PubRank

Weida Tong

Author PubWeight™ 180.72‹?›

Top papers

Rank Title Journal Year PubWeight™‹?›
1 The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol 2006 30.90
2 The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. Nat Biotechnol 2010 7.08
3 Performance comparison of one-color and two-color platforms within the MicroArray Quality Control (MAQC) project. Nat Biotechnol 2006 5.92
4 ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level. Bioinformatics 2010 5.60
5 Rat toxicogenomic study reveals analytical consistency across microarray platforms. Nat Biotechnol 2006 5.14
6 Toward interoperable bioscience data. Nat Genet 2012 4.72
7 The first RSBI (ISA-TAB) workshop: "can a simple format work for complex studies?". OMICS 2008 4.15
8 Cross-platform comparability of microarray technology: intra-platform consistency and appropriate data analysis procedures are essential. BMC Bioinformatics 2005 3.93
9 A strategy capitalizing on synergies: the Reporting Structure for Biological Investigation (RSBI) working group. OMICS 2006 3.51
10 QA/QC: challenges and pitfalls facing the microarray community and regulatory agencies. Expert Rev Mol Diagn 2004 2.73
11 The balance of reproducibility, sensitivity, and specificity of lists of differentially expressed genes in microarray studies. BMC Bioinformatics 2008 2.54
12 High lipophilicity and high daily dose of oral medications are associated with significant risk for drug-induced liver injury. Hepatology 2013 2.02
13 Microarray scanner calibration curves: characteristics and implications. BMC Bioinformatics 2005 2.02
14 Assessing batch effects of genotype calling algorithm BRLMM for the Affymetrix GeneChip Human Mapping 500 K array set using 270 HapMap samples. BMC Bioinformatics 2008 1.98
15 GOFFA: gene ontology for functional analysis--a FDA gene ontology tool for analysis of genomic and proteomic data. BMC Bioinformatics 2006 1.72
16 Reproducible and reliable microarray results through quality control: good laboratory proficiency and appropriate data analysis practices are essential. Curr Opin Biotechnol 2007 1.71
17 ArrayTrack: an FDA and public genomic tool. Methods Mol Biol 2009 1.71
18 DNA microarrays are predictive of cancer prognosis: a re-evaluation. Clin Cancer Res 2010 1.69
19 Study of 202 natural, synthetic, and environmental chemicals for binding to the androgen receptor. Chem Res Toxicol 2003 1.61
20 Mining FDA drug labels using an unsupervised learning technique--topic modeling. BMC Bioinformatics 2011 1.53
21 Current status of methods for defining the applicability domain of (quantitative) structure-activity relationships. The report and recommendations of ECVAM Workshop 52. Altern Lab Anim 2005 1.52
22 FDA-approved drug labeling for the study of drug-induced liver injury. Drug Discov Today 2011 1.42
23 Comparing next-generation sequencing and microarray technologies in a toxicological study of the effects of aristolochic acid on rat kidneys. Chem Res Toxicol 2011 1.41
24 Technical reproducibility of genotyping SNP arrays used in genome-wide association studies. PLoS One 2012 1.36
25 Next-generation sequencing and its applications in molecular diagnostics. Expert Rev Mol Diagn 2011 1.33
26 Prediction of estrogen receptor binding for 58,000 chemicals using an integrated system of a tree-based model with structural alerts. Environ Health Perspect 2002 1.31
27 Phytoestrogens and mycoestrogens bind to the rat uterine estrogen receptor. J Nutr 2002 1.27
28 Quality control and quality assessment of data from surface-enhanced laser desorption/ionization (SELDI) time-of flight (TOF) mass spectrometry (MS). BMC Bioinformatics 2005 1.25
29 Investigating drug repositioning opportunities in FDA drug labels through topic modeling. BMC Bioinformatics 2012 1.22
30 Multi-class cancer classification by total principal component regression (TPCR) using microarray gene expression data. Nucleic Acids Res 2005 1.19
31 Perspectives on validation of high-throughput assays supporting 21st century toxicity testing. ALTEX 2013 1.19
32 A decade of toxicogenomic research and its contribution to toxicological science. Toxicol Sci 2012 1.14
33 Mold(2), molecular descriptors from 2D structures for chemoinformatics and toxicoinformatics. J Chem Inf Model 2008 1.09
34 Voluntary exploratory data submissions to the US FDA and the EMA: experience and impact. Nat Rev Drug Discov 2010 1.08
35 Multi-class tumor classification by discriminant partial least squares using microarray gene expression data and assessment of classification models. Comput Biol Chem 2004 1.07
36 Translating clinical findings into knowledge in drug safety evaluation--drug induced liver injury prediction system (DILIps). PLoS Comput Biol 2011 1.06
37 Identification of genes and pathways involved in kidney renal clear cell carcinoma. BMC Bioinformatics 2014 1.05
38 Gene expression profile exploration of a large dataset on chronic fatigue syndrome. Pharmacogenomics 2006 1.04
39 Quantitative structure-activity relationship methods: perspectives on drug discovery and toxicology. Environ Toxicol Chem 2003 1.03
40 The EDKB: an established knowledge base for endocrine disrupting chemicals. BMC Bioinformatics 2010 1.03
41 Chemical effects in biological systems--data dictionary (CEBS-DD): a compendium of terms for the capture and integration of biological study design description, conventional phenotypes, and 'omics data. Toxicol Sci 2005 1.01
42 Meeting report: Validation of toxicogenomics-based test systems: ECVAM-ICCVAM/NICEATM considerations for regulatory use. Environ Health Perspect 2006 0.98
43 Differential gene expression in mouse primary hepatocytes exposed to the peroxisome proliferator-activated receptor alpha agonists. BMC Bioinformatics 2006 0.98
44 An FDA bioinformatics tool for microbial genomics research on molecular characterization of bacterial foodborne pathogens using microarrays. BMC Bioinformatics 2010 0.97
45 Meta-analysis of microarray data using a pathway-based approach identifies a 37-gene expression signature for systemic lupus erythematosus in human peripheral blood mononuclear cells. BMC Med 2011 0.96
46 Three new consensus QSAR models for the prediction of Ames genotoxicity. Mutagenesis 2004 0.96
47 Toward a checklist for exchange and interpretation of data from a toxicology study. Toxicol Sci 2007 0.95
48 Decision forest analysis of 61 single nucleotide polymorphisms in a case-control study of esophageal cancer; a novel method. BMC Bioinformatics 2005 0.95
49 Integrating time-course microarray gene expression profiles with cytotoxicity for identification of biomarkers in primary rat hepatocytes exposed to cadmium. Bioinformatics 2005 0.94
50 The liver toxicity biomarker study: phase I design and preliminary results. Toxicol Pathol 2009 0.93
51 In silico drug repositioning: what we need to know. Drug Discov Today 2012 0.93
52 Evaluation of gene expression data generated from expired Affymetrix GeneChip® microarrays using MAQC reference RNA samples. BMC Bioinformatics 2010 0.92
53 Two new ArrayTrack libraries for personalized biomedical research. BMC Bioinformatics 2010 0.92
54 Biomarkers for drug-induced liver injury. Expert Rev Gastroenterol Hepatol 2010 0.92
55 An integrated study of acute effects of valproic acid in the liver using metabonomics, proteomics, and transcriptomics platforms. OMICS 2006 0.91
56 EADB: an estrogenic activity database for assessing potential endocrine activity. Toxicol Sci 2013 0.91
57 Consensus analysis of multiple classifiers using non-repetitive variables: diagnostic application to microarray gene expression data. Comput Biol Chem 2007 0.90
58 ArrayTrack: a free FDA bioinformatics tool to support emerging biomedical research--an update. Hum Genomics 2010 0.89
59 Whole genome sequencing of 35 individuals provides insights into the genetic architecture of Korean population. BMC Bioinformatics 2014 0.88
60 An investigation of biomarkers derived from legacy microarray data for their utility in the RNA-seq era. Genome Biol 2014 0.88
61 Critical role of bioinformatics in translating huge amounts of next-generation sequencing data into personalized medicine. Sci China Life Sci 2013 0.88
62 Evaluating variations of genotype calling: a potential source of spurious associations in genome-wide association studies. J Genet 2010 0.88
63 Mining hidden knowledge for drug safety assessment: topic modeling of LiverTox as a case study. BMC Bioinformatics 2014 0.88
64 Toward predictive models for drug-induced liver injury in humans: are we there yet? Biomark Med 2014 0.88
65 High daily dose and being a substrate of cytochrome P450 enzymes are two important predictors of drug-induced liver injury. Drug Metab Dispos 2014 0.87
66 Comparative analysis of predictive models for nongenotoxic hepatocarcinogenicity using both toxicogenomics and quantitative structure-activity relationships. Chem Res Toxicol 2011 0.87
67 Multiclass Decision Forest--a novel pattern recognition method for multiclass classification in microarray data analysis. DNA Cell Biol 2004 0.87
68 Maximizing biomarker discovery by minimizing gene signatures. BMC Genomics 2011 0.86
69 A testing strategy to predict risk for drug-induced liver injury in humans using high-content screen assays and the 'rule-of-two' model. Arch Toxicol 2014 0.86
70 Shifting from population-wide to personalized cancer prognosis with microarrays. PLoS One 2012 0.86
71 Microarray analysis distinguishes differential gene expression patterns from large and small colony Thymidine kinase mutants of L5178Y mouse lymphoma cells. BMC Bioinformatics 2006 0.85
72 Discovering functional modules by topic modeling RNA-Seq based toxicogenomic data. Chem Res Toxicol 2014 0.85
73 atBioNet--an integrated network analysis tool for genomics and biomarker discovery. BMC Genomics 2012 0.85
74 Homology modeling, molecular docking, and molecular dynamics simulations elucidated α-fetoprotein binding modes. BMC Bioinformatics 2013 0.85
75 An approach to comparative analysis of chromatographic fingerprints for assuring the quality of botanical drugs. J Chem Inf Comput Sci 2003 0.84
76 Differential gene expression profiling of mouse skin after sulfur mustard exposure: Extended time response and inhibitor effect. Toxicol Appl Pharmacol 2008 0.84
77 Competitive molecular docking approach for predicting estrogen receptor subtype α agonists and antagonists. BMC Bioinformatics 2014 0.84
78 QA/QC issues to aid regulatory acceptance of microarray gene expression data. Environ Mol Mutagen 2007 0.84
79 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 Bioinformatics 2011 0.84
80 Investigation of reproducibility of differentially expressed genes in DNA microarrays through statistical simulation. BMC Proc 2009 0.82
81 Constructing a robust protein-protein interaction network by integrating multiple public databases. BMC Bioinformatics 2011 0.82
82 Incorporating the human gene annotations in different databases significantly improved transcriptomic and genetic analyses. RNA 2013 0.82
83 Understanding and predicting binding between human leukocyte antigens (HLAs) and peptides by network analysis. BMC Bioinformatics 2015 0.82
84 Self-self hybridization as an alternative experiment design to dye swap for two-color microarrays. OMICS 2007 0.82
85 Predicting idiosyncratic drug-induced liver injury: some recent advances. Expert Rev Gastroenterol Hepatol 2014 0.81
86 Is toxicogenomics a more reliable and sensitive biomarker than conventional indicators from rats to predict drug-induced liver injury in humans? Chem Res Toxicol 2011 0.81
87 Modeling chemical interaction profiles: II. Molecular docking, spectral data-activity relationship, and structure-activity relationship models for potent and weak inhibitors of cytochrome P450 CYP3A4 isozyme. Molecules 2012 0.81
88 A systems approach for analysis of high content screening assay data with topic modeling. BMC Bioinformatics 2013 0.81
89 Modeling chemical interaction profiles: I. Spectral data-activity relationship and structure-activity relationship models for inhibitors and non-inhibitors of cytochrome P450 CYP3A4 and CYP2D6 isozymes. Molecules 2012 0.81
90 Comprehensively identifying and characterizing the missing gene sequences in human reference genome with integrated analytic approaches. Hum Genet 2013 0.80
91 Next generation sequencing for profiling expression of miRNAs: technical progress and applications in drug development. J Biomed Sci Eng 2011 0.80
92 Molecular docking to identify associations between drugs and class I human leukocyte antigens for predicting idiosyncratic drug reactions. Comb Chem High Throughput Screen 2015 0.80
93 Very Important Pool (VIP) genes--an application for microarray-based molecular signatures. BMC Bioinformatics 2008 0.80
94 Maximum predictive power of the microarray-based models for clinical outcomes is limited by correlation between endpoint and gene expression profile. BMC Genomics 2011 0.80
95 Does applicability domain exist in microarray-based genomic research? PLoS One 2010 0.80
96 ebTrack: an environmental bioinformatics system built upon ArrayTrack. BMC Proc 2009 0.80
97 The accurate prediction of protein family from amino acid sequence by measuring features of sequence fragments. J Comput Biol 2009 0.80
98 Evaluations of the trans-sulfuration pathway in multiple liver toxicity studies. Toxicol Appl Pharmacol 2008 0.79
99 Correlation analysis of external RNA controls reveals its utility for assessment of microarray assay. Anal Biochem 2008 0.79
100 Cross-platform comparison of microarray-based multiple-class prediction. PLoS One 2011 0.79
101 Classification of cDNA array genes that have a highly significant discriminative power due to their unique distribution in four brain regions. DNA Cell Biol 2004 0.79
102 Rat α-Fetoprotein binding affinities of a large set of structurally diverse chemicals elucidated the relationships between structures and binding affinities. Chem Res Toxicol 2012 0.79
103 Estimating relative noise to signal in DNA microarray data. Int J Bioinform Res Appl 2013 0.78
104 Influence of the structural diversity of data sets on the statistical quality of three-dimensional quantitative structure-activity relationship (3D-QSAR) models: predicting the estrogenic activity of xenoestrogens. Chem Res Toxicol 2002 0.78
105 Emerging efforts for discovering new biomarkers of liver disease and hepatotoxicity. Biomark Med 2014 0.78
106 Molecular biomarkers: a US FDA effort. Biomark Med 2010 0.78
107 A phenome-guided drug repositioning through a latent variable model. BMC Bioinformatics 2014 0.78
108 Building an organ-specific carcinogenic database for SAR analyses. J Toxicol Environ Health A 2004 0.77
109 Identification of New SRF Binding Sites in Genes Modulated by SRF Over-Expression in Mouse Hearts. Gene Regul Syst Bio 2011 0.77
110 Self-Inclusion Complexes Derived from Cyclodextrins: Synthesis and Characterization of 6(A),6(B)-Bis-O-[p-(allyloxy)phenyl]-Substituted beta-Cyclodextrins. J Org Chem 1996 0.77
111 Advances in translational bioinformatics facilitate revealing the landscape of complex disease mechanisms. BMC Bioinformatics 2014 0.76
112 Dissecting the Characteristics and Dynamics of Human Protein Complexes at Transcriptome Cascade Using RNA-Seq Data. PLoS One 2013 0.76
113 miRNAs and their application in drug-induced liver injury. Biomark Med 2014 0.76
114 LC/ESI-MS method for the determination of trimetazidine in human plasma: application to a bioequivalence study on Chinese volunteers. J Pharm Biomed Anal 2007 0.76
115 Quantitative structure-activity relationship models for predicting drug-induced liver injury based on FDA-approved drug labeling annotation and using a large collection of drugs. Toxicol Sci 2013 0.76
116 Drug-induced rhabdomyolysis: from systems pharmacology analysis to biochemical flux. Chem Res Toxicol 2014 0.76
117 SNPTrack™ : an integrated bioinformatics system for genetic association studies. Hum Genomics 2012 0.75
118 The emerging genomics and systems biology research lead to systems genomics studies. BMC Genomics 2014 0.75
119 Proceedings of the First International Conference on Toxicogenomics Integrated with Environmental Sciences (TIES-2007). BMC Proc 2009 0.75
120 Towards interoperable reporting standards for omics data: hopes and hurdles. Summit on Translat Bioinforma 2009 0.75
121 Correction: Species Identification of Food Contaminating Beetles by Recognizing Patterns in Microscopic Images of Elytra Fragments. PLoS One 2016 0.75
122 A unifying ontology to integrate histological and clinical observations for drug-induced liver injury. Am J Pathol 2013 0.75
123 Comparing genetic variants detected in the 1000 genomes project with SNPs determined by the International HapMap Consortium. J Genet 2015 0.75
124 2012 Global Summit on Regulatory Science (GSRS-2012)--modernizing toxicology. Toxicol Sci 2012 0.75
125 Assessing consistency between versions of genotype-calling algorithm Birdseed for the Genome-Wide Human SNP Array 6.0 using HapMap samples. Adv Exp Med Biol 2010 0.75
126 The liver toxicity biomarker study phase I: markers for the effects of tolcapone or entacapone. Toxicol Pathol 2012 0.75