Yu Shyr - RankMe

49 papers Misc 1Journal 48

Year	Rank	Type	Title / 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`	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`	scKWARN: Kernel-weighted-average robust normalization for single-cell RNA-seq data. Bioinform. Chih-Yuan Hsu, Chia-Jung Chang, Qi Liu, Yu Shyr
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	J	`jnl`	Dysregulated ligand-receptor interactions from single-cell transcriptomics. Bioinform. Qi Liu, Chih-Yuan Hsu, Jia Li, Yu Shyr
2021	J	`jnl`	MetaGSCA: A tool for meta-analysis of gene set differential coexpression. PLoS Comput. Biol. Yan Guo, Hui Yu, Haocan Song, Jiapeng He, Olufunmilola Oyebamiji, Huining Kang, Jie Ping, Scott Ness, Yu Shyr, Fei Ye
2021	J	`jnl`	PheWAS-ME: a web-app for interactive exploration of multimorbidity patterns in PheWAS. Bioinform. Nick Strayer, Jana K. Shirey-Rice, Yu Shyr, Joshua C. Denny, Jill M. Pulley, Yaomin Xu
2020	J	`jnl`	Bayesian Inference of Lymph Node Ratio Estimation and Survival Prognosis for Breast Cancer Patients. IEEE J. Biomed. Health Informatics Jing Teng, Assem Abdygametova, Jing Du, Bian Ma, Rong Zhou, Yu Shyr, Fei Ye
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`	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
2018	J	`jnl`	Power and sample size calculations for high-throughput sequencing-based experiments. Briefings Bioinform. Chung-I Li, David C. Samuels, Ying-Yong Zhao, Yu Shyr, Yan Guo
2018	J	`jnl`	RnaSeqSampleSize: real data based sample size estimation for RNA sequencing. BMC Bioinform. Shilin Zhao, Chung-I Li, Yan Guo, Quanhu Sheng, Yu Shyr
2018	J	`jnl`	Strategies for processing and quality control of Illumina genotyping arrays. Briefings Bioinform. Shilin Zhao, Jing Wang, David C. Samuels, Quanghu Sheng, Yu Shyr, Yan Guo
2017	J	`jnl`	Functional data classification using covariate-adjusted subspace projection. Comput. Stat. Data Anal. Pai-Ling Li, Jeng-Min Chiou, Yu Shyr
2017	J	`jnl`	StrandScript: evaluation of Illumina genotyping array design and strand correction. Bioinform. Jing Wang, David C. Samuels, Yu Shyr, Yan Guo
2016	J	`jnl`	Evidence Combination From an Evolutionary Game Theory Perspective. IEEE Trans. Cybern. Xinyang Deng, Deqiang Han, Jean Dezert, Yong Deng, Yu Shyr
2016	J	`jnl`	Mitochondria sequence mapping strategies and practicability of mitochondria variant detection from exome and RNA sequencing data. Briefings Bioinform. Pan Zhang, David C. Samuels, Brian D. Lehmann, Thomas Stricker, Jennifer A. Pietenpol, Yu Shyr, Yan Guo
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
2015	J	`jnl`	Genome measures used for quality control are dependent on gene function and ancestry. Bioinform. Jing Wang, Leon Raskin, David C. Samuels, Yu Shyr, Yan Guo
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`	NGSPERL: a semi-automated framework for large scale next generation sequencing data analysis. Int. J. Comput. Biol. Drug Des. Quanhu Sheng, Shilin Zhao, Mingsheng Guo, Yu Shyr
2015	Misc	`conf`	PheWAS Network Analysis and Visualization. AMIA 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
2015	J	`jnl`	Population structure analysis on 2504 individuals across 26 ancestries using bioinformatics approaches. BMC Bioinform. Jing Wang, David C. Samuels, Yu Shyr, Yan Guo
2015	J	`jnl`	Practicality of identifying mitochondria variants from exome and RNAseq data. BMC Bioinform. Pan Zhang, David C. Samuels, Brian D. Lehmann, Thomas Stricker, Jennifer A. Pietenpol, Yu Shyr, Yan Guo
2015	J	`jnl`	SWATH-MS in proteomics: current status. Int. J. Comput. Biol. Drug Des. Jing Wang, Quanhu Sheng, Yu Shyr
2014	J	`jnl`	A comparison of microRNA sequencing reproducibility and noise reduction using mirVana and TRIzol isolation methods. Int. J. Comput. Biol. Drug Des. Yan Guo, Amma Bosompem, Xue Zhong, Travis Clark, Yu Shyr, Annette S. Kim
2014	J	`jnl`	CLIP-EZ: a computational tool for HITS-CLIP data analysis. BMC Bioinform. Xue Zhong, Qi Liu, Yu Shyr
2014	J	`jnl`	Detection of internal exon deletion with exon Del. BMC Bioinform. Yan Guo, Shilin Zhao, Brian D. Lehmann, Quanhu Sheng, Timothy M. Shaver, Thomas Stricker, Jennifer A. Pietenpol, Yu Shyr
2014	J	`jnl`	DupChecker: a bioconductor package for checking high-throughput genomic data redundancy in meta-analysis. BMC Bioinform. Quanhu Sheng, Yu Shyr, Xi Chen
2014	J	`jnl`	Heatmap3: an improved heatmap package with more powerful and convenient features. BMC Bioinform. Shilin Zhao, Yan Guo, Quanhu Sheng, Yu Shyr
2014	J	`jnl`	Implementation and evaluation of an integrated computerized asthma management system in a pediatric emergency department: A randomized clinical trial. Int. J. Medical Informatics Judith W. Dexheimer, Thomas J. Abramo, Donald H. Arnold, Kevin B. Johnson, Yu Shyr, Fei Ye, Kang-Hsien Fan, Neal Patel, Dominik Aronsky
2014	J	`jnl`	Sample size determination for paired right-censored data based on the difference of Kaplan-Meier estimates. Comput. Stat. Data Anal. Pei-Fang Su, Chung-I Li, Yu Shyr
2013	J	`jnl`	An asthma management system in a pediatric emergency department. Int. J. Medical Informatics Judith W. Dexheimer, Thomas J. Abramo, Donald H. Arnold, Kevin B. Johnson, Yu Shyr, Fei Ye, Kang-Hsien Fan, Neal Patel, Dominik Aronsky
2013	J	`jnl`	Co-expression network analysis identifies Spleen Tyrosine Kinase (SYK) as a candidate oncogenic driver in a subset of small-cell lung cancer. BMC Syst. Biol. Akshata R. Udyavar, Megan D. Hoeksema, Jonathan E. Clark, Yong Zou, Zuojian Tang, Zhiguo Li, Ming Li, Heidi Chen, Alexander R. Statnikov, Yu Shyr, Daniel C. Liebler, John K. Field, Rosana Eisenberg, Lourdes Estrada, Pierre P. Massion, Vito Quaranta
2013	J	`jnl`	MitoSeek: extracting mitochondria information and performing high-throughput mitochondria sequencing analysis. Bioinform. Yan Guo, Jiang Li, Chung-I Li, Yu Shyr, David C. Samuels
2013	J	`jnl`	Sample size calculation based on exact test for assessing differential expression analysis in RNA-seq data. BMC Bioinform. Chung-I Li, Pei-Fang Su, Yu Shyr
2013	J	`jnl`	Sample size calculation for differential expression analysis of RNA-seq data under Poisson distribution. Int. J. Comput. Biol. Drug Des. Chung-I Li, Pei-Fang Su, Yan Guo, Yu Shyr
2012	J	`jnl`	Advances in systems biology: computational algorithms and applications. BMC Syst. Biol. Yufei Huang, Zhongming Zhao, Hua Xu, Yu Shyr, Bing Zhang
2012	J	`jnl`	Statistical aspects of omics data analysis using the random compound covariate. BMC Syst. Biol. Pei-Fang Su, Xi Chen, Heidi Chen, Yu Shyr
2011	J	`jnl`	Analyzing survival curves at a fixed point in time for paired and clustered right-censored data. Comput. Stat. Data Anal. Pei-Fang Su, Yunchan Chi, Chung-I Li, Yu Shyr, Yi-De Liao
2011	J	`jnl`	Wave-spec: a preprocessing package for mass spectrometry data. Bioinform. Ming Li, Shuo Chen, Joan Zhang, Heidi Chen, Yu Shyr
2009	J	`jnl`	A novel comprehensive wave-form MS data processing method. Bioinform. Shuo Chen, Ming Li, Don Hong, Dean Billheimer, Huiming Li, Baogang J. Xu, Yu Shyr
2009	J	`jnl`	Web-based interrogation of gene expression signatures using EXALT. BMC Bioinform. Jun Wu, Qingchao Qiu, Lu Xie, Joseph Fullerton, Jian Yu, Yu Shyr, Alfred L. George Jr., Yajun Yi
2008	J	`jnl`	Use of normalization methods for analysis of microarrays containing a high degree of gene effects. BMC Bioinform. Terri T. Ni, William J. Lemon, Yu Shyr, Tao P. Zhong
2007	J	`jnl`	A Practical Question Based on Cross-Platform microarray Data Normalization: are Boec More Like Large Vessel or microvascular Endothelial Cells or Neither of Them? J. Bioinform. Comput. Biol. Aixiang Jiang, Wei Pan, Liming C. Milbauer, Yu Shyr, Robert P. Hebbel
2007	J	`jnl`	Wavelet-based procedures for proteomic mass spectrometry data processing. Comput. Stat. Data Anal. Shuo Chen, Don Hong, Yu Shyr
2000	J	`jnl`	Registration of Physical Space to Laparoscopic Image Space for use in Minimally Invasive Hepatic Surgery. IEEE Trans. Medical Imaging James D. Stefansic, Alan J. Herline, Yu Shyr, William C. Chapman, J. Michael Fitzpatrick, Robert L. Galloway
1998	J	`jnl`	Visual Assessment of the Accuracy of Retrospective Registration of MR and CT Images of the Brain. IEEE Trans. Medical Imaging J. Michael Fitzpatrick, Derek L. G. Hill, Yu Shyr, Jay B. West, Colin Studholme, Calvin R. Maurer Jr.