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Journal Articles
- 2023
[j35]Wenbin Li
, Lin Gao, Xin Yi, Shuangfeng Shi, Jie Huang, Leming Shi, Xiaoyan Zhou, Lingying Wu, Jianming Ying:
Patient Assessment and Therapy Planning Based on Homologous Recombination Repair Deficiency. Genom. Proteom. Bioinform. 21(5): 962-975 (2023)- 2019
- [j34]Bohu Pan, Rebecca Kusko, Wenming Xiao, Yuanting Zheng, Zhichao Liu, Chunlin Xiao, Sugunadevi Sakkiah, Wenjing Guo, Ping Gong, Chaoyang Zhang, Weigong Ge, Leming Shi, Weida Tong, Huixiao Hong:
Correction to: Similarities and differences between variants called with human reference genome HG19 or HG38. BMC Bioinform. 20(1): 252:1 (2019) - [j33]Bohu Pan, Rebecca Kusko, Wenming Xiao, Yuanting Zheng, Zhichao Liu, Chunlin Xiao, Sugunadevi Sakkiah, Wenjing Guo, Ping Gong, Chaoyang Zhang, Weigong Ge, Leming Shi, Weida Tong, Huixiao Hong:
Similarities and differences between variants called with human reference genome HG19 or HG38. BMC Bioinform. 20-S(2): 17-29 (2019) - [j32]Ying Yu, Yunjin Wang, Zhaojie Xia, Xiangyu Zhang, Kailiang Jin, Jingcheng Yang, Luyao Ren, Zheng Zhou, Dong Yu, Tao Qing, Chengdong Zhang, Li Jin, Yuanting Zheng, Li Guo, Leming Shi:
PreMedKB: an integrated precision medicine knowledgebase for interpreting relationships between diseases, genes, variants and drugs. Nucleic Acids Res. 47(Database-Issue): D1090-D1101 (2019) - 2015
- [j31]Heng Luo, Hao Ye, Hui Wen Ng, Leming Shi, Weida Tong, William Mattes, Donna Mendrick, Huixiao Hong:
Understanding and predicting binding between human leukocyte antigens (HLAs) and peptides by network analysis. BMC Bioinform. 16(S13): S9 (2015) - [j30]Christopher J. Mitchell, Derese Getnet, Min Sik Kim, Srinivas Manda Srikanth, Praveen Kumar, Tai-Chung Huang, Sneha M. Pinto, Nirujogi Raja Sekhar, Mio Iwasaki, Patrick G. Shaw, Xinyan Wu, Jun Zhong, Raghothama Chaerkady, Arivusudar Marimuthu, Babylakshmi Muthusamy, Nandini A. Sahasrabuddhe, Rajesh Raju, Caitlyn Bowman, Ludmila V. Danilova, Jevon Cutler, Dhanashree S. Kelkar, Charles G. Drake, T. S. Keshava Prasad, Luigi Marchionni, Peter N. Murakami, Alan F. Scott, Leming Shi, Jean Thierry-Mieg, Danielle Thierry-Mieg, Rafael A. Irizarry, Leslie Cope, Yasushi Ishihama, Charles Wang, Harsha Gowda, Akhilesh Pandey:
A multi-omic analysis of human naïve CD4+ T cells. BMC Syst. Biol. 9: 75 (2015) - 2014
- [j29]Heng Luo, Ping Zhang, Hui Huang, Jialiang Huang, Emily Kao, Leming Shi, Lin He, Lun Yang:
DDI-CPI, a server that predicts drug-drug interactions through implementing the chemical-protein interactome. Nucleic Acids Res. 42(Webserver-Issue): 46-52 (2014) - 2013
- [j28]Jie Cheng, Joel Greshock, Leming Shi, Shu Zheng, Alan Menius, Kwan Lee:
Good practice guidelines for biomarker discovery from array data: a case study for breast cancer prognosis. BMC Syst. Biol. 7(S-4): S2 (2013) - [j27]Huixiao Hong, Qilong Hong, Jie Liu, Weida Tong, Leming Shi:
Estimating relative noise to signal in DNA microarray data. Int. J. Bioinform. Res. Appl. 9(5): 433-448 (2013) - 2011
- [j26]Minjun Chen, Leming M. Shi, Reagan Kelly, Roger Perkins, Hong Fang, Weida Tong:
Selecting a single model or combining multiple models for microarray-based classifier development? - A comparative analysis based on large and diverse datasets generated from the MAQC-II project. BMC Bioinform. 12(S-10): S3 (2011) - [j25]Heng Luo, Jian Chen, Leming Shi, Mike Mikailov, Huang Zhu, Kejian Wang, Lin He, Lun Yang:
DRAR-CPI: a server for identifying drug repositioning potential and adverse drug reactions via the chemical-protein interactome. Nucleic Acids Res. 39(Web-Server-Issue): 492-498 (2011) - [j24]Lun Yang, Kejian Wang, Jian Chen, Anil G. Jegga, Heng Luo, Leming Shi, Chunling Wan, Xizhi Guo, Shengying Qin, Guang He, Guoyin Feng, Lin He:
Exploring Off-Targets and Off-Systems for Adverse Drug Reactions via Chemical-Protein Interactome - Clozapine-Induced Agranulocytosis as a Case Study. PLoS Comput. Biol. 7(3) (2011) - 2010
- [j23]Zhining Wen, Charles Wang, Quan Shi, Ying Huang, Zhenqiang Su, Huixiao Hong, Weida Tong, Leming Shi:
Evaluation of gene expression data generated from expired Affymetrix GeneChip® microarrays using MAQC reference RNA samples. BMC Bioinform. 11(S-6): S10 (2010) - [j22]Don Ding, Lei Xu, Hong Fang, Huixiao Hong, Roger Perkins, Steve Harris, Edward D. Bearden, Leming Shi, Weida Tong:
The EDKB: an established knowledge base for endocrine disrupting chemicals. BMC Bioinform. 11(S-6): S5 (2010) - 2009
- [j21]Zhiguang Li, Zhenqiang Su, Zhining Wen, Leming M. Shi, Tao Chen:
Microarray platform consistency is revealed by biologically functional analysis of gene expression profiles. BMC Bioinform. 10(S-11): 12 (2009) - [j20]Huixiao Hong, Qilong Hong, Roger Perkins, Leming M. Shi, Hong Fang, Zhenqiang Su, Yvonne P. Dragan, James C. Fuscoe, Weida Tong:
The Accurate Prediction of Protein Family from Amino Acid Sequence by Measuring Features of Sequence Fragments. J. Comput. Biol. 16(12): 1671-1688 (2009) - 2008
- [j19]Huixiao Hong, Zhenqiang Su, Weigong Ge, Leming M. Shi, Roger Perkins, Hong Fang, Joshua Xu, James J. Chen, Tao Han, Jim Kaput, James C. Fuscoe, Weida Tong:
Assessing batch effects of genotype calling algorithm BRLMM for the Affymetrix GeneChip Human Mapping 500 K array set using 270 HapMap samples. BMC Bioinform. 9(S-9) (2008) - [j18]Leming M. Shi, Wendell D. Jones, Roderick V. Jensen, Stephen C. Harris, Roger Perkins, Federico M. Goodsaid, Lei Guo, Lisa J. Croner, Cecilie Boysen, Hong Fang, Feng Qian, Shashi Amur, Wenjun Bao, Catalin C. Barbacioru, Vincent Bertholet, Xiaoxi Megan Cao, Tzu-Ming Chu, Patrick J. Collins, Xiao-hui Fan, Felix W. Frueh:
The balance of reproducibility, sensitivity, and specificity of lists of differentially expressed genes in microarray studies. BMC Bioinform. 9(S-9) (2008) - [j17]Zhenqiang Su, Huixiao Hong, Hong Fang, Leming M. Shi, Roger Perkins, Weida Tong:
Very Important Pool (VIP) genes - an application for microarray-based molecular signatures. BMC Bioinform. 9(S-9) (2008) - [j16]Huixiao Hong, Qian Xie, Weigong Ge, Feng Qian, Hong Fang, Leming Shi, Zhenqiang Su, Roger Perkins, Weida Tong:
Mold2, Molecular Descriptors from 2D Structures for Chemoinformatics and Toxicoinformatics. J. Chem. Inf. Model. 48(7): 1337-1344 (2008) - 2006
- [j15]Yongxi Tan, Leming M. Shi, Saber M. Hussain, Jun Xu, Weida Tong, John M. Frazier, Charles Wang:
Integrating time-course microarray gene expression profiles with cytotoxicity for identification of biomarkers in primary rat hepatocytes exposed to cadmium. Bioinform. 22(1): 77-87 (2006) - [j14]Tao Chen, Lei Guo, Lu Zhang, Leming M. Shi, Hong Fang, Yongming Sun, James C. Fuscoe, Nan Mei:
Gene Expression Profiles Distinguish the Carcinogenic Effects of Aristolochic Acid in Target (Kidney) and Non-target (Liver) Tissues in Rats. BMC Bioinform. 7(S-2) (2006) - [j13]Lei Guo, Hong Fang, Jim Collins, Xiao-hui Fan, Stacey L. Dial, Alex Wong, Kshama Mehta, Ernice Blann, Leming M. Shi, Weida Tong, Yvonne P. Dragan:
Differential gene expression in mouse primary hepatocytes exposed to the peroxisome proliferator-activated receptor alpha agonists. BMC Bioinform. 7(S-2) (2006) - [j12]Tao Han, Cathy D. Melvin, Leming M. Shi, William S. Branham, Carrie L. Moland, P. Scott Pine, Karol L. Thompson, James C. Fuscoe:
Improvement in the Reproducibility and Accuracy of DNA Microarray Quantification by Optimizing Hybridization Conditions. BMC Bioinform. 7(S-2) (2006) - [j11]Nan Mei, Lei Guo, Lu Zhang, Leming M. Shi, Yongming Andrew Sun, Chris Fung, Carrie L. Moland, Stacey L. Dial, James C. Fuscoe, Tao Chen:
Analysis of gene expression changes in relation to toxicity and tumorigenesis in the livers of Big Blue transgenic rats fed comfrey (Symphytum officinale). BMC Bioinform. 7(S-2) (2006) - 2005
- [j10]Hong Fang, Weida Tong, Roger Perkins, Leming M. Shi, Huixiao Hong, X. Cao, Qian Xie, S. H. Yim, J. M. Ward, Henry C. Pitot, Yvonne P. Dragan:
Bioinformatics approaches for cross-species liver cancer analysis based on microarray gene expression profiling. BMC Bioinform. 6(S-2) (2005) - [j9]Huixiao Hong, Yvonne P. Dragan, Joshua Epstein, Candee Teitel, Bangzheng Chen, Qian Xie, Hong Fang, Leming M. Shi, Roger Perkins, Weida Tong:
Quality control and quality assessment of data from surface-enhanced laser desorption/ionization (SELDI) time-of flight (TOF) mass spectrometry (MS). BMC Bioinform. 6(S-2) (2005) - [j8]Leming M. Shi, Weida Tong, Hong Fang, Uwe Scherf, Jing Han, Raj K. Puri, Felix W. Frueh, Federico M. Goodsaid, Lei Guo, Zhenqiang Su, Tao Han, James C. Fuscoe, Z. Alex Xu, Tucker A. Patterson, Huixiao Hong, Qian Xie, Roger Perkins, James J. Chen, Daniel A. Casciano:
Cross-platform comparability of microarray technology: Intra-platform consistency and appropriate data analysis procedures are essential. BMC Bioinform. 6(S-2) (2005) - [j7]Leming M. Shi, Weida Tong, Zhenqiang Su, Tao Han, Jing Han, Raj K. Puri, Hong Fang, Felix W. Frueh, Federico M. Goodsaid, Lei Guo, William S. Branham, James J. Chen, Z. Alex Xu, Stephen C. Harris, Huixiao Hong, Qian Xie, Roger Perkins, James C. Fuscoe:
Microarray scanner calibration curves: characteristics and implications. BMC Bioinform. 6(S-2) (2005) - [j6]Zengjun Xu, Tucker A. Patterson, Jonathan D. Wren, Tao Han, Leming M. Shi, Helen Duhart, Syed F. Ali, William Slikker Jr.:
A microarray study of MPP+-treated PC12 Cells: Mechanisms of toxicity (MOT) analysis using bioinformatics tools. BMC Bioinform. 6(S-2) (2005) - 2004
- [j5]Yongxi Tan, Leming M. Shi, Weida Tong, G. T. Gene Hwang, Charles Wang:
Multi-class tumor classification by discriminant partial least squares using microarray gene expression data and assessment of classification models. Comput. Biol. Chem. 28(3): 235-243 (2004) - [j4]Chenzhong Liao, Aihua Xie, Leming M. Shi, Jiaju Zhou, Xianping Lu:
Eigenvalue Analysis of Peroxisome Proliferator-Activated Receptor gamma Agonists. J. Chem. Inf. Model. 44(1): 230-238 (2004) - 2001
- [j3]Leming M. Shi, Hong Fang, Weida Tong, Jie Wu, Roger Perkins, Robert M. Blair, William S. Branham, Stacey L. Dial, Carrie L. Moland, Daniel M. Sheehan:
QSAR Models Using a Large Diverse Set of Estrogens. J. Chem. Inf. Comput. Sci. 41(1): 186-195 (2001) - 2000
- [j2]Leming M. Shi, Yi Fan, Jae K. Lee, Mark Waltham, Darren T. Andrews, Uwe Scherf, Kenneth D. Paull, John N. Weinstein:
Mining and Visualizing Large Anticancer Drug Discovery Databases. J. Chem. Inf. Comput. Sci. 40(2): 367-379 (2000) - 1998
- [j1]Leming M. Shi, Yi Fan, Timothy G. Myers, Patrick M. O'Connor, Kenneth D. Paull, Stephen H. Friend, John N. Weinstein:
Mining the NCI Anticancer Drug Discovery Databases: Genetic Function Approximation for the QSAR Study of Anticancer Ellipticine Analogues. J. Chem. Inf. Comput. Sci. 38(2): 189-199 (1998)
Conference and Workshop Papers
- 2012
- [c2]Jie Cheng, Joel Greshock, Leming Shi, Jeffery Painter, Xiwu Lin, Kwan Lee, Shu Zheng, Richard Wooster, Lajos Pusztai, Alan Menius:
An adaptive feature selection method for microarray data analysis. BIBM 2012: 1-6 - 1997
- [c1]Leming M. Shi, Yi Fan, Timothy G. Myers, John N. Weinstein:
Genetic function approximation in the molecular pharmacology of cancer. ICNN 1997: 2490-2493
Parts in Books or Collections
- 2011
- [p1]Zhining Wen, Zhenqiang Su, Jie Liu, Baitang Ning, Lei Guo, Weida Tong, Leming M. Shi:
The MicroArray Quality Control (MAQC) Project and Cross-Platform Analysis of Microarray Data. Handbook of Statistical Bioinformatics 2011: 171-192
Coauthor Index
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