Miao Yu

Miao Yu
Icahn School of Medicine at Mount Sinai | MSSM · Department of environmental medicine and public health

Doctor of Philosophy

About

58
Publications
10,057
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
880
Citations
Introduction
Mass spectrum data analysis for metabolomics and exposome study/in vivo solid phase micro-extraction/environmental statistics
Additional affiliations
April 2022 - present
The Jackson Laboratory
Position
  • Associate Computational Scientist
September 2018 - April 2022
Icahn School of Medicine at Mount Sinai
Position
  • PostDoc Position
August 2016 - September 2018
University of Waterloo
Position
  • PostDoc Position
Education
August 2010 - June 2016
Chinese Academy of Sciences
Field of study
  • Environmental Sciences
September 2006 - June 2010
Shandong University
Field of study
  • Environmental Sciences

Publications

Publications (58)
Article
Full-text available
Untargeted metabolomics analysis captures chemical reactions among small molecules. Common mass spectrometry-based metabolomics workflows first identify the small molecules significantly associated with the outcome of interest, then begin exploring their biochemical relationships to understand biological fate or impact. We suggest an alternative by...
Article
Full-text available
Unknown features in untargeted metabolomics and non-targeted analysis (NTA) are identified using fragment ions from MS/MS spectra to predict the structures of the unknown compounds. The precursor ion selected for fragmentation is commonly performed using data dependent acquisition (DDA) strategies or following statistical analysis using targeted MS...
Article
Full-text available
Background: Teeth have unique histology that make this biomatrix a time-capsule for retrospective exposure analysis of fetal and early life. However, most analytic methods require pulverizing the whole tooth, which eliminates exposure timing information. Further, the range of chemicals and endogenous exposures that can be measured in teeth has yet...
Article
Full-text available
Solid-phase microextraction (SPME) is a well-established sample-preparation technique for environmental studies. The application of SPME has extended from the headspace extraction of volatile compounds to the capture of active components in living organisms via the direct immersion of SPME probes into the tissue (in vivo SPME). The development of b...
Preprint
Full-text available
Motivation Unknown features in untargeted metabolomics and non-targeted analysis (NTA) are identified using fragment ions from MS/MS spectra to predict the structures of the unknown compounds. The precursor ion selected for fragmentation is commonly performed using data dependent acquisition (DDA) strategies or following statistical analysis using...
Preprint
Motivation Unknown features in untargeted metabolomics and non-targeted analysis (NTA) are identified using fragment ions from MS/MS spectra to predict the structures of the unknown compounds. The precursor ion selected for fragmentation is commonly performed using data dependent acquisition (DDA) strategies or following statistical analysis using...
Article
Full-text available
IntroductionPsoriatic arthritis (PsA), an inflammatory arthritis that develops in individuals with psoriasis, is associated with reduced quality of life. Identifying biomarkers associated with development of PsA as well as with PsA disease activity may help management of psoriatic disease.Objectives To use metabolomic fingerprinting to determine po...
Preprint
Full-text available
The exposome reflects the many exposures to various factors across the life-course that can affect health. Sensitive techniques like metabolomics can reveal the underlying molecular basis linking exposures to disease and generate hypotheses for future quantitative toxicological studies. Current applications of metabolomics are primarily to identify...
Article
Full-text available
A Correction to this paper has been published: https://doi.org/10.1038/s42004-021-00479-1
Preprint
p>Unknown features in untargeted metabolomics and non-targeted analysis (NTA) are identified using fragment ions from MS/MS spectra to predict the structures of the unknown compounds. The precursor ion selected for fragmentation is commonly performed using data dependent acquisition (DDA) strategies or following statistical analysis using targeted...
Preprint
Full-text available
Unknown features in untargeted metabolomics and non-targeted analysis (NTA) are identified using fragment ions from MS/MS spectra to predict the structures of the unknown compounds. The precursor ion selected for fragmentation is commonly performed using data dependent acquisition (DDA) strategies or following statistical analysis using targeted MS...
Article
Unstable tissue components (metabolites) are not easily captured and evaluated by traditional metabolomics methods. In this study, a comprehensive investigation of various sampling methods and storage conditions on the metabolomic profile of fish muscle was performed based on in vivo and ex vivo sampling. The GlobalStd algorithm and structure/react...
Article
Archived dried blood spots (DBS) following newborn screening are an attractive resource for interrogating early-life biology using untargeted metabolomics. Therefore, they have the potential to substantially aid etiological studies, particularly for rare and low-frequency childhood diseases and disorders. However, metabolite quantification in DBS i...
Article
Short chain and medium chain chlorinated paraffins (SCCPs and MCCPs) are mixtures of complex chemical compounds with intensive usage. They are frequently detected in various environmental samples. However, the interaction between CPs and plants, especially the biotransformation behaviors of CPs within plants are poorly understood. In this study, 1,...
Article
Analysis of brain samples obtained post mortem remains a standard approach in neuroscience, despite often being sub-optimal for inferring roles of small molecules in the pathophysiology of brain diseases. Sample collection and preservation further hinders conclusive interpretation of biomarker analysis in autopsy samples. We investigate purely deat...
Preprint
Full-text available
Background Glyphosate-based herbicides (GBHs) have previously been considered safe to humans. However, emerging evidence indicates that GBHs can disrupt the host microbiota and influence human health. To build upon our previous findings of gut dysbiosis and other adverse health effects resulting from low-dose exposure of GBHs (glyphosate and Roundu...
Chapter
Solid-phase microextraction (SPME) is a well-established sample preparation technique in the field of environmental and toxicological studies. The application of SPME has extended from the headspace extraction of volatile compounds to the capturing of short-lived and unstable components of the ecosystem extracted from the living organism via direct...
Preprint
Full-text available
Batch effects will influence the interpretation of metabolomics data. In order to avoid misleading results, batch effects should be corrected and normalized prior to statistical analysis. Metabolomics studies are usually performed without targeted compounds (e.g., internal standards) and it is a challenging task to validate batch effects correction...
Preprint
Chemical reactions among small molecules enable untargeted metabolomics analysis, in which small molecules within tissue samples are identified through high-throughput assays. In standard mass spectrometry-based metabolomics, first significant small molecules are identified, then their biochemical relationships are probed to reveal biological fate...
Article
Tetrabromobisphenol A (TBBPA) is the most widely used brominated flame retardant (BFR) and it bioaccumulates throughout the food chains. Its fate in the first trophic level, plants, is of special interest. In this study, a four-day hydroponic exposure of TBBPA to pumpkin seedlings was conducted at a concentration of 1 μmol L-1. A non-target screeni...
Article
Various environmental studies have employed the biomonitoring of fish in their aquatic ecosystems in order to identify potential metabolic responses to the exposome. In this study, we applied in vivo solid-phase microextraction (SPME) to perform non-lethal sampling on the muscle tissue of living fish to extract toxicants and various endogenous meta...
Code
Paired mass distance (PMD) analysis proposed in Yu, Olkowicz and Pawliszyn (2018) <doi:10.1016/j.aca.2018.10.062> for gas/liquid chromatography–mass spectrometry (GC/LC-MS) based non-targeted analysis. PMD analysis including GlobalStd algorithm and structure/reaction directed analysis. GlobalStd algorithm could found independent peaks in m/z-retent...
Article
In LC-MS based untargeted analysis, data is collected at the peak or ion level, although the investigated biochemistry processes occur at the compound or reaction level. To this end, the presence of redundancy peaks such as co-eluted peaks, multi-chargers, adducts, neutral loss, isotopologues, and fragments ions often muddle subsequent statistical...
Article
In vivo solid-phase microextraction (SPME) of endogenous compounds may depict changes in the biochemical pathways in organisms that have been affected by various stimuli, such as environmental pollutants. In this paper, we use low-invasive in vivo SPME to analyze metabolic profile changes in the muscle tissue of living fish that have been exposed t...
Article
As the metabolites of tetrabromobisphenol A (TBBPA), tetrabromobisphenol A mono- and di-methyl ethers (TBBPA MME and TBBPA DME) have been detected in various environmental media. However, knowledge of the contribution of plants to their environmental fates, especially to the interactions between TBBPA DME and TBBPA, is quite limited. In this study,...
Article
Full-text available
Low-invasive in vivo solid-phase microextraction (SPME) was used to investigate the lipid profiles of muscle tissue of living fish. Briefly, mixed mode SPME fibers were inserted into the muscle for 20 min extraction, and then the fibers were desorbed in an optimal mixture of solvents. The obtained lipid profile was then compared and contrasted to t...
Article
Biotransformation of organic pollutants may result in the formation of oxidation products more toxic than the parent contaminants. However, to trace and identify those products, and the metabolic pathways involved in their formation, is still challenging within complex environmental samples. We applied stable isotope-assisted metabolomics (SIAM) to...
Article
Airborne particulate pollution is a critical environmental problem affecting human health and sustainable development. Understanding of the sources of aerosol particles is of extreme importance for regional air pollution control. Here we show that natural Si isotopic signature can be used as a new tool to elucidate the sources of fine particulate m...
Article
Hydroxylated (OH-) and methoxylated (MeO-) polybrominated diphenyl ethers (PBDEs) have been identified ubiquitous in wildlife and environment. However, understanding on their trophic accumulation and human exposure was hitherto limited. In this study, the occurrences and trophic behaviors were demonstrated for OH- and MeO-PBDEs using the biota samp...
Article
Hexachlorobutadiene (HCBD) has been listed as persistent organic pollutants (POPs) in the Stockholm Convention, and is now drawing more and more research interests. However, the understanding on its bioaccumulation, especially in plants, is still very limited. In this work, the behavior of HCBD in aqueous solution and pumpkin seedlings were studied...
Article
The on-site screening of target analytes in complex matrices, such as biofluids and food specimens, not only requires reliable and portable analytical instrumentation, but also solvent-free and easy-to-use sampling/sample preparation approaches that allow analytes of interest to be isolated from such matrices. The integration of sampling devices wi...
Article
Full-text available
To date, solid-phase microextraction (SPME) fibers used for in-vivo bio-analysis can be too fragile and flexible, which limits suitability for direct tissue sampling. As a result, these devices often require a sheathing needle to pre-puncture robust sample matrices and protect the extraction phase from mechanical damage. To address this limitation,...
Article
Full-text available
In view of the final destination of nanomaterials, the water system would be the important sink. However, the environmental behavior of nanomaterials is rather confusing due to the complexity of the real environment. In this study, a fresh water ecosystem, including water, sediment, water lettuce, water silk, Asian clam, snail, water flea, the Japa...
Article
F-53B, the commercial product of chlorinated polyfluoroalkyl ether sulfonic acids (Cl-PFESAs), has been used in Chinese chrome plating industry for 30 years, and was recently identified in the environment, which caused great concerns. So far, limited investigations have been performed on their environmental occurrence, fate and impact. In this stud...
Article
Short chain chlorinated paraffins (SCCPs) are ubiquitously present as persistent organic pollutants in the environment. However, little information on the interaction of SCCPs with plants is currently available. In this work, young pumpkin plants (Cucurbita maxima × C. Moschata) were hydroponically exposed to the congener of chlorinated decane, 1,2...
Code
Gas Chromatography-Mass Spectrometer(GC-MS) Data Analysis for Environmental Science. This package covered topics such as raw data process, molecular isotope ratio, matrix effects, etc. in environmental analysis. This package has been published on CRAN(https://cran.r-project.org/web/packages/enviGCMS/index.html)
Article
A reliable and effective method for simultaneous analysis of trace amount of bromophenols (BPs) in various aqueous samples was developed in this study. The aqueous samples must be acidified after sampling to prevent the fast degradation of bromophenols. Solid-phase extraction was chosen to extract and purify the water samples. High performance liqu...
Article
The uncertainties in analysis of trace environmental pollutants may come from sample matrix and sample pretreatment process. In this study, a boundary model was developed based on the visualized data of mass spectrometry to evaluate the influences from sample matrix and pretreatment process. The factors affecting the pretreatment procedures, such a...
Article
Tetrabromobisphenol-A/S (TBBPA/S) analogs have raised substantial concern because of their adverse effects and potential bioaccumulative properties, such as TBBPA bis(allyl ether) (TBBPA-BAE) and TBBPA bis(2,3-dibromopropyl ether) (TBBPA-BDBPE). In this study, a comprehensive method for simultaneous determination of TBBPA/S and nine novel analogs,...
Article
It is hard to quantify the trace pollutants in the environment without the corresponding reference standards. Structure identifications of unknown organic pollutants are thus of great importance in environmental analysis. As for polybrominated diphenyl ethers (PBDE) with one substituent of methoxyl group, there are 837 congeners, but only 32 standa...
Article
Real time online calibration of mass shift and intensity fluctuation to improve the accuracy of measurements for identification and quantitation in trace mass spectrometric analysis was demonstrated using extractive electrospray ionization mass spectrometry (EESI-MS). The signals of authentic compounds (e.g., lysine (Lys), proline (Pro) and histidi...
Article
Full-text available
Identification of novel brominated contaminants in the environment, especially the derivatives and byproducts of brominated flame retardants (BFRs), has become a wide concern because of their adverse effects on human health. Herein, we qualitatively and quantitatively identified three byproducts of tetrabromobisphenol-S bis(2,3-dibromopropyl ether)...
Article
Relationships among polybrominated diphenyl ethers (PBDEs), hydroxylated PBDEs (OH-PBDEs), and methoxylated PBDEs (MeO-PBDEs) have attracted considerable scientific interest. However, few studies have focused on the in vivo metabolism of these compounds by intact whole plants. In this work, interconversion between OH-tetraBDEs and MeO-tetraBDEs in...
Article
Although hexachlorobutadiene (HCBD) was recently proposed as a candidate persistent organic pollutant (POP) under the Stockholm Convention, information about its environmental levels and distributions is still very limited. In this work, HCBD was determined in the sewage sludge from 37 wastewater treatment plants (WWTPs) in 23 cities and 17 soils n...
Code
This package was created to analyze multi-level one-way experimental designs. It is designed to handle vectorized observation and factor data where there are unequal sample sizes and population variance homogeneity can not be assumed. To conduct the Gabriel test, create two vectors: one for your observations and one for the factor level of each obs...
Article
There is currently limited knowledge on the PBDEs metabolism in plants although they could play an important role in the environmental transformation of these persistent organic pollutants. In this study, pumpkin (Cucurbita maxima × C. moschata) was chosen as the model to understand the fate of BDE-28 in plants. The metabolites MeO-tri-BDEs, OH-tri...
Article
A new method using ultrasonic extraction and solid phase extraction (SPE) clean-up pretreatments was developed for the analysis of mono-, di- and tri-substituted polyfluoroalkyl phosphates (abbreviated as mono-PAPs, di-PAPs and tri-PAPs) and perfluorinated phosphonic acids (PFPAs) in sludge from wastewater treatment plants (WWTPs). For the ultrason...
Article
Tetrabromobisphenol A (TBBPA) is one of the most widely used brominated flame retardants (BFRs) and has been frequently detected in the environment and biota. Recent studies have found that derivatives of TBBPA, such as TBBPA bis(allyl) ether (TBBPA BAE) and TBBPA bis(2,3-dibromopropyl) ether (TBBPA BDBPE) are present in various environmental compa...
Article
Polybrominated diphenyl ethers (PBDEs) are widely distributed persistent organic pollutants. In vitro and in vivo research using various animal models have shown that PBDEs might be transformed to hydroxylated PBDEs, but there are few studies on in vivo metabolism of PBDEs by intact whole plants. In this research, pumpkin plants (Cucurbita maxima ×...

Network

Cited By

Projects

Projects (5)
Project
Find the molecular (metabolites, protein, gene) linking exposure(s) and other metabolites by network analysis. Test the health related sensitivity of those gatekeepers. Causal inference for the mediation roles of gatekeepers between exposome and health outcome.
Project
Fundamental and applications of mass spectrometry based reactomics
Project
Investigation of storage condition on in vivo SPME sampling