Visual Assessment of the Accuracy of Retrospective Registration of MR and CT Images of the Brain. - J. Michael Fitzpatrick; Derek L. G. Hill; Yu Shyr; Jay B. West; Colin Studholme; Calvin R. Maurer Jr. (IEEE Trans. Medical Imaging, 1998)

Registration of Physical Space to Laparoscopic Image Space for use in Minimally Invasive Hepatic Surgery. - James D. Stefansic; Alan J. Herline; Yu Shyr; William C. Chapman; J. Michael Fitzpatrick; Robert L. Galloway (IEEE Trans. Medical Imaging, 2000)

Wavelet-based procedures for proteomic mass spectrometry data processing. - Shuo Chen; Don Hong; Yu Shyr (Comput. Stat. Data Anal., 2007)

A Practical Question Based on Cross-Platform microarray Data Normalization: are Boec More Like Large Vessel or microvascular Endothelial Cells or Neither of Them? - Aixiang Jiang; Wei Pan 011; Liming C. Milbauer; Yu Shyr; Robert P. Hebbel (J. Bioinform. Comput. Biol., 2007)

Use of normalization methods for analysis of microarrays containing a high degree of gene effects. - Terri T. Ni; William J. Lemon; Yu Shyr; Tao P. Zhong (BMC Bioinform., 2008)

A novel comprehensive wave-form MS data processing method. - Shuo Chen; Ming Li 022; Don Hong; Dean Billheimer; Huiming Li; Baogang J. Xu; Yu Shyr (Bioinform., 2009)

Web-based interrogation of gene expression signatures using EXALT. - Jun Wu; Qingchao Qiu; Lu Xie; Joseph Fullerton; Jian Yu; Yu Shyr; Alfred L. George Jr.; Yajun Yi (BMC Bioinform., 2009)

Wave-spec: a preprocessing package for mass spectrometry data. - Ming Li 022; Shuo Chen; Joan Zhang; Heidi Chen; Yu Shyr (Bioinform., 2011)

Analyzing survival curves at a fixed point in time for paired and clustered right-censored data. - Pei-Fang Su; Yunchan Chi; Chung-I Li; Yu Shyr; Yi-De Liao (Comput. Stat. Data Anal., 2011)

Advances in systems biology: computational algorithms and applications. - Yufei Huang 001; Zhongming Zhao; Hua Xu 001; Yu Shyr; Bing Zhang 003 (BMC Syst. Biol., 2012)

Statistical aspects of omics data analysis using the random compound covariate. - Pei-Fang Su; Xi Chen; Heidi Chen; Yu Shyr (BMC Syst. Biol., 2012)

MitoSeek: extracting mitochondria information and performing high-throughput mitochondria sequencing analysis. - Yan Guo; Jiang Li; Chung-I Li; Yu Shyr; David C. Samuels (Bioinform., 2013)

Sample size calculation based on exact test for assessing differential expression analysis in RNA-seq data. - Chung-I Li; Pei-Fang Su; Yu Shyr (BMC Bioinform., 2013)

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)

Co-expression network analysis identifies Spleen Tyrosine Kinase (SYK) as a candidate oncogenic driver in a subset of small-cell lung cancer. - Akshata R. Udyavar; Megan D. Hoeksema; Jonathan E. Clark; Yong Zou; Zuojian Tang; Zhiguo Li; Ming Li 022; Heidi Chen; Alexander R. Statnikov; Yu Shyr; Daniel C. Liebler; John K. Field; et al. (BMC Syst. Biol., 2013)

Sample size calculation for differential expression analysis of RNA-seq data under Poisson distribution. - Chung-I Li; Pei-Fang Su; Yan Guo; Yu Shyr (Int. J. Comput. Biol. Drug Des., 2013)

An asthma management system in a pediatric emergency department. - Judith W. Dexheimer; Thomas J. Abramo; Donald H. Arnold; Kevin B. Johnson; Yu Shyr; Fei Ye; Kang-Hsien Fan; Neal Patel; Dominik Aronsky (Int. J. Medical Informatics, 2013)

Detection of internal exon deletion with exon Del. - Yan Guo; Shilin Zhao; Brian D. Lehmann; Quanhu Sheng; Timothy M. Shaver; Thomas Stricker; Jennifer A. Pietenpol; Yu Shyr (BMC Bioinform., 2014)

DupChecker: a bioconductor package for checking high-throughput genomic data redundancy in meta-analysis. - Quanhu Sheng; Yu Shyr; Xi Chen (BMC Bioinform., 2014)

Heatmap3: an improved heatmap package with more powerful and convenient features. - Shilin Zhao; Yan Guo; Quanhu Sheng; Yu Shyr (BMC Bioinform., 2014)

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

Sample size determination for paired right-censored data based on the difference of Kaplan-Meier estimates. - Pei-Fang Su; Chung-I Li; Yu Shyr (Comput. Stat. Data Anal., 2014)

A comparison of microRNA sequencing reproducibility and noise reduction using mirVana and TRIzol isolation methods. - Yan Guo; Amma Bosompem; Xue Zhong; Travis Clark; Yu Shyr; Annette S. Kim (Int. J. Comput. Biol. Drug Des., 2014)

Implementation and evaluation of an integrated computerized asthma management system in a pediatric emergency department: A randomized clinical trial. - Judith W. Dexheimer; Thomas J. Abramo; Donald H. Arnold; Kevin B. Johnson; Yu Shyr; Fei Ye; Kang-Hsien Fan; Neal Patel; Dominik Aronsky (Int. J. Medical Informatics, 2014)

PheWAS Network Analysis and Visualization. - Yaomin Xu; Todd L. Edwards; Lisa Bastarache; Rebecca N. Jerome; Shilin Zho; Eric Torstenson; Wei-Qi Wei; Jana Shirey-Rice; Erica A. Bowton; Yu Shyr; Jill M. Pulley; Joshua C. Denny (AMIA, 2015)

Genome measures used for quality control are dependent on gene function and ancestry. - Jing Wang 026; Leon Raskin; David C. Samuels; Yu Shyr; Yan Guo (Bioinform., 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)

NGSPERL: a semi-automated framework for large scale next generation sequencing data analysis. - Quanhu Sheng; Shilin Zhao; Mingsheng Guo; Yu Shyr (Int. J. Comput. Biol. Drug Des., 2015)

SWATH-MS in proteomics: current status. - Jing Wang 026; Quanhu Sheng; Yu Shyr (Int. J. Comput. Biol. Drug Des., 2015)

Population structure analysis on 2504 individuals across 26 ancestries using bioinformatics approaches. - Jing Wang 026; David C. Samuels; Yu Shyr; Yan Guo (BMC Bioinform., 2015)

Practicality of identifying mitochondria variants from exome and RNAseq data. - Pan Zhang; David C. Samuels; Brian D. Lehmann; Thomas Stricker; Jennifer A. Pietenpol; Yu Shyr; Yan Guo (BMC Bioinform., 2015)

Mitochondria sequence mapping strategies and practicability of mitochondria variant detection from exome and RNA sequencing data. - Pan Zhang; David C. Samuels; Brian D. Lehmann; Thomas Stricker; Jennifer A. Pietenpol; Yu Shyr; Yan Guo (Briefings Bioinform., 2016)

Evidence Combination From an Evolutionary Game Theory Perspective. - Xinyang Deng; Deqiang Han; Jean Dezert; Yong Deng 001; Yu Shyr (IEEE Trans. Cybern., 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)

StrandScript: evaluation of Illumina genotyping array design and strand correction. - Jing Wang 026; David C. Samuels; Yu Shyr; Yan Guo (Bioinform., 2017)

Functional data classification using covariate-adjusted subspace projection. - Pai-Ling Li; Jeng-Min Chiou; Yu Shyr (Comput. Stat. Data Anal., 2017)

Power and sample size calculations for high-throughput sequencing-based experiments. - Chung-I Li; David C. Samuels; Ying-Yong Zhao; Yu Shyr; Yan Guo (Briefings Bioinform., 2018)

Strategies for processing and quality control of Illumina genotyping arrays. - Shilin Zhao; Jing Wang 026; David C. Samuels; Quanghu Sheng; Yu Shyr; Yan Guo (Briefings Bioinform., 2018)

RnaSeqSampleSize: real data based sample size estimation for RNA sequencing. - Shilin Zhao; Chung-I Li; Yan Guo; Quanhu Sheng; Yu Shyr (BMC Bioinform., 2018)

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)

Bayesian Inference of Lymph Node Ratio Estimation and Survival Prognosis for Breast Cancer Patients. - Jing Teng; Assem Abdygametova; Jing Du; Bian Ma; Rong Zhou; Yu Shyr; Fei Ye (IEEE J. Biomed. Health Informatics, 2020)

PheWAS-ME: a web-app for interactive exploration of multimorbidity patterns in PheWAS. - Nick Strayer; Jana K. Shirey-Rice; Yu Shyr; Joshua C. Denny; Jill M. Pulley; Yaomin Xu (Bioinform., 2021)

MetaGSCA: A tool for meta-analysis of gene set differential coexpression. - Yan Guo; Hui Yu; Haocan Song; Jiapeng He; Olufunmilola Oyebamiji; Huining Kang; Jie Ping; Scott Ness; Yu Shyr; Fei Ye (PLoS Comput. Biol., 2021)

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)

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

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)