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Journal Articles
- 2024
[j45]Hua-Chang Chen, Jing Wang, Yu Shyr, Qi Liu
:
FindAdapt: A python package for fast and accurate adapter detection in small RNA sequencing. PLoS Comput. Biol. 20(1) (2024)- 2022
- [j44]Shih-Kai Chu, Shilin Zhao, Yu Shyr, Qi Liu:
Comprehensive evaluation of noise reduction methods for single-cell RNA sequencing data. Briefings Bioinform. 23(2) (2022) - [j43]Qi Liu, Chih-Yuan Hsu, Jia Li, Yu Shyr:
Dysregulated ligand-receptor interactions from single-cell transcriptomics. Bioinform. 38(12): 3216-3221 (2022) - 2021
- [j42]Nick Strayer, Jana K. Shirey-Rice, Yu Shyr, Joshua C. Denny, Jill M. Pulley, Yaomin Xu:
PheWAS-ME: a web-app for interactive exploration of multimorbidity patterns in PheWAS. Bioinform. 37(12): 1778-1780 (2021) - [j41]Yan Guo, Hui Yu, Haocan Song, Jiapeng He, Olufunmilola Oyebamiji, Huining Kang, Jie Ping, Scott Ness, Yu Shyr, Fei Ye:
MetaGSCA: A tool for meta-analysis of gene set differential coexpression. PLoS Comput. Biol. 17(5) (2021) - 2020
- [j40]Jing Teng, Assem Abdygametova, Jing Du, Bian Ma, Rong Zhou, Yu Shyr, Fei Ye:
Bayesian Inference of Lymph Node Ratio Estimation and Survival Prognosis for Breast Cancer Patients. IEEE J. Biomed. Health Informatics 24(2): 354-364 (2020) - 2019
- [j39]Qi Liu, Quanhu Sheng, Jie Ping, Marisol Adelina Ramirez, Ken S. Lau, Robert J. Coffey, Yu Shyr:
scRNABatchQC: multi-samples quality control for single cell RNA-seq data. Bioinform. 35(24): 5306-5308 (2019) - [j38]Jing Wang, Xizhen Dai, Lynne D. Berry, Joy D. Cogan, Qi Liu, Yu Shyr:
HACER: an atlas of human active enhancers to interpret regulatory variants. Nucleic Acids Res. 47(Database-Issue): D106-D112 (2019) - 2018
- [j37]Shilin Zhao, Jing Wang, David C. Samuels, Quanghu Sheng, Yu Shyr, Yan Guo:
Strategies for processing and quality control of Illumina genotyping arrays. Briefings Bioinform. 19(5): 765-775 (2018) - [j36]Chung-I Li, David C. Samuels, Ying-Yong Zhao, Yu Shyr, Yan Guo:
Power and sample size calculations for high-throughput sequencing-based experiments. Briefings Bioinform. 19(6): 1247-1255 (2018) - [j35]Shilin Zhao, Chung-I Li, Yan Guo, Quanhu Sheng, Yu Shyr:
RnaSeqSampleSize: real data based sample size estimation for RNA sequencing. BMC Bioinform. 19(1): 191:1-191:8 (2018) - 2017
- [j34]Jing Wang, David C. Samuels, Yu Shyr, Yan Guo:
StrandScript: evaluation of Illumina genotyping array design and strand correction. Bioinform. 33(15): 2399-2401 (2017) - [j33]Pai-Ling Li, Jeng-Min Chiou, Yu Shyr:
Functional data classification using covariate-adjusted subspace projection. Comput. Stat. Data Anal. 115: 21-34 (2017) - 2016
- [j32]Pan Zhang, David C. Samuels, Brian D. Lehmann, Thomas Stricker, Jennifer A. Pietenpol, Yu Shyr, Yan Guo:
Mitochondria sequence mapping strategies and practicability of mitochondria variant detection from exome and RNA sequencing data. Briefings Bioinform. 17(2): 224-232 (2016) - [j31]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:
Proceedings of the 15th Annual UT-KBRIN Bioinformatics Summit 2016: Cadiz, KY, USA. 8-10 April 2016. BMC Bioinform. 17(S-10) (2016) - [j30]Xinyang Deng, Deqiang Han, Jean Dezert, Yong Deng, Yu Shyr:
Evidence Combination From an Evolutionary Game Theory Perspective. IEEE Trans. Cybern. 46(9): 2070-2082 (2016) - 2015
- [j29]Jing Wang, Leon Raskin, David C. Samuels, Yu Shyr, Yan Guo:
Genome measures used for quality control are dependent on gene function and ancestry. Bioinform. 31(3): 318-323 (2015) - [j28]Jing Wang, David C. Samuels, Yu Shyr, Yan Guo:
Population structure analysis on 2504 individuals across 26 ancestries using bioinformatics approaches. BMC Bioinform. 16(S15): P19 (2015) - [j27]Pan Zhang, David C. Samuels, Brian D. Lehmann, Thomas Stricker, Jennifer A. Pietenpol, Yu Shyr, Yan Guo:
Practicality of identifying mitochondria variants from exome and RNAseq data. BMC Bioinform. 16(S15): P6 (2015) - [j26]Jing Wang, Quanhu Sheng, Yu Shyr:
SWATH-MS in proteomics: current status. Int. J. Comput. Biol. Drug Des. 8(3): 192-202 (2015) - [j25]Quanhu Sheng, Shilin Zhao, Mingsheng Guo, Yu Shyr:
NGSPERL: a semi-automated framework for large scale next generation sequencing data analysis. Int. J. Comput. Biol. Drug Des. 8(3): 203-211 (2015) - 2014
- [j24]Quanhu Sheng, Yu Shyr, Xi Chen:
DupChecker: a bioconductor package for checking high-throughput genomic data redundancy in meta-analysis. BMC Bioinform. 15: 323 (2014) - [j23]Yan Guo, Shilin Zhao, Brian D. Lehmann, Quanhu Sheng, Timothy M. Shaver, Thomas Stricker, Jennifer A. Pietenpol, Yu Shyr:
Detection of internal exon deletion with exon Del. BMC Bioinform. 15: 332 (2014) - [j22]Xue Zhong, Qi Liu, Yu Shyr:
CLIP-EZ: a computational tool for HITS-CLIP data analysis. BMC Bioinform. 15(S-10): P1 (2014) - [j21]Shilin Zhao, Yan Guo, Quanhu Sheng, Yu Shyr:
Heatmap3: an improved heatmap package with more powerful and convenient features. BMC Bioinform. 15(S-10): P16 (2014) - [j20]Pei-Fang Su, Chung-I Li, Yu Shyr:
Sample size determination for paired right-censored data based on the difference of Kaplan-Meier estimates. Comput. Stat. Data Anal. 74: 39-51 (2014) - [j19]Yan Guo, Amma Bosompem, Xue Zhong, Travis Clark, Yu Shyr, Annette S. Kim:
A comparison of microRNA sequencing reproducibility and noise reduction using mirVana and TRIzol isolation methods. Int. J. Comput. Biol. Drug Des. 7(2/3): 102-112 (2014) - [j18]Judith W. Dexheimer, Thomas J. Abramo, Donald H. Arnold, Kevin B. Johnson, Yu Shyr, Fei Ye, Kang-Hsien Fan, Neal Patel, Dominik Aronsky:
Implementation and evaluation of an integrated computerized asthma management system in a pediatric emergency department: A randomized clinical trial. Int. J. Medical Informatics 83(11): 805-813 (2014) - 2013
- [j17]Yan Guo, Jiang Li, Chung-I Li, Yu Shyr, David C. Samuels:
MitoSeek: extracting mitochondria information and performing high-throughput mitochondria sequencing analysis. Bioinform. 29(9): 1210-1211 (2013) - [j16]Chung-I Li, Pei-Fang Su, Yu Shyr:
Sample size calculation based on exact test for assessing differential expression analysis in RNA-seq data. BMC Bioinform. 14: 357 (2013) - [j15]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:
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. 7(S-5): S1 (2013) - [j14]Qi Liu, Shilin Zhao, Pei-Fang Su, Shyr Yu:
Gene and isoform expression signatures associated with tumor stage in kidney renal clear cell carcinoma. BMC Syst. Biol. 7(S-5): S7 (2013) - [j13]Chung-I Li, Pei-Fang Su, Yan Guo, Yu Shyr:
Sample size calculation for differential expression analysis of RNA-seq data under Poisson distribution. Int. J. Comput. Biol. Drug Des. 6(4): 358-375 (2013) - [j12]Judith W. Dexheimer, Thomas J. Abramo, Donald H. Arnold, Kevin B. Johnson, Yu Shyr, Fei Ye, Kang-Hsien Fan, Neal Patel, Dominik Aronsky:
An asthma management system in a pediatric emergency department. Int. J. Medical Informatics 82(4): 230-238 (2013) - 2012
- [j11]Yufei Huang, Zhongming Zhao, Hua Xu, Yu Shyr, Bing Zhang:
Advances in systems biology: computational algorithms and applications. BMC Syst. Biol. 6(S-3): S1 (2012) - [j10]Pei-Fang Su, Xi Chen, Heidi Chen, Yu Shyr:
Statistical aspects of omics data analysis using the random compound covariate. BMC Syst. Biol. 6(S-3): S11 (2012) - 2011
- [j9]Ming Li, Shuo Chen, Joan Zhang, Heidi Chen, Yu Shyr:
Wave-spec: a preprocessing package for mass spectrometry data. Bioinform. 27(5): 739-740 (2011) - [j8]Pei-Fang Su, Yunchan Chi, Chung-I Li, Yu Shyr, Yi-De Liao:
Analyzing survival curves at a fixed point in time for paired and clustered right-censored data. Comput. Stat. Data Anal. 55(4): 1617-1628 (2011) - 2009
- [j7]Shuo Chen, Ming Li, Don Hong, Dean Billheimer, Huiming Li, Baogang J. Xu, Yu Shyr:
A novel comprehensive wave-form MS data processing method. Bioinform. 25(6): 808-814 (2009) - [j6]Jun Wu, Qingchao Qiu, Lu Xie, Joseph Fullerton, Jian Yu, Yu Shyr, Alfred L. George Jr., Yajun Yi:
Web-based interrogation of gene expression signatures using EXALT. BMC Bioinform. 10: 420 (2009) - 2008
- [j5]Terri T. Ni, William J. Lemon, Yu Shyr, Tao P. Zhong:
Use of normalization methods for analysis of microarrays containing a high degree of gene effects. BMC Bioinform. 9 (2008) - 2007
- [j4]Shuo Chen, Don Hong, Yu Shyr:
Wavelet-based procedures for proteomic mass spectrometry data processing. Comput. Stat. Data Anal. 52(1): 211-220 (2007) - [j3]Aixiang Jiang, Wei Pan, Liming C. Milbauer, Yu Shyr, Robert P. Hebbel:
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. 5(4): 875-893 (2007) - 2000
- [j2]James D. Stefansic, Alan J. Herline, Yu Shyr, William C. Chapman, J. Michael Fitzpatrick, Robert L. Galloway:
Registration of Physical Space to Laparoscopic Image Space for use in Minimally Invasive Hepatic Surgery. IEEE Trans. Medical Imaging 19(10): 1012-1023 (2000) - 1998
- [j1]J. Michael Fitzpatrick, Derek L. G. Hill, Yu Shyr, Jay B. West, Colin Studholme, Calvin R. Maurer Jr.:
Visual Assessment of the Accuracy of Retrospective Registration of MR and CT Images of the Brain. IEEE Trans. Medical Imaging 17(4): 571-585 (1998)
Conference and Workshop Papers
- 2015
- [c1]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:
PheWAS Network Analysis and Visualization. AMIA 2015
Informal and Other Publications
- 2015
- [i1]Xinyang Deng, Zhen Wang, Qi Liu, Yong Deng, Yu Shyr:
Impact of Preference and Equivocators on Opinion Dynamics with Evolutionary Game Framework. CoRR abs/1507.07950 (2015)
Coauthor Index
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