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Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection.
Ewing AD, Houlahan KE, Hu Y, Ellrott K, Caloian C, Yamaguchi TN, Bare JC, P'ng C, Waggott D, Sabelnykova VY; ICGC-TCGA DREAM Somatic Mutation Calling Challenge participants; Kellen MR, Norman TC, Haussler D, Friend SH, Stolovitzky G, Margolin AA, Stuart JM, Boutros PC. Ewing AD, et al. Among authors: hu y. Nat Methods. 2015 Jul;12(7):623-30. doi: 10.1038/nmeth.3407. Epub 2015 May 18. Nat Methods. 2015. PMID: 25984700 Free PMC article.
Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection.
Lee AY, Ewing AD, Ellrott K, Hu Y, Houlahan KE, Bare JC, Espiritu SMG, Huang V, Dang K, Chong Z, Caloian C, Yamaguchi TN; ICGC-TCGA DREAM Somatic Mutation Calling Challenge Participants; Kellen MR, Chen K, Norman TC, Friend SH, Guinney J, Stolovitzky G, Haussler D, Margolin AA, Stuart JM, Boutros PC. Lee AY, et al. Among authors: hu y. Genome Biol. 2018 Nov 6;19(1):188. doi: 10.1186/s13059-018-1539-5. Genome Biol. 2018. PMID: 30400818 Free PMC article.
A community challenge to evaluate RNA-seq, fusion detection, and isoform quantification methods for cancer discovery.
Creason A, Haan D, Dang K, Chiotti KE, Inkman M, Lamb A, Yu T, Hu Y, Norman TC, Buchanan A, van Baren MJ, Spangler R, Rollins MR, Spellman PT, Rozanov D, Zhang J, Maher CA, Caloian C, Watson JD, Uhrig S, Haas BJ, Jain M, Akeson M, Ahsen ME; SMC-RNA Challenge Participants; Stolovitzky G, Guinney J, Boutros PC, Stuart JM, Ellrott K. Creason A, et al. Among authors: hu y. Cell Syst. 2021 Aug 18;12(8):827-838.e5. doi: 10.1016/j.cels.2021.05.021. Epub 2021 Jun 18. Cell Syst. 2021. PMID: 34146471 Free PMC article.
Sex Differences in Long COVID.
Shah DP, Thaweethai T, Karlson EW, Bonilla H, Horne BD, Mullington JM, Wisnivesky JP, Hornig M, Shinnick DJ, Klein JD, Erdmann NB, Brosnahan SB, Lee-Iannotti JK, Metz TD, Maughan C, Ofotokun I, Reeder HT, Stiles LE, Shaukat A, Hess R, Ashktorab H, Bartram L, Bassett IV, Becker JH, Brim H, Charney AW, Chopra T, Clifton RG, Deeks SG, Erlandson KM, Fierer DS, Flaherman VJ, Fonseca V, Gander JC, Hodder SL, Jacoby VL, Kotini-Shah P, Krishnan JA, Kumar A, Levy BD, Lieberman D, Lin JJ, Martin JN, McComsey GA, Moukabary T, Okumura MJ, Peluso MJ, Rosen CJ, Saade G, Shah PK, Sherif ZA, Taylor BS, Tuttle KR, Urdaneta AE, Wallick JA, Wiley Z, Zhang D, Horwitz LI, Foulkes AS, Singer NG; RECOVER Consortium. Shah DP, et al. JAMA Netw Open. 2025 Jan 2;8(1):e2455430. doi: 10.1001/jamanetworkopen.2024.55430. JAMA Netw Open. 2025. PMID: 39841477
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