open
View article: Omic Risk Scores are Associated with COPD-related Traits Across Three Cohorts
Omic Risk Scores are Associated with COPD-related Traits Across Three Cohorts Open
Background Chronic obstructive pulmonary disease (COPD) exhibits marked heterogeneity in lung function decline, mortality, exacerbations, and other disease-related outcomes. Omic risk scores (ORS) estimate the cumulative contribution of om…
View article: The glycolytic reaction PGAM restrains Th17 pathogenicity and Th17-dependent autoimmunity
The glycolytic reaction PGAM restrains Th17 pathogenicity and Th17-dependent autoimmunity Open
View article: Neural Spectral Prediction for Structure Elucidation with Tandem Mass Spectrometry
Neural Spectral Prediction for Structure Elucidation with Tandem Mass Spectrometry Open
Structural elucidation using untargeted tandem mass spectrometry (MS/MS) has played a critical role in advancing scientific discovery [1, 2]. However, differentiating molecular fragmentation patterns between isobaric structures remains a p…
View article: Pre-treatment untargeted cerebrospinal fluid metabolomic profiling in tuberculous meningitis uncovers pathways associated with mortality
Pre-treatment untargeted cerebrospinal fluid metabolomic profiling in tuberculous meningitis uncovers pathways associated with mortality Open
National Institute of Health; Wellcome Trust, UK.