Xi Emmett Peng 彭玺 Péng Xǐ

Ph.D. in Ecology (2026) / Molecular ecology & bioinformatics researcher

Xi Emmett Peng

For a long time, science to me meant learning what was already known. Growing up in an exam-oriented education system, I became used to treating biology as a collection of established knowledge to be understood, remembered, and occasionally demonstrated through experiments. Even when I first encountered laboratory work, the goal was often to reproduce principles whose answers were already known. After years of studying biochemistry, genetics, and molecular biology, I still found myself unsure of what kind of science I truly wanted to pursue. I enjoyed biology, but often felt that the experiments in front of me were only very small pieces of a much larger question that I had not yet learned how to see.

That began to change when I entered graduate training in ecology. My attention shifted from molecules and cells to populations, communities, and ecosystems, and with that shift came a different understanding of research itself. I became fascinated by the idea that microorganisms, despite existing at the scale of individual cells, are deeply embedded in much larger systems. Their interactions, metabolism, competition, cooperation, and communication collectively connect the microscopic world to the environment around them. Studying these communities also taught me that meaningful scientific questions rarely belong to one discipline alone. Biology constantly meets chemistry, physics, mathematics, computer science, and even ideas that resemble those used to understand social systems.

Looking back, I have come to think that finding a research direction is not simply about choosing a topic. It is about finding the scale and perspective from which the world becomes most interesting to you. Sometimes that perspective is not obvious at the beginning. It emerges gradually, as we move beyond learning existing answers and begin to discover the kinds of questions we genuinely want to ask.

Right now, I am in a gap period.

Updates

MEE story-behind

Published the story behind our study of read length, metagenome assembly and binning.

Ph.D. defense!

Ph.D. thesis: A Metagenomics-Based Framework for Analyzing Microbial Metabolic and Quorum Sensing Networks (2019-2025)

New paper on iMeta

iNAP 2.0: Harnessing metabolic complementarity in microbial network analysis

CSC Award!

Awarded the CSC (China Scholarship Council) scholarship.

Selected Publications

  1. Methods in Ecology and Evolution, 2026

    From short to long: The impact of read length on metagenome assembly and binning

    Xi Peng, Xingsheng Yang, Danrui Wang, Bo Zhao, Kai Feng, Qing He, Shang Wang, Ye Deng*

    Paper

  2. Nature Communications, 2024

    Metabolic interdependencies in thermophilic communities are revealed using co-occurrence and complementarity networks

    Xi Peng, Shang Wang, Miaoxiao Wang, Kai Feng, Qing He, Xingsheng Yang, Weiguo Hou, Fangru Li, Yuxiang Zhao, Baolan Hu, Xiao Zou, Ye Deng*.

    Paper

  3. iMeta, 2024

    iNAP 2.0: Harnessing metabolic complementarity in microbial network analysis

    Xi Peng, Kai Feng, Xingsheng Yang, Qing He, Bo Zhao, Tong Li, Shang Wang, Ye Deng*

    Paper

Full publication list

Notes

All notes

CV & Experience

Visiting Ph.D. Student

Department of Microbiology, Immunology and Transplantation, KU Leuven

Ph.D. in Microbial Ecology

Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences

B.Sc. in Biological Sciences

China Agricultural University

Full CV and experience

Links

MEM - Deng Lab
Lab of Microbial Systems Biology - KU Leuven