Tianyi Liu My Works & Thoughts

Research

Introduction

My dissertation research mainly focuses on cell type deconvolution, investigating theories and algorithms of non-negative matrix factorization. I also join research efforts in precision medicine with my colleagues, studying the optimal timings of individual treatments under disease progression and resource constraints.

On the collaborative side, I work with a group of scientists on quantifying genetic impacts of inorganic arsenics on type-II diabetes using mouse models and consult on studying efficacies of neonatal physical therapeutic interventions as well as the impacts social determinants of health on getting physical therapy services for patients.

Highlighted

ARTdeConv: adaptive regularized tri-factor non-negative matrix factorization for cell type deconvolution
ARTdeConv: adaptive regularized tri-factor non-negative matrix factorization for cell type deconvolution
Tianyi Liu, Chuwen Liu, Quefeng Li, Xiaojing Zheng, Fei Zou
NAR Genomics and Bioinformatics   ·   29 Mar 2025   ·   doi:10.1093/nargab/lqaf046

All Publications

2025

Transgenerational diabetogenic effects of preconception exposure to inorganic arsenic in C57BL/6 mice are associated with dysregulation of DNA methylation and gene expression in G1 and G2 offspring
Transgenerational diabetogenic effects of preconception exposure to inorganic arsenic in C57BL/6 mice are associated with dysregulation of DNA methylation and gene expression in G1 and G2 offspring
Bingzhen Shang, Tianyi Liu, Hadley Hartwell, Christelle Douillet, Abhishek Venkatratnam, ..., Sergey A. Krupenko, Folami Y. Ideraabdullah, Fernando Pardo-Manuel de Villena, Rebecca C. Fry, Miroslav Stýblo
Archives of Toxicology   ·   12 Jun 2025   ·   doi:10.1007/s00204-025-04107-y
ARTdeConv: adaptive regularized tri-factor non-negative matrix factorization for cell type deconvolution
ARTdeConv: adaptive regularized tri-factor non-negative matrix factorization for cell type deconvolution
Tianyi Liu, Chuwen Liu, Quefeng Li, Xiaojing Zheng, Fei Zou
NAR Genomics and Bioinformatics   ·   29 Mar 2025   ·   doi:10.1093/nargab/lqaf046
Heritable dysregulation of DNA methylation may underlie the diabetogenic effects of paternal preconception exposure to inorganic arsenic in C57BL/6J mice
Heritable dysregulation of DNA methylation may underlie the diabetogenic effects of paternal preconception exposure to inorganic arsenic in C57BL/6J mice
Hadley J. Hartwell, Bingzhen Shang, Christelle Douillet, Audrey G. Bousquet, Tianyi Liu, Fei Zou, Folami Ideraabdullah, Miroslav Stýblo, Rebecca C. Fry
Toxicology and Applied Pharmacology   ·   01 Mar 2025   ·   doi:10.1016/j.taap.2025.117242

2024

Temporal High-Resolution Atlas of Human Blood Leukocyte Composition in Response to Respiratory Virus Inoculation
Temporal High-Resolution Atlas of Human Blood Leukocyte Composition in Response to Respiratory Virus Inoculation
Yu Zhang, Tianyi Liu, Chuwen Liu, Xuejun Sun, Pei Liu, James S. Hagood, Raymond J. Pickles, Fei Zou, Xiaojing Zheng
Cold Spring Harbor Laboratory   ·   03 Oct 2024   ·   doi:10.1101/2024.10.01.616122
Interdisciplinary collaborative eye examinations to protect preterm infant neurodevelopment: a quality improvement project
Interdisciplinary collaborative eye examinations to protect preterm infant neurodevelopment: a quality improvement project
Dana B. McCarty, Erika Clary-Williams, Kristen D. LeBLond, Tianyi Liu, Tika Zbornik-Thompson, J. Niklas Ulrich, Michelle S. Go
Frontiers in Psychology   ·   06 May 2024   ·   doi:10.3389/fpsyg.2024.1354033

2023

Adaptive Regularized Tri-Factor Non-Negative Matrix Factorization for Cell Type Deconvolution
Adaptive Regularized Tri-Factor Non-Negative Matrix Factorization for Cell Type Deconvolution
Tianyi Liu, Chuwen Liu, Quefeng Li, Xiaojing Zheng, Fei Zou
Cold Spring Harbor Laboratory   ·   08 Dec 2023   ·   doi:10.1101/2023.12.07.570631
A Feasibility Study of a Physical and Occupational Therapy-Led and Parent-Administered Program to Improve Parent Mental Health and Infant Development
A Feasibility Study of a Physical and Occupational Therapy-Led and Parent-Administered Program to Improve Parent Mental Health and Infant Development
Dana B. McCarty, Stacey C. Dusing, Deborah Thorpe, Morris Weinberger, Susan Pusek, Alana Gilbert, Tianyi Liu, Kerry Blazek, Sara Hammond, T. Michael O’Shea
Physical & Occupational Therapy In Pediatrics   ·   22 Oct 2023   ·   doi:10.1080/01942638.2023.2271102
Sex-specific transgenerational effects of preconception exposure to arsenite: metabolic phenotypes of C57BL/6 offspring
Sex-specific transgenerational effects of preconception exposure to arsenite: metabolic phenotypes of C57BL/6 offspring
Bingzhen Shang, Abhishek Venkatratnam, Tianyi Liu, Christelle Douillet, Qing Shi, ..., Peter Cable, Fei Zou, Folami Y. Ideraabdullah, Rebecca C. Fry, Miroslav Stýblo
Archives of Toxicology   ·   24 Aug 2023   ·   doi:10.1007/s00204-023-03582-5

2022

Ex vivo exposures to arsenite and its methylated trivalent metabolites alter gene transcription in mouse sperm cells
Ex vivo exposures to arsenite and its methylated trivalent metabolites alter gene transcription in mouse sperm cells
Bingzhen Shang, Abhishek Venkatratnam, Hadley Hartwell, Christelle Douillet, Peter Cable, Tianyi Liu, Fei Zou, Folami Y. Ideraabdullah, Rebecca C. Fry, Miroslav Stýblo
Toxicology and Applied Pharmacology   ·   01 Nov 2022   ·   doi:10.1016/j.taap.2022.116266
An interaction of inorganic arsenic exposure with body weight and composition on type 2 diabetes indicators in Diversity Outbred mice
An interaction of inorganic arsenic exposure with body weight and composition on type 2 diabetes indicators in Diversity Outbred mice
James G. Xenakis, Christelle Douillet, Timothy A. Bell, Pablo Hock, Joseph Farrington, ..., Abhishek Venkatratnam, Fei Zou, Rebecca C. Fry, Miroslav Stýblo, Fernando Pardo-Manuel de Villena
Mammalian Genome   ·   11 Jul 2022   ·   doi:10.1007/s00335-022-09957-w

2021

NuMorph: Tools for cortical cellular phenotyping in tissue-cleared whole-brain images
NuMorph: Tools for cortical cellular phenotyping in tissue-cleared whole-brain images
Oleh Krupa, Giulia Fragola, Ellie Hadden-Ford, Jessica T. Mory, Tianyi Liu, ..., William D. Snider, Mark J. Zylka, Guorong Wu, Lei Xing, Jason L. Stein
Cell Reports   ·   01 Oct 2021   ·   doi:10.1016/j.celrep.2021.109802

2017

Accurate and High Throughput Cell Segmentation Method for Mouse Brain Nuclei Using Cascaded Convolutional Neural Network
Accurate and High Throughput Cell Segmentation Method for Mouse Brain Nuclei Using Cascaded Convolutional Neural Network
Qian Wang, Shaoyu Wang, Xiaofeng Zhu, Tianyi Liu, Zachary Humphrey, ..., Kira Bradford, Mark J. Zylka, Ashok Krishnamurthy, Jason L. Stein, Guorong Wu
Lecture Notes in Computer Science   ·   01 Jan 2017   ·   doi:10.1007/978-3-319-67434-6_7