CV

Education

• Ph.D in Civil & Environmental Engineering, Massachusetts Institute of Technology, 2024 (expected)
  • Advisor: Prof. David Des Marais
  • Related graduate course work: Systems Biology, Statistic Computation & Applications, Graphical Models, Evolutionary & Quantative Genomics, Plants and Climate, Land Water Food and Climate, Resilience of Living Systems to Environmental Change
• M.S. in Civil & Environmental Engineering, Carnegie Mellon University, 2017
• B.S. in Water Supply and Sewerage Engineering, Shenyang Jianzhu University, 2016

Awards & Honors

• Graduate Student Fellowship award at Abdul Latif Jameel Water & Food Systems Lab (J-WAFS) at MIT 09/2023 - 12/2023
• Department scholarship at CMU 08/2016 - 12/2017
• Outstanding Graduate, Shenyang Jianzhu University 2016
• Outstanding Student Scholarships, 8 times during undergraduate 2012 - 2016

Skills

• Computer
  • R Language
  • Python
  • Linux
  • High-Performance Computing
  • Raspberry Pi Image Systel Setup
  • Cellpose
  • Imagej
• Biology
  • Drought study
  • RNASequencing
  • Allele Specific Expression
  • Metabolites Assay
  • Plant Photosynthesis and Gas-exchange Measurement (Li-COR)
  • Hydraulic Potential Measurement
  • Genetic crossing
• Analytical
  • Bioinformatics
  • Genomics
  • Transcriptomic Study
  • Graphical Models
  • Co-Expression Network Analysis
  • Machine Learning Applications
  • Statistical Analysis

Publications

Genetic Diversity In Gene Regulatory Interactions Underlies The Response To Soil Drying In The Model Grass Brachypodium Distachyon

Yun, Jie, Angela Burnett, Alistair Rogers, David L. Des Marais. (2024). "Genetic Diversity In Gene Regulatory Interactions Underlies The Response To Soil Drying In The Model Grass Brachypodium Distachyon." bioRxiv doi:10.1101/2024.06.17.597683

Critical Review: Role of Inorganic Nanoparticle Properties on Their Foliar Uptake and in Planta Translocation (The third joint winner for best 2021 review in ES&T)

Astrid Avellan, Jie Yun, Bruno P. Morais, Emma T. Clement, Sonia M. Rodrigues, and Gregory V. Lowry. (2021). "Critical Review: Role of Inorganic Nanoparticle Properties on Their Foliar Uptake and in Planta ." Environmental Science & Technology.

CuO nanoparticles alter the rhizospheric bacterial community and local nitrogen cycling for wheat grown in a calcareous soil

Xiangyu Guan, Xiaoyu Gao, Astrid Avellan, Eleanor Spielman-Sun, Jiang Xu, Stephanie Laughton, Jie Yun, Yilin Zhang, Garret D. Bland, Ying Zhang, Ruirui Zhang, Xusheng Wang, Elizabeth A. Casman, and Gregory V. Lowry (2020). "CuO nanoparticles alter the rhizospheric bacterial community and local nitrogen cycling for wheat grown in a calcareous soil." Environmental Science and Technology.

Nanoparticle size and coating chemistry control foliar uptake pathways, translocation, and leaf-to-rhizosphere transport in wheat

Avellan, Astrid, Jie Yun, Yilin Zhang, Eleanor Spielman-Sun, Jason M. Unrine, Juergen Thieme, Jieran Li, Enzo Lombi, Garret Bland, and Gregory V. Lowry. (2010). "Nanoparticle size and coating chemistry control foliar uptake pathways, translocation, and leaf-to-rhizosphere transport in wheat." ACS nano.

Effect of silver concentration and chemical transformations on release and antibacterial efficacy in silver-containing textiles

Eleanor Spielman-Sun, Tatiana Zaikova, Theresa Dankovich, Jie Yun, Margret Ryan, James E. Hutchison, Gregory V. Lowry. (2018). "Effect of silver concentration and chemical transformations on release and antibacterial efficacy in silver-containing textiles." NanoImpact.

The Effect of Divalent Metal Ions and Recycle Ratio of UASB Reactor on the Formation of Anammox Granules and Its Treatment Performance

Jinxiang Fu, Mingjun Zhou, Jie Yun, Yang Su, Pengfei Yu, Ming Sun, Xinqi Ji. (2017). "The Effect of Divalent Metal Ions and Recycle Ratio of UASB Reactor on the Formation of Anammox Granules and Its Treatment Performance." Water, Air, & Soil Pollution.

Talks

Genotype-by-environment interaction (GxE) in gene regulatory networks in Brachypodium distachyon under soil water deficit (poster)​

November 30, 2023

CSHL Plant Genomes, Systems Biology & Engineering at CSHL, Cold Spring Harbor, NY

Different carbon allocation strategies in annual and perennial species of Brachypodium at reproductive stage under carbon limitation induced by drought​

November 27, 2023

Holbrook Lab Meetings at Harvard at BioLab, Cambridge, MA

Different carbon allocation strategies in annual and perennial species of Brachypodium at reproductive stage under carbon limitation induced by drought (poster)

August 05, 2023

ASPB plant biology 2023 at Savannah Convention Center, Savanah, GA

Using Biodiversity to Increase Crop Drought Resistance– Comparison of Leaf Growth among Barley, Oat, Wheat and Brachypodium under drought (poster)

August 05, 2023

ASPB plant biology 2023 at Savannah Convention Center, Savanah, GA

Using Biodiversity to Increase Crop Drought Resistance–A Comparison of Leaf Growth among Barley, Oat, Wheat and Brachypodium under drought (poster)​

April 19, 2023

MITEI Earth Day Colloquium at Wong Auditorium and Ting Foyer, Cambridge, MA

Genotype-by-environment interaction (GxE) in gene regulatory networks in Brachypodium distachyon under soil water deficit (talk and poster)​

June 26, 2022

Evolution Meetings at Huntington Convention Center, Cleveland, OH

Genotype-by-environment interaction (GxE) in gene regulatory networks in Brachypodium distachyon under soil water deficit

June 15, 2022

Brachypodium conference 2022 at Zoom, virtual

Genotype-by-environment interaction (GxE) in gene regulatory networks in Brachypodium distachyon under soil water deficit (talk and poster)

May 21, 2022

Salt and Water Stress in Plants Gordon Research Seminar (GRS) and Gordon Research Conference(GRC) at Les Diablerets Conference Center, Les Diablerets, Switzerland

Genotype by Environment Interaction in gene regulatory networks​ (poster)

April 19, 2022

MIT CEE Annual Research Day at MIT’s Media Lab, Cambridge, MA

Genotype by Environment Interaction in gene regulatory networks​

July 31, 2020

Parsons Graduate Student Seminar at MIT at Zoom, Cambridge, MA

Teaching

Mentor - MIT MINI UROP (Undergraduate Research Opportunities Program)

Teaching Assistant - MIT CEE Traveling Research Environmental Experience

Mentor - MIT UROP (Undergraduate Research Opportunities Program)

Mentor - MIT UROP (Undergraduate Research Opportunities Program)

Grader - Numerical Methods

Leadership experience and training

• Participant and LEAPS Fellow, Leadership and Professional Strategies (LEAPS) programs (8.396/8.397), MIT, Spring 2024

Scientific communication and outreach

• Volunteer in Boston Public Library Science Outreach Program, Boston, Massachusetts, US 3/2024-4/2024
• Volunteer in Arnold Arboretum Summer Institute 2022, Boston, Massachusetts, US 8/2022