Xin Xie

About

Xin Xie is an Assistant Professor at the Department of Language Science at UC Irvine. He earned his Ph.D. from the University of Connecticut in 2015. His research focuses on psycholinguistics, speech perception and production, cross-language communication, computational modeling, and neuroimaging. His work aims to understand the cognitive and neural mechanisms underlying language processing and communication across different languages.

Research topics

• Computer Science
• Artificial Intelligence
• Biology
• Genetics
• Computational biology
• Medicine
• Sociology
• Machine Learning
• Socioeconomics
• Environmental planning

Selected publications

• Identifying viruses from metagenomic data using deep learning

  Quantitative Biology · 2020 · 665 citations

  BACKGROUND: The recent development of metagenomic sequencing makes it possible to massively sequence microbial genomes including viral genomes without the need for laboratory culture. Existing reference-based and gene homology-based methods are not efficient in identifying unknown viruses or short viral sequences from metagenomic data. METHODS: Here we developed a reference-free and alignment-free machine learning method, DeepVirFinder, for identifying viral sequences in metagenomic data using d…

  DOI

• UFold: fast and accurate RNA secondary structure prediction with deep learning

  Nucleic Acids Research · 2021 · 273 citations

  Senior authorCorresponding

  For many RNA molecules, the secondary structure is essential for the correct function of the RNA. Predicting RNA secondary structure from nucleotide sequences is a long-standing problem in genomics, but the prediction performance has reached a plateau over time. Traditional RNA secondary structure prediction algorithms are primarily based on thermodynamic models through free energy minimization, which imposes strong prior assumptions and is slow to run. Here, we propose a deep learning-based met…

  DOI

• A deep learning-based auto-segmentation system for organs-at-risk on whole-body computed tomography images for radiation therapy

  Radiotherapy and Oncology · 2021 · 158 citations

  DOI

• Lineage tracing and analog recording in mammalian cells by single-site DNA writing

  Nature Chemical Biology · 2021 · 83 citations

  PublisherOA PDFDOI

• Using machine learning to examine street green space types at a high spatial resolution: Application in Los Angeles County on socioeconomic disparities in exposure

  The Science of The Total Environment · 2021 · 76 citations

  DOI

Recent grants

• III: Small: Integrating and Interpreting Heterogeneous Genomic Data Through Deep Learning

  NSF · $471k · 2017–2021

• CAREER: Computational Tools for Interpreting Genomes

  NSF · $752k · 2009–2014

• NIH Grant RC2HG005613

  NIH · $736k · 2012

Frequent coauthors

• Wenju Lu

  Guangzhou Medical University

  51 shared

• Eric S. Lander

  Broad Institute

  44 shared

• Yuan Liang

  North Sichuan Medical University

  36 shared

• Jian Wang

  Guangzhou Medical University

  33 shared

• Shanlin Sun

  26 shared

• Erik J. Sánchez

  New York University

  23 shared

• Zili Zhang

  23 shared

• Vamsi K. Mootha

  Broad Institute

  23 shared

Labs

• the meaning labPI

  1-2 sentence research focus

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