List of works - Leming Shi

A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages

scientific article

A testing strategy to predict risk for drug-induced liver injury in humans using high-content screen assays and the 'rule-of-two' model

scientific article published on 11 June 2014

An integrated bioinformatics infrastructure essential for advancing pharmacogenomics and personalized medicine in the context of the FDA's Critical Path Initiative

scientific article published on January 2007

An investigation of biomarkers derived from legacy microarray data for their utility in the RNA-seq era

scientific article

ArrayTrack--supporting toxicogenomic research at the U.S. Food and Drug Administration National Center for Toxicological Research

scientific article

ArrayTrack: An FDA and Public Genomic Tool

scientific article published on January 2017

ArrayTrack: an FDA and public genomic tool

2009 scientific article

Assessing QSAR Limitations - A Regulatory Perspective

Assessing batch effects of genotype calling algorithm BRLMM for the Affymetrix GeneChip Human Mapping 500 K array set using 270 HapMap samples

scientific article

Assessing technical performance in differential gene expression experiments with external spike-in RNA control ratio mixtures

scientific article

Assessment of prediction confidence and domain extrapolation of two structure-activity relationship models for predicting estrogen receptor binding activity

scientific article

Classification of cDNA array genes that have a highly significant discriminative power due to their unique distribution in four brain regions

scientific article published on 01 October 2004

Comparing next-generation sequencing and microarray technologies in a toxicological study of the effects of aristolochic acid on rat kidneys

scientific article published on 23 August 2011

Comparison of RNA-seq and microarray-based models for clinical endpoint prediction

scientific article published on 25 June 2015

Comprehensive RNA-Seq transcriptomic profiling across 11 organs, 4 ages, and 2 sexes of Fischer 344 rats

scientific article

Comprehensively identifying and characterizing the missing gene sequences in human reference genome with integrated analytic approaches ⬇️

scientific article published on April 10, 2013

Correction to: Similarities and differences between variants called with human reference genome HG19 or HG38

scholarly article published in BMC Bioinformatics

Correlation analysis of external RNA controls reveals its utility for assessment of microarray assay

scientific article published on 6 December 2008

Critical role of bioinformatics in translating huge amounts of next-generation sequencing data into personalized medicine

scientific article

Cross-platform comparability of microarray technology: intra-platform consistency and appropriate data analysis procedures are essential

scientific article

Cross-platform ultradeep transcriptomic profiling of human reference RNA samples by RNA-Seq

scientific article

DNA microarrays are predictive of cancer prognosis: a re-evaluation

scientific article published on 12 January 2010

Development of public toxicogenomics software for microarray data management and analysis

scientific article

Differential gene expression in mouse primary hepatocytes exposed to the peroxisome proliferator-activated receptor alpha agonists

scientific article published on 6 September 2006

Dissecting the Characteristics and Dynamics of Human Protein Complexes at Transcriptome Cascade Using RNA-Seq Data

scientific article

Emerging technologies for food and drug safety

scientific article published on 23 July 2018

Estimating relative noise to signal in DNA microarray data

scientific article

Evaluating variations of genotype calling: a potential source of spurious associations in genome-wide association studies

scientific article

Evaluation of external RNA controls for the assessment of microarray performance

scientific article published on September 2006

Evaluation of gene expression data generated from expired Affymetrix GeneChip® microarrays using MAQC reference RNA samples

scientific article

Gaining Confidence on Molecular Classification through Consensus Modeling and Validation

scientific article published on January 2006

Incorporating the human gene annotations in different databases significantly improved transcriptomic and genetic analyses

scientific article published on 19 February 2013

Integrating time-course microarray gene expression profiles with cytotoxicity for identification of biomarkers in primary rat hepatocytes exposed to cadmium

scientific article

Investigation of reproducibility of differentially expressed genes in DNA microarrays through statistical simulation

scientific article

Machine Learning Methods for Predicting HLA-Peptide Binding Activity

scientific article

Microarray scanner calibration curves: characteristics and implications

scientific article published on 15 July 2005

Mold(2), molecular descriptors from 2D structures for chemoinformatics and toxicoinformatics

scientific article

Molecular biomarkers: a US FDA effort

scientific article published on April 2010

Molecular docking to identify associations between drugs and class I human leukocyte antigens for predicting idiosyncratic drug reactions.

scientific article

Multi-class cancer classification by total principal component regression (TPCR) using microarray gene expression data

scientific article

Multi-class tumor classification by discriminant partial least squares using microarray gene expression data and assessment of classification models

scientific article

Multiclass Decision Forest--a novel pattern recognition method for multiclass classification in microarray data analysis

scientific article

Multiple microRNAs function as self-protective modules in acetaminophen-induced hepatotoxicity in humans

scientific article

Next-generation sequencing and its applications in molecular diagnostics

scientific article published on April 2011

Performance comparison of one-color and two-color platforms within the MicroArray Quality Control (MAQC) project

scientific article published on 01 September 2006

Phytoestrogens and mycoestrogens bind to the rat uterine estrogen receptor

scientific article published on 01 April 2002

Prediction of estrogen receptor binding for 58,000 chemicals using an integrated system of a tree-based model with structural alerts

scientific article

QA/QC issues to aid regulatory acceptance of microarray gene expression data

scientific article

QA/QC: challenges and pitfalls facing the microarray community and regulatory agencies

scientific article

Quality control and quality assessment of data from surface-enhanced laser desorption/ionization (SELDI) time-of flight (TOF) mass spectrometry (MS).

scientific article published on 15 July 2005

Rat toxicogenomic study reveals analytical consistency across microarray platforms

scientific article

Reproducible and reliable microarray results through quality control: good laboratory proficiency and appropriate data analysis practices are essential

scientific article

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 ⬇️

scientific article published on October 18, 2011

Self-self hybridization as an alternative experiment design to dye swap for two-color microarrays

scientific article published on 01 January 2007

Sequencing XMET genes to promote genotype-guided risk assessment and precision medicine

scientific article published on 20 May 2019

Significant variations in alternative splicing patterns and expression profiles between human-mouse orthologs in early embryos

scientific article published on 4 July 2016

Similarities and differences between variants called with human reference genome HG19 or HG38

Structure-activity relationship approaches and applications

scientific article

Technical reproducibility of genotyping SNP arrays used in genome-wide association studies

scientific article

The EDKB: an established knowledge base for endocrine disrupting chemicals

scientific article

The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements

scientific article

The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models

scientific article

The accurate prediction of protein family from amino acid sequence by measuring features of sequence fragments

scientific article published in December 2009

The balance of reproducibility, sensitivity, and specificity of lists of differentially expressed genes in microarray studies

scientific article

The concordance between RNA-seq and microarray data depends on chemical treatment and transcript abundance

scientific article

The international MAQC Society launches to enhance reproducibility of high-throughput technologies

scientific article published in December 2017

Towards the development of an omics data analysis framework

scientific article published on 19 February 2020

Transcriptomic profiling of rat liver samples in a comprehensive study design by RNA-Seq

scientific article

Understanding and predicting binding between human leukocyte antigens (HLAs) and peptides by network analysis

scientific article

Using decision forest to classify prostate cancer samples on the basis of SELDI-TOF MS data: assessing chance correlation and prediction confidence

scientific article

Very Important Pool (VIP) genes--an application for microarray-based molecular signatures

scientific article

Voluntary exploratory data submissions to the US FDA and the EMA: experience and impact

scientific article published in June 2010

List of works by Leming Shi

A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages

A testing strategy to predict risk for drug-induced liver injury in humans using high-content screen assays and the 'rule-of-two' model

An integrated bioinformatics infrastructure essential for advancing pharmacogenomics and personalized medicine in the context of the FDA's Critical Path Initiative

An investigation of biomarkers derived from legacy microarray data for their utility in the RNA-seq era

ArrayTrack--supporting toxicogenomic research at the U.S. Food and Drug Administration National Center for Toxicological Research

ArrayTrack: An FDA and Public Genomic Tool

ArrayTrack: an FDA and public genomic tool

Assessing QSAR Limitations - A Regulatory Perspective

Assessing batch effects of genotype calling algorithm BRLMM for the Affymetrix GeneChip Human Mapping 500 K array set using 270 HapMap samples

Assessing technical performance in differential gene expression experiments with external spike-in RNA control ratio mixtures

Assessment of prediction confidence and domain extrapolation of two structure-activity relationship models for predicting estrogen receptor binding activity

Classification of cDNA array genes that have a highly significant discriminative power due to their unique distribution in four brain regions

Comparing next-generation sequencing and microarray technologies in a toxicological study of the effects of aristolochic acid on rat kidneys

Comparison of RNA-seq and microarray-based models for clinical endpoint prediction

Comprehensive RNA-Seq transcriptomic profiling across 11 organs, 4 ages, and 2 sexes of Fischer 344 rats

Comprehensively identifying and characterizing the missing gene sequences in human reference genome with integrated analytic approaches ⬇️

Correction to: Similarities and differences between variants called with human reference genome HG19 or HG38

Correlation analysis of external RNA controls reveals its utility for assessment of microarray assay

Critical role of bioinformatics in translating huge amounts of next-generation sequencing data into personalized medicine

Cross-platform comparability of microarray technology: intra-platform consistency and appropriate data analysis procedures are essential

Cross-platform ultradeep transcriptomic profiling of human reference RNA samples by RNA-Seq

DNA microarrays are predictive of cancer prognosis: a re-evaluation

Development of public toxicogenomics software for microarray data management and analysis

Differential gene expression in mouse primary hepatocytes exposed to the peroxisome proliferator-activated receptor alpha agonists

Dissecting the Characteristics and Dynamics of Human Protein Complexes at Transcriptome Cascade Using RNA-Seq Data

Emerging technologies for food and drug safety

Estimating relative noise to signal in DNA microarray data

Evaluating variations of genotype calling: a potential source of spurious associations in genome-wide association studies

Evaluation of external RNA controls for the assessment of microarray performance

Evaluation of gene expression data generated from expired Affymetrix GeneChip® microarrays using MAQC reference RNA samples

Gaining Confidence on Molecular Classification through Consensus Modeling and Validation

Incorporating the human gene annotations in different databases significantly improved transcriptomic and genetic analyses

Integrating time-course microarray gene expression profiles with cytotoxicity for identification of biomarkers in primary rat hepatocytes exposed to cadmium

Investigation of reproducibility of differentially expressed genes in DNA microarrays through statistical simulation

Machine Learning Methods for Predicting HLA-Peptide Binding Activity

Microarray scanner calibration curves: characteristics and implications

Mold(2), molecular descriptors from 2D structures for chemoinformatics and toxicoinformatics

Molecular biomarkers: a US FDA effort

Molecular docking to identify associations between drugs and class I human leukocyte antigens for predicting idiosyncratic drug reactions.

Multi-class cancer classification by total principal component regression (TPCR) using microarray gene expression data

Multi-class tumor classification by discriminant partial least squares using microarray gene expression data and assessment of classification models

Multiclass Decision Forest--a novel pattern recognition method for multiclass classification in microarray data analysis

Multiple microRNAs function as self-protective modules in acetaminophen-induced hepatotoxicity in humans

Next-generation sequencing and its applications in molecular diagnostics

Performance comparison of one-color and two-color platforms within the MicroArray Quality Control (MAQC) project

Phytoestrogens and mycoestrogens bind to the rat uterine estrogen receptor

Prediction of estrogen receptor binding for 58,000 chemicals using an integrated system of a tree-based model with structural alerts

QA/QC issues to aid regulatory acceptance of microarray gene expression data

QA/QC: challenges and pitfalls facing the microarray community and regulatory agencies

Quality control and quality assessment of data from surface-enhanced laser desorption/ionization (SELDI) time-of flight (TOF) mass spectrometry (MS).

Rat toxicogenomic study reveals analytical consistency across microarray platforms

Reproducible and reliable microarray results through quality control: good laboratory proficiency and appropriate data analysis practices are essential

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 ⬇️

Self-self hybridization as an alternative experiment design to dye swap for two-color microarrays

Sequencing XMET genes to promote genotype-guided risk assessment and precision medicine

Significant variations in alternative splicing patterns and expression profiles between human-mouse orthologs in early embryos

Similarities and differences between variants called with human reference genome HG19 or HG38

Structure-activity relationship approaches and applications

Technical reproducibility of genotyping SNP arrays used in genome-wide association studies

The EDKB: an established knowledge base for endocrine disrupting chemicals

The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements

The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models

The accurate prediction of protein family from amino acid sequence by measuring features of sequence fragments

The balance of reproducibility, sensitivity, and specificity of lists of differentially expressed genes in microarray studies

The concordance between RNA-seq and microarray data depends on chemical treatment and transcript abundance

The international MAQC Society launches to enhance reproducibility of high-throughput technologies

Towards the development of an omics data analysis framework

Transcriptomic profiling of rat liver samples in a comprehensive study design by RNA-Seq

Understanding and predicting binding between human leukocyte antigens (HLAs) and peptides by network analysis

Using decision forest to classify prostate cancer samples on the basis of SELDI-TOF MS data: assessing chance correlation and prediction confidence

Very Important Pool (VIP) genes--an application for microarray-based molecular signatures

Voluntary exploratory data submissions to the US FDA and the EMA: experience and impact