MicroArray/Sequencing Quality Control (MAQC/SEQC) Publications
Journal Special Issues or Manuscript Collections Featuring MAQC/SECQ
Nature Biotechnology — SEQC2 Article Collection (2020-2022)
Genome Biology — SEQC2 Article Collection (2021-2022)
Nature Biotechnology — 2014 Special Issue
Nature Biotechnology — August 2010 Issue
Pharmacogenomics Journal — August 2010 Issue
Nature Biotechnology — September 2006
| Year | Title | Authors | Full Citation |
|---|---|---|---|
| 2022 | Achieving Robust Somatic Mutation Detection with Deep Learning Models Derived from Reference Data Sets of a Cancer Sample | Sahraeian S.M.E., Fang L.T., Karagiannis K., Moos M., Smith S., Santana-Quintero L., Xiao C., Colgan M., Hong H., Mohiyuddin M., et al. | Achieving Robust Somatic Mutation Detection with Deep Learning Models Derived from Reference Data Sets of a Cancer Sample. Sahraeian S.M.E., Fang L.T., Karagiannis K., Moos M., Smith S., Santana-Quintero L., Xiao C., Colgan M., Hong H., Mohiyuddin M., et al. Genome Biol. 2022, 23(1):12. |
| 2022 | Assessing Reproducibility of Inherited Variants Detected with Short-Read Whole Genome Sequencing | Pan B., Ren L., Onuchic V., Guan M., Kusko R., Bruinsma S., Trigg L., Scherer A., Ning B., Zhang C., et al. | Assessing Reproducibility of Inherited Variants Detected with Short-Read Whole Genome Sequencing. Pan B., Ren L., Onuchic V., Guan M., Kusko R., Bruinsma S., Trigg L., Scherer A., Ning B., Zhang C., et al. Genome Biol. 2022, 23(1):2. |
| 2022 | Deep Oncopanel Sequencing Reveals Within Block Position-Dependent Quality Degradation in FFPE Processed Samples | Zhang Y., Blomquist T.M., Kusko R., Stetson D., Zhang Z., Yin L., Sebra R., Gong B., Lococo J.S., Mittal V.K., et al. | Deep Oncopanel Sequencing Reveals Within Block Position-Dependent Quality Degradation in FFPE Processed Samples. Zhang Y., Blomquist T.M., Kusko R., Stetson D., Zhang Z., Yin L., Sebra R., Gong B., Lococo J.S., Mittal V.K., et al. Genome Biol. 2022, 23(1):141. |
| 2022 | Personalized Genome Assembly for Accurate Cancer Somatic Mutation Discovery Using Tumor-Normal Paired Reference Samples | Xiao C., Chen Z., Chen W., Padilla C., Colgan M., Wu W., Fang L.T., Liu T., Yang Y., Schneider V., et al. |
Personalized Genome Assembly for Accurate Cancer Somatic Mutation Discovery Using Tumor-Normal Paired Reference Samples. |
| 2022 | Structural Variant Analysis of a Cancer Reference Cell Line Sample Using Multiple Sequencing Technologies | Talsania K., Shen T.W., Chen X., Jaeger E., Li Z., Chen Z., Chen W., Tran B., Kusko R., Wang L., et al. | Structural Variant Analysis of a Cancer Reference Cell Line Sample Using Multiple Sequencing Technologies. Talsania K., Shen T.W., Chen X., Jaeger E., Li Z., Chen Z., Chen W., Tran B., Kusko R., Wang L., et al. Genome Biol. 2022, 23(1):255. |
| 2022 | Ultra-Deep Multi-Oncopanel Sequencing of Benchmarking Samples with a Wide Range of Variant Allele Frequencies | Gong B., Kusko R., Jones W., Tong W., and Xu J. | Ultra-Deep Multi-Oncopanel Sequencing of Benchmarking Samples with a Wide Range of Variant Allele Frequencies. Gong B., Kusko R., Jones W., Tong W., and Xu J. Sci Data. 2022, 9(1):288. |
| 2022 | Ultra-Deep Sequencing Data from a Liquid Biopsy Proficiency Study Demonstrating Analytic Validity | Gong B., Deveson I.W., Mercer T., Johann D.J. Jr., Jones W., Tong W., and Xu J. | Ultra-Deep Sequencing Data from a Liquid Biopsy Proficiency Study Demonstrating Analytic Validity. Gong B., Deveson I.W., Mercer T., Johann D.J. Jr., Jones W., Tong W., and Xu J. Sci Data. 2022, 9(1):170. |
| 2022 | Using Synthetic Chromosome Controls to Evaluate the Sequencing of Difficult Regions within the Human Genome | Reis A.L.M., Deveson I.W., Madala B.S., Wong T., Barker C., Xu J., Lennon N., Tong W., Mercer T.R., and Consortium S. | Using Synthetic Chromosome Controls to Evaluate the Sequencing of Difficult Regions within the Human Genome. Reis A.L.M., Deveson I.W., Madala B.S., Wong T., Barker C., Xu J., Lennon N., Tong W., Mercer T.R., and Consortium S. Genome Biol. 2022, 23(1):19. |
| 2021 | A Multi-Center Cross-Platform Single-Cell RNA Sequencing Reference Dataset | Chen X., Yang Z., Chen W., Zhao Y., Farmer A., Tran B., Furtak V., Moos M. Jr., Xiao W., and Wang C. | A Multi-Center Cross-Platform Single-Cell RNA Sequencing Reference Dataset. Chen X., Yang Z., Chen W., Zhao Y., Farmer A., Tran B., Furtak V., Moos M. Jr., Xiao W., and Wang C. Sci Data. 2021, 8(1):39. |
| 2021 | A Multicenter Study Benchmarking Single-Cell RNA Sequencing Technologies Using Reference Samples | Chen W., Zhao Y., Chen X., Yang Z., Xu X., Bi Y., Chen V., Li J., Choi H., Ernest B., et al. | A Multicenter Study Benchmarking Single-Cell RNA Sequencing Technologies Using Reference Samples. Chen W., Zhao Y., Chen X., Yang Z., Xu X., Bi Y., Chen V., Li J., Choi H., Ernest B., et al. Nat Biotechnol. 2021, 39(9):1103-1114. |
| 2021 | A Verified Genomic Reference Sample for Assessing Performance of Cancer Panels Detecting Small Variants of Low Allele Frequency | Jones W., Gong B., Novoradovskaya N., Li D., Kusko R., Richmond T.A., Johann D.J. Jr., Bisgin H., Sahraeian S.M.E., Bushel P.R., et al. | A Verified Genomic Reference Sample for Assessing Performance of Cancer Panels Detecting Small Variants of Low Allele Frequency. Jones W., Gong B., Novoradovskaya N., Li D., Kusko R., Richmond T.A., Johann D.J. Jr., Bisgin H., Sahraeian S.M.E., Bushel P.R., et al. Genome Biol. 2021, 22(1):111. |
| 2021 | Advancing NGS Quality Control to Enable Measurement of Actionable Mutations in Circulating Tumor DNA | Willey J.C., Morrison T.B., Austermiller B., Crawford E.L., Craig D.J., Blomquist T.M., Jones W.D., Wali A., Lococo J.S., Haseley N., et al. | Advancing NGS Quality Control to Enable Measurement of Actionable Mutations in Circulating Tumor DNA. Willey J.C., Morrison T.B., Austermiller B., Crawford E.L., Craig D.J., Blomquist T.M., Jones W.D., Wali A., Lococo J.S., Haseley N., et al. Cell Rep Methods. 2021, 1(7):100106. |
| 2021 | Cross-Oncopanel Study Reveals High Sensitivity and Accuracy with Overall Analytical Performance Depending on Genomic Regions | Gong B., Li D., Kusko R., Novoradovskaya N., Zhang Y., Wang S., Pabon-Pena C., Zhang Z., Lai K., Cai W., et al. | Cross-Oncopanel Study Reveals High Sensitivity and Accuracy with Overall Analytical Performance Depending on Genomic Regions. Gong B., Li D., Kusko R., Novoradovskaya N., Zhang Y., Wang S., Pabon-Pena C., Zhang Z., Lai K., Cai W., et al. Genome Biol. 2021, 22(1):109. |
| 2021 | Establishing Community Reference Samples, Data and Call Sets for Benchmarking Cancer Mutation Detection Using Whole-Genome Sequencing | Fang L.T., Zhu B., Zhao Y., Chen W., Yang Z., Kerrigan L., Langenbach K., de Mars M., Lu C., Idler K., et al. | Establishing Community Reference Samples, Data and Call Sets for Benchmarking Cancer Mutation Detection Using Whole-Genome Sequencing. Fang L.T., Zhu B., Zhao Y., Chen W., Yang Z., Kerrigan L., Langenbach K., de Mars M., Lu C., Idler K., et al. Nat Biotechnol. 2021, 39(9):1151-1160. |
| 2021 | Evaluating the Analytical Validity of Circulating Tumor DNA Sequencing Assays for Precision Oncology | Deveson I.W., Gong B., Lai K., LoCoco J.S., Richmond T.A., Schageman J., Zhang Z., Novoradovskaya N., Willey J.C., Jones W., et al. | Evaluating the Analytical Validity of Circulating Tumor DNA Sequencing Assays for Precision Oncology. Deveson I.W., Gong B., Lai K., LoCoco J.S., Richmond T.A., Schageman J., Zhang Z., Novoradovskaya N., Willey J.C., Jones W., et al. Nat Biotechnol. 2021, 39(9):1115-1128. |
| 2021 | FDA-Led Consortium Studies Advance Quality Control of Targeted Next Generation Sequencing Assays for Precision Oncology | Li D., Kusko R., Ning B., Tong W., Johann D.J. Jr., and Xu J. | FDA-Led Consortium Studies Advance Quality Control of Targeted Next Generation Sequencing Assays for Precision Oncology. Li D., Kusko R., Ning B., Tong W., Johann D.J. Jr., and Xu J. Precis Cancer Med. 2021, 4:32. |
| 2021 | Hidden Biases in Germline Structural Variant Detection | Khayat M.M., Sahraeian S.M.E., Zarate S., Carroll A., Hong H., Pan B., Shi L., Gibbs R.A., Mohiyuddin M., Zheng Y., et al. | Hidden Biases in Germline Structural Variant Detection. Khayat M.M., Sahraeian S.M.E., Zarate S., Carroll A., Hong H., Pan B., Shi L., Gibbs R.A., Mohiyuddin M., Zheng Y., et al. Genome Biol. 2021, 22(1):347. |
| 2021 | Orchestrating and Sharing Large Multimodal Data for Transparent and Reproducible Research | Mammoliti A., Smirnov P., Nakano M., Safikhani Z., Eeles C., Seo H., Nair S.K., Mer A.S., Smith I., Ho C., et al. | Orchestrating and Sharing Large Multimodal Data for Transparent and Reproducible Research. Mammoliti A., Smirnov P., Nakano M., Safikhani Z., Eeles C., Seo H., Nair S.K., Mer A.S., Smith I., Ho C., et al. Nat Commun. 2021, 12(1):5797. |
| 2021 | Performance Assessment of DNA Sequencing Platforms in the ABRF Next-Generation Sequencing Study | Foox J., Tighe S.W., Nicolet C.M., Zook J.M., Byrska-Bishop M., Clarke W.E., Khayat M.M., Mahmoud M., Laaguiby P.K., Herbert Z.T., et al. | Performance Assessment of DNA Sequencing Platforms in the ABRF Next-Generation Sequencing Study. Foox J., Tighe S.W., Nicolet C.M., Zook J.M., Byrska-Bishop M., Clarke W.E., Khayat M.M., Mahmoud M., Laaguiby P.K., Herbert Z.T., et al. Nat Biotechnol. 2021, 39(9):1129-1140. |
| 2021 | Reporting Guidelines for Human Microbiome Research: the STORMS Checklist | Mirzayi C., Renson A., Genomic Standards C., Massive A., Quality Control S., Zohra F., Elsafoury S., Geistlinger L., Kasselman L.J., Eckenrode K., et al. | Reporting Guidelines for Human Microbiome Research: the STORMS Checklist. Mirzayi C., Renson A., Genomic Standards C., Massive A., Quality Control S., Zohra F., Elsafoury S., Geistlinger L., Kasselman L.J., Eckenrode K., et al. Nat Med. 2021, 27(11):1885-1892. |
| 2021 | The SEQC2 Epigenomics Quality Control (EpiQC) Study | Foox J., Nordlund J., Lalancette C., Gong T., Lacey M., Lent S., Langhorst B.W., Ponnaluri V.K.C., Williams L., Padmanabhan K.R., et al. | The SEQC2 Epigenomics Quality Control (EpiQC) Study. Foox J., Nordlund J., Lalancette C., Gong T., Lacey M., Lent S., Langhorst B.W., Ponnaluri V.K.C., Williams L., Padmanabhan K.R., et al. Genome Biol. 2021, 22(1):332. |
| 2021 | The Sequencing Quality Control 2 Study: Establishing Community Standards for Sequencing in Precision Medicine | Mercer T.R., Xu J., Mason C.E., Tong W., MAQC/SEQC2 Consortium. | The Sequencing Quality Control 2 Study: Establishing Community Standards for Sequencing in Precision Medicine. Mercer T.R., Xu J., Mason C.E., Tong W., MAQC/SEQC2 Consortium. Genome Biol. 2021, 22(1):306. |
| 2021 | Toward Best Practice in Cancer Mutation Detection with Whole-Genome and Whole-Exome Sequencing | Xiao W., Ren L., Chen Z., Fang L.T., Zhao Y., Lack J., Guan M., Zhu B., Jaeger E., Kerrigan L., et al. | Toward Best Practice in Cancer Mutation Detection with Whole-Genome and Whole-Exome Sequencing. Xiao W., Ren L., Chen Z., Fang L.T., Zhao Y., Lack J., Guan M., Zhu B., Jaeger E., Kerrigan L., et al. Nat Biotechnol. 2021, 39(9):1141-1150. |
| 2021 | Whole Genome and Exome Sequencing Reference Datasets from a Multi-Center and Cross-Platform Benchmark Study | Zhao Y., Fang L.T., Shen T.W., Choudhari S., Talsania K., Chen X., Shetty J., Kriga Y., Tran B., Zhu B., et al. | Whole Genome and Exome Sequencing Reference Datasets from a Multi-Center and Cross-Platform Benchmark Study. Zhao Y., Fang L.T., Shen T.W., Choudhari S., Talsania K., Chen X., Shetty J., Kriga Y., Tran B., Zhu B., et al. Sci Data. 2021, 8(1):296. |
| 2021 | X-CNV: Genome-Wide Prediction of the Pathogenicity of Copy Number Variations | Zhang L., Shi J., Ouyang J., Zhang R., Tao Y., Yuan D., Lv C., Wang R., Ning B., Roberts R., et al. | X-CNV: Genome-Wide Prediction of the Pathogenicity of Copy Number Variations. Zhang L., Shi J., Ouyang J., Zhang R., Tao Y., Yuan D., Lv C., Wang R., Ning B., Roberts R., et al. Genome Med. 2021, 13(1):132. |
| 2014 | A Comprehensive Assessment of RNA-Seq Accuracy, Reproducibility and Information Content by the Sequence Quality Control Consortium | SEQC/MAQC-III Consortium | A Comprehensive Assessment of RNA-Seq Accuracy, Reproducibility and Information Content by the Sequence Quality Control Consortium. SEQC/MAQC-III Consortium. Nature Biotechnology. 2014, 32(9):903-14. doi: 10.1038/nbt.2957. |
| 2014 | An Investigation of Biomarkers Derived from Legacy Microarray Data for their Utility in the RNA-Seq Era | Su Z., Fang H., Hong H., Shi L., Zhang W., Zhang W., Zhang Y., Dong Z., Lancashire L.J., Bessarabova M., Yang X., Ning B., Gong B., Meehan J., Xu J., Ge W., Perkins R., Fischer M., and Tong W. | An Investigation of Biomarkers Derived from Legacy Microarray Data for their Utility in the RNA-Seq Era. Su Z., Fang H., Hong H., Shi L., Zhang W., Zhang W., Zhang Y., Dong Z., Lancashire L.J., Bessarabova M., Yang X., Ning B., Gong B., Meehan J., Xu J., Ge W., Perkins R., Fischer M., and Tong W. Genome Biology. 2014, 15(12):523. doi: 10.1186/s13059-014-0523-y. |
| 2014 | Assessing Technical Performance in RNA-Seq Experiments with External Spike-in RNA Controls. | Munro S.A., Lund S.P., Pine P.S., Binder H., Clevert D.A., Conesa A., Dopazo J., Fasold M., Hochreiter S., Hong H., Jafari N., Kreil D.P., Łabaj P.P., Li S., Liao Y., Lin S.M., Meehan J., Mason C.E., Santoyo-Lopez J., Setterquist R.A., Shi L., Shi W., Smyth G.K., Stralis-Pavese N., Su Z., Tong W., Wang C., Wang J., Xu J., Ye Z., Yang Y., Yu Y., and Salit M. | Assessing Technical Performance in RNA-Seq Experiments with External Spike-in RNA Controls. Munro S.A., Lund S.P., Pine P.S., Binder H., Clevert D.A., Conesa A., Dopazo J., Fasold M., Hochreiter S., Hong H., Jafari N., Kreil D.P., Łabaj P.P., Li S., Liao Y., Lin S.M., Meehan J., Mason C.E., Santoyo-Lopez J., Setterquist R.A., Shi L., Shi W., Smyth G.K., Stralis-Pavese N., Su Z., Tong W., Wang C., Wang J., Xu J., Ye Z., Yang Y., Yu Y., and Salit M. Nature Communications. 2014, 5:5125. doi: 10.1038/ncomms6125. |
| 2014 | Comprehensive RNA-Seq Transcriptomic Profiling Across 11 Organs, 4 Ages, and 2 Sexes of Fischer 344 Rats | Yu Y., Zhao C., Su Z., Wang C., Fuscoe J.C., Tong W., and Shi L. | Comprehensive RNA-Seq Transcriptomic Profiling Across 11 Organs, 4 Ages, and 2 Sexes of Fischer 344 Rats. Yu Y., Zhao C., Su Z., Wang C., Fuscoe J.C., Tong W., and Shi L. Scientific Data. 2014, 1:140013. doi: 10.1038/sdata.2014.13. |
| 2014 | The Concordance Between RNA-Seq and Microarray Data Depends on Chemical Treatment and Transcript Abundance | Wang C., Gong B., Bushel P.R., Thierry-Mieg J., Thierry-Mieg D., Xu J., Fang H., Hong H., Shen J., Su Z., Meehan J., Li X., Yang L., Li H., Łabaj P.P., Kreil D.P., Megherbi D., Gaj S., Caiment F., van Delft J., Kleinjans J., Scherer A., Devanarayan V., Wang J., Yang Y., Qian H.R., Lancashire L.J., Bessarabova M., Nikolsky Y., Furlanello C., Chierici M., Albanese D., Jurman G., Riccadonna S., Filosi M., Visintainer R., Zhang K.K., Li J., Hsieh J.H., Svoboda D.L., Fuscoe J.C., Deng Y., Shi L., Paules R.S., Auerbach S.S., and Tong W. | The Concordance Between RNA-Seq and Microarray Data Depends on Chemical Treatment and Transcript Abundance. Wang C., Gong B., Bushel P.R., Thierry-Mieg J., Thierry-Mieg D., Xu J., Fang H., Hong H., Shen J., Su Z., Meehan J., Li X., Yang L., Li H., Łabaj P.P., Kreil D.P., Megherbi D., Gaj S., Caiment F., van Delft J., Kleinjans J., Scherer A., Devanarayan V., Wang J., Yang Y., Qian H.R., Lancashire L.J., Bessarabova M., Nikolsky Y., Furlanello C., Chierici M., Albanese D., Jurman G., Riccadonna S., Filosi M., Visintainer R., Zhang K.K., Li J., Hsieh J.H., Svoboda D.L., Fuscoe J.C., Deng Y., Shi L., Paules R.S., Auerbach S.S., and Tong W. Nature Biotechnology. 2014, 32(9):926-32. doi: 10.1038/nbt.3001. |
| 2014 | Cross-Platform Ultradeep Transcriptomic Profiling of Human Reference RNA Samples by RNA-Seq | Xu J., Su Z., Hong H., Kreil D.P., Mason C.E., Tong W., and Shi L. | Cross-Platform Ultradeep Transcriptomic Profiling of Human Reference RNA Samples by RNA-Seq. Xu J., Su Z., Hong H., Kreil D.P., Mason C.E., Tong W., and Shi L. Scientific Data. 2014, 1:140020. doi: 10.1038/sdata.2014.20. |
| 2014 | Detecting and Correcting Systematic Variation in Large-Scale RNA Sequencing Data | Li S., Łabaj P.P., Zumbo P., Sykacek P., Shi W., Shi L., Phan J., Wu P.Y., Wang M., Wang C., Thierry-Mieg D., Thierry-Mieg J., Kreil D.P., and Mason C.E. | Detecting and Correcting Systematic Variation in Large-Scale RNA Sequencing Data. Li S., Łabaj P.P., Zumbo P., Sykacek P., Shi W., Shi L., Phan J., Wu P.Y., Wang M., Wang C., Thierry-Mieg D., Thierry-Mieg J., Kreil D.P., and Mason C.E. Nat Biotechnol. 2014, 32(9):888-95. doi: 10.1038/nbt.3000. |
| 2014 | A Rat RNA-Seq Transcriptomic BodyMap Across 11 Organs and 4 Developmental Stages | Yu Y., Fuscoe J.C., Zhao C., Guo C., Jia M., Qing T., Bannon D.I., Lancashire L., Bao W., Du T., Luo H., Su Z., Jones W.D., Moland C.L., Branham W.S., Qian F., Ning B., Li Y., Hong H., Guo L., Mei N., Shi T., Wang K.Y., Wolfinger R.D., Nikolsky Y., Walker S.J., Duerksen-Hughes P., Mason C.E., Tong W., Thierry-Mieg J., Thierry-Mieg D., Shi L., and Wang C. | A Rat RNA-Seq Transcriptomic BodyMap Across 11 Organs and 4 Developmental Stages. Yu Y., Fuscoe J.C., Zhao C., Guo C., Jia M., Qing T., Bannon D.I., Lancashire L., Bao W., Du T., Luo H., Su Z., Jones W.D., Moland C.L., Branham W.S., Qian F., Ning B., Li Y., Hong H., Guo L., Mei N., Shi T., Wang K.Y., Wolfinger R.D., Nikolsky Y., Walker S.J., Duerksen-Hughes P., Mason C.E., Tong W., Thierry-Mieg J., Thierry-Mieg D., Shi L., and Wang C. Nature Communications. 2014, 5:3230. doi: 10.1038/ncomms4230. |
| 2014 | Transcriptomic Profiling of Rat Liver Samples in a Comprehensive Study Design by RNA-Seq | Gong B., Wang C., Su Z., Hong H., Auerbach A., Shi L., Tong W., and Xu J. |
Transcriptomic Profiling of Rat Liver Samples in a Comprehensive Study Design by RNA-Seq. |
| 2010 | A Comparison of Batch Effect Removal Methods for Enhancement of Prediction Performance Using MAQC-II Microarray Gene Expression Data | Luo J., Schumacher M., Scherer A., Sanoudou D., Megherbi D., Davison T., Shi T., Tong W., Shi L., Hong H., Zhao C., Elloumi F., Shi W., Thomas R., Lin S., Tillinghast G., Liu G., Zhou Y., Herman D., Li Y., Deng Y., Fang H., Bushel P., Woods M., and Zhang J. | A Comparison of Batch Effect Removal Methods for Enhancement of Prediction Performance Using MAQC-II Microarray Gene Expression Data. Luo J., Schumacher M., Scherer A., Sanoudou D., Megherbi D., Davison T., Shi T., Tong W., Shi L., Hong H., Zhao C., Elloumi F., Shi W., Thomas R., Lin S., Tillinghast G., Liu G., Zhou Y., Herman D., Li Y., Deng Y., Fang H., Bushel P., Woods M., and Zhang J. Pharmacogenomics J. 2010, 10: 278-291. |
| 2010 | An Interactive Effect of Batch Size and Composition Contributes to Discordant Results in GWAS with the CHIAMO Genotyping Algorithm | Chierici M., Miclaus K., Vega S., and Furlanello C. | An Interactive Effect of Batch Size and Composition Contributes to Discordant Results in GWAS with the CHIAMO Genotyping Algorithm. Chierici M., Miclaus K., Vega S., and Furlanello C. Pharmacogenomics J. 2010, 10: 355-363. |
| 2010 | Assessing Sources of Inconsistencies in Genotypes and Their Effects on Genome-Wide Association Studies with HapMap Samples | Hong H., Shi L., Su Z., Ge W., Jones W.D., Czika W., Miclaus K., Lambert C.G., Vega S.C., Zhang J., Ning B., Liu J., Green B., Xu L., Fang H., Perkins R., Lin S.M., Jafari N., Park K., Ahn T., Chierici M., Furlanello C., Zhang L., Wolfinger R.D., Goodsaid F., and Tong W. | Assessing Sources of Inconsistencies in Genotypes and Their Effects on Genome-Wide Association Studies with HapMap Samples. Hong H., Shi L., Su Z., Ge W., Jones W.D., Czika W., Miclaus K., Lambert C.G., Vega S.C., Zhang J., Ning B., Liu J., Green B., Xu L., Fang H., Perkins R., Lin S.M., Jafari N., Park K., Ahn T., Chierici M., Furlanello C., Zhang L., Wolfinger R.D., Goodsaid F., and Tong W. Pharmacogenomics J. 2010, 10: 364-374. |
| 2010 | Assessment of Variability in GWAS with CRLMM Genotyping Algorithm on WTCCC Coronary Artery Disease | Zhang L., Yin S., Miclaus K., Chierici M., Vega S., Lambert C., Hong H., Wolfinger R.D., Furlanello C., and Goodsaid F. | Assessment of Variability in GWAS with CRLMM Genotyping Algorithm on WTCCC Coronary Artery Disease. Zhang L., Yin S., Miclaus K., Chierici M., Vega S., Lambert C., Hong H., Wolfinger R.D., Furlanello C., and Goodsaid F. Pharmacogenomics J. 2010, 10: 347-354. |
| 2010 | Batch Effects in the BRLMM Genotype Calling Algorithm Influence GWAS Results for the Affymetrix 500K Array | Miclaus K., Wolfinger R., Vega S., Chierici M., Furlanello C., Lambert C., Hong H., Zhang L., Yin S., and Goodsaid F. | Batch Effects in the BRLMM Genotype Calling Algorithm Influence GWAS Results for the Affymetrix 500K Array. Miclaus K., Wolfinger R., Vega S., Chierici M., Furlanello C., Lambert C., Hong H., Zhang L., Yin S., and Goodsaid F. Pharmacogenomics J. 2010, 10: 336-346. |
| 2010 | Comparison of Performance of One-Color and Two-Color Gene-Expression Analyses in Predicting Clinical Endpoints of Neuroblastoma Patients | Oberthuer A., Juraeva D., Li L., Kahlert Y., Westermann F., Eils R., Berthold F., Shi L., Wolfinger R.D., Fischer M., and Brors B. | Comparison of Performance of One-Color and Two-Color Gene-Expression Analyses in Predicting Clinical Endpoints of Neuroblastoma Patients. Oberthuer A., Juraeva D., Li L., Kahlert Y., Westermann F., Eils R., Berthold F., Shi L., Wolfinger R.D., Fischer M., and Brors B. Pharmacogenomics J. 2010, 10: 258-266. |
| 2010 | Consistency of Predictive Signature Genes and Classifiers Generated Using Different Microarray Platforms | Fan X., Lobenhofer E.K., Chen M., Shi W., Huang J., Luo J., Zhang J., Walker S.J., Chu T.M., Li L., Wolfinger R., Bao W., Paules R.S., Bushel P.R., Li J., Shi T., Nikolskaya T., Nikolsky Y., Hong H., Deng Y., Cheng Y., Fang H., Shi L., and Tong W. | Consistency of Predictive Signature Genes and Classifiers Generated Using Different Microarray Platforms. Fan X., Lobenhofer E.K., Chen M., Shi W., Huang J., Luo J., Zhang J., Walker S.J., Chu T.M., Li L., Wolfinger R., Bao W., Paules R.S., Bushel P.R., Li J., Shi T., Nikolskaya T., Nikolsky Y., Hong H., Deng Y., Cheng Y., Fang H., Shi L., and Tong W. Pharmacogenomics J. 2010, 10: 247-257. |
| 2010 | Functional Analysis of Multiple Genomic Signatures Demonstrates that Classification Algorithms Choose Phenotype-Related Genes | Dosymbekov D., Dezso Z., Nikolskaya T., Dudoladova M., Serebryiskaya T., Bugrim A., Guryanov A., Brennan R.J., Shah R., Dopazo J., Chen M., Deng Y., Shi T., Jurman G., Furlanello C., Thomas R.S., Corton J.C., Tong W., Shi L., and Nikolsky Y. | Functional Analysis of Multiple Genomic Signatures Demonstrates that Classification Algorithms Choose Phenotype-Related Genes. Shi W., Bessarabova M., Dosymbekov D., Dezso Z., Nikolskaya T., Dudoladova M., Serebryiskaya T., Bugrim A., Guryanov A., Brennan R.J., Shah R., Dopazo J., Chen M., Deng Y., Shi T., Jurman G., Furlanello C., Thomas R.S., Corton J.C., Tong W., Shi L., and Nikolsky Y. Pharmacogenomics J. 2010, 10: 310-323. |
| 2010 | Genomic Indicators in the Blood Predict Drug-Induced Liver Injury | Huang J., Shi W., Zhang J., Chou J.W., Paules R.S., Gerrish K., Li J., Luo J., Wolfinger R.D., Bao W., Chu T.M., Nikolsky Y., Nikolskaya T., Dosymbekov D., Tsyganova M.O., Shi L., Fan X., Corton J.C., Chen M., Cheng Y., Tong W., Fang H., and Bushel P.R. | Genomic Indicators in the Blood Predict Drug-Induced Liver Injury. Huang J., Shi W., Zhang J., Chou J.W., Paules R.S., Gerrish K., Li J., Luo J., Wolfinger R.D., Bao W., Chu T.M., Nikolsky Y., Nikolskaya T., Dosymbekov D., Tsyganova M.O., Shi L., Fan X., Corton J.C., Chen M., Cheng Y., Tong W., Fang H., and Bushel P.R. Pharmacogenomics J. 2010, 10: 267-277. |
| 2010 | k-Nearest Neighbor Models for Microarray Gene Expression Analysis and Clinical Outcome Prediction | Parry R.M., Jones W., Stokes T.H., Phan J.H., Moffitt R.A., Fang H., Shi L., Oberthuer A., Fischer M., Tong W., and Wang M.D. | k-Nearest Neighbor Models for Microarray Gene Expression Analysis and Clinical Outcome Prediction. Parry R.M., Jones W., Stokes T.H., Phan J.H., Moffitt R.A., Fang H., Shi L., Oberthuer A., Fischer M., Tong W., and Wang M.D. Pharmacogenomics J. 2010, 10: 292-309. |
| 2010 | MAQC-II: Analyze That! (Editorial) | MAQC-II: Analyze That! Nat Biotechnol. 2010, 28: 761. |
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| 2010 | Microarrays in the Clinic | Tillinghast G.W. | Microarrays in the Clinic. Tillinghast G.W. Nat Biotechnol. 2010, 28: 810-812. |
| 2010 | The MicroArray Quality Control (MAQC)-II Study of Common Practices for the Development and Validation of Microarray-Based Predictive Models | MAQC Consortium | The MicroArray Quality Control (MAQC)-II Study of Common Practices for the Development and Validation of Microarray-Based Predictive Models. MAQC Consortium. Nat Biotechnol. 2010, 28: 827-838. |
| 2010 | Of Genomics and Bioinformatics (Editorial) | Slikker W., Jr. | Of Genomics and Bioinformatics. Slikker W., Jr. Pharmacogenomics J. 2010, 10: 245-246. |
| 2010 | Variability in GWAS Analysis: The Impact of Genotype Calling Algorithm Inconsistencies | Miclaus K., Chierici M., Lambert C., Zhang L., Vega S., Hong H., Yin S., Furlanello C., Wolfinger R., and Goodsaid F. | Variability in GWAS Analysis: The Impact of Genotype Calling Algorithm Inconsistencies. Miclaus K., Chierici M., Lambert C., Zhang L., Vega S., Hong H., Yin S., Furlanello C., Wolfinger R., and Goodsaid F. Pharmacogenomics J. 2010, 10: 324-335. |
| 2009 | Correlation Analysis of External RNA Controls Reveals its Utility for Assessment of Microarray Assay | Fan X., Fang H., Hong H., Perkins R.G., She L., and Tong W. | Correlation Analysis of External RNA Controls Reveals its Utility for Assessment of Microarray Assay. Fan X., Fang H., Hong H., Perkins R.G., She L., and Tong W. Anal Biochem. 2009, 385(2):203-207. |
| 2009 | Investigation of Reproducibility of Differentially Expressed Genes in DNA Microarrays Through Statistical Simulation | Fan X., Shi L., Fang H., Harris S., Perkins R.G., and Tong W. | Investigation of Reproducibility of Differentially Expressed Genes in DNA Microarrays Through Statistical Simulation. Fan X., Shi L., Fang H., Harris S., Perkins R.G., and Tong W. BMC Proc. 2009, 3 Suppl 2:S4. |
| 2008 | The Balance of Reproducibility, Sensitivity, and Specificity of Lists of Differenctially Expressed Genes in Microarray Studies | Shi L., Jones W.D., Jensen R.V., Harris S.C., Perkins R.G., Goodsaid F.M., Guo L., Croner L.J., Boysen C., Fang H., et al. | The Balance of Reproducibility, Sensitivity, and Specificity of Lists of Differenctially Expressed Genes in Microarray Studies. Shi L., Jones W.D., Jensen R.V., Harris S.C., Perkins R.G., Goodsaid F.M., Guo L., Croner L.J., Boysen C., Fang H., et al. BMC Bioinformatics. 2008, 9 Suppl 9:S10. |
| 2008 | Reproducible and Reliable Microarray Results Through Quality Control: Good Laboratory Proficiency and Appropriate Data Analysis Practices are Essential | Shi L., Perkins R.G., Fang H., and Tong W. | Reproducible and Reliable Microarray Results Through Quality Control: Good Laboratory Proficiency and Appropriate Data Analysis Practices are Essential. Shi L., Perkins R.G., Fang H., and Tong W. Curr Opin Biotechnol. 2008, 19(1):10-18. |
| 2006 | Evaluation of DNA Microarray Results with Quantitative Gene Expression Platforms | Canales R.D., Luo Y., Willey J.C., Austermiller B., Barbacioru C.C., Boysen C., Hunkapiller K., Jensen R.V., Knight C.R., Lee K.Y., et al. | Evaluation of DNA Microarray Results with Quantitative Gene Expression Platforms. Canales R.D., Luo Y., Willey J.C., Austermiller B., Barbacioru C.C., Boysen C., Hunkapiller K., Jensen R.V., Knight C.R., Lee K.Y., et al. Nat Biotechnol. 2006, 24(9):1115-1122. |
| 2006 | Evaluation of External RNA Controls for the Assessment of Microarray Performance | Tong W., Lucas A.B., Shippy R., Fan X., Fang H., Hong H., Orr M.S., Chu T.M., Guo X., Collins P.J., et al. | Evaluation of External RNA Controls for the Assessment of Microarray Performance. Tong W., Lucas A.B., Shippy R., Fan X., Fang H., Hong H., Orr M.S., Chu T.M., Guo X., Collins P.J., et al. Nat Biotechnol. 2006, 24(9):1132-1139. |
| 2006 | The MicroArray Quality Control (MAQC) Project Shows Inter- and Intraplatform Reproducibility of Gene Expression Measurements | Shi L., Reid L.H., Jones W.D., Shippy R., Warrington J.A., Baker S.C., Collins P.J., de Longueville F., Kawasaki E.S., Lee K.Y., et al. | The MicroArray Quality Control (MAQC) Project Shows Inter- and Intraplatform Reproducibility of Gene Expression Measurements. Shi L., Reid L.H., Jones W.D., Shippy R., Warrington J.A., Baker S.C., Collins P.J., de Longueville F., Kawasaki E.S., Lee K.Y. et al. Nat Biotechnol. 2006, 24(9):1151-1161. |
| 2006 | Performance Comparison of One-Color and Two-Color Platforms Within the MicroArray Quality Control (MAQC) Project | Patterson T.A., Lobenhofer E.K., Fulmer-Smentek S.B., Collins P.J., Chu T.M., Bao W., Fang H., Kawasaki E.S., Hager J., Tikhonova I.R., et al. | Performance Comparison of One-Color and Two-Color Platforms Within the MicroArray Quality Control (MAQC) Project. Patterson T.A., Lobenhofer E.K., Fulmer-Smentek S.B., Collins P.J., Chu T.M., Bao W., Fang H., Kawasaki E.S., Hager J., Tikhonova I.R., et al. Nat Biotechnol. 2006, 24(9):1140-1150. |
| 2006 | Rat Toxicogenomic Study Reveals Analytical Consistency Across Microarray Platforms | Guo L., Lobenhofer E., Wang C., Shippy R., Harris S., Zhang L., Mei N., Chen T., Herman D., and Goodsaid F. | Rat Toxicogenomic Study Reveals Analytical Consistency Across Microarray Platforms. Guo L., Lobenhofer E., Wang C., Shippy R., Harris S., Zhang L., Mei N., Chen T., Herman D., and Goodsaid F. Nat Biotechnol. 2006, 24:1162-1169. |
| 2006 | Using RNA Sample Titrations to Assess Microarray Platform Performance and Normalization Techniques | Shippy R., Fulmer-Smentek S., Jensen R.V., Jones W.D., Wolber P.K., Johnson C.D., Pine P.S., Boysen C., Guo X., Chudin E., et al. | Using RNA Sample Titrations to Assess Microarray Platform Performance and Normalization Techniques. Shippy R., Fulmer-Smentek S., Jensen R.V., Jones W.D., Wolber P.K., Johnson C.D., Pine P.S., Boysen C., Guo X., Chudin E., et al. Nat Biotechnol. 2006, 24(9):1123-1131. |