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The concordance between RNA-seq and microarray data depends on chemical treatment and transcript abundance.
Wang C, Gong B, Bushel PR, 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 PP, Kreil DP, Megherbi D, Gaj S, Caiment F, van Delft J, Kleinjans J, Scherer A, Devanarayan V, Wang J, Yang Y, Qian HR, Lancashire LJ, Bessarabova M, Nikolsky Y, Furlanello C, Chierici M, Albanese D, Jurman G, Riccadonna S, Filosi M, Visintainer R, Zhang KK, Li J, Hsieh JH, Svoboda DL, Fuscoe JC, Deng Y, Shi L, Paules RS, Auerbach SS, Tong W. Wang C, et al. Among authors: scherer a. Nat Biotechnol. 2014 Sep;32(9):926-32. doi: 10.1038/nbt.3001. Epub 2014 Aug 24. Nat Biotechnol. 2014. PMID: 25150839 Free PMC article.
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 TA, Johann DJ Jr, Bisgin H, Sahraeian SME, Bushel PR, Pirooznia M, Wilkins K, Chierici M, Bao W, Basehore LS, Lucas AB, Burgess D, Butler DJ, Cawley S, Chang CJ, Chen G, Chen T, Chen YC, Craig DJ, Del Pozo A, Foox J, Francescatto M, Fu Y, Furlanello C, Giorda K, Grist KP, Guan M, Hao Y, Happe S, Hariani G, Haseley N, Jasper J, Jurman G, Kreil DP, Łabaj P, Lai K, Li J, Li QZ, Li Y, Li Z, Liu Z, López MS, Miclaus K, Miller R, Mittal VK, Mohiyuddin M, Pabón-Peña C, Parsons BL, Qiu F, Scherer A, Shi T, Stiegelmeyer S, Suo C, Tom N, Wang D, Wen Z, Wu L, Xiao W, Xu C, Yu Y, Zhang J, Zhang Y, Zhang Z, Zheng Y, Mason CE, Willey JC, Tong W, Shi L, Xu J. Jones W, et al. Among authors: scherer a. Genome Biol. 2021 Apr 16;22(1):111. doi: 10.1186/s13059-021-02316-z. Genome Biol. 2021. PMID: 33863366 Free PMC article.
Whole genome and exome sequencing reference datasets from a multi-center and cross-platform benchmark study.
Zhao Y, Fang LT, Shen TW, Choudhari S, Talsania K, Chen X, Shetty J, Kriga Y, Tran B, Zhu B, Chen Z, Chen W, Wang C, Jaeger E, Meerzaman D, Lu C, Idler K, Ren L, Zheng Y, Shi L, Petitjean V, Sultan M, Hung T, Peters E, Drabek J, Vojta P, Maestro R, Gasparotto D, Kõks S, Reimann E, Scherer A, Nordlund J, Liljedahl U, Foox J, Mason CE, Xiao C, Hong H, Xiao W. Zhao Y, et al. Among authors: scherer a. Sci Data. 2021 Nov 9;8(1):296. doi: 10.1038/s41597-021-01077-5. Sci Data. 2021. PMID: 34753956 Free PMC article.
Robust and tissue-independent gender-specific transcript biomarkers.
Staedtler F, Hartmann N, Letzkus M, Bongiovanni S, Scherer A, Marc P, Johnson KJ, Schumacher MM. Staedtler F, et al. Among authors: scherer a. Biomarkers. 2013 Aug;18(5):436-45. doi: 10.3109/1354750X.2013.811538. Epub 2013 Jul 8. Biomarkers. 2013. PMID: 23829492
Evaluating the analytical validity of circulating tumor DNA sequencing assays for precision oncology.
Deveson IW, Gong B, Lai K, LoCoco JS, Richmond TA, Schageman J, Zhang Z, Novoradovskaya N, Willey JC, Jones W, Kusko R, Chen G, Madala BS, Blackburn J, Stevanovski I, Bhandari A, Close D, Conroy J, Hubank M, Marella N, Mieczkowski PA, Qiu F, Sebra R, Stetson D, Sun L, Szankasi P, Tan H, Tang LY, Arib H, Best H, Burgher B, Bushel PR, Casey F, Cawley S, Chang CJ, Choi J, Dinis J, Duncan D, Eterovic AK, Feng L, Ghosal A, Giorda K, Glenn S, Happe S, Haseley N, Horvath K, Hung LY, Jarosz M, Kushwaha G, Li D, Li QZ, Li Z, Liu LC, Liu Z, Ma C, Mason CE, Megherbi DB, Morrison T, Pabón-Peña C, Pirooznia M, Proszek PZ, Raymond A, Rindler P, Ringler R, Scherer A, Shaknovich R, Shi T, Smith M, Song P, Strahl M, Thodima VJ, Tom N, Verma S, Wang J, Wu L, Xiao W, Xu C, Yang M, Zhang G, Zhang S, Zhang Y, Shi L, Tong W, Johann DJ Jr, Mercer TR, Xu J; SEQC2 Oncopanel Sequencing Working Group. Deveson IW, et al. Among authors: scherer a. Nat Biotechnol. 2021 Sep;39(9):1115-1128. doi: 10.1038/s41587-021-00857-z. Epub 2021 Apr 12. Nat Biotechnol. 2021. PMID: 33846644 Free PMC article.
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, Pabón-Peña C, Zhang Z, Lai K, Cai W, LoCoco JS, Lader E, Richmond TA, Mittal VK, Liu LC, Johann DJ Jr, Willey JC, Bushel PR, Yu Y, Xu C, Chen G, Burgess D, Cawley S, Giorda K, Haseley N, Qiu F, Wilkins K, Arib H, Attwooll C, Babson K, Bao L, Bao W, Lucas AB, Best H, Bhandari A, Bisgin H, Blackburn J, Blomquist TM, Boardman L, Burgher B, Butler DJ, Chang CJ, Chaubey A, Chen T, Chierici M, Chin CR, Close D, Conroy J, Cooley Coleman J, Craig DJ, Crawford E, Del Pozo A, Deveson IW, Duncan D, Eterovic AK, Fan X, Foox J, Furlanello C, Ghosal A, Glenn S, Guan M, Haag C, Hang X, Happe S, Hennigan B, Hipp J, Hong H, Horvath K, Hu J, Hung LY, Jarosz M, Kerkhof J, Kipp B, Kreil DP, Łabaj P, Lapunzina P, Li P, Li QZ, Li W, Li Z, Liang Y, Liu S, Liu Z, Ma C, Marella N, Martín-Arenas R, Megherbi DB, Meng Q, Mieczkowski PA, Morrison T, Muzny D, Ning B, Parsons BL, Paweletz CP, Pirooznia M, Qu W, Raymond A, Rindler P, Ringler R, Sadikovic B, Scherer A, Schulze E, Sebra R, Shaknovich R, Shi Q, Shi T, Silla-Castro JC, Smith M, López MS, Song P, Stetson D, Strahl M, Stuart A, Supplee J, Szankasi P, Tan H, Tang LY, Tao Y, Thakkar S, Thi… See abstract for full author list ➔ Gong B, et al. Among authors: scherer a. Genome Biol. 2021 Apr 16;22(1):109. doi: 10.1186/s13059-021-02315-0. Genome Biol. 2021. PMID: 33863344 Free PMC article.
549 results