A HMM-based method to predict the transmembrane regions of beta-barrel membrane proteins. - Qi Liu 024; Yisheng Zhu; Baohua Wang; Yi-Xue Li (Comput. Biol. Chem., 2003)

Identification of -barrel membrane proteins based on amino acid composition properties and predicted secondary structure. - Qi Liu 024; Yisheng Zhu; Baohua Wang; Yi-Xue Li (Comput. Biol. Chem., 2003)

Scoring hidden Markov models to discriminate -barrel membrane proteins. - Yong Deng 001; Qi Liu 024; Yi-Xue Li (Comput. Biol. Chem., 2004)

Combining belief functions based on distance of evidence. - Yong Deng 001; Wenkang Shi; Zhenfu Zhu; Qi Liu 024 (Decis. Support Syst., 2004)

A new similarity measure of generalized fuzzy numbers and its application to pattern recognition. - Yong Deng 001; Wenkang Shi; Feng Du; Qi Liu 024 (Pattern Recognit. Lett., 2004)

Refined phylogenetic profiles method for predicting protein-protein interactions. - Jingchun Sun; Jinlin Xu; Zhen Liu; Qi Liu 024; Aimin Zhao; Tieliu Shi; Yi-Xue Li (Bioinform., 2005)

A topsis-based centroid-index ranking method of fuzzy numbers and its application in decision-making. - Yong Deng 001; Qi Liu 024 (Cybern. Syst., 2005)

Ranking fuzzy numbers with an area method using radius of gyration. - Yong Deng 001; Zhenfu Zhu; Qi Liu 024 (Comput. Math. Appl., 2006)

Insights into the Coupling of Duplication Events and Macroevolution from an Age Profile of Animal Transmembrane Gene Families. - Guohui Ding 001; Jiuhong Kang; Qi Liu 024; Tieliu Shi; Gang Pei; Yixue Li (PLoS Comput. Biol., 2006)

InPrePPI: an integrated evaluation method based on genomic context for predicting protein-protein interactions in prokaryotic genomes. - Jingchun Sun; Yan Sun; Guohui Ding 001; Qi Liu 024; Chuan Wang; Youyu He; Tieliu Shi; Yixue Li; Zhongming Zhao (BMC Bioinform., 2007)

A subjective methodology for risk quantification based on generalized fuzzy numbers. - Qi Liu 024; Jia Xiong; Yong Deng 001 (Int. J. Gen. Syst., 2008)

Dysfunctional gene/protein networks in hepatitis C virus-induced hepatocellular cirrhosis and carcinoma. - Tao Huang 004; Guohui Ding 001; Yixue Li; Lei Liu; Eugene Tan; Hongyue Dai; Qi Liu 024; Zhidong Tu; Lu Xie (BCB, 2010)

TF-centered downstream gene set enrichment analysis: Inference of causal regulators by integrating TF-DNA interactions and protein post-translational modifications information. - Qi Liu 024; Yejun Tan; Tao Huang 004; Guohui Ding 001; Zhidong Tu; Lei Liu; Yixue Li; Hongyue Dai; Lu Xie (BMC Bioinform., 2010)

Erratum to "Combining belief functions based on distance of evidence" [Decision Support Systems Volume(38/3)489-493]. - Deqiang Han; Yong Deng 001; Qi Liu 024 (Decis. Support Syst., 2010)

The role of Hepatitis C Virus in the dynamic protein interaction networks of hepatocellular cirrhosis and carcinoma. - Tao Huang 004; Lei Liu; Qi Liu 024; Guohui Ding 001; Yejun Tan; Zhidong Tu; Yixue Li; Hongyue Dai; Lu Xie (Int. J. Comput. Biol. Drug Des., 2011)

Gene and isoform expression signatures associated with tumor stage in kidney renal clear cell carcinoma. - Qi Liu 024; Shilin Zhao; Pei-Fang Su; Shyr Yu (BMC Syst. Biol., 2013)

An Adaptive Amoeba Algorithm for Shortest Path Tree Computation in Dynamic Graphs. - Xiaoge Zhang 001; Qi Liu 024; Yong Hu 002; Felix T. S. Chan; Sankaran Mahadevan; Zili Zhang 001; Yong Deng 001 (CoRR, 2013)

CLIP-EZ: a computational tool for HITS-CLIP data analysis. - Xue Zhong; Qi Liu 024; Yu Shyr (BMC Bioinform., 2014)

Generalized prisoner's dilemma. - Xinyang Deng; Qi Liu 024; Yong Deng 001 (CoRR, 2014)

A belief-based evolutionarily stable strategy. - Xinyang Deng; Zhen Wang; Qi Liu 024; Yong Deng 001; Sankaran Mahadevan (CoRR, 2014)

Newborns prediction based on a belief Markov chain model. - Xinyang Deng; Qi Liu 024; Yong Deng 001 (Appl. Intell., 2015)

A quantum extension to inspection game. - Xinyang Deng; Yong Deng 001; Qi Liu 024; Zhen Wang (CoRR, 2015)

Quantum games of opinion formation based on the Marinatto-Weber quantum game scheme. - Xinyang Deng; Yong Deng 001; Qi Liu 024; Zhen Wang (CoRR, 2015)

Impact of Preference and Equivocators on Opinion Dynamics with Evolutionary Game Framework. - Xinyang Deng; Zhen Wang; Qi Liu 024; Yong Deng 001; Yu Shyr (CoRR, 2015)

Identification of influential nodes in network of networks. - Meizhu Li; Qi Zhang 022; Qi Liu 024; Yong Deng 001 (CoRR, 2015)

Matrix games with payoffs of belief structures. - Xinyang Deng; Qi Liu 024; Yong Deng 001 (Appl. Math. Comput., 2016)

Self-adaptive win-stay-lose-shift reference selection mechanism promotes cooperation on a square lattice. - Xinyang Deng; Zhipeng Zhang; Yong Deng 001; Qi Liu 024; Shuhua Chang (Appl. Math. Comput., 2016)

An improved method to construct basic probability assignment based on the confusion matrix for classification problem. - Xinyang Deng; Qi Liu 024; Yong Deng 001; Sankaran Mahadevan (Inf. Sci., 2016)

Proceedings of the 15th Annual UT-KBRIN Bioinformatics Summit 2016: Cadiz, KY, USA. 8-10 April 2016. - 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.; et al. (BMC Bioinform., 2016)

Investigating MicroRNA and transcription factor co-regulatory networks in colorectal cancer. - Hao Wang; Jiamao Luo; Chun Liu; Huilin Niu; Jing Wang 026; Qi Liu 024; Zhongming Zhao; Hua Xu 001; Yanqing Ding; Jingchun Sun; Qingling Zhang 003 (BMC Bioinform., 2017)

A systematic analysis of FDA-approved anticancer drugs. - Jingchun Sun; Qiang Wei 002; Yubo Zhou; Jingqi Wang; Qi Liu 024; Hua Xu 001 (BMC Syst. Biol., 2017)

scRNABatchQC: multi-samples quality control for single cell RNA-seq data. - Qi Liu 024; Quanhu Sheng; Jie Ping; Marisol Adelina Ramirez; Ken S. Lau; Robert J. Coffey; Yu Shyr (Bioinform., 2019)

HACER: an atlas of human active enhancers to interpret regulatory variants. - Jing Wang 026; Xizhen Dai; Lynne D. Berry; Joy D. Cogan; Qi Liu 024; Yu Shyr (Nucleic Acids Res., 2019)

Systems-level network modeling of Small Cell Lung Cancer subtypes identifies master regulators and destabilizers. - David J. Wooten; Sarah M. Groves; Darren R. Tyson; Qi Liu 024; Jing S. Lim; Réka Albert; Carlos F. Lopez; Julien Sage; Vito Quaranta (PLoS Comput. Biol., 2019)

MxIF Q-score: Biology-Informed Quality Assurance for Multiplexed Immunofluorescence Imaging. - Shunxing Bao; Jia Li 027; Can Cui 006; Yucheng Tang; Ruining Deng; Lucas W. Remedios; Ho Hin Lee; Sophie Chiron; Nathan Heath Patterson; Ken S. Lau; Lori A. Coburn; Keith T. Wilson; et al. (MOVI@MICCAI, 2022)

Cross-Scale Attention Guided Multi-instance Learning for Crohn's Disease Diagnosis with Pathological Images. - Ruining Deng; Can Cui 006; Lucas W. Remedios; Shunxing Bao; R. Michael Womick; Sophie Chiron; Jia Li 027; Joseph T. Roland; Ken S. Lau; Qi Liu 024; Keith T. Wilson; Yaohong Wang; et al. (MMMI@MICCAI, 2022)

Comprehensive evaluation of noise reduction methods for single-cell RNA sequencing data. - Shih-Kai Chu; Shilin Zhao; Yu Shyr; Qi Liu 024 (Briefings Bioinform., 2022)

Quantifying and correcting slide-to-slide variation in multiplexed immunofluorescence images. - Coleman R. Harris; Eliot T. McKinley; Joseph T. Roland; Qi Liu 024; Martha J. Shrubsole; Ken S. Lau; Robert J. Coffey; Julia Wrobel; Simon N. Vandekar (Bioinform., 2022)

Dysregulated ligand-receptor interactions from single-cell transcriptomics. - Qi Liu 024; Chih-Yuan Hsu; Jia Li 027; Yu Shyr (Bioinform., 2022)

Feasibility of Universal Anomaly Detection Without Knowing the Abnormality in Medical Images. - Can Cui 006; Yaohong Wang; Shunxing Bao; Yucheng Tang; Ruining Deng; Lucas W. Remedios; Zuhayr Asad; Joseph T. Roland; Ken S. Lau; Qi Liu 024; Lori A. Coburn; Keith T. Wilson; et al. (MILLanD@MICCAI, 2023)

Alleviating tiling effect by random walk sliding window in high-resolution histological whole slide image synthesis. - Shunxing Bao; Ho Hin Lee; Qi Yang 004; Lucas Walker Remedios; Ruining Deng; Can Cui 006; Leon Yichen Cai; Kaiwen Xu; Xin Yu 010; Sophie Chiron; Yike Li; Nathan Heath Patterson; et al. (MIDL, 2023)

Topological-preserving membrane skeleton segmentation in multiplex immunofluorescence imaging. - Shunxing Bao; Can Cui 006; Jia Li 027; Yucheng Tang; Ho Hin Lee; Ruining Deng; Lucas W. Remedios; Xin Yu 010; Qi Yang 004; Sophie Chiron; Nathan Heath Patterson; Ken S. Lau; et al. (Digital and Computational Pathology, 2023)

Influence of cell-type ratio on spatially resolved single-cell transcriptomes using the Tangram algorithm: based on implementation on single-cell and MxIF data. - Can Cui 006; Shunxing Bao; Jia Li 027; Ruining Deng; Lucas W. Remedios; Zuhayr Asad; Sophie Chiron; Ken S. Lau; Yaohong Wang; Lori A. Coburn; Keith T. Wilson; Joseph T. Roland; et al. (Digital and Computational Pathology, 2023)

Cell Spatial Analysis in Crohn's Disease: Unveiling Local Cell Arrangement Pattern with Graph-based Signatures. - Shunxing Bao; Sichen Zhu; Vasantha L. Kolachala; Lucas W. Remedios; Yeonjoo Hwang; Yutong Sun; Ruining Deng; Can Cui 006; Yike Li; Jia Li 027; Joseph T. Roland; Qi Liu 024; et al. (CoRR, 2023)

Nucleus subtype classification using inter-modality learning. - Lucas W. Remedios; Shunxing Bao; Samuel W. Remedios; Ho Hin Lee; Leon Y. Cai; Thomas Z. Li; Ruining Deng; Can Cui 006; Jia Li 027; Qi Liu 024; Ken S. Lau; Joseph T. Roland; et al. (CoRR, 2024)

Data-driven Nucleus Subclassification on Colon H&E using Style-transferred Digital Pathology. - 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 006; Jia Li 027; Qi Liu 024; et al. (CoRR, 2024)

Cross-scale multi-instance learning for pathological image diagnosis. - Ruining Deng; Can Cui 006; Lucas W. Remedios; Shunxing Bao; R. Michael Womick; Sophie Chiron; Jia Li 027; Joseph T. Roland; Ken S. Lau; Qi Liu 024; Keith T. Wilson; Yaohong Wang; et al. (Medical Image Anal., 2024)

FindAdapt: A python package for fast and accurate adapter detection in small RNA sequencing. - Hua-Chang Chen; Jing Wang 026; Yu Shyr; Qi Liu 024 (PLoS Comput. Biol., 2024)

stImage: a versatile framework for optimizing spatial transcriptomic analysis through customizable deep histology and location informed integration. - Yu Wang; Haichun Yang; Ruining Deng; Yuankai Huo; Qi Liu 024; Yu Shyr; Shilin Zhao (Briefings Bioinform., 2025)