About

Shankar Subramaniam is a Professor of Bioengineering at UCSD. His research activities and funding include leading the Graduate Training Program in Bioinformatics and overseeing various NIH-funded projects such as the Biomedical Data Commons Workbench, the Metabolomics Data Center, and systems biology analyses related to vascular homeostasis and disease pathways. His work involves clinical trials, multiomics, and systems biology approaches to understanding molecular networks, disease mechanisms, and biomedical data integration. He has contributed to the development of bioinformatics workflows, molecular landscape analysis in cancer, and the application of multiomics to inflammation and neurodegenerative diseases.

Research topics

• Gastroenterology
• Medicine
• Internal medicine
• Endocrinology
• Environmental health
• Radiology

Selected publications

• Reproducibility and Repeatability of US Shear-Wave and Transient Elastography in Nonalcoholic Fatty Liver Disease

  Radiology · 2024-09-01 · 35 citations

  articleOpen access

  This prospective study defines expected US elastography measurement variability to guide clinical interpretation, enable diagnostic enrichment in clinical trials, and support U.S. Food and Drug Administration biomarker validation for nonalcoholic fatty liver disease.

  PublisherOA PDFDOI

• Safety and Efficacy of Novel Incretin Co-agonist Cotadutide in Biopsy-proven Noncirrhotic MASH With Fibrosis

  Clinical Gastroenterology and Hepatology · 2024-05-09 · 39 citations

  articleOpen access1st authorCorresponding
  PublisherDOI

• Repeatability of MRI Biomarkers in Nonalcoholic Fatty Liver Disease: The NIMBLE Consortium

  Radiology · 2023-10-01 · 43 citations

  articleOpen access

  There is a need for reliable noninvasive methods for diagnosing and monitoring nonalcoholic fatty liver disease (NAFLD). Thus, the multidisciplinary Non-invasive Biomarkers of Metabolic Liver disease (NIMBLE) consortium was formed to identify and advance the regulatory qualification of NAFLD imaging biomarkers.

  PublisherOA PDFDOI

• The Nimble Stage 1 Study Validates Diagnostic Circulating Biomarkers for Nonalcoholic Steatohepatitis

  Research Square · 2023-01-19 · 8 citations

  preprintOpen access
  PublisherOA PDFDOI

• Performance of non-invasive tests and histology for the prediction of clinical outcomes in patients with non-alcoholic fatty liver disease: an individual participant data meta-analysis

  ˜The œLancet. Gastroenterology & hepatology · 2023 · 179 citations

  • Medicine
  • Internal medicine
  • Gastroenterology

  BACKGROUND: Histologically assessed liver fibrosis stage has prognostic significance in patients with non-alcoholic fatty liver disease (NAFLD) and is accepted as a surrogate endpoint in clinical trials for non-cirrhotic NAFLD. Our aim was to compare the prognostic performance of non-invasive tests with liver histology in patients with NAFLD. METHODS: This was an individual participant data meta-analysis of the prognostic performance of histologically assessed fibrosis stage (F0-4), liver stiffness measured by vibration-controlled transient elastography (LSM-VCTE), fibrosis-4 index (FIB-4), and NAFLD fibrosis score (NFS) in patients with NAFLD. The literature was searched for a previously published systematic review on the diagnostic accuracy of imaging and simple non-invasive tests and updated to Jan 12, 2022 for this study. Studies were identified through PubMed/MEDLINE, EMBASE, and CENTRAL, and authors were contacted for individual participant data, including outcome data, with a minimum of 12 months of follow-up. The primary outcome was a composite endpoint of all-cause mortality, hepatocellular carcinoma, liver transplantation, or cirrhosis complications (ie, ascites, variceal bleeding, hepatic encephalopathy, or progression to a MELD score ≥15). We calculated aggregated survival curves for trichotomised groups and compared them using stratified log-rank tests (histology: F0-2 vs F3 vs F4; LSM: <10 vs 10 to <20 vs ≥20 kPa; FIB-4: <1·3 vs 1·3 to ≤2·67 vs >2·67; NFS: <-1·455 vs -1·455 to ≤0·676 vs >0·676), calculated areas under the time-dependent receiver operating characteristic curves (tAUC), and performed Cox proportional-hazards regression to adjust for confounding. This study was registered with PROSPERO, CRD42022312226. FINDINGS: Of 65 eligible studies, we included data on 2518 patients with biopsy-proven NAFLD from 25 studies (1126 [44·7%] were female, median age was 54 years [IQR 44-63), and 1161 [46·1%] had type 2 diabetes). After a median follow-up of 57 months [IQR 33-91], the composite endpoint was observed in 145 (5·8%) patients. Stratified log-rank tests showed significant differences between the trichotomised patient groups (p<0·0001 for all comparisons). The tAUC at 5 years were 0·72 (95% CI 0·62-0·81) for histology, 0·76 (0·70-0·83) for LSM-VCTE, 0·74 (0·64-0·82) for FIB-4, and 0·70 (0·63-0·80) for NFS. All index tests were significant predictors of the primary outcome after adjustment for confounders in the Cox regression. INTERPRETATION: Simple non-invasive tests performed as well as histologically assessed fibrosis in predicting clinical outcomes in patients with NAFLD and could be considered as alternatives to liver biopsy in some cases. FUNDING: Innovative Medicines Initiative 2.

  DOI

• Diagnostic performance of circulating biomarkers for non-alcoholic steatohepatitis

  Nature Medicine · 2023-09-07 · 110 citations

  articleOpen access

  There are no approved diagnostic biomarkers for at-risk non-alcoholic steatohepatitis (NASH), defined by the presence of NASH, high histological activity and fibrosis stage ≥2, which is associated with higher incidence of liver-related events and mortality. FNIH-NIMBLE is a multi-stakeholder project to support regulatory approval of NASH-related biomarkers. The diagnostic performance of five blood-based panels was evaluated in an observational (NASH CRN DB2) cohort (n = 1,073) with full spectrum of non-alcoholic fatty liver disease (NAFLD). The panels were intended to diagnose at-risk NASH (NIS4), presence of NASH (OWLiver) or fibrosis stages >2, >3 or 4 (enhanced liver fibrosis (ELF) test, PROC3 and FibroMeter VCTE). The prespecified performance metric was an area under the receiver operating characteristic curve (AUROC) ≥0.7 and superiority over alanine aminotransferase for disease activity and the FIB-4 test for fibrosis severity. Multiple biomarkers met these metrics. NIS4 had an AUROC of 0.81 (95% confidence interval: 0.78-0.84) for at-risk NASH. The AUROCs of the ELF test, PROC3 and FibroMeterVCTE for clinically significant fibrosis (≥stage 2), advanced fibrosis (≥stage 3) or cirrhosis (stage 4), respectively, were all ≥0.8. ELF and FibroMeter VCTE outperformed FIB-4 for all fibrosis endpoints. These data represent a milestone toward qualification of several biomarker panels for at-risk NASH and also fibrosis severity in individuals with NAFLD.

  PublisherOA PDFDOI

• Validation of the ADAPT score for the diagnosis of clinically significant fibrosis in patients with non-alcoholic fatty liver disease (NAFLD)

  Journal of Hepatology · 2022-07-01

  article
  PublisherDOI

• Results of the Non-invasive Biomarkers of Metabolic Liver Disease (NIMBLE) study 1.1 on the reproducibility and repeatability of shear-wave and transient elastography in non-alcoholic fatty liver disease

  Journal of Hepatology · 2022-07-01 · 1 citations

  article
  PublisherDOI

• Changes in hepatic fat fraction as assessed by MRI-PDFF are correlated with changes in markers of hepatic inflammation, disease activity and fibrosis in biopsy-proven non-cirrhotic NASH with fibrosis

  Journal of Hepatology · 2022-07-01

  articleSenior author
  PublisherDOI

• Non-Invasive Biomarkers of Nonalcoholic Steatohepatitis: the FNIH NIMBLE project

  Nature Medicine · 2022-02-10 · 55 citations

  letterOpen access
  PublisherOA PDFDOI

Recent grants

• NIH Grant M01RR000750

  NIH · $17.5M · 2009

• NIH Grant K23AI052852

  NIH · $383k · 2008

Frequent coauthors

• Roberto A. Calle

  172 shared

• Tania Kamphaus

  Foundation for the National Institutes of Health

  165 shared

• Sarah P. Sherlock

  Pfizer (United States)

  163 shared

• Arun J. Sanyal

  Virginia Commonwealth University

  162 shared

• Anthony E. Samir

  156 shared

• Claude B. Sirlin

  The University of Texas Southwestern Medical Center

  155 shared

• Kathryn J. Fowler

  155 shared

• Rohit Loomba

  155 shared