Qi Liu

54 papers Journal 47Unranked 7
YearRankTypeTitle / Venue / Authors
2025 J jnl
stImage: a versatile framework for optimizing spatial transcriptomic analysis through customizable deep histology and location informed integration.
Briefings Bioinform.
Yu Wang, Haichun Yang, Ruining Deng, Yuankai Huo, Qi Liu, Yu Shyr, Shilin Zhao
2024 J jnl
A distribution-free and analytic method for power and sample size calculation in single-cell differential expression.
Bioinform.
Chih-Yuan Hsu, Qi Liu, Yu Shyr
2024 J jnl
Cross-scale multi-instance learning for pathological image diagnosis.
Medical Image Anal.
Ruining Deng, Can Cui, Lucas W. Remedios, Shunxing Bao, R. Michael Womick, Sophie Chiron, Jia Li, Joseph T. Roland, Ken S. Lau, Qi Liu, Keith T. Wilson, Yaohong Wang, Lori A. Coburn, Bennett A. Landman, Yuankai Huo
2024 J jnl
Data-driven Nucleus Subclassification on Colon H&E using Style-transferred Digital Pathology.
CoRR
Lucas W. Remedios, Shunxing Bao, Samuel W. Remedios, Ho Hin Lee, Leon Y. Cai, Thomas Z. Li, Ruining Deng, Nancy R. Newlin, Adam M. Saunders, Can Cui, Jia Li, Qi Liu, Ken S. Lau, Joseph T. Roland, Mary K. Washington, Lori A. Coburn, Keith T. Wilson, Yuankai Huo, Bennett A. Landman
2024 J jnl
FindAdapt: A python package for fast and accurate adapter detection in small RNA sequencing.
PLoS Comput. Biol.
Hua-Chang Chen, Jing Wang, Yu Shyr, Qi Liu
2024 J jnl
Nucleus subtype classification using inter-modality learning.
CoRR
Lucas W. Remedios, Shunxing Bao, Samuel W. Remedios, Ho Hin Lee, Leon Y. Cai, Thomas Z. Li, Ruining Deng, Can Cui, Jia Li, Qi Liu, Ken S. Lau, Joseph T. Roland, Mary K. Washington, Lori A. Coburn, Keith T. Wilson, Yuankai Huo, Bennett A. Landman
2024 J jnl
scKWARN: Kernel-weighted-average robust normalization for single-cell RNA-seq data.
Bioinform.
Chih-Yuan Hsu, Chia-Jung Chang, Qi Liu, Yu Shyr
2023 — conf
Alleviating tiling effect by random walk sliding window in high-resolution histological whole slide image synthesis.
MIDL
Shunxing Bao, Ho Hin Lee, Qi Yang, Lucas Walker Remedios, Ruining Deng, Can Cui, Leon Yichen Cai, Kaiwen Xu, Xin Yu, Sophie Chiron, Yike Li, Nathan Heath Patterson, Yaohong Wang, Jia Li, Qi Liu, Ken S. Lau, Joseph T. Roland, Lori A. Coburn, Keith T. Wilson, Bennett A. Landman, Yuankai Huo
2023 J jnl
Cell Spatial Analysis in Crohn's Disease: Unveiling Local Cell Arrangement Pattern with Graph-based Signatures.
CoRR
Shunxing Bao, Sichen Zhu, Vasantha L. Kolachala, Lucas W. Remedios, Yeonjoo Hwang, Yutong Sun, Ruining Deng, Can Cui, Yike Li, Jia Li, Joseph T. Roland, Qi Liu, Ken S. Lau, Subra Kugathasan, Peng Qiu, Keith T. Wilson, Lori A. Coburn, Bennett A. Landman, Yuankai Huo
2023 J jnl
Cross-scale Multi-instance Learning for Pathological Image Diagnosis.
CoRR
Ruining Deng, Can Cui, Lucas W. Remedios, Shunxing Bao, R. Michael Womick, Sophie Chiron, Jia Li, Joseph T. Roland, Ken S. Lau, Qi Liu, Keith T. Wilson, Yaohong Wang, Lori A. Coburn, Bennett A. Landman, Yuankai Huo
2023 — conf
Feasibility of Universal Anomaly Detection Without Knowing the Abnormality in Medical Images.
MILLanD@MICCAI
Can Cui, Yaohong Wang, Shunxing Bao, Yucheng Tang, Ruining Deng, Lucas W. Remedios, Zuhayr Asad, Joseph T. Roland, Ken S. Lau, Qi Liu, Lori A. Coburn, Keith T. Wilson, Bennett A. Landman, Yuankai Huo
2023 J jnl
Feasibility of Universal Anomaly Detection without Knowing the Abnormality in Medical Images.
CoRR
Can Cui, Yaohong Wang, Shunxing Bao, Yucheng Tang, Ruining Deng, Lucas W. Remedios, Zuhayr Asad, Joseph T. Roland, Ken S. Lau, Qi Liu, Lori A. Coburn, Keith T. Wilson, Bennett A. Landman, Yuankai Huo
2023 — conf
Influence of cell-type ratio on spatially resolved single-cell transcriptomes using the Tangram algorithm: based on implementation on single-cell and MxIF data.
Digital and Computational Pathology
Can Cui, Shunxing Bao, Jia Li, Ruining Deng, Lucas W. Remedios, Zuhayr Asad, Sophie Chiron, Ken S. Lau, Yaohong Wang, Lori A. Coburn, Keith T. Wilson, Joseph T. Roland, Bennett A. Landman, Qi Liu, Yuankai Huo
2023 — conf
Topological-preserving membrane skeleton segmentation in multiplex immunofluorescence imaging.
Digital and Computational Pathology
Shunxing Bao, Can Cui, Jia Li, Yucheng Tang, Ho Hin Lee, Ruining Deng, Lucas W. Remedios, Xin Yu, Qi Yang, Sophie Chiron, Nathan Heath Patterson, Ken S. Lau, Qi Liu, Joseph T. Roland, Lori A. Coburn, Keith T. Wilson, Bennett A. Landman, Yuankai Huo
2022 J jnl
Comprehensive evaluation of noise reduction methods for single-cell RNA sequencing data.
Briefings Bioinform.
Shih-Kai Chu, Shilin Zhao, Yu Shyr, Qi Liu
2022 — conf
Cross-Scale Attention Guided Multi-instance Learning for Crohn's Disease Diagnosis with Pathological Images.
MMMI@MICCAI
Ruining Deng, Can Cui, Lucas W. Remedios, Shunxing Bao, R. Michael Womick, Sophie Chiron, Jia Li, Joseph T. Roland, Ken S. Lau, Qi Liu, Keith T. Wilson, Yaohong Wang, Lori A. Coburn, Bennett A. Landman, Yuankai Huo
2022 J jnl
Cross-scale Attention Guided Multi-instance Learning for Crohn's Disease Diagnosis with Pathological Images.
CoRR
Ruining Deng, Can Cui, Lucas W. Remedios, Shunxing Bao, R. Michael Womick, Sophie Chiron, Jia Li, Joseph T. Roland, Ken S. Lau, Qi Liu, Keith T. Wilson, Yaohong Wang, Lori A. Coburn, Bennett A. Landman, Yuankai Huo
2022 J jnl
Dysregulated ligand-receptor interactions from single-cell transcriptomics.
Bioinform.
Qi Liu, Chih-Yuan Hsu, Jia Li, Yu Shyr
2022 — conf
MxIF Q-score: Biology-Informed Quality Assurance for Multiplexed Immunofluorescence Imaging.
MOVI@MICCAI
Shunxing Bao, Jia Li, Can Cui, Yucheng Tang, Ruining Deng, Lucas W. Remedios, Ho Hin Lee, Sophie Chiron, Nathan Heath Patterson, Ken S. Lau, Lori A. Coburn, Keith T. Wilson, Joseph T. Roland, Bennett A. Landman, Qi Liu, Yuankai Huo
2022 J jnl
Quantifying and correcting slide-to-slide variation in multiplexed immunofluorescence images.
Bioinform.
Coleman R. Harris, Eliot T. McKinley, Joseph T. Roland, Qi Liu, Martha J. Shrubsole, Ken S. Lau, Robert J. Coffey, Julia Wrobel, Simon N. Vandekar
2019 J jnl
HACER: an atlas of human active enhancers to interpret regulatory variants.
Nucleic Acids Res.
Jing Wang, Xizhen Dai, Lynne D. Berry, Joy D. Cogan, Qi Liu, Yu Shyr
2019 J jnl
Systems-level network modeling of Small Cell Lung Cancer subtypes identifies master regulators and destabilizers.
PLoS Comput. Biol.
David J. Wooten, Sarah M. Groves, Darren R. Tyson, Qi Liu, Jing S. Lim, Réka Albert, Carlos F. Lopez, Julien Sage, Vito Quaranta
2019 J jnl
scRNABatchQC: multi-samples quality control for single cell RNA-seq data.
Bioinform.
Qi Liu, Quanhu Sheng, Jie Ping, Marisol Adelina Ramirez, Ken S. Lau, Robert J. Coffey, Yu Shyr
2017 J jnl
A systematic analysis of FDA-approved anticancer drugs.
BMC Syst. Biol.
Jingchun Sun, Qiang Wei, Yubo Zhou, Jingqi Wang, Qi Liu, Hua Xu
2017 J jnl
Investigating MicroRNA and transcription factor co-regulatory networks in colorectal cancer.
BMC Bioinform.
Hao Wang, Jiamao Luo, Chun Liu, Huilin Niu, Jing Wang, Qi Liu, Zhongming Zhao, Hua Xu, Yanqing Ding, Jingchun Sun, Qingling Zhang
2016 J jnl
An improved method to construct basic probability assignment based on the confusion matrix for classification problem.
Inf. Sci.
Xinyang Deng, Qi Liu, Yong Deng, Sankaran Mahadevan
2016 J jnl
Matrix games with payoffs of belief structures.
Appl. Math. Comput.
Xinyang Deng, Qi Liu, Yong Deng
2016 J jnl
Proceedings of the 15th Annual UT-KBRIN Bioinformatics Summit 2016: Cadiz, KY, USA. 8-10 April 2016.
BMC Bioinform.
Eric C. Rouchka, Julia H. Chariker, Benjamin J. Harrison, Juw Won Park, Xueyuan Cao, Stanley Pounds, Susana C. Raimondi, James R. Downing, Raul C. Ribeiro, Jeffrey Rubnitz, Jatinder Lamba, Bernie J. Daigle Jr., Deborah Burgess, Stephanie Gehrlich, John C. Carmen, Nicholas Johnson, Chandrakanth Emani, Kalpani De Silva, Michael P. Heaton, Theodore S. Kalbfleisch, Teeradache Viangteeravat, Rahul Mudunuri, Oluwaseun Ajayi, Fatih Sen, Eunice Y. Huang, Mohammad Mohebbi, Luaire Florian, Douglas J. Jackson, John F. Naber, Akm Sabbir, Sally R. Ellingson, Yuping Lu, Charles A. Phillips, Michael A. Langston, Rahul Kumar Sevakula, Raghuveer Thirukovalluru, Nishchal K. Verma, Yan Cui, Mohammed Sayed, Jing Wang, Qi Liu, Yu Shyr, Xiaofei Zhang, Naresh Prodduturi, Gavin R. Oliver, Diane Grill, Jie Na, Jeanette Eckel-Passow, Eric W. Klee, Michael M. Goodin, Mark L. Farman, Harrison Inocencio, Chanyong Jang, Jerzy W. Jaromczyk, Neil Moore, Kelly L. Sovacool, Leon Dent, Mike Izban, Sammed N. Mandape, Shruti S. Sakhare, Siddharth Pratap, Dana Marshall, M. Scotty Depriest, James N. MacLeod, Hanady Adam, Ethan Blandford, Joel Campbell, Joshua Castlen, Brittany Dixon, Ginger Gilbert, Aaron Hall, Philip Kreisle, Jessica Lasher, Bethany Oakes, Allison Speer, Maximilian Valentine, Naga Satya Venkateswara Ra Nagisetty, Rony Jose, Robert W. Rooney, David Hains
2016 J jnl
Self-adaptive win-stay-lose-shift reference selection mechanism promotes cooperation on a square lattice.
Appl. Math. Comput.
Xinyang Deng, Zhipeng Zhang, Yong Deng, Qi Liu, Shuhua Chang
2015 J jnl
A quantum extension to inspection game.
CoRR
Xinyang Deng, Yong Deng, Qi Liu, Zhen Wang
2015 J jnl
Identification of influential nodes in network of networks.
CoRR
Meizhu Li, Qi Zhang, Qi Liu, Yong Deng
2015 J jnl
Impact of Preference and Equivocators on Opinion Dynamics with Evolutionary Game Framework.
CoRR
Xinyang Deng, Zhen Wang, Qi Liu, Yong Deng, Yu Shyr
2015 J jnl
Newborns prediction based on a belief Markov chain model.
Appl. Intell.
Xinyang Deng, Qi Liu, Yong Deng
2015 J jnl
Quantum games of opinion formation based on the Marinatto-Weber quantum game scheme.
CoRR
Xinyang Deng, Yong Deng, Qi Liu, Zhen Wang
2014 J jnl
A belief-based evolutionarily stable strategy.
CoRR
Xinyang Deng, Zhen Wang, Qi Liu, Yong Deng, Sankaran Mahadevan
2014 J jnl
CLIP-EZ: a computational tool for HITS-CLIP data analysis.
BMC Bioinform.
Xue Zhong, Qi Liu, Yu Shyr
2014 J jnl
Generalized prisoner's dilemma.
CoRR
Xinyang Deng, Qi Liu, Yong Deng
2013 J jnl
An Adaptive Amoeba Algorithm for Shortest Path Tree Computation in Dynamic Graphs.
CoRR
Xiaoge Zhang, Qi Liu, Yong Hu, Felix T. S. Chan, Sankaran Mahadevan, Zili Zhang, Yong Deng
2013 J jnl
Gene and isoform expression signatures associated with tumor stage in kidney renal clear cell carcinoma.
BMC Syst. Biol.
Qi Liu, Shilin Zhao, Pei-Fang Su, Shyr Yu
2011 J jnl
The role of Hepatitis C Virus in the dynamic protein interaction networks of hepatocellular cirrhosis and carcinoma.
Int. J. Comput. Biol. Drug Des.
Tao Huang, Lei Liu, Qi Liu, Guohui Ding, Yejun Tan, Zhidong Tu, Yixue Li, Hongyue Dai, Lu Xie
2010 — conf
Dysfunctional gene/protein networks in hepatitis C virus-induced hepatocellular cirrhosis and carcinoma.
BCB
Tao Huang, Guohui Ding, Yixue Li, Lei Liu, Eugene Tan, Hongyue Dai, Qi Liu, Zhidong Tu, Lu Xie
2010 J jnl
Erratum to "Combining belief functions based on distance of evidence" [Decision Support Systems Volume(38/3)489-493].
Decis. Support Syst.
Deqiang Han, Yong Deng, Qi Liu
2010 J jnl
TF-centered downstream gene set enrichment analysis: Inference of causal regulators by integrating TF-DNA interactions and protein post-translational modifications information.
BMC Bioinform.
Qi Liu, Yejun Tan, Tao Huang, Guohui Ding, Zhidong Tu, Lei Liu, Yixue Li, Hongyue Dai, Lu Xie
2008 J jnl
A subjective methodology for risk quantification based on generalized fuzzy numbers.
Int. J. Gen. Syst.
Qi Liu, Jia Xiong, Yong Deng
2007 J jnl
InPrePPI: an integrated evaluation method based on genomic context for predicting protein-protein interactions in prokaryotic genomes.
BMC Bioinform.
Jingchun Sun, Yan Sun, Guohui Ding, Qi Liu, Chuan Wang, Youyu He, Tieliu Shi, Yixue Li, Zhongming Zhao
2006 J jnl
Insights into the Coupling of Duplication Events and Macroevolution from an Age Profile of Animal Transmembrane Gene Families.
PLoS Comput. Biol.
Guohui Ding, Jiuhong Kang, Qi Liu, Tieliu Shi, Gang Pei, Yixue Li
2006 J jnl
Ranking fuzzy numbers with an area method using radius of gyration.
Comput. Math. Appl.
Yong Deng, Zhenfu Zhu, Qi Liu
2005 J jnl
A topsis-based centroid-index ranking method of fuzzy numbers and its application in decision-making.
Cybern. Syst.
Yong Deng, Qi Liu
2005 J jnl
Refined phylogenetic profiles method for predicting protein-protein interactions.
Bioinform.
Jingchun Sun, Jinlin Xu, Zhen Liu, Qi Liu, Aimin Zhao, Tieliu Shi, Yi-Xue Li
2004 J jnl
A new similarity measure of generalized fuzzy numbers and its application to pattern recognition.
Pattern Recognit. Lett.
Yong Deng, Wenkang Shi, Feng Du, Qi Liu
2004 J jnl
Combining belief functions based on distance of evidence.
Decis. Support Syst.
Yong Deng, Wenkang Shi, Zhenfu Zhu, Qi Liu
2004 J jnl
Scoring hidden Markov models to discriminate -barrel membrane proteins.
Comput. Biol. Chem.
Yong Deng, Qi Liu, Yi-Xue Li
2003 J jnl
A HMM-based method to predict the transmembrane regions of \beta-barrel membrane proteins.
Comput. Biol. Chem.
Qi Liu, Yisheng Zhu, Baohua Wang, Yi-Xue Li
2003 J jnl
Identification of -barrel membrane proteins based on amino acid composition properties and predicted secondary structure.
Comput. Biol. Chem.
Qi Liu, Yisheng Zhu, Baohua Wang, Yi-Xue Li