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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: furlanello c. Genome Biol. 2021 Apr 16;22(1):109. doi: 10.1186/s13059-021-02315-0. Genome Biol. 2021. PMID: 33863344 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: furlanello c. Genome Biol. 2021 Apr 16;22(1):111. doi: 10.1186/s13059-021-02316-z. Genome Biol. 2021. PMID: 33863366 Free PMC article.
Comparison of RNA-seq and microarray-based models for clinical endpoint prediction.
Zhang W, Yu Y, Hertwig F, Thierry-Mieg J, Zhang W, Thierry-Mieg D, Wang J, Furlanello C, Devanarayan V, Cheng J, Deng Y, Hero B, Hong H, Jia M, Li L, Lin SM, Nikolsky Y, Oberthuer A, Qing T, Su Z, Volland R, Wang C, Wang MD, Ai J, Albanese D, Asgharzadeh S, Avigad S, Bao W, Bessarabova M, Brilliant MH, Brors B, Chierici M, Chu TM, Zhang J, Grundy RG, He MM, Hebbring S, Kaufman HL, Lababidi S, Lancashire LJ, Li Y, Lu XX, Luo H, Ma X, Ning B, Noguera R, Peifer M, Phan JH, Roels F, Rosswog C, Shao S, Shen J, Theissen J, Tonini GP, Vandesompele J, Wu PY, Xiao W, Xu J, Xu W, Xuan J, Yang Y, Ye Z, Dong Z, Zhang KK, Yin Y, Zhao C, Zheng Y, Wolfinger RD, Shi T, Malkas LH, Berthold F, Wang J, Tong W, Shi L, Peng Z, Fischer M. Zhang W, et al. Among authors: furlanello c. Genome Biol. 2015 Jun 25;16(1):133. doi: 10.1186/s13059-015-0694-1. Genome Biol. 2015. PMID: 26109056 Free PMC article.
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: furlanello c. 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.
Multi-omics integration for neuroblastoma clinical endpoint prediction.
Francescatto M, Chierici M, Rezvan Dezfooli S, Zandonà A, Jurman G, Furlanello C. Francescatto M, et al. Among authors: furlanello c. Biol Direct. 2018 Apr 3;13(1):5. doi: 10.1186/s13062-018-0207-8. Biol Direct. 2018. PMID: 29615097 Free PMC article.
Predictability of drug-induced liver injury by machine learning.
Chierici M, Francescatto M, Bussola N, Jurman G, Furlanello C. Chierici M, et al. Among authors: furlanello c. Biol Direct. 2020 Feb 13;15(1):3. doi: 10.1186/s13062-020-0259-4. Biol Direct. 2020. PMID: 32054490 Free PMC article.
93 results