Research

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Open collaborative writing with Manubot

Daniel S. Himmelstein, Vincent Rubinetti, David R. Slochower, Dongbo Hu, Venkat S. Malladi, Casey S. Greene, Anthony Gitter

PLOS Computational Biology  ·  04 Dec 2020  ·  doi:10.1371/journal.pcbi.1007128

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2024

The DIKW of Transcriptomics in Ecotoxicology: Extracting Information, Knowledge, and Wisdom From Big Data

Jessica A. Head, Jessica D. Ewald, Niladri Basu

Environmental Toxicology and Chemistry  ·  12 Aug 2024  ·  doi:10.1002/etc.5954

Evaluating batch correction methods for image-based cell profiling

John Arevalo, Ellen Su, Jessica D. Ewald, Robert van Dijk, Anne E. Carpenter, Shantanu Singh

Nature Communications  ·  02 Aug 2024  ·  doi:10.1038/s41467-024-50613-5

Proteomic predictors of individualized nutrient-specific insulin secretion in health and disease

Jelena Kolic, WenQing Grace Sun, Haoning Howard Cen, Jessica D. Ewald, Jason C. Rogalski, …, Francis C. Lynn, Anna L. Gloyn, Leonard J. Foster, Patrick E. MacDonald, James D. Johnson

Cell Metabolism  ·  01 Jul 2024  ·  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

Sophia C. Noel, Jeanne F. Madranges, Jean-David M. Gothié, Jessica Ewald, Austen J. Milnerwood, Timothy E. Kennedy, Marilyn E. Scott

Scientific Reports  ·  10 May 2024  ·  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

Meredith Sherrill, Alexandre Bernier-Graveline, Jessica Ewald, Zhiqiang Pang, Michel Moisan, Mathieu Marzelière, Maris Muzzy, Tracy A. Romano, Robert Michaud, Jonathan Verreault

Frontiers in Marine Science  ·  19 Apr 2024  ·  doi:10.3389/fmars.2024.1360374

Web-based multi-omics integration using the Analyst software suite

Jessica D. Ewald, Guangyan Zhou, Yao Lu, Jelena Kolic, Cara Ellis, James D. Johnson, Patrick E. Macdonald, Jianguo Xia

Nature Protocols  ·  14 Feb 2024  ·  doi:10.1038/s41596-023-00950-4

Hepatic Transcriptomic Responses to Ethinylestradiol in Embryonic Japanese Quail and Double‐Crested Cormorant

Yeon‐Seon Jeon, Jonathan Sangiovanni, Emily Boulanger, Doug Crump, Peng Liu, Jessica Ewald, Niladri Basu, Jianguo Xia, Markus Hecker, Jessica Head

Environmental Toxicology and Chemistry  ·  25 Jan 2024  ·  doi:10.1002/etc.5811

Comparing Transcriptomic Responses to Chemicals Across Six Species Using the EcoToxChip RNASeq Database

Krittika Mittal, Jessica Ewald, Doug Crump, Jessica Head, Markus Hecker, Natacha Hogan, Jianguo Xia, Niladri Basu

Environmental Toxicology and Chemistry  ·  17 Jan 2024  ·  doi:10.1002/etc.5803

A data-centric perspective on exposomics data analysis

Le Chang, Jessica Ewald, Fiona Hui, Stéphane Bayen, Jianguo Xia

Exposome  ·  01 Jan 2024  ·  doi:10.1093/exposome/osae005

2023

Using ExpressAnalyst for Comprehensive Gene Expression Analysis in Model and Non‐Model Organisms

Jessica Ewald, Guangyan Zhou, Yao Lu, Jianguo Xia

Current Protocols  ·  01 Nov 2023  ·  doi:10.1002/cpz1.922

ExpressAnalyst: A unified platform for RNA-sequencing analysis in non-model species

Peng Liu, Jessica Ewald, Zhiqiang Pang, Elena Legrand, Yeon Seon Jeon, …, Orcun Hacariz, Guangyan Zhou, Jessica A. Head, Niladri Basu, Jianguo Xia

Nature Communications  ·  24 May 2023  ·  doi:10.1038/s41467-023-38785-y

MicrobiomeAnalyst 2.0: comprehensive statistical, functional and integrative analysis of microbiome data

Yao Lu, Guangyan Zhou, Jessica Ewald, Zhiqiang Pang, Tanisha Shiri, Jianguo Xia

Nucleic Acids Research  ·  11 May 2023  ·  doi:10.1093/nar/gkad407

2022

Transcriptomic points of departure calculated from human intestinal cells exposed to dietary nanoparticles

Ke Xu, Krittika Mittal, Jessica Ewald, Samuel Rulli, Jennifer L. Jakubowski, Saji George, Niladri Basu

Food and Chemical Toxicology  ·  01 Dec 2022  ·  doi:10.1016/j.fct.2022.113501

A unified platform for RNA-seq analysis in non-model species

Peng Liu, Jessica Ewald, Elena Legrand, Yeon-Seon Jeon, Jonathan Sangiovanni, …, Zhiqiang Pang, Guangyan Zhou, Jessica Head, Niladri Basu, Jianguo Xia

Research Square Platform LLC  ·  08 Nov 2022  ·  doi:10.21203/rs.3.rs-2187066/v1

A Systematic Review of Mercury Exposures from Skin-Lightening Products

Ashley Bastiansz, Jessica Ewald, Verónica Rodríguez Saldaña, Andrea Santa-Rios, Niladri Basu

Environmental Health Perspectives  ·  01 Nov 2022  ·  doi:10.1289/ehp10808

Characterizing Variability and Uncertainty Associated with Transcriptomic Dose–Response Modeling

Jessica D. Ewald, Niladri Basu, Doug Crump, Emily Boulanger, Jessica Head

Environmental Science & Technology  ·  21 Oct 2022  ·  doi:10.1021/acs.est.2c04665

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)

H. Marchand, B. D. Barst, E. Boulanger, N. Vachon, M. Houde, …, P. Liu, J. D. Ewald, S. Bayen, L. Liu, J. A. Head

Environmental Toxicology and Chemistry  ·  30 Jun 2022  ·  doi:10.1002/etc.5391

Transcriptomic Points of Departure Calculated from Rainbow Trout Gill, Liver, and Gut Cell Lines Exposed to Methylmercury and Fluoxetine

Krittika Mittal, Jessica Ewald, Niladri Basu

Environmental Toxicology and Chemistry  ·  28 Jun 2022  ·  doi:10.1002/etc.5395

Using MetaboAnalyst 5.0 Part I: Optimizing parameters for LC-HRMS spectra processing

Zhiqiang Pang, Guangyan Zhou, Jessica Ewald, Le Chang, Orcun Hacariz, Niladri Basu, Jianguo Xia

Research Square Platform LLC  ·  17 Jun 2022  ·  doi:10.21203/rs.3.pex-1917/v1

Using MetaboAnalyst 5.0 for LC–HRMS spectra processing, multi-omics integration and covariate adjustment of global metabolomics data

Zhiqiang Pang, Guangyan Zhou, Jessica Ewald, Le Chang, Orcun Hacariz, Niladri Basu, Jianguo Xia

Nature Protocols  ·  17 Jun 2022  ·  doi:10.1038/s41596-022-00710-w

OmicsNet 2.0: a web-based platform for multi-omics integration and network visual analytics

Guangyan Zhou, Zhiqiang Pang, Yao Lu, Jessica Ewald, Jianguo Xia

Nucleic Acids Research  ·  26 May 2022  ·  doi:10.1093/nar/gkac376

Comparative analysis of transcriptomic points-of-departure (tPODs) and apical responses in embryo-larval fathead minnows exposed to fluoxetine

Alper James G. Alcaraz, Shaina Baraniuk, Kamil Mikulášek, Bradley Park, Taylor Lane, …, Doug Crump, Niladri Basu, Natacha Hogan, Markus Brinkmann, Markus Hecker

Environmental Pollution  ·  01 Feb 2022  ·  doi:10.1016/j.envpol.2021.118667

2021

EcoToxXplorer: Leveraging Design Thinking to Develop a Standardized Web‐Based Transcriptomics Analytics Platform for Diverse Users

Othman Soufan, Jessica Ewald, Guangyan Zhou, Orcun Hacariz, Emily Boulanger, …, Markus Hecker, Doug Crump, Jessica Head, Niladri Basu, Jianguo Xia

Environmental Toxicology and Chemistry  ·  29 Dec 2021  ·  doi:10.1002/etc.5251

Using Transcriptomics and Metabolomics to Understand Species Differences in Sensitivity to Chlorpyrifos in Japanese Quail and Double‐Crested Cormorant Embryos

Jean‐Pierre Desforges, Elena Legrand, Emily Boulager, Peng Liu, Jianguo Xia, …, Jessica Ewald, Niladri Basu, Markus Hecker, Jessica Head, Doug Crump

Environmental Toxicology and Chemistry  ·  15 Sep 2021  ·  doi:10.1002/etc.5174

Assessing the Toxicity of 17α-Ethinylestradiol in Rainbow Trout Using a 4-Day Transcriptomics Benchmark Dose (BMD) Embryo Assay

Alper James G. Alcaraz, Kamil Mikulášek, David Potěšil, Bradley Park, Kamran Shekh, …, David Schneider, Jianguo Xia, Doug Crump, Niladri Basu, Markus Hecker

Environmental Science & Technology  ·  22 Jul 2021  ·  doi:10.1021/acs.est.1c02401

OmicsAnalyst: a comprehensive web-based platform for visual analytics of multi-omics data

Guangyan Zhou, Jessica Ewald, Jianguo Xia

Nucleic Acids Research  ·  21 May 2021  ·  doi:10.1093/nar/gkab394

Ultrafast functional profiling of RNA-seq data for nonmodel organisms

Peng Liu, Jessica Ewald, Jose Hector Galvez, Jessica Head, Doug Crump, Guillaume Bourque, Niladri Basu, Jianguo Xia

Genome Research  ·  17 Mar 2021  ·  doi:10.1101/gr.269894.120

2020

Open collaborative writing with Manubot

Daniel S. Himmelstein, Vincent Rubinetti, David R. Slochower, Dongbo Hu, Venkat S. Malladi, Casey S. Greene, Anthony Gitter

PLOS Computational Biology  ·  04 Dec 2020  ·  doi:10.1371/journal.pcbi.1007128

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Manubot

Manuscript Source

Website

open-science collaboration

FastBMD: an online tool for rapid benchmark dose–response analysis of transcriptomics data

Jessica Ewald, Othman Soufan, Jianguo Xia, Niladri Basu

Bioinformatics  ·  06 Aug 2020  ·  doi:10.1093/bioinformatics/btaa700

Selenium and stable mercury isotopes provide new insights into mercury toxicokinetics in pilot whales

Miling Li, C. Alicia Juang, Jessica D. Ewald, Runsheng Yin, Bjarni Mikkelsen, David P. Krabbenhoft, Prentiss H. Balcom, Clifton Dassuncao, Elsie M. Sunderland

Science of The Total Environment  ·  01 Mar 2020  ·  doi:10.1016/j.scitotenv.2019.136325

EcoToxModules: Custom Gene Sets to Organize and Analyze Toxicogenomics Data from Ecological Species

Jessica D. Ewald, Othman Soufan, Doug Crump, Markus Hecker, Jianguo Xia, Niladri Basu

Environmental Science & Technology  ·  28 Feb 2020  ·  doi:10.1021/acs.est.9b06607

Constructing knowledge graphs and their biomedical applications

David N. Nicholson, Casey S. Greene

Computational and Structural Biotechnology Journal  ·  01 Jan 2020  ·  doi:10.1016/j.csbj.2020.05.017

2019

T1000: A reduced toxicogenomics gene set for improved decision making

Othman Soufan, Jessica Ewald, Charles Viau, Doug Crump, Markus Hecker, Niladri Basu, Jianguo Xia

PeerJ  ·  03 Jul 2019  ·  doi:10.7287/peerj.preprints.27839v1

T1000: A reduced toxicogenomics gene set for improved decision making

Othman Soufan, Jessica Ewald, Charles Viau, Doug Crump, Markus Hecker, Niladri Basu, Jianguo Xia

PeerJ  ·  03 Jul 2019  ·  doi:10.7287/peerj.preprints.27839

NetworkAnalyst 3.0: a visual analytics platform for comprehensive gene expression profiling and meta-analysis

Guangyan Zhou, Othman Soufan, Jessica Ewald, Robert E W Hancock, Niladri Basu, Jianguo Xia

Nucleic Acids Research  ·  01 Apr 2019  ·  doi:10.1093/nar/gkz240

Organ-specific differences in mercury speciation and accumulation across ringed seal (Phoca hispida) life stages

Jessica D. Ewald, Jane L. Kirk, Miling Li, Elsie M. Sunderland

Science of The Total Environment  ·  01 Feb 2019  ·  doi:10.1016/j.scitotenv.2018.09.299

2018

Sci-Hub provides access to nearly all scholarly literature

Daniel S Himmelstein, Ariel Rodriguez Romero, Jacob G Levernier, Thomas Anthony Munro, Stephen Reid McLaughlin, Bastian Greshake Tzovaras, Casey S Greene

eLife  ·  01 Mar 2018  ·  doi:10.7554/eLife.32822

2016

Environmental Origins of Methylmercury Accumulated in Subarctic Estuarine Fish Indicated by Mercury Stable Isotopes

Miling Li, Amina T. Schartup, Amelia P. Valberg, Jessica D. Ewald, David P. Krabbenhoft, Runsheng Yin, Prentiss H. Balcom, Elsie M. Sunderland

Environmental Science & Technology  ·  19 Oct 2016  ·  doi:10.1021/acs.est.6b03206