Genetic function approximation in the molecular pharmacology of cancer. - Leming M. Shi; Yi Fan; Timothy G. Myers 001; John N. Weinstein (ICNN, 1997)

Mining the NCI Anticancer Drug Discovery Databases: Genetic Function Approximation for the QSAR Study of Anticancer Ellipticine Analogues. - Leming M. Shi; Yi Fan; Timothy G. Myers 001; Patrick M. O'Connor; Kenneth D. Paull; Stephen H. Friend; John N. Weinstein (J. Chem. Inf. Comput. Sci., 1998)

Mining and Visualizing Large Anticancer Drug Discovery Databases. - Leming M. Shi; Yi Fan; Jae K. Lee; Mark Waltham; Darren T. Andrews; Uwe Scherf; Kenneth D. Paull; John N. Weinstein (J. Chem. Inf. Comput. Sci., 2000)

QSAR Models Using a Large Diverse Set of Estrogens. - Leming M. Shi; Hong Fang; Weida Tong; Jie Wu 008; Roger Perkins; Robert M. Blair; William S. Branham; Stacey L. Dial; Carrie L. Moland; Daniel M. Sheehan (J. Chem. Inf. Comput. Sci., 2001)

Multi-class tumor classification by discriminant partial least squares using microarray gene expression data and assessment of classification models. - Yongxi Tan; Leming M. Shi; Weida Tong; G. T. Gene Hwang; Charles Wang (Comput. Biol. Chem., 2004)

Eigenvalue Analysis of Peroxisome Proliferator-Activated Receptor gamma Agonists. - Chenzhong Liao; Aihua Xie; Leming M. Shi; Jiaju Zhou; Xianping Lu (J. Chem. Inf. Model., 2004)

Bioinformatics approaches for cross-species liver cancer analysis based on microarray gene expression profiling. - Hong Fang; Weida Tong; Roger Perkins; Leming M. Shi; Huixiao Hong; X. Cao; Qian Xie 004; S. H. Yim; J. M. Ward; Henry C. Pitot; Yvonne P. Dragan (BMC Bioinform., 2005)

Quality control and quality assessment of data from surface-enhanced laser desorption/ionization (SELDI) time-of flight (TOF) mass spectrometry (MS). - Huixiao Hong; Yvonne P. Dragan; Joshua Epstein; Candee Teitel; Bangzheng Chen; Qian Xie 004; Hong Fang; Leming M. Shi; Roger Perkins; Weida Tong (BMC Bioinform., 2005)

Cross-platform comparability of microarray technology: Intra-platform consistency and appropriate data analysis procedures are essential. - Leming M. Shi; Weida Tong; Hong Fang; Uwe Scherf; Jing Han 003; Raj K. Puri; Felix W. Frueh; Federico M. Goodsaid; Lei Guo 006; Zhenqiang Su; Tao Han 007; James C. Fuscoe; et al. (BMC Bioinform., 2005)

Microarray scanner calibration curves: characteristics and implications. - Leming M. Shi; Weida Tong; Zhenqiang Su; Tao Han 007; Jing Han 003; Raj K. Puri; Hong Fang; Felix W. Frueh; Federico M. Goodsaid; Lei Guo 006; William S. Branham; James J. Chen; et al. (BMC Bioinform., 2005)

A microarray study of MPP+-treated PC12 Cells: Mechanisms of toxicity (MOT) analysis using bioinformatics tools. - Zengjun Xu; Tucker A. Patterson; Jonathan D. Wren; Tao Han 007; Leming M. Shi; Helen Duhart; Syed F. Ali; William Slikker Jr. (BMC Bioinform., 2005)

Integrating time-course microarray gene expression profiles with cytotoxicity for identification of biomarkers in primary rat hepatocytes exposed to cadmium. - Yongxi Tan; Leming M. Shi; Saber M. Hussain; Jun Xu; Weida Tong; John M. Frazier; Charles Wang (Bioinform., 2006)

Gene Expression Profiles Distinguish the Carcinogenic Effects of Aristolochic Acid in Target (Kidney) and Non-target (Liver) Tissues in Rats. - Tao Chen; Lei Guo 006; Lu Zhang 013; Leming M. Shi; Hong Fang; Yongming Sun; James C. Fuscoe; Nan Mei (BMC Bioinform., 2006)

Differential gene expression in mouse primary hepatocytes exposed to the peroxisome proliferator-activated receptor alpha agonists. - Lei Guo 006; Hong Fang; Jim Collins; Xiao-hui Fan; Stacey L. Dial; Alex Wong; Kshama Mehta; Ernice Blann; Leming M. Shi; Weida Tong; Yvonne P. Dragan (BMC Bioinform., 2006)

Improvement in the Reproducibility and Accuracy of DNA Microarray Quantification by Optimizing Hybridization Conditions. - Tao Han 007; Cathy D. Melvin; Leming M. Shi; William S. Branham; Carrie L. Moland; P. Scott Pine; Karol L. Thompson; James C. Fuscoe (BMC Bioinform., 2006)

Analysis of gene expression changes in relation to toxicity and tumorigenesis in the livers of Big Blue transgenic rats fed comfrey (Symphytum officinale). - Nan Mei; Lei Guo 006; Lu Zhang 013; Leming M. Shi; Yongming Andrew Sun; Chris Fung; Carrie L. Moland; Stacey L. Dial; James C. Fuscoe; Tao Chen (BMC Bioinform., 2006)

Assessing batch effects of genotype calling algorithm BRLMM for the Affymetrix GeneChip Human Mapping 500 K array set using 270 HapMap samples. - Huixiao Hong; Zhenqiang Su; Weigong Ge; Leming M. Shi; Roger Perkins; Hong Fang; Joshua Xu; James J. Chen; Tao Han 007; Jim Kaput; James C. Fuscoe; Weida Tong (BMC Bioinform., 2008)

The balance of reproducibility, sensitivity, and specificity of lists of differentially expressed genes in microarray studies. - Leming M. Shi; Wendell D. Jones; Roderick V. Jensen; Stephen C. Harris; Roger Perkins; Federico M. Goodsaid; Lei Guo 006; Lisa J. Croner; Cecilie Boysen; Hong Fang; Feng Qian; Shashi Amur; et al. (BMC Bioinform., 2008)

Very Important Pool (VIP) genes - an application for microarray-based molecular signatures. - Zhenqiang Su; Huixiao Hong; Hong Fang; Leming M. Shi; Roger Perkins; Weida Tong (BMC Bioinform., 2008)

Mold2, Molecular Descriptors from 2D Structures for Chemoinformatics and Toxicoinformatics. - Huixiao Hong; Qian Xie 004; Weigong Ge; Feng Qian; Hong Fang; Leming Shi; Zhenqiang Su; Roger Perkins; Weida Tong (J. Chem. Inf. Model., 2008)

Microarray platform consistency is revealed by biologically functional analysis of gene expression profiles. - Zhiguang Li; Zhenqiang Su; Zhining Wen; Leming M. Shi; Tao Chen (BMC Bioinform., 2009)

The Accurate Prediction of Protein Family from Amino Acid Sequence by Measuring Features of Sequence Fragments. - Huixiao Hong; Qilong Hong; Roger Perkins; Leming M. Shi; Hong Fang; Zhenqiang Su; Yvonne P. Dragan; James C. Fuscoe; Weida Tong (J. Comput. Biol., 2009)

The EDKB: an established knowledge base for endocrine disrupting chemicals. - Don Ding; Lei Xu; Hong Fang; Huixiao Hong; Roger Perkins; Steve Harris; Edward D. Bearden; Leming Shi; Weida Tong (BMC Bioinform., 2010)

Evaluation of gene expression data generated from expired Affymetrix GeneChip® microarrays using MAQC reference RNA samples. - Zhining Wen; Charles Wang; Quan Shi; Ying Huang; Zhenqiang Su; Huixiao Hong; Weida Tong; Leming Shi (BMC Bioinform., 2010)

The MicroArray Quality Control (MAQC) Project and Cross-Platform Analysis of Microarray Data. - Zhining Wen; Zhenqiang Su; Jie Liu; Baitang Ning; Lei Guo 006; Weida Tong; Leming M. Shi (Handbook of Statistical Bioinformatics, 2011)

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. - Minjun Chen; Leming M. Shi; Reagan Kelly; Roger Perkins; Hong Fang; Weida Tong (BMC Bioinform., 2011)

DRAR-CPI: a server for identifying drug repositioning potential and adverse drug reactions via the chemical-protein interactome. - Heng Luo 002; Jian Chen; Leming Shi; Mike Mikailov; Huang Zhu; Kejian Wang; Lin He 007; Lun Yang (Nucleic Acids Res., 2011)

Exploring Off-Targets and Off-Systems for Adverse Drug Reactions via Chemical-Protein Interactome - Clozapine-Induced Agranulocytosis as a Case Study. - Lun Yang; Kejian Wang; Jian Chen; Anil G. Jegga; Heng Luo 002; Leming Shi; Chunling Wan; Xizhi Guo; Shengying Qin; Guang He; Guoyin Feng; Lin He 007 (PLoS Comput. Biol., 2011)

An adaptive feature selection method for microarray data analysis. - Jie Cheng; Joel Greshock; Leming Shi; Jeffery Painter; Xiwu Lin; Kwan Lee; Shu Zheng; Richard Wooster; Lajos Pusztai; Alan Menius (BIBM, 2012)

Good practice guidelines for biomarker discovery from array data: a case study for breast cancer prognosis. - Jie Cheng; Joel Greshock; Leming Shi; Shu Zheng; Alan Menius; Kwan Lee (BMC Syst. Biol., 2013)

Estimating relative noise to signal in DNA microarray data. - Huixiao Hong; Qilong Hong; Jie Liu; Weida Tong; Leming Shi (Int. J. Bioinform. Res. Appl., 2013)

DDI-CPI, a server that predicts drug-drug interactions through implementing the chemical-protein interactome. - Heng Luo 002; Ping Zhang 016; Hui Huang; Jialiang Huang; Emily Kao; Leming Shi; Lin He 007; Lun Yang (Nucleic Acids Res., 2014)

A multi-omic analysis of human naïve CD4+ T cells. - 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; et al. (BMC Syst. Biol., 2015)

Understanding and predicting binding between human leukocyte antigens (HLAs) and peptides by network analysis. - Heng Luo 002; Hao Ye; Hui Wen Ng; Leming Shi; Weida Tong; William Mattes; Donna Mendrick; Huixiao Hong (BMC Bioinform., 2015)

Similarities and differences between variants called with human reference genome HG19 or HG38. - Bohu Pan; Rebecca Kusko; Wenming Xiao; Yuanting Zheng; Zhichao Liu; Chunlin Xiao; Sugunadevi Sakkiah; Wenjing Guo; Ping Gong 001; Chaoyang Zhang; Weigong Ge; Leming Shi; et al. (BMC Bioinform., 2019)

Correction to: Similarities and differences between variants called with human reference genome HG19 or HG38. - Bohu Pan; Rebecca Kusko; Wenming Xiao; Yuanting Zheng; Zhichao Liu; Chunlin Xiao; Sugunadevi Sakkiah; Wenjing Guo; Ping Gong 001; Chaoyang Zhang; Weigong Ge; Leming Shi; et al. (BMC Bioinform., 2019)

PreMedKB: an integrated precision medicine knowledgebase for interpreting relationships between diseases, genes, variants and drugs. - Ying Yu; Yunjin Wang; Zhaojie Xia; Xiangyu Zhang; Kailiang Jin; Jingcheng Yang; Luyao Ren; Zheng Zhou; Dong Yu; Tao Qing; Chengdong Zhang; Li Jin 002; et al. (Nucleic Acids Res., 2019)

Patient Assessment and Therapy Planning Based on Homologous Recombination Repair Deficiency. - Wenbin Li; Lin Gao; Xin Yi; Shuangfeng Shi; Jie Huang 026; Leming Shi; Xiaoyan Zhou; Lingying Wu; Jianming Ying (Genom. Proteom. Bioinform., 2023)

Evaluative Methodology for HRD Testing: Development of Standard Tools for Consistency Assessment. - Zheng Jia; Yaqing Liu; Shoufang Qu; Wenbin Li; Lin Gao; Lin Dong; Yun Xing; Yadi Cheng; Huan Fang 005; Yuting Yi; Yuxing Chu; Chao Zhang; et al. (Genom. Proteom. Bioinform., 2025)