Publications
Highlighted
Web-based multi-omics integration using the Analyst software suite
Nature Protocols
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14 Feb 2024
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doi:10.1038/s41596-023-00950-4
A protocol for multi-omics integration with user-friendly web-based tools that enable researchers to efficiently integrate different data types for scientific discovery.
Evaluating batch correction methods for image-based cell profiling
Nature Communications
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02 Aug 2024
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doi:10.1038/s41467-024-50613-5
All
2025
Linking molecular pathways and islet cell dysfunction in human type 1 diabetes
Cold Spring Harbor Laboratory
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21 Feb 2025
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doi:10.1101/2025.02.20.639325
Cell Painting for cytotoxicity and mode-of-action analysis in primary human hepatocytes
Cold Spring Harbor Laboratory
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24 Jan 2025
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doi:10.1101/2025.01.22.634152
2024
Bioinformatic workflows for deriving transcriptomic points of departure: current status, data gaps, and research priorities
Toxicological Sciences
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05 Nov 2024
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doi:10.1093/toxsci/kfae145
HumanIslets.com: Improving accessibility, integration, and usability of human research islet data
Cell Metabolism
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01 Oct 2024
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doi:10.1016/j.cmet.2024.09.001
The DIKW of transcriptomics in ecotoxicology: extracting information, knowledge, and wisdom from big data
Environmental Toxicology and Chemistry
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12 Aug 2024
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doi:10.1002/etc.5954
Evaluating batch correction methods for image-based cell profiling
Nature Communications
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02 Aug 2024
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doi:10.1038/s41467-024-50613-5
Inconsistent Transcriptomic Responses to Hexabromocyclododecane in Japanese Quail: A Comparative Analysis of Results From Four Different Study Designs
Environmental Toxicology and Chemistry
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29 Jul 2024
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doi:10.1002/etc.5955
Proteomic predictors of individualized nutrient-specific insulin secretion in health and disease
Cell Metabolism
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01 Jul 2024
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doi:10.1016/j.cmet.2024.06.001
Maternal gastrointestinal nematode infection alters hippocampal neuroimmunity, promotes synaptic plasticity, and improves resistance to direct infection in offspring
Scientific Reports
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10 May 2024
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doi:10.1038/s41598-024-60865-2
Scaled mass index derived from aerial photogrammetry associated with predicted metabolic pathway disruptions in free-ranging St. Lawrence Estuary belugas
Frontiers in Marine Science
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19 Apr 2024
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doi:10.3389/fmars.2024.1360374
Web-based multi-omics integration using the Analyst software suite
Nature Protocols
·
14 Feb 2024
·
doi:10.1038/s41596-023-00950-4
A protocol for multi-omics integration with user-friendly web-based tools that enable researchers to efficiently integrate different data types for scientific discovery.
A data-centric perspective on exposomics data analysis
Exposome
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01 Jan 2024
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doi:10.1093/exposome/osae005
2023
Comparing transcriptomic responses to chemicals across six species using the EcoToxChip RNASeq database
Environmental Toxicology and Chemistry
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12 Dec 2023
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doi:10.1002/etc.5803
Hepatic Transcriptomic Responses to Ethinylestradiol in Embryonic Japanese Quail and Double-Crested Cormorant
Environmental Toxicology and Chemistry
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01 Dec 2023
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doi:10.1002/etc.5811
Using ExpressAnalyst for Comprehensive Gene Expression Analysis in Model and Non‐Model Organisms
Current Protocols
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01 Nov 2023
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doi:10.1002/cpz1.922
ExpressAnalyst: A unified platform for RNA-sequencing analysis in non-model species
Nature Communications
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24 May 2023
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doi:10.1038/s41467-023-38785-y
MicrobiomeAnalyst 2.0: comprehensive statistical, functional and integrative analysis of microbiome data
Nucleic Acids Research
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11 May 2023
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doi:10.1093/nar/gkad407
2022
Transcriptomic points of departure calculated from human intestinal cells exposed to dietary nanoparticles
Food and Chemical Toxicology
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01 Dec 2022
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doi:10.1016/j.fct.2022.113501
A Systematic Review of Mercury Exposures from Skin-Lightening Products
Environmental Health Perspectives
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01 Nov 2022
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doi:10.1289/ehp10808
Characterizing Variability and Uncertainty Associated with Transcriptomic Dose–Response Modeling
Environmental Science & Technology
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21 Oct 2022
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doi:10.1021/acs.est.2c04665
Using MetaboAnalyst 5.0 for LC–HRMS spectra processing, multi-omics integration and covariate adjustment of global metabolomics data
Nature Protocols
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17 Jun 2022
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doi:10.1038/s41596-022-00710-w
Transcriptomic Points of Departure Calculated from Rainbow Trout Gill, Liver, and Gut Cell Lines Exposed to Methylmercury and Fluoxetine
Environmental Toxicology and Chemistry
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27 May 2022
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doi:10.1002/etc.5395
Exposure to Contaminated River Water is Associated with Early Hatching and Dysregulation of Gene Expression in Early Life Stages of the Endangered Copper Redhorse (Moxostoma hubbsi)
Environmental Toxicology and Chemistry
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27 May 2022
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doi:10.1002/etc.5391
OmicsNet 2.0: a web-based platform for multi-omics integration and network visual analytics
Nucleic Acids Research
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26 May 2022
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doi:10.1093/nar/gkac376
Comparative analysis of transcriptomic points-of-departure (tPODs) and apical responses in embryo-larval fathead minnows exposed to fluoxetine
Environmental Pollution
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01 Feb 2022
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doi:10.1016/j.envpol.2021.118667
2021
EcoToxXplorer: Leveraging Design Thinking to Develop a Standardized Web-Based Transcriptomics Analytics Platform for Diverse Users
Environmental Toxicology and Chemistry
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11 Nov 2021
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doi:10.1002/etc.5251
Assessing the Toxicity of 17α-Ethinylestradiol in Rainbow Trout Using a 4-Day Transcriptomics Benchmark Dose (BMD) Embryo Assay
Environmental Science & Technology
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22 Jul 2021
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doi:10.1021/acs.est.1c02401
Using Transcriptomics and Metabolomics to Understand Species Differences in Sensitivity to Chlorpyrifos in Japanese Quail and Double-Crested Cormorant Embryos
Environmental Toxicology and Chemistry
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22 Jul 2021
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doi:10.1002/etc.5174
OmicsAnalyst: a comprehensive web-based platform for visual analytics of multi-omics data
Nucleic Acids Research
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21 May 2021
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doi:10.1093/nar/gkab394
Ultrafast functional profiling of RNA-seq data for nonmodel organisms
Genome Research
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17 Mar 2021
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doi:10.1101/gr.269894.120
2020
FastBMD: an online tool for rapid benchmark dose–response analysis of transcriptomics data
Bioinformatics
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06 Aug 2020
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doi:10.1093/bioinformatics/btaa700
Selenium and stable mercury isotopes provide new insights into mercury toxicokinetics in pilot whales
Science of The Total Environment
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01 Mar 2020
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doi:10.1016/j.scitotenv.2019.136325
EcoToxModules: Custom Gene Sets to Organize and Analyze Toxicogenomics Data from Ecological Species
Environmental Science & Technology
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28 Feb 2020
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doi:10.1021/acs.est.9b06607
2019
T1000: A reduced toxicogenomics gene set for improved decision making
PeerJ
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03 Jul 2019
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doi:10.7287/peerj.preprints.27839
NetworkAnalyst 3.0: a visual analytics platform for comprehensive gene expression profiling and meta-analysis
Nucleic Acids Research
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01 Apr 2019
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doi:10.1093/nar/gkz240
Organ-specific differences in mercury speciation and accumulation across ringed seal (Phoca hispida) life stages
Science of The Total Environment
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01 Feb 2019
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doi:10.1016/j.scitotenv.2018.09.299
2016
Environmental Origins of Methylmercury Accumulated in Subarctic Estuarine Fish Indicated by Mercury Stable Isotopes
Environmental Science & Technology
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19 Oct 2016
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doi:10.1021/acs.est.6b03206