CV
View pdf CV here
Education
- Ph.D. Crop and Soil Science – Environmental Toxicology, Michigan State University, 2020
- Ph.D. dual major, Environmental Science and Policy, Michigan State University, 2020
- B.Sc. Environmental and Conservation Sciences, University of Alberta, 2016
Interests
- Environmental health data science
- Microbiome
- Machine learning
- High dimensional data analysis
- Bioinformatics
- Multi-omics
- Environmental exposures
Work experience
- 2020.6-present: Postdoctoral Research Scientist
- Department of Environmental Health Sciences, Columbia University
- Mentor: Andrea Baccarelli, MD, Ph.D.
- 2016.8-2020.5: Graduate Research Assistant
- Department of Plant, Soil, and Microbial Sciences, Michigan State University
- Advisor, mentor: Wei Zhang, Ph.D.
- Committe Members: Drs. Hui Li, Elliot T. Ryser, Ashley Shade
- 2016.8-2020.5: Environmental Science and Policy Fellow
- Environmental Science and Policy Program, Michigan State University
- 2015.6-2016.2: Student Research Assistant, University of Alberta
- Department of Renewable Resources
- Mentors: Drs. Scott Chang & Bin Ma
Skills
- Programming
- R, Python, Unix, Shell Scripts, High-Performance Computing, Amazon Web Service, GitHub
- Data analysis
- Microbiome bioinformatics (amplicon, shotgun metagenome, shotgun metatranscriptome), Machine learning, Big data analytics, Data visualization
- Wet Lab
- Various molecular biology and analytical chemistry hands on laboratory skills
Coauthor word cloud as of 12/18/22
Publications
Shen Y, Stedtfeld RD, Guo X, Bhalsod GD, Jeon S, Tiedje JM, Li H, Zhang W* (2019). Pharmaceutical exposure changed antibiotic resistance genes and bacterial communities in soil-surface-and overhead-irrigated greenhouse lettuce. Environment international, 131, 105031.
Shen Y, Li H, Ryser ET, Zhang W* (2021). Comparing root concentration factors of antibiotics for lettuce (Lactuca sativa) measured in rhizosphere and bulk soils. Chemosphere, 262, 127677.
Shen Y, Hamm J, Gao F, Ryser ET, Zhang W*. 2021. Assessing consumer buy and pay preferences for labeled food products with statistical and machine learning methods. Journal of Food Protection.
Shen Y, Ryser ET, Li H, Zhang W*. (2021). Bacterial community assembly and antibiotic resistance genes in the lettuce-soil system upon antibiotic exposure. Science of The Total Environment, 778, 146255.
Gao F, Shen Y, Sallach JB, Li H, Liu C*, Li Y*. (2021). Direct prediction of bioaccumulation of organic contaminants in plant roots from soils with machine learning models based on molecular structures. Environmental Science & Technology. 55, 16358-26368
Shen Y*, Laue HE, Shrubsole MJ, Wu H, Bloomquist TR, Larouche A, Zhao K, Gao F, Boivin A, Prada D, Hunting DJ. Gillet V, Takser L, Baccarelli AA. (2022). Associations of childhood and perinatal blood metals with children’s gut microbiomes in a Canadian gestation cohort. Environmental Health Perspectives. 130(1).
Gao F#, Shen Y#, Sallach JB, Li H, Zhang W, Li Y*, Liu C*. 2022. Predicting crop root concentration factors of organic contaminants with machine learning models. Journal of Hazardous Materials. 424, 127437. #Equal Contribution
Gao F, Zhang W, Baccarelli AA, Shen Y*. (2022). Predicting Chemical Ecotoxicity by Learning Latent Space Chemical Representations. Environment international, 163, 107224.
Laue HE*#, Shen Y#, Bloomquist TR, Wu H, Brennan, KJM, Raphael C, Wilkie E, Gillet V, Desautels A, Abdelouahab N, Bellenger JP, Burris HH, Coull BA, Weisskopf MG, Zhang W, Takser L, Baccarelli AA. (2022). In utero exposure to caffeine and acetaminophen, the gut microbiome, and neurodevelopmental outcomes, a prospective birth cohort study. International Journal of Environmental Research and Public Health 19(15), 9357.#equal contribution
Shen Y, Zhao E, Zhang W*, Baccarelli AA, Gao F*. (2022). Predicting pesticide dissipation half-life intervals in plants with machine learning models. Journal of Hazardous Materials. 436, 129177
Talks
March 22, 2017
Conference Oral Presentation at American Society for Microbiology Conference - Innovative Microbial Ecology for Mitigation of Antibiotic Resistance and Bacterial Diseases. , Crystal City, VA
August 13, 2017
Conference Oral Presentation at 4th International Symposium on the Environmental Dimension of Antibiotic Resistance, East Lansing, MI
December 25, 2017
Invited Talk at Zhejiang University, Invited by Dr. Bin Ma., Hangzhou, Zhejiang, China
August 20, 2018
Conference Oral Presentation at American Chemical Society National Meeting #256, Boston, MA
August 26, 2019
Conference Oral Presentation at American Chemical Society National Meeting #257, San Diego, CA
October 02, 2019
Conference Poster Presentation at US-China Environment and Sustainability Forum at the University of Michigan, Ann Arbor, MI
January 01, 2020
Invited Talk at Various location in China, China
February 18, 2020
Job Interview Talk at The Baccarelli Laboratory, Columbia University Mailman School of Public Health, New York, NY
April 01, 2020
Seminar Talk at Environmental Science and Policy Program, Michigan State University, East Lansing, MI
June 18, 2020
Conference Poster Presentation at American Society of Microbiology Conference – ASM Microbe 2020, Chicago, IL (Virtue due to COVID19)
June 21, 2021
Conference Poster Presentation at American Society of Microbiology Conference – ASM World Microbe Forum, Virtue Conference
June 22, 2021
Invited Talk at Takser Lab, Université de Sherbrooke. Invited by Dr. Larrisa Takser, Quebec, Canada
August 24, 2021
Conference Spotlight Oral Presentation at International Society for Environmental Epidemiology, New York, NY (online)
February 21, 2022
Seminar talk at Department of Environmental Health Sciences, Columbia University, New York, NY
March 20, 2022
Conference Oral Presentation at American Chemical Society National Meeting Spring 2022, San Diego, CA
May 23, 2022
Conference Poster Presentation at 8th New York City Epidemiology Forum, New York, NY
July 14, 2022
Conference Poster Presentation at NIEHS Environmental Health Sciences Core Centers (EHSCC) 2022 Annual Meeting, New York, NY
September 13, 2022
Invited Presentation at Columbia University P30 Center – The NIEHS Center for Environmental Health and Justice in Northern Manhattan, New York, NY
September 15, 2022
Invited Presentation at Journal of Eco-Environment & Health (Over 2000 audiences listened to the webinar), Jiangsu, Nanjing, China
September 20, 2022
Conference Poster Presentation at International Society for Environmental Epidemiology annual meeting – ISEE2022, Athens, Greece
November 12, 2019
Conference Oral Presentation at ASA-CSSA-SSSA International Annual Meeting, San Antonio, TX
Teaching Assistant (TA)
- SHARP Python Boot Camp, Columbia University, Summer 2021
- SHARP Epigenetics Boot Camp, Columbia University, Summer 2020
- CSS 340: Applied Soil Physics, Michigan State University, Spring 2018 and Spring 2019
- CSS 330: Soil Chemistry, Michigan State University, Spring 2019
- RenR 299: Environmental and Forestry Spring Field School, University of Alberta, Spring 2015
Review Services
- Environmental Science & Technology (ACS)
- ACS Environmental Science & Technology Water (ACS)
- Chemical Research in Toxicology (ACS)
- The Innovation (CellPress)
- Environmental Research (Elsevier)
- Science of the Total Environment (Elsevier)
- Environmental Pollution (Elsevier)
- Chemosphere (Elsevier)
- Applied Soil Ecology (Elsevier)
- Food Chemistry (Elsevier)
- Current Research in Food Science (Elsevier)
- Journal of Environmental Management (Elsevier)
- BMC Medicine (BioMed Central)
- BMC Genomics (BioMed Central)
- Frontiers in Microbiology (Frontiers)
- Current Environmental Health Reports (Springer Nature)
- Reviews of Environmental Contamination and Toxicology (Springer Nature)
- Scientific Reports (Springer Nature)
- Journal of Trust Research (Taylor & Francis Online)
- International Journal of Environmental Research and Public Health (MDPI)
- Pathogens (MDPI)
- Nutrients (MDPI)
- Microorganisms (MDPI)
Honors & Awards
Awards from Michigan State University:
- Graduate Research Assistantship, 2016 – 2020
- Institute for Integrative Toxicology Summer Travel Award, 2017 – 2020
- Dissertation Completion Fellowship, 2019
- Graduate School Travel Funds, 2019
- College of Agriculture and Natural Resources Food Systems Fellowship, 2019
- Environmental Science and Policy Program Travel Grant, 2017,2019
- Environmental Science and Policy Doctoral Recruitment Fellowship, 2016 External Awards
- ASM Travel Grant (American Society for Microbiology), 2017
- First Class Standing (University of Alberta), 2015, 2016
- Undergraduate Research Grant (Natural Science and Engineering Research Council of Canada - CREATE Grant), 2015
- ALES Student Engagement Fund (University of Alberta), 2015
- ZAFU - UofA (ALES) Award (University of Alberta), 2013
- National Scholarship of China (Ministry of Education in China), 2013
*Updated 04/06/2023