Jianguo (Jeff) Xia

Jianguo (Jeff) Xia
McGill University | McGill · Institute of Parasitology, Animal Science, Microbiology and Immunology

MD, PhD

About

210
Publications
87,674
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
40,547
Citations
Introduction
Bioinformatics and statistics for high-throughput omics data; host-parasite-gut microbiome interactions; big data analytics and systems biology.
Additional affiliations
January 2015 - present
McGill University
Position
  • Professor (Assistant)
August 2012 - December 2014
University of British Columbia
Position
  • PostDoc Position
Description
  • Next generation sequence analysis, RNA-seq, meta-analysis, network and systems biology
September 2011 - July 2012
University of Alberta
Position
  • PostDoc Position
Description
  • Clinical biomarker analysis, metagenomics, metabolomics
Education
August 2012 - December 2014
University of British Columbia
Field of study
  • RNAseq, network analysis, data integration & meta-anlysis
September 2011 - July 2012
University of Alberta
Field of study
  • Metabolomics, Biomarker Analysis
September 2006 - August 2011
University of Alberta
Field of study
  • Metabolomics, Bioinformatics

Publications

Publications (210)
Article
Full-text available
The widespread application of next-generation sequencing technologies has revolutionized microbiome research by enabling high-throughput profiling of the genetic contents of microbial communities. How to analyze the resulting large complex datasets remains a key challenge in current microbiome studies. Over the past decade, powerful computational p...
Article
Full-text available
MicroRNAs (miRNAs) can regulate nearly all biological processes and their dysregulation is implicated in various complex diseases and pathological conditions. Recent years have seen a growing number of functional studies of miRNAs using high-throughput experimental technologies, which have produced a large amount of high-quality data regarding miRN...
Article
Full-text available
MetaboAnalyst (www.metaboanalyst.ca) is a web server designed to permit comprehensive metabolomic data analysis, visualization and interpretation. It supports a wide range of complex statistical calculations and high quality graphical rendering functions that require significant computational resources. First introduced in 2009, MetaboAnalyst has e...
Article
Full-text available
Meta-analysis of gene expression data sets is increasingly performed to help identify robust molecular signatures and to gain insights into underlying biological processes. The complicated nature of such analyses requires both advanced statistics and innovative visualization strategies to support efficient data comparison, interpretation and hypoth...
Article
Full-text available
Metabolomics is increasingly being applied towards the identification of biomarkers for disease diagnosis, prognosis and risk prediction. Unfortunately among the many published metabolomic studies focusing on biomarker discovery, there is very little consistency and relatively little rigor in how researchers select, assess or report their candidate...
Article
Full-text available
Missing values are prevalent in high-throughput measurements due to various experimental or analytical reasons. Imputation, the process of replacing missing values in a dataset with estimated values, plays an important role in multivariate and machine learning analyses. The three missingness patterns, including missing completely at random (MCAR),...
Article
Full-text available
Background: Electronic and electrical waste (e-waste) production has emerged to be of global environmental public health concern. E-waste workers, who are frequently exposed to hazardous chemicals through occupational activities, face considerable health risks. Methods: To investigate the metabolic and exposomic changes in these workers, we analyze...
Article
The growing volumes of microbiome studies over the past decade have revealed a wide repertoire of microbial associations under diverse conditions. Microbes produce small molecules to interact with each other as well as to modulate their environments. Their metabolic profiles hold the key to understanding these association patterns for translational...
Article
Full-text available
Efforts to use transcriptomics for toxicity testing have classically relied on the assumption that chemicals consistently produce characteristic transcriptomic signatures that are reflective of their mechanism of action. However, the degree to which transcriptomic responses are conserved across different test methodologies has seldom been explored....
Article
Population-level variation and mechanisms behind insulin secretion in response to carbohydrate, protein, and fat remain uncharacterized. We defined prototypical insulin secretion responses to three macronutrients in islets from 140 cadaveric donors, including those with type 2 diabetes. The majority of donors’ islets exhibited the highest insulin r...
Preprint
Full-text available
Comprehensive molecular and cellular phenotyping of human islets can enable deep mechanistic insights for diabetes research. We established the Human Islet Data Analysis and Sharing (HI-DAS) consortium to advance goals in accessibility, usability, and integration of data from human islets isolated from donors with and without diabetes at the Albert...
Article
Full-text available
To standardize metabolomics data analysis and facilitate future computational developments, it is essential to have a set of well-defined templates for common data structures. Here we describe a collection of data structures involved in metabolomics data processing and illustrate how they are utilized in a full-featured Python-centric pipeline. We...
Article
Full-text available
The wide applications of liquid chromatography - mass spectrometry (LC-MS) in untargeted metabolomics demand an easy-to-use, comprehensive computational workflow to support efficient and reproducible data analysis. However, current tools were primarily developed to perform specific tasks in LC-MS based metabolomics data analysis. Here we introduce...
Article
Exposomics represents a systematic approach to investigate the etiology of diseases by formally integrating individuals’ entire environmental exposures and associated biological responses into the traditional genotype-phenotype framework. The field is largely enabled by various omics technologies which offer practical means to comprehensively measu...
Article
Full-text available
We introduce MetaboAnalyst version 6.0 as a unified platform for processing, analyzing, and interpreting data from targeted as well as untargeted metabolomics studies using liquid chromatography - mass spectrometry (LC–MS). The two main objectives in developing version 6.0 are to support tandem MS (MS2) data processing and annotation, as well as to...
Article
The growing number of multi-omics studies demands clear conceptual workflows coupled with easy-to-use software tools to facilitate data analysis and interpretation. This protocol covers three key components involved in multi-omics analysis, including single-omics data analysis, knowledge-driven integration using biological networks and data-driven...
Preprint
Full-text available
To standardize metabolomics data analysis and facilitate future computational developments, it is essential is have a set of well-defined templates for common data structures. Here we describe a collection of data structures involved in metabolomics data processing and illustrate how they are utilized in a full-featured Python-centric pipeline. We...
Article
Full-text available
Understanding species differences in sensitivity to toxicants is a critical issue in ecotoxicology. We recently established that double‐crested cormorant (DCCO) embryos are more sensitive than Japanese quail (JQ) to the developmental effects of ethinylestradiol (EE2). Here, we explore how this difference in sensitivity between species is reflected...
Article
The EcoToxChip project includes RNA‐sequencing data from experiments involving model (Japanese quail, fathead minnow, African clawed frog) and ecological (double‐crested cormorant, rainbow trout, northern leopard frog) species, at multiple life stages (whole embryo and adult), exposed to eight chemicals of environmental concern known to perturb a w...
Article
ExpressAnalyst is a web‐based platform that enables intuitive, end‐to‐end transcriptomics and proteomics data analysis. Users can start from FASTQ files, gene/protein abundance tables, or gene/protein lists. ExpressAnalyst will perform read quantification, gene expression table processing and normalization, differential expression analysis, or meta...
Article
Full-text available
Gut-microbiota derived metabolites are important regulators of host biology and metabolism. To understand the impacts of the microbial metabolite 4-cresol sulfate (4-CS) on four chronic diseases [type 2 diabetes mellitus, metabolic syndrome (MetS), non-alcoholic fatty liver disease, and chronic kidney disease (CKD)], we conducted association analys...
Article
Full-text available
Aging is the system-wide loss of homeostasis, eventually leading to death. There is growing evidence that the microbiome not only evolves with its aging host, but also directly affects aging via the modulation of metabolites involved in important cellular functions. The widely used model organism C. elegans exhibits high selectivity towards its nat...
Article
Full-text available
Metabolomics-based genome-wide association studies (mGWAS) are key to understanding the genetic regulations of metabolites in complex phenotypes. We previously developed mGWAS-Explorer 1.0 to link single-nucleotide polymorphisms (SNPs), metabolites, genes and phenotypes for hypothesis generation. It has become clear that identifying potential causa...
Preprint
Population level variation and molecular mechanisms behind insulin secretion in response to carbohydrate, protein, and fat remain uncharacterized despite ramifications for personalized nutrition. We now define prototypical insulin secretion dynamics in response to the three macronutrients in islets from 140 cadaveric donors, including those diagnos...
Article
Full-text available
The increasing application of RNA sequencing to study non-model species demands easy-to-use and efficient bioinformatics tools to help researchers quickly uncover biological and functional insights. We developed ExpressAnalyst (www.expressanalyst.ca), a web-based platform for processing, analyzing, and interpreting RNA-sequencing data from any euka...
Article
New approach methods (NAMs) are increasingly important to help accelerate the pace of ecological risk assessment and offer more ethical, affordable, and efficient alternatives to traditional toxicity tests. In the present study, we describe the development, technical characterization and initial testing of a toxicogenomics tool, EcoToxChip (384-wel...
Article
Full-text available
Microbiome studies have become routine in biomedical, agricultural and environmental sciences with diverse aims, including diversity profiling, functional characterization, and translational applications. The resulting complex, often multi-omics datasets demand powerful, yet user-friendly bioinformatics tools to reveal key patterns, important bioma...
Article
Full-text available
The 2nd CASMS conference was held virtually through Gather.Town platform from October 17 to 21, 2022, with a total of 363 registrants including an outstanding and diverse group of scientists at the forefront of their research fields from both academia and industry worldwide, especially in the US and China. The conference offered a 5-day agenda with...
Article
Full-text available
Staphylococcus aureus is one of the prevalent etiological agents of contagious bovine mastitis, causing a significant economic burden on the global dairy industry. Given the emergence of antibiotic resistance (ABR) and possible zoonotic spillovers, S aureus from mastitic cattle pose threat to both veterinary and public health. Therefore, assessment...
Article
Full-text available
The composition and metabolism of the human gut microbiota are strongly influenced by dietary complex glycans, which cause downstream effects on the physiology and health of hosts. Despite recent advances in our understanding of glycan metabolism by human gut bacteria, we still need methods to link glycans to their consuming bacteria. Here, we use...
Article
Full-text available
Background: Global or untargeted metabolomics is widely used to comprehensively investigate metabolic profiles under various pathophysiological conditions such as inflammations, infections, responses to exposures or interactions with microbial communities. However, biological interpretation of global metabolomics data remains a daunting task. Rece...
Article
Progress in mass spectrometry lipidomics has led to a rapid proliferation of studies across biology and biomedicine. These generate extremely large raw datasets requiring sophisticated solutions to support automated data processing. To address this, numerous software tools have been developed and tailored for specific tasks. However, for researcher...
Chapter
MicroRNAs exert their effects in the context of gene regulatory networks. The recent development of high-throughput experimental approaches and the growing availability of gene expression data have permitted comprehensive functional studies of miRNAs. However, the data interpretation is often challenging due to the fact that miRNAs not only act coo...
Preprint
Full-text available
The increasing application of RNA-seq to study non-model organisms demands easy-to-use and efficient bioinformatics tools to help researchers quickly uncover biological and functional insights from large datasets. Here, we present a unified software suite for processing, analyzing, and interpreting RNA-seq data from any eukaryotic species. This sui...
Article
The muscle quality of farmed fish has attracted widespread public attention. To understand a comprehensive molecular mechanism underlying the effects of artificial formula feed- (AF) and grass-feeding (GF) on muscle quality and growth of grass carp (Ctenopharyngodon idellus), muscular transcriptomics and proteomics of GF and AF C. idellus were char...
Article
Chemical risk assessment for avian species typically depends on information from toxicity tests performed in adult birds. Early‐life stage (ELS) toxicity tests have been proposed as an alternative, but incorporation of these data into existing frameworks will require knowledge about the similarities/differences between ELS and adult responses. The...
Poster
Full-text available
A unique Nano-enabled Antibacterial Combination Therapy (NACT) was developed to combat multi-drug resistant Salmonella-mediated intestinal infection. The NACT was efficient against intracellular Salmonella in Caco-2 cells and remediated intestinal infection in C. elegans. The NACT promises potential application in animal agriculture to counter the...
Article
Full-text available
Tens of thousands of single-nucleotide polymorphisms (SNPs) have been identified to be significantly associated with metabolite abundance in over 65 genome-wide association studies with metabolomics (mGWAS) to date. Obtaining mechanistic or functional insights from these associations for translational applications has become a key research area in...
Article
Liquid chromatography coupled with high-resolution mass spectrometry (LC–HRMS) has become a workhorse in global metabolomics studies with growing applications across biomedical and environmental sciences. However, outstanding bioinformatics challenges in terms of data processing, statistical analysis and functional interpretation remain critical ba...
Preprint
Full-text available
Liquid-chromatography coupled with high-resolution mass spectrometry (LC-HRMS) has become a workhorse in global metabolomics studies with growing applications across biomedical and environmental sciences. However, outstanding bioinformatics challenges in terms of data processing, statistical analysis and functional interpretation remain critical ba...
Preprint
Liquid-chromatography coupled with high-resolution mass spectrometry (LC-HRMS) has become a workhorse in global metabolomics studies with growing applications across biomedical and environmental sciences. However, outstanding bioinformatics challenges in terms of data processing, statistical analysis and functional interpretation remain critical ba...
Preprint
Full-text available
Liquid-chromatography coupled with high-resolution mass spectrometry (LC-HRMS) has become a workhorse in global metabolomics studies with growing applications across biomedical and environmental sciences. However, outstanding bioinformatics challenges in terms of data processing, statistical analysis and functional interpretation remain critical ba...
Article
Full-text available
Researchers are increasingly seeking to interpret molecular data within a multi-omics context to gain a more comprehensive picture of their study system. OmicsNet (www.omicsnet.ca) is a web-based tool developed to allow users to easily build, visualize, and analyze multi-omics networks to study rich relationships among lists of 'omics features of i...
Preprint
Full-text available
Liquid-chromatography coupled with high-resolution mass spectrometry (LC-HRMS) has become a workhorse in global metabolomics studies with growing applications across biomedical and environmental sciences. However, outstanding bioinformatics challenges in terms of data processing, statistical analysis and functional interpretation remain critical ba...
Article
Early-life stage (ELS) avian toxicity tests have been proposed as a more ethical alternative to traditional standardized tests with adult birds. At the same time, 'omics approaches are gaining traction in the field of avian toxicology, but little has been done to characterize the metabolome and transcriptome at different life stages. The present st...
Article
Full-text available
The copper redhorse (Moxostoma hubbsi) is an endangered fish that spawns exclusively in the Richelieu River (Quebec, Canada). Tributaries of the Richelieu are contaminated with high levels of current‐use pesticides, which may impact early life stage (ELS) copper redhorse and other native fishes. We assessed the effects of exposure to contaminated r...
Preprint
Full-text available
Toxicity testing is under transformation as it aims to harness the potential of New Approach Methods (NAMs) as alternative test methods that may be less resource-intensive (i.e., fewer animals, cheaper costs, quicker assays) than traditional approaches while also providing more data and information. While many stakeholders are of the opinion that t...
Article
Full-text available
The roles of the healthy microbiome on the host and the relationships between members of the microbiome remain to be fully characterized. Due to the complexity of the interactions between the mammalian microbiome and its host, the use of model organisms such as the nematode worm Caenorhabditis elegans is a promising strategy to study host-microbiom...
Article
Current ecotoxicity testing programs are impeded as they predominantly rely on slow and expensive animal tests measuring adverse outcomes. Therefore, new approach methodologies (NAMs) increasingly involve short-term mechanistic assays that employ molecular endpoints to predict adverse outcomes of regulatory relevance. This study aimed to elucidate...
Article
Full-text available
Crosstalk between the gut microbiome and the host plays an important role in animal development and health. Small compounds are key mediators in this host–gut microbiome dialogue. For instance, tryptophan metabolites, generated by biotransformation of tryptophan through complex host–microbiome co-metabolism can trigger immune, metabolic, and neuron...
Article
Functional peptides were obtained via enzymatic hydrolysis of smooth dogfish (Mustelus canis) skin. The enzyme-assisted process was optimized to achieve high yield of smooth dogfish skin peptides (SDSP). Fractions of SDSP (MW < 2 kDa, 2-5 kDa, 5-10 kDa and >10 kDa) showed in vitro antioxidant activities. The peptides <2 kDa (SDSP<2 kDa) significant...
Article
Full-text available
This proof-of-concept study characterizes the Japanese quail (Coturnix japonica) hepatic metabolome following exposure to benzo[a]pyrene, chlorpyrifos, ethinylestradiol, fluoxetine hydrochloride, hexabromocyclododecane, lead(II)nitrate, seleno-L-methionine, and trenbolone in embryos and adults. The analysis revealed effects on lipid metabolism foll...
Article
Current approaches in chemical hazard assessment face significant challenges because they rely on live animal testing, which is time-consuming, expensive, and ethically questionable. These concerns serve as an impetus to develop new approach methodologies (NAMs) that do not rely on live animal tests. This study explored a molecular benchmark dose (...
Article
Modern 21st century toxicity testing makes use of omics technologies to address critical questions in toxicology and chemical management. Of interest are questions relating to chemical mechanisms of toxicity, differences in species sensitivity, and translation of molecular effects to observable apical endpoints. Our study addressed these questions...
Article
Full-text available
Since its first release over a decade ago, the MetaboAnalyst web-based platform has become widely used for comprehensive metabolomics data analysis and interpretation. Here we introduce MetaboAnalyst version 5.0, aiming to narrow the gap from raw data to functional insights for global metabolomics based on high-resolution mass spectrometry (HRMS)....
Article
Full-text available
Data analysis and interpretation remain a critical bottleneck in current multi-omics studies. Here, we introduce OmicsAnalyst, a user-friendly, web-based platform that allows users to perform a wide range of well-established data-driven approaches for multi-omics integration, and visually explore their results in a clear and meaningful manner. To h...
Article
Full-text available
Background A healthy microbiome influences host physiology through a mutualistic relationship, which can be important for the host to cope with cellular stress by promoting fitness and survival. The mammalian microbiome is highly complex and attributing host phenotypes to a specific member of the microbiome can be difficult. The model organism Caen...
Article
There is increasing pressure to develop alternative ecotoxicological risk assessment approaches that do not rely on expensive, time-consuming, and ethically questionable live animal testing. This study aimed to develop a comprehensive early life stage toxicity pathway model for the exposure of fish to estrogenic chemicals that is rooted in mechanis...
Article
Full-text available
Computational time and cost remain a major bottleneck for RNA-seq data analysis of nonmodel organisms without reference genomes. To address this challenge, we have developed Seq2Fun, a novel, all-in-one, ultrafast tool to directly perform functional quantification of RNA-seq reads without transcriptome de novo assembly. The pipeline starts with raw...
Article
Full-text available
A growing number of software tools have been developed for metabolomics data processing and analysis. Many new tools are contributed by metabolomics practitioners who have limited prior experience with software development, and the tools are subsequently implemented by users with expertise that ranges from basic point-and-click data analysis to adv...
Article
Full-text available
The novel coronavirus SARS-CoV-2 has spread across the world since 2019, causing a global pandemic. The pathogenesis of the viral infection and the associated clinical presentations depend primarily on host factors such as age and immunity, rather than the viral load or its genetic variations. A growing number of omics studies have been conducted t...
Article
Full-text available
Arctic Mesorhizobium sp. N33 isolated from nodules of Oxytropis arctobia in Canada’s eastern Arctic has a growth temperature range from 0uC to 30C and is a well-known cold-adapted rhizobia. The key molecular mechanisms underlying cold adaptation in Arctic rhizobia remains totally unknown. Since the concentration and contents of metabolites are clos...
Article
Full-text available
Motivation: Transcriptomics dose-response analysis is a promising new approach method for toxicity testing. While international regulatory agencies have spent substantial effort establishing a standardized statistical approach, existing software that follows this approach is computationally inefficient and must be locally installed. Results: Fas...
Article
Full-text available
miRNet is an easy-to-use, web-based platform designed to help elucidate microRNA (miRNA) functions by integrating users' data with existing knowledge via network-based visual analytics. Since its first release in 2016, miRNet has been accessed by >20 000 researchers worldwide, with ∼100 users on a daily basis. While version 1.0 was focused primaril...
Article
Full-text available
Liquid chromatography coupled to high-resolution mass spectrometry platforms are increasingly employed to comprehensively measure metabolome changes in systems biology and complex diseases. Over the past decade, several powerful computational pipelines have been developed for spectral processing, annotation, and analysis. However, significant obsta...