Yike Shen, Ph.D.

Yike Shen, Ph.D.

Assistant Professor

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Pages

Shen Environmental Health Data Science Laboratory

Posts

Amazon Web Service RONIN Cloud Computing Tutorial

less than 1 minute read

Published:

  • This is the AWS RONIN tutorials for Baccarelli Lab at Columbia University
  • Author: Yike Shen
  • Tutorial Link: https://github.com/YikeShen/BaccarelliLab_AWSRONIN_tutorials
  • 06/04/2021
    • Confidential video tutorials to Baccarelli Lab available at lab shared drive under AWS RONIN tutorials
    • Tutorial_1: RONIN Machine and cluster configuration and navigation
    • Tutorial_2: AWS CLI and file transfer.
    • Tutorial_3: Example for small amplicon sequencing data processing using python and unix command in Linux system.
    • Tutorial_4: Example for large shotgun metagenome sequencing data processing using python and unix command in Linux system.

portfolio

publications

Pharmaceutical exposure changed antibiotic resistance genes and bacterial communities in soil-surface- and overhead-irrigated greenhouse lettuce

Published in Environment International, 2019

Code, https://github.com/YikeShen/Shen-et-al.-2019_Environment-International

Recommended citation: 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. https://www.sciencedirect.com/science/article/pii/S016041201931270X

Bacterial community assembly and antibiotic resistance genes in the lettuce-soil system upon antibiotic exposure

Published in Science of The Total Environment, 2021

Code, https://github.com/YikeShen/Shen-et-al.-2021_Science-of-the-Total-Environment.

Recommended citation: 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. https://www.sciencedirect.com/science/article/pii/S0048969721013231

Direct prediction of bioaccumulation of organic contaminants in plant roots from soils with machine learning models based on molecular structures

Published in Environmental Science & Technology, 2021

Code, https://github.com/FengGmsu/RCF.

Recommended citation: 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 https://pubs.acs.org/doi/full/10.1021/acs.est.1c02376

Associations of childhood and perinatal blood metals with children’s gut microbiomes in a Canadian gestation cohort

Published in Environmental Health Perspectives, 2022

Code, https://github.com/YikeShen/Shen-et-al.-2022_Environmental-Health-Perspectives.

Recommended citation: 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). https://ehp.niehs.nih.gov/doi/full/10.1289/EHP9674

Predicting crop root concentration factors of organic contaminants with machine learning models

Published in Journal of Hazardous Materials, 2022

Code, https://github.com/YikeShen/Gao-and-Shen-et-al_Journal-of-Hazardous-Materials_2022

Recommended citation: 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 https://www.sciencedirect.com/science/article/pii/S0304389421024055

In Utero Exposure to Caffeine and Acetaminophen, the Gut Microbiome, and Neurodevelopmental Outcomes: A Prospective Birth Cohort Study

Published in International Journal of Environmental Research and Public Health, 2022

Code, https://github.com/YikeShen/Laue-and-Shen-et-al_2022_IJERPH

Recommended citation: 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 https://doi.org/10.3390/ijerph19159357

talks

Assessing Antibiotics, Antibiotic Resistance Genes and Microbiome in Lettuce and Food Safety Related Consumer Preference

Published:

  • EMBLab, Westlake University, Hangzhou, Zhejiang, China. January 17, 2020. Invited by Dr. Feng Ju.
  • Institute of Nuclear-Agricultural Science, Zhejiang University, Hangzhou, Zhejiang, China. January 16, 2020. Invited by Dr. Haiyan Wang.
  • College of Environmental Science and Engineering, Nankai University, Tianjin, China. January 14, 2020. Invited by Dr. Zeyou Chen.
  • Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China. January 13, 2020. Invited by Dr. Yuanbo Li.
  • Institute of Soil-Water Resource and Environment, Zhejiang University, Hangzhou, Zhejiang, China. January 6, 2020. Invited by Dr. Bin Ma.
  • The International Youth Scholars Forum of Zhejiang A&F University, Zhejiang A&F University, Hangzhou, Zhejiang, China. December 28, 2019. Invited by School of Environmental and Resource Sciences.

teaching

Teaching experience 1

Undergraduate course, University 1, Department, 2014

This is a description of a teaching experience. You can use markdown like any other post.

Teaching experience 2

Workshop, University 1, Department, 2015

This is a description of a teaching experience. You can use markdown like any other post.