MicroArray/Sequencing Quality Control (MAQC/SEQC) Publications

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class="content-title text-center">MicroArray/Sequencing Quality Control (MAQC/SEQC) Publications</h1> <div class="lcds-toolbar lcds-toolbar--social"> <ul class="lcds-share lcds-share--default"> <li class="lcds-share__item"> <a href="https://www.facebook.com/sharer/sharer.php?u=https://www.fda.gov%2Fscience-research%2Fmicroarraysequencing-quality-control-maqcseqc%2Fmicroarraysequencing-quality-control-maqcseqc-publications" class="lcds-share__btn lcds-share--default__btn-facebook js-share" id="fb-share" target="_blank"><span class="fa icon-facebook" aria-hidden="true"></span>Share</a> </li> <li class="lcds-share__item"> <a href="https://x.com/intent/tweet/?text=MicroArray%2FSequencing%20Quality%20Control%20%28MAQC%2FSEQC%29%20Publications&url=https://www.fda.gov%2Fscience-research%2Fmicroarraysequencing-quality-control-maqcseqc%2Fmicroarraysequencing-quality-control-maqcseqc-publications" target="_blank" class="lcds-share__btn lcds-share--default__btn-x-twitter js-share" id="twitter-share"> <svg class="icon-svg-inline" aria-hidden="true"> <use href="/themes/custom/preview/assets/images/fa-icons.svg#icon-x-twitter"> </svg> Post </a> </li> <li class="lcds-share__item hidden-xs"> <a href="https://www.linkedin.com/shareArticle?mini=true&url=https://www.fda.gov%2Fscience-research%2Fmicroarraysequencing-quality-control-maqcseqc%2Fmicroarraysequencing-quality-control-maqcseqc-publications&title=MicroArray%2FSequencing%20Quality%20Control%20%28MAQC%2FSEQC%29%20Publications&source=FDA" class="lcds-share__btn lcds-share--default__btn-linkedin js-share" id="linkedin-share" target="_blank"><span class="fa icon-linkedin" aria-hidden="true"></span>Linkedin</a> </li> <li class="lcds-share__item"> <a href="mailto:?subject=MicroArray%2FSequencing%20Quality%20Control%20%28MAQC%2FSEQC%29%20Publications&body=https://www.fda.gov%2Fscience-research%2Fmicroarraysequencing-quality-control-maqcseqc%2Fmicroarraysequencing-quality-control-maqcseqc-publications" 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href="http://www.nature.com/nbt/journal/v28/n8/index.html" target="_blank"><em>Nature Biotechnology</em> — August 2010 Issue</a></p> <p><a href="http://www.nature.com/tpj/journal/v10/n4/index.html"><em>Pharmacogenomics Journal</em> — August 2010 Issue</a></p> <p><a href="http://www.nature.com/nbt/focus/maqc/index.html"><em>Nature Biotechnology</em> — September 2006</a></p> <p> </p> <p> </p> <div> <div class="table-responsive lcds-datatable lcds-datatable--ckeditor"> <table class="table table-bordered table-striped" data-column-defs="[ {"targets": 0, "type": "date"} ]" data-excel-button="true" data-order="[ 0, "desc" ]" data-page-length="-1" data-paging="true" data-searching="true"> <thead> <tr> <th scope="col">Year</th> <th scope="col">Title</th> <th scope="col">Authors</th> <th scope="col">Full Citation</th> </tr> </thead> <tbody> <tr> <td>2022</td> <td style="width: 516px;"><a href="https://pubmed.ncbi.nlm.nih.gov/34996510/">Achieving Robust Somatic Mutation Detection with Deep Learning Models Derived from Reference Data Sets of a Cancer Sample</a></td> <td style="width: 274px;">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. </td> <td style="width: 445px;"><strong>Achieving Robust Somatic Mutation Detection with Deep Learning Models Derived from Reference Data Sets of a Cancer Sample</strong>. <br> 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. <br> <em>Genome Biol</em>. 2022, 23(1):12.</td> </tr> <tr> <td>2022</td> <td style="width: 516px;"><a href="https://pubmed.ncbi.nlm.nih.gov/34980216/">Assessing Reproducibility of Inherited Variants Detected with Short-Read Whole Genome Sequencing</a></td> <td style="width: 274px;">Pan B., Ren L., Onuchic V., Guan M., Kusko R., Bruinsma S., Trigg L., Scherer A., Ning B., Zhang C., et al.</td> <td style="width: 445px;"><strong>Assessing Reproducibility of Inherited Variants Detected with Short-Read Whole Genome Sequencing</strong>. <br> Pan B., Ren L., Onuchic V., Guan M., Kusko R., Bruinsma S., Trigg L., Scherer A., Ning B., Zhang C., et al.<br> <em>Genome Biol</em>. 2022, 23(1):2.</td> </tr> <tr> <td>2022</td> <td style="width: 516px;"><a href="https://pubmed.ncbi.nlm.nih.gov/35768876/">Deep Oncopanel Sequencing Reveals Within Block Position-Dependent Quality Degradation in FFPE Processed Samples</a></td> <td style="width: 274px;">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. </td> <td style="width: 445px;"><strong>Deep Oncopanel Sequencing Reveals Within Block Position-Dependent Quality Degradation in FFPE Processed Samples</strong>. <br> 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. <br> <em>Genome Biol</em>. 2022, 23(1):141.</td> </tr> <tr> <td>2022</td> <td style="width: 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Concordance Between RNA-Seq and Microarray Data Depends on Chemical Treatment and Transcript Abundance</strong>.<br> 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. <br> <em>Nature Biotechnology</em>. 2014, 32(9):926-32. doi: 10.1038/nbt.3001.</td> </tr> <tr> <td>2014</td> <td style="width: 516px;"><a href="https://pubmed.ncbi.nlm.nih.gov/25977777/">Cross-Platform Ultradeep Transcriptomic Profiling of Human Reference RNA Samples by RNA-Seq</a></td> <td style="width: 274px;">Xu J., Su Z., Hong H., Kreil D.P., Mason C.E., Tong W., and Shi L.</td> <td style="width: 445px;"><strong>Cross-Platform Ultradeep Transcriptomic Profiling of Human Reference RNA Samples by RNA-Seq</strong>.<br> Xu J., Su Z., Hong H., Kreil D.P., Mason C.E., Tong W., and Shi L.<br> <em>Scientific Data</em>. 2014, 1:140020. doi: 10.1038/sdata.2014.20. </td> </tr> <tr> <td>2014</td> <td style="width: 516px;"><a href="https://pubmed.ncbi.nlm.nih.gov/25150837/">Detecting and Correcting Systematic Variation in Large-Scale RNA Sequencing Data</a></td> <td style="width: 274px;">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. </td> <td style="width: 445px;"><strong>Detecting and Correcting Systematic Variation in Large-Scale RNA Sequencing Data</strong>.<br> 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. <br> <em>Nat Biotechnol</em>. 2014, 32(9):888-95. doi: 10.1038/nbt.3000. </td> </tr> <tr> <td>2014</td> <td style="width: 516px;"><a href="https://pubmed.ncbi.nlm.nih.gov/24510058/">A Rat RNA-Seq Transcriptomic BodyMap Across 11 Organs and 4 Developmental Stages</a></td> <td style="width: 274px;">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. </td> <td style="width: 445px;"><strong>A Rat RNA-Seq Transcriptomic BodyMap Across 11 Organs and 4 Developmental Stages</strong>.<br> 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. <br> <em>Nature Communications</em>. 2014, 5:3230. doi: 10.1038/ncomms4230.</td> </tr> <tr> <td>2014</td> <td style="width: 516px;"><a href="https://pubmed.ncbi.nlm.nih.gov/25977778/">Transcriptomic Profiling of Rat Liver Samples in a Comprehensive Study Design by RNA-Seq</a></td> <td style="width: 274px;">Gong B., Wang C., Su Z., Hong H., Auerbach A., Shi L., Tong W., and Xu J.</td> <td style="width: 445px;"> <p><strong>Transcriptomic Profiling of Rat Liver Samples in a Comprehensive Study Design by RNA-Seq.</strong><br> Gong B., Wang C., Su Z., Hong H., Auerbach A., Shi L., Tong W., and Xu J.<br> <em>Scientific Data</em>. 2014, 1:140021. doi: 10.1038/sdata.2014.21.</p> </td> </tr> <tr> <td>2010</td> <td style="width: 516px;"><a href="https://pubmed.ncbi.nlm.nih.gov/20676067/">A Comparison of Batch Effect Removal Methods for Enhancement of Prediction Performance Using MAQC-II Microarray Gene Expression Data</a></td> <td style="width: 274px;">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.</td> <td style="width: 445px;"><strong>A Comparison of Batch Effect Removal Methods for Enhancement of Prediction Performance Using MAQC-II Microarray Gene Expression Data</strong>. <br> 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.<br> <em>Pharmacogenomics J.</em> 2010, 10: 278-291.</td> </tr> <tr> <td>2010</td> <td style="width: 516px;"><a href="https://pubmed.ncbi.nlm.nih.gov/20676073/">An Interactive Effect of Batch Size and Composition Contributes to Discordant Results in GWAS with the CHIAMO Genotyping Algorithm</a></td> <td style="width: 274px;">Chierici M., Miclaus K., Vega S., and Furlanello C. </td> <td style="width: 445px;"><strong>An Interactive Effect of Batch Size and Composition Contributes to Discordant Results in GWAS with the CHIAMO Genotyping Algorithm</strong>.<br> Chierici M., Miclaus K., Vega S., and Furlanello C. <br> <em>Pharmacogenomics J. </em>2010, 10: 355-363.</td> </tr> <tr> <td>2010</td> <td style="width: 516px;"><a href="https://pubmed.ncbi.nlm.nih.gov/20368714/">Assessing Sources of Inconsistencies in Genotypes and Their Effects on Genome-Wide Association Studies with HapMap Samples</a></td> <td style="width: 274px;">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.</td> <td style="width: 445px;"><strong>Assessing Sources of Inconsistencies in Genotypes and Their Effects on Genome-Wide Association Studies with HapMap Samples</strong>.<br> 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.<br> <em>Pharmacogenomics J.</em> 2010, 10: 364-374.</td> </tr> <tr> <td>2010</td> <td style="width: 516px;"><a href="https://pubmed.ncbi.nlm.nih.gov/20676072/">Assessment of Variability in GWAS with CRLMM Genotyping Algorithm on WTCCC Coronary Artery Disease</a></td> <td style="width: 274px;">Zhang L., Yin S., Miclaus K., Chierici M., Vega S., Lambert C., Hong H., Wolfinger R.D., Furlanello C., and Goodsaid F.</td> <td style="width: 445px;"><strong>Assessment of Variability in GWAS with CRLMM Genotyping Algorithm on WTCCC Coronary Artery Disease</strong>.<br> Zhang L., Yin S., Miclaus K., Chierici M., Vega S., Lambert C., Hong H., Wolfinger R.D., Furlanello C., and Goodsaid F. <em>Pharmacogenomics J.</em> 2010, 10: 347-354.</td> </tr> <tr> <td>2010</td> <td style="width: 516px;"><a href="https://pubmed.ncbi.nlm.nih.gov/20676071/">Batch Effects in the BRLMM Genotype Calling Algorithm Influence GWAS Results for the Affymetrix 500K Array</a></td> <td style="width: 274px;">Miclaus K., Wolfinger R., Vega S., Chierici M., Furlanello C., Lambert C., Hong H., Zhang L., Yin S., and Goodsaid F.</td> <td style="width: 445px;"><strong>Batch Effects in the BRLMM Genotype Calling Algorithm Influence GWAS Results for the Affymetrix 500K Array</strong>.<br> Miclaus K., Wolfinger R., Vega S., Chierici M., Furlanello C., Lambert C., Hong H., Zhang L., Yin S., and Goodsaid F. <em>Pharmacogenomics J.</em> 2010, 10: 336-346.</td> </tr> <tr> <td>2010</td> <td style="width: 516px;"><a href="https://pubmed.ncbi.nlm.nih.gov/20676065/">Comparison of Performance of One-Color and Two-Color Gene-Expression Analyses in Predicting Clinical Endpoints of Neuroblastoma Patients</a></td> <td style="width: 274px;">Oberthuer A., Juraeva D., Li L., Kahlert Y., Westermann F., Eils R., Berthold F., Shi L., Wolfinger R.D., Fischer M., and Brors B.</td> <td style="width: 445px;"><strong>Comparison of Performance of One-Color and Two-Color Gene-Expression Analyses in Predicting Clinical Endpoints of Neuroblastoma Patients.</strong><br> Oberthuer A., Juraeva D., Li L., Kahlert Y., Westermann F., Eils R., Berthold F., Shi L., Wolfinger R.D., Fischer M., and Brors B. <em>Pharmacogenomics J.</em> 2010, 10: 258-266.</td> </tr> <tr> <td>2010</td> <td style="width: 516px;"><a href="https://pubmed.ncbi.nlm.nih.gov/20676064/">Consistency of Predictive Signature Genes and Classifiers Generated Using Different Microarray Platforms</a></td> <td style="width: 274px;">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.</td> <td style="width: 445px;"><strong>Consistency of Predictive Signature Genes and Classifiers Generated Using Different Microarray Platforms</strong>.<br> 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. <br> <em>Pharmacogenomics J.</em> 2010, 10: 247-257.</td> </tr> <tr> <td>2010</td> <td style="width: 516px;"><a href="https://pubmed.ncbi.nlm.nih.gov/20676069/">Functional Analysis of Multiple Genomic Signatures Demonstrates that Classification Algorithms Choose Phenotype-Related Genes</a></td> <td style="width: 274px;">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.</td> <td style="width: 445px;"><strong>Functional Analysis of Multiple Genomic Signatures Demonstrates that Classification Algorithms Choose Phenotype-Related Genes</strong>. 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. <em>Pharmacogenomics J.</em> 2010, 10: 310-323.</td> </tr> <tr> <td>2010</td> <td style="width: 516px;"><a href="https://pubmed.ncbi.nlm.nih.gov/20676066/">Genomic Indicators in the Blood Predict Drug-Induced Liver Injury</a></td> <td style="width: 274px;">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.</td> <td style="width: 445px;"><strong>Genomic Indicators in the Blood Predict Drug-Induced Liver Injury</strong>.<br> 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.<br> <em>Pharmacogenomics J.</em> 2010, 10: 267-277.</td> </tr> <tr> <td>2010</td> <td style="width: 516px;"><a href="https://pubmed.ncbi.nlm.nih.gov/20676068/">k-Nearest Neighbor Models for Microarray Gene Expression Analysis and Clinical Outcome Prediction</a></td> <td style="width: 274px;">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.</td> <td style="width: 445px;"><strong>k-Nearest Neighbor Models for Microarray Gene Expression Analysis and Clinical Outcome Prediction</strong>.<br> 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.<br> <em>Pharmacogenomics J.</em> 2010, 10: 292-309.</td> </tr> <tr> <td>2010</td> <td style="width: 516px;"><a href="https://www.nature.com/articles/nbt0810-761b">MAQC-II: Analyze That!</a> (Editorial)</td> <td style="width: 274px;"> </td> <td style="width: 445px;"><strong>MAQC-II: Analyze That!</strong><br> <em>Nat Biotechnol.</em> 2010, 28: 761.</td> </tr> <tr> <td>2010</td> <td style="width: 516px;"><a href="https://www.nature.com/articles/nbt0810-810">Microarrays in the Clinic</a></td> <td style="width: 274px;">Tillinghast G.W.</td> <td style="width: 445px;"><strong>Microarrays in the Clinic</strong>.<br> Tillinghast G.W.<br> <em>Nat Biotechnol.</em> 2010, 28: 810-812.</td> </tr> <tr> <td>2010</td> <td style="width: 516px;"><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3315840/">The MicroArray Quality Control (MAQC)-II Study of Common Practices for the Development and Validation of Microarray-Based Predictive Models</a></td> <td style="width: 274px;">MAQC Consortium</td> <td style="width: 445px;"><strong>The MicroArray Quality Control (MAQC)-II Study of Common Practices for the Development and Validation of Microarray-Based Predictive Models</strong>.<br> MAQC Consortium.<br> <em>Nat Biotechnol.</em> 2010, 28: 827-838.</td> </tr> <tr> <td>2010</td> <td style="width: 516px;"><a href="https://www.nature.com/articles/tpj201059">Of Genomics and Bioinformatics</a> (Editorial)</td> <td style="width: 274px;">Slikker W., Jr.</td> <td style="width: 445px;"><strong>Of Genomics and Bioinformatics</strong>.<br> Slikker W., Jr.<br> <em>Pharmacogenomics J.</em> 2010, 10: 245-246.</td> </tr> <tr> <td>2010</td> <td style="width: 516px;"><a href="https://www.nature.com/articles/tpj201046">Variability in GWAS Analysis: The Impact of Genotype Calling Algorithm Inconsistencies</a></td> <td style="width: 274px;">Miclaus K., Chierici M., Lambert C., Zhang L., Vega S., Hong H., Yin S., Furlanello C., Wolfinger R., and Goodsaid F.</td> <td style="width: 445px;"><strong>Variability in GWAS Analysis: The Impact of Genotype Calling Algorithm Inconsistencies</strong>.<br> Miclaus K., Chierici M., Lambert C., Zhang L., Vega S., Hong H., Yin S., Furlanello C., Wolfinger R., and Goodsaid F. <em>Pharmacogenomics J.</em> 2010, 10: 324-335.</td> </tr> <tr> <td>2009</td> <td style="width: 516px;"><a href="https://pubmed.ncbi.nlm.nih.gov/19059192/">Correlation Analysis of External RNA Controls Reveals its Utility for Assessment of Microarray Assay</a></td> <td style="width: 274px;">Fan X., Fang H., Hong H., Perkins R.G., She L., and Tong W.</td> <td style="width: 445px;"><strong>Correlation Analysis of External RNA Controls Reveals its Utility for Assessment of Microarray Assay.</strong><br> Fan X., Fang H., Hong H., Perkins R.G., She L., and Tong W.<br> <em>Anal Biochem.</em> 2009, 385(2):203-207.</td> </tr> <tr> <td>2009</td> <td style="width: 516px;"><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2654487/">Investigation of Reproducibility of Differentially Expressed Genes in DNA Microarrays Through Statistical Simulation</a></td> <td style="width: 274px;">Fan X., Shi L., Fang H., Harris S., Perkins R.G., and Tong W.</td> <td style="width: 445px;"><strong>Investigation of Reproducibility of Differentially Expressed Genes in DNA Microarrays Through Statistical Simulation</strong>.<br> Fan X., Shi L., Fang H., Harris S., Perkins R.G., and Tong W.<br> <em>BMC Proc.</em> 2009, 3 Suppl 2:S4.</td> </tr> <tr> <td>2008</td> <td style="width: 516px;"><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2537561/">The Balance of Reproducibility, Sensitivity, and Specificity of Lists of Differenctially Expressed Genes in Microarray Studies</a></td> <td style="width: 274px;">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., <em>et al.</em></td> <td style="width: 445px;"><strong>The Balance of Reproducibility, Sensitivity, and Specificity of Lists of Differenctially Expressed Genes in Microarray Studies.</strong><br> 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., <em>et al.</em><br> <em>BMC Bioinformatics.</em> 2008, 9 Suppl 9:S10.</td> </tr> <tr> <td>2008</td> <td style="width: 516px;"><a href="https://pubmed.ncbi.nlm.nih.gov/18155896/">Reproducible and Reliable Microarray Results Through Quality Control: Good Laboratory Proficiency and Appropriate Data Analysis Practices are Essential</a></td> <td style="width: 274px;">Shi L., Perkins R.G., Fang H., and Tong W.</td> <td style="width: 445px;"><strong>Reproducible and Reliable Microarray Results Through Quality Control: Good Laboratory Proficiency and Appropriate Data Analysis Practices are Essential.</strong><br> Shi L., Perkins R.G., Fang H., and Tong W.<br> <em>Curr Opin Biotechnol.</em> 2008, 19(1):10-18.</td> </tr> <tr> <td>2006</td> <td style="width: 516px;"><a href="https://pubmed.ncbi.nlm.nih.gov/16964225/">Evaluation of DNA Microarray Results with Quantitative Gene Expression Platforms</a></td> <td style="width: 274px;">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., <em>et al.</em></td> <td style="width: 445px;"><strong>Evaluation of DNA Microarray Results with Quantitative Gene Expression Platforms</strong>.<br> 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., <em>et al.</em><br> <em>Nat Biotechnol. </em>2006<em>, </em>24(9):1115-1122.</td> </tr> <tr> <td>2006</td> <td style="width: 516px;"><a href="https://pubmed.ncbi.nlm.nih.gov/16964227/">Evaluation of External RNA Controls for the Assessment of Microarray Performance</a></td> <td style="width: 274px;">Tong W., Lucas A.B., Shippy R., Fan X., Fang H., Hong H., Orr M.S., Chu T.M., Guo X., Collins P.J., <em>et al.</em></td> <td style="width: 445px;"><strong>Evaluation of External RNA Controls for the Assessment of Microarray Performanc</strong>e<strong>.</strong><br> Tong W., Lucas A.B., Shippy R., Fan X., Fang H., Hong H., Orr M.S., Chu T.M., Guo X., Collins P.J., <em>et al.</em><br> <em>Nat Biotechnol.</em> 2006, 24(9):1132-1139.</td> </tr> <tr> <td>2006</td> <td style="width: 516px;"><a href="https://pubmed.ncbi.nlm.nih.gov/16964229/">The MicroArray Quality Control (MAQC) Project Shows Inter- and Intraplatform Reproducibility of Gene Expression Measurements</a></td> <td style="width: 274px;">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., <em>et al</em>.</td> <td style="width: 445px;"><strong>The MicroArray Quality Control (MAQC) Project Shows Inter- and Intraplatform Reproducibility of Gene Expression Measurements</strong><strong>.</strong><br> 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. <em>et al</em>.<br> <em>Nat Biotechnol.</em> 2006, 24(9):1151-1161.</td> </tr> <tr> <td>2006</td> <td style="width: 516px;"><a href="https://pubmed.ncbi.nlm.nih.gov/16964228/">Performance Comparison of One-Color and Two-Color Platforms Within the MicroArray Quality Control (MAQC) Project</a></td> <td style="width: 274px;">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., <em>et al.</em></td> <td style="width: 445px;"><strong>Performance Comparison of One-Color and Two-Color Platforms Within the MicroArray Quality Control (MAQC) Project.</strong><br> 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., <em>et al.</em><br> <em>Nat Biotechnol.</em> 2006, 24(9):1140-1150.  </td> </tr> <tr> <td>2006</td> <td style="width: 516px;"><a href="https://pubmed.ncbi.nlm.nih.gov/17061323/">Rat Toxicogenomic Study Reveals Analytical Consistency Across Microarray Platforms</a></td> <td style="width: 274px;">Guo L., Lobenhofer E., Wang C., Shippy R., Harris S., Zhang L., Mei N., Chen T., Herman D., and Goodsaid F.</td> <td style="width: 445px;"><strong>Rat Toxicogenomic Study Reveals Analytical Consistency Across Microarray Platforms.</strong><br> Guo L., Lobenhofer E., Wang C., Shippy R., Harris S., Zhang L., Mei N., Chen T., Herman D., and Goodsaid F.<br> <em>Nat Biotechnol. </em>2006<em>, </em>24:1162-1169.</td> </tr> <tr> <td>2006</td> <td style="width: 516px;"><a href="https://pubmed.ncbi.nlm.nih.gov/16964226/">Using RNA Sample Titrations to Assess Microarray Platform Performance and Normalization Techniques</a></td> <td style="width: 274px;">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., <em>et al.</em></td> <td style="width: 445px;"><strong>Using RNA Sample Titrations to Assess Microarray Platform Performance and Normalization Techniques.</strong><br> Shippy R., Fulmer-Smentek S., Jensen R.V., Jones W.D., Wolber P.K., Johnson C.D., Pine P.S., Boysen C., Guo X., 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