Scholars@Duke
Pixu Shi

Pixu Shi

Assistant Professor of Biostatistics & Bioinformatics
Biostatistics & Bioinformatics, Division of Integrative Genomics

Selected Publications

Longitudinal analysis of rhesus macaque metabolome during acute SIV infection reveals disruption in broad metabolite classes.

Journal Article J Virol · March 18, 2025 UNLABELLED: Persons living with HIV experience significant metabolic dysregulation, frequently resulting in immune and other cellular dysfunction. However, our understanding of metabolism and its relationship to immunity in the context of HIV remains incom ... Full text Link to item Cite

Branched chain amino acid metabolism and microbiome in adolescents with obesity during weight loss therapy.

Journal Article medRxiv · February 4, 2025 BACKGROUND: Towards improving outcomes for adolescents with obesity, we aimed to define metabolic and microbiome phenotypes at baseline and post-weight loss intervention. METHODS: The Pediatric Obesity Microbiome and Metabolism Study enrolled 220 adolescen ... Full text Link to item Cite

Glucagon-Like Peptide 1 Receptor (Glp1r) Deficiency Does Not Appreciably Alter Airway Inflammation or Gut-Lung Microbiome Axis in a Mouse Model of Obese Allergic Airways Disease and Bariatric Surgery.

Journal Article J Asthma Allergy · 2025 PURPOSE: High body mass index (≥30 kg/m2) is associated with asthma severity, and nearly 40% of asthma patients exhibit obesity. Furthermore, over 40% of patients with obesity and asthma that receive bariatric surgery no longer require asthma medication. I ... Full text Link to item Cite

TEMPTED: time-informed dimensionality reduction for longitudinal microbiome studies.

Journal Article Genome Biol · December 19, 2024 Longitudinal studies are crucial for understanding complex microbiome dynamics and their link to health. We introduce TEMPoral TEnsor Decomposition (TEMPTED), a time-informed dimensionality reduction method for high-dimensional longitudinal data that treat ... Full text Link to item Cite

Abstract PO4-14-07: Genomic and immune profiling of breast cancer brain metastases

Conference Cancer Research · May 2, 2024 AbstractBACKGROUND: Brain metastases (BrM) arising from breast cancer (BC) are an increasing consequence of advanced disease, with up to half of patients (pts) with metastatic HER2+ or triple negative breast ... Full text Cite

A conserved interdomain microbial network underpins cadaver decomposition despite environmental variables.

Journal Article Nat Microbiol · March 2024 Microbial breakdown of organic matter is one of the most important processes on Earth, yet the controls of decomposition are poorly understood. Here we track 36 terrestrial human cadavers in three locations and show that a phylogenetically distinct, interd ... Full text Link to item Cite

Guaranteed Functional Tensor Singular Value Decomposition.

Journal Article J Am Stat Assoc · 2024 This paper introduces the functional tensor singular value decomposition (FTSVD), a novel dimension reduction framework for tensors with one functional mode and several tabular modes. The problem is motivated by high-order longitudinal data analysis. Our m ... Full text Link to item Cite

Serum and CSF metabolomics analysis shows Mediterranean Ketogenic Diet mitigates risk factors of Alzheimer's disease.

Journal Article NPJ Metab Health Dis · 2024 Alzheimer's disease (AD) is influenced by a variety of modifiable risk factors, including a person's dietary habits. While the ketogenic diet (KD) holds promise in reducing metabolic risks and potentially affecting AD progression, only a few studies have e ... Full text Link to item Cite

A Modified Mediterranean Ketogenic Diet mitigates modifiable risk factors of Alzheimer's Disease: a serum and CSF-based metabolic analysis.

Journal Article medRxiv · November 27, 2023 Alzheimer's disease (AD) is influenced by a variety of modifiable risk factors, including a person's dietary habits. While the ketogenic diet (KD) holds promise in reducing metabolic risks and potentially affecting AD progression, only a few studies have e ... Full text Link to item Cite

NIH SenNet Consortium to map senescent cells throughout the human lifespan to understand physiological health.

Journal Article Nature aging · December 2022 Cells respond to many stressors by senescing, acquiring stable growth arrest, morphologic and metabolic changes, and a proinflammatory senescence-associated secretory phenotype. The heterogeneity of senescent cells (SnCs) and senescence-associated secretor ... Full text Cite

High-dimensional log-error-in-variable regression with applications to microbial compositional data analysis

Journal Article Biometrika · June 1, 2022 In microbiome and genomic studies, the regression of compositional data has been a crucial tool for identifying microbial taxa or genes that are associated with clinical phenotypes. To account for the variation in sequencing depth, the classic log-contrast ... Full text Cite

Generalized Linear Models With Linear Constraints for Microbiome Compositional Data

Journal Article Biometrics · March 1, 2019 SummaryMotivated by regression analysis for microbiome compositional data, this article considers generalized linear regression analysis with compositional covariates, where a group of linear constraints on ... Full text Cite

A Model for Paired-Multinomial Data and Its Application to Analysis of Data on a Taxonomic Tree

Journal Article Biometrics · December 1, 2017 SummaryIn human microbiome studies, sequencing reads data are often summarized as counts of bacterial taxa at various taxonomic levels specified by a taxonomic tree. This article considers the problem of analyzing two repea ... Full text Cite

Regression analysis for microbiome compositional data

Journal Article The Annals of Applied Statistics · June 1, 2016 Full text Cite