About me

I am currently in the market for Tenure Track Assistant Professor positions in Environmental Health Sciences/Environmental Sciences.

Welcome to my website! I am currently a postdoctoral research scientist at Columbia University working with Dr. Andrea Baccarelli. I dedicate my career and research to environmental health data science. I approach this theme through computational precision environmental health and biomarker discovery from high dimensional omics and environmental exposure data. In my doctoral and postdoctoral training, I gained proficient knowledge and skills in microbiome, machine learning, high dimensional data analytics, bioinformatics, environmental toxicology, and wet lab techniques. My major research interests are listed as follows:

  1. Linking environmental exposures and microbiome
    Humans are exposed to a myriad of environmental pollutants (e.g., pharmaceuticals and personal care products, metals, PFAS, flame retardants, etc.) every day. Individual or mixture of pollutants may relate to changes in human gut microbiome and/or soil-plant microbiome, and subsequently impact human health. I have studied the associations of metal exposures with human gut microbiomes Shen et al., 2022. Environmental Health Perspectives; antimicrobial resistance and bacterial microbiome in lettuce-soil systems Shen et al., 2019. Environment International; Shen et al., 2021. Science of the Total Environment; associations of caffeine/acetaminophen with human gut microbiome Laue and Shen et al., 2022. IJERPH. Future works include associations of flame retardants/replacements and PFAS exposures with gut microbiome. Dedicated to end-to-end microbiome research, I have explored bacterial RNA quality and shotgun metatranscriptome sequencing Shen et al., manuscript in prepration and streamlined microbiome bioinformatics (i.e., amplicon sequencing, shotgun metagenome sequencing, and shotgun metatranscriptome sequencing) (Bioinformatics Collaboration).

  2. Harnessing high-dimensional chemical and omics data
    High dimensional data are becoming increasingly common in environmental and biomedical research (e.g., omics). While we obtain much more information from high-dimensional data, they may contain redundant information. Therefore, the ability to learn from high-dimensional data is challenging. I have developed deep learning models such as autoencoder models to learn latent space chemical representations to predict chemical ecotoxicity Gao, ……, Shen*. 2022. Environment International. I also developed a AESur: autoencoder survival analysis model to assist early prediction of coronary heart disease Shen et al., manuscript in prepration. Future works include exposomics, metagenomics, etc.

  3. Exploring the fate and transport of contaminants in the environment
    Accurate prediction of fate and transport of contaminants in the environment is a critical step in chemical risk assessment. I am interested in systematically predicting toxicity and understanding properties of interest with the help of machine learning, deep learning, and experiments. My work includes: 1) predicted pesticide dissipation half-life intervals in plants using molecular fingerprints Shen et al., 2022. Journal of Hazardous Materials; 2) predicted bioaccumulation of organic contaminants in plant roots from soils Gao and Shen et al., 2022. Journal of Hazardous Materials; Gao et al., 2021. Environmental Science & Technology; 3) conducted a laboratory experiment on comparing root concentration factors of antibiotics for lettuce measured in rhizosphere and bulk soils Shen et al., 2021. Chemosphere.

  4. Network analysis in epidemiology cohort studies.
    Exciting updates are coming soon Shen et al., manuscript in prepration. Stay tuned!

I support open and transparent research, all code for my publications (leading and/or corresponding authors) are available at my GitHub Repository;
list of my publications;
list of my talks;
my CV


Feature article about my research
Shen Y. (2022). Harnessing high-dimensional data in environmental health sciences. Research Features. DOI: 10.26904/RF-144-3452044615. Feature article link

Contact Information

Yike Shen
Department of Environmental Health Sciences
Columbia University Mailman School of Public Health
630 West 168th Street
P&S Building, Room 16-416
New York, New York 10032
Email: yike.shen@columbia.edu
Email: ys3419@cumc.columbia.edu

Updated 11/15/2022