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Key Parameters of Tumor Epitope Immunogenicity Revealed Through a Consortium Approach Improve Neoantigen Prediction.
Wells DK, van Buuren MM, Dang KK, Hubbard-Lucey VM, Sheehan KCF, Campbell KM, Lamb A, Ward JP, Sidney J, Blazquez AB, Rech AJ, Zaretsky JM, Comin-Anduix B, Ng AHC, Chour W, Yu TV, Rizvi H, Chen JM, Manning P, Steiner GM, Doan XC; Tumor Neoantigen Selection Alliance; Merghoub T, Guinney J, Kolom A, Selinsky C, Ribas A, Hellmann MD, Hacohen N, Sette A, Heath JR, Bhardwaj N, Ramsdell F, Schreiber RD, Schumacher TN, Kvistborg P, Defranoux NA. Wells DK, et al. Among authors: yu tv. Cell. 2020 Oct 29;183(3):818-834.e13. doi: 10.1016/j.cell.2020.09.015. Epub 2020 Oct 9. Cell. 2020. PMID: 33038342 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. 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.
A community challenge to predict clinical outcomes after immune checkpoint blockade in non-small cell lung cancer.
Mason M, Lapuente-Santana Ó, Halkola AS, Wang W, Mall R, Xiao X, Kaufman J, Fu J, Pfeil J, Banerjee J, Chung V, Chang H, Chasalow SD, Lin HY, Chai R, Yu T, Finotello F, Mirtti T, Mäyränpää MI, Bao J, Verschuren EW, Ahmed EI, Ceccarelli M, Miller LD, Monaco G, Hendrickx WRL, Sherif S, Yang L, Tang M, Gu SS, Zhang W, Zhang Y, Zeng Z, Das Sahu A, Liu Y, Yang W, Bedognetti D, Tang J, Eduati F, Laajala TD, Geese WJ, Guinney J, Szustakowski JD, Vincent BG, Carbone DP. Mason M, et al. J Transl Med. 2024 Feb 21;22(1):190. doi: 10.1186/s12967-023-04705-3. J Transl Med. 2024. PMID: 38383458 Free PMC article.
A high-throughput molecular data resource for cutaneous neurofibromas.
Gosline SJ, Weinberg H, Knight P, Yu T, Guo X, Prasad N, Jones A, Shrestha S, Boone B, Levy SE, La Rosa S, Guinney J, Bakker A. Gosline SJ, et al. Sci Data. 2017 Apr 11;4:170045. doi: 10.1038/sdata.2017.45. Sci Data. 2017. PMID: 28398289 Free PMC article.
A Scalable Quality Assurance Process for Curating Oncology Electronic Health Records: The Project GENIE Biopharma Collaborative Approach.
Lavery JA, Lepisto EM, Brown S, Rizvi H, McCarthy C, LeNoue-Newton M, Yu C, Lee J, Guo X, Yu T, Rudolph J, Sweeney S; AACR Project GENIE Consortium; Park BH, Warner JL, Bedard PL, Riely G, Schrag D, Panageas KS. Lavery JA, et al. JCO Clin Cancer Inform. 2022 Feb;6:e2100105. doi: 10.1200/CCI.21.00105. JCO Clin Cancer Inform. 2022. PMID: 35192403 Free PMC article.
Prediction of overall survival for patients with metastatic castration-resistant prostate cancer: development of a prognostic model through a crowdsourced challenge with open clinical trial data.
Guinney J, Wang T, Laajala TD, Winner KK, Bare JC, Neto EC, Khan SA, Peddinti G, Airola A, Pahikkala T, Mirtti T, Yu T, Bot BM, Shen L, Abdallah K, Norman T, Friend S, Stolovitzky G, Soule H, Sweeney CJ, Ryan CJ, Scher HI, Sartor O, Xie Y, Aittokallio T, Zhou FL, Costello JC; Prostate Cancer Challenge DREAM Community. Guinney J, et al. Lancet Oncol. 2017 Jan;18(1):132-142. doi: 10.1016/S1470-2045(16)30560-5. Epub 2016 Nov 16. Lancet Oncol. 2017. PMID: 27864015 Free PMC article. Clinical Trial.
Linked Entity Attribute Pair (LEAP): A Harmonization Framework for Data Pooling.
Thomas S, Lichtenberg T, Dang K, Fitzsimons M, Grossman RL, Kundra R, Lavery JA, Lenoue-Newton ML, Panageas KS, Sawyers C, Schultz ND, Sirintrapun SJ, Topaloglu U, Welch A, Yu T, Zehir A, Gardos S. Thomas S, et al. JCO Clin Cancer Inform. 2020 Aug;4:691-699. doi: 10.1200/CCI.20.00037. JCO Clin Cancer Inform. 2020. PMID: 32755461 Free PMC article.
Gene selection for optimal prediction of cell position in tissues from single-cell transcriptomics data.
Tanevski J, Nguyen T, Truong B, Karaiskos N, Ahsen ME, Zhang X, Shu C, Xu K, Liang X, Hu Y, Pham HV, Xiaomei L, Le TD, Tarca AL, Bhatti G, Romero R, Karathanasis N, Loher P, Chen Y, Ouyang Z, Mao D, Zhang Y, Zand M, Ruan J, Hafemeister C, Qiu P, Tran D, Nguyen T, Gabor A, Yu T, Guinney J, Glaab E, Krause R, Banda P; DREAM SCTC Consortium; Stolovitzky G, Rajewsky N, Saez-Rodriguez J, Meyer P. Tanevski J, et al. Life Sci Alliance. 2020 Sep 24;3(11):e202000867. doi: 10.26508/lsa.202000867. Print 2020 Nov. Life Sci Alliance. 2020. PMID: 32972997 Free PMC article.
28 results