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Jie Liu

Assistant Professor

University of Michigan

Liu Lab

Dr. Liu’s research lab aims to develop machine learning approaches for real-world bioinformatics and medical informatics problems. We believe that computational methods are essential in order to understand many of these molecular biology problems, including the dynamics of genome conformation and nuclear organization, gene regulation, cellular networks, and the genetic basis of human diseases.

Liu Lab currently has openings for graduate students and postdocs. Please reach out to Dr. Jie Liu via email if you are interested.

Interests

  • Machine Learning
  • Bioinformatics
  • Computational Genomics
  • Medical Informatics

Education

  • PhD in Computer Science, 2014

    University of Wisconsin - Madison

Recent News

All news»

04/2021 scHiCTools paper was accepted for publication in PLOS Computational Biology. Congratulations to Xinjun, Fan, Hongxi and Wai Yan.

04/2021 Shuze Wang’s work was published on Genome Research https://genome.cshlp.org/content/early/2021/04/09/gr.271080.120.abstract

03/2021 Sean Moran decided to join the lab after his rotation. Welcome, Sean!

10/2020 Zhenhao Zhang joined the lab and entered BIOINFO PhD program after finishing his master of IOE. Welcome, Zhenhao!

09/2020 Liu Lab received the NHGRI Innovator Award (R35) to develop deep learning approaches to understand the relationship between chromatin state features and chromatin organization.

Projects

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single-cell multi-omics integration

An unsupervised manifold alignment algorithm, MMD-MA, for integrating multiple measurements carried out on disjoint aliquots of a given population of single cells.

scHi-C embedding

The first computational embedding method for single cells in terms of their chromatin organization.

Multiple Testing Under Dependence

A graphical model based multiple testing procedure which captures dependence among the hypotheses.

Personalized Breast Cancer Diagnosis

Our results show that radiologists can potentially use genetic variants (SNPs) to improve personalized breast cancer diagnosis (Marco Ramoni Distinguished Paper Award).

Tumor Heterogeneity Anaysis

Comprehensive statistical inference of the clonal structure of cancer from multiple biopsies (Supported by Moore-Sloan Data Science Environment Fellowship).

Publications

(2021). scHiCTools: a computational toolbox for analyzing single-cell Hi-C data. PLOS Computational Biology.

PDF Code Project

(2021). Mapping the regulatory landscape of auditory hair cells from single-cell multi-omics data. In Genome Res.

DOI

(2020). Capturing cell type-specific chromatin structural patterns by applying topic modeling to single-cell Hi-C data. PLOS Computational Biology.

PDF Project

(2020). p53 Integrates Temporal WDR5 Inputs during Neuroectoderm and Mesoderm Differentiation of Mouse Embryonic Stem Cells. In Cell Reports.

DOI

(2019). Jointly embedding multiple single-cell omics measurements. In The Workshop on Algorithms in Bioinformatics.

PDF Code Project

People

Principal Investigator

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Jie Liu

Assistant Professor

Students

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Fan Feng

PhD student
DCMB

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Shuze Wang

PhD student
DCMB
co-advised by Dr. Joerg Waldhaus

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Yuanhao Huang

PhD student
DCMB

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Sean Moran

PhD student
DCMB

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Zhenhao Zhang

PhD student
DCMB

Ziqiao Ma

Undergraduate
EECS

Tianjun Li

Undergraduate
EECS

Yuan Yao

Undergraduate
EECS

Linghua Jiang

Master Student
Bioinformatics

Chenghao Shuangguan

Master Student
Biostatistics

Xinyu Lu

Undergraduate
EECS

Yiyang Qiu

Undergraduate
EECS

Simin Fan

Undergraduate
EECS

Jiahao Qiu

Undergraduate
EECS

Hongxi Pu

Undergraduate
CS(LSA)

Feitong Tang

Undergraduate
EECS

Alumni

Yufeng Zhang

MS Biostatistics
Current - PhD student
DCMB
University of Michigan

Mingyu Du

MS Biostatistics
Current - PhD Student
Bioinformatics
University of California-Irvine

Yijiao Qin

BS EECS
Current - Master student
Info Networking
Carnegie Mellon University

Xinjun Li

Master student
Statistics

Yujuan Fu

BS EECS
Current - PhD student
Biomedical Informatics
University of Washington - Seattle

Zheyu Zhang

BS Statistics (CUHK-SZ)
Current - Master student
Industrial Engineering
Georgia Institute of Technology

Bingjiang Wang

Undergraduate EECS
Current - Graduate Student
CSE
University of California at San Diego

Chenghao Xu

BS Statistics (CUHK-SZ)
Current - Master student
Math
New York University

Zhuowen Shen

BS EECS
Current - Graduate Student
CSE
University of Michigan

Ben Wurman

Undergraduate
CS & MCDB

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