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Page 1
Systematic analysis of challenge-driven improvements in molecular prognostic models for breast cancer.
Margolin AA, Bilal E, Huang E, Norman TC, Ottestad L, Mecham BH, Sauerwine B, Kellen MR, Mangravite LM, Furia MD, Vollan HK, Rueda OM, Guinney J, Deflaux NA, Hoff B, Schildwachter X, Russnes HG, Park D, Vang VO, Pirtle T, Youseff L, Citro C, Curtis C, Kristensen VN, Hellerstein J, Friend SH, Stolovitzky G, Aparicio S, Caldas C, Børresen-Dale AL. Margolin AA, et al. Among authors: hoff b. Sci Transl Med. 2013 Apr 17;5(181):181re1. doi: 10.1126/scitranslmed.3006112. Sci Transl Med. 2013. PMID: 23596205 Free PMC article.
Summary of the DREAM8 Parameter Estimation Challenge: Toward Parameter Identification for Whole-Cell Models.
Karr JR, Williams AH, Zucker JD, Raue A, Steiert B, Timmer J, Kreutz C; DREAM8 Parameter Estimation Challenge Consortium; Wilkinson S, Allgood BA, Bot BM, Hoff BR, Kellen MR, Covert MW, Stolovitzky GA, Meyer P. Karr JR, et al. Among authors: hoff br. PLoS Comput Biol. 2015 May 28;11(5):e1004096. doi: 10.1371/journal.pcbi.1004096. eCollection 2015 May. PLoS Comput Biol. 2015. PMID: 26020786 Free PMC article.
A Community Challenge for Inferring Genetic Predictors of Gene Essentialities through Analysis of a Functional Screen of Cancer Cell Lines.
Gönen M, Weir BA, Cowley GS, Vazquez F, Guan Y, Jaiswal A, Karasuyama M, Uzunangelov V, Wang T, Tsherniak A, Howell S, Marbach D, Hoff B, Norman TC, Airola A, Bivol A, Bunte K, Carlin D, Chopra S, Deran A, Ellrott K, Gopalacharyulu P, Graim K, Kaski S, Khan SA, Newton Y, Ng S, Pahikkala T, Paull E, Sokolov A, Tang H, Tang J, Wennerberg K, Xie Y, Zhan X, Zhu F; Broad-DREAM Community; Aittokallio T, Mamitsuka H, Stuart JM, Boehm JS, Root DE, Xiao G, Stolovitzky G, Hahn WC, Margolin AA. Gönen M, et al. Among authors: hoff b. Cell Syst. 2017 Nov 22;5(5):485-497.e3. doi: 10.1016/j.cels.2017.09.004. Epub 2017 Oct 4. Cell Syst. 2017. PMID: 28988802 Free PMC article.
Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis.
Sieberts SK, Zhu F, García-García J, Stahl E, Pratap A, Pandey G, Pappas D, Aguilar D, Anton B, Bonet J, Eksi R, Fornés O, Guney E, Li H, Marín MA, Panwar B, Planas-Iglesias J, Poglayen D, Cui J, Falcao AO, Suver C, Hoff B, Balagurusamy VSK, Dillenberger D, Neto EC, Norman T, Aittokallio T, Ammad-Ud-Din M, Azencott CA, Bellón V, Boeva V, Bunte K, Chheda H, Cheng L, Corander J, Dumontier M, Goldenberg A, Gopalacharyulu P, Hajiloo M, Hidru D, Jaiswal A, Kaski S, Khalfaoui B, Khan SA, Kramer ER, Marttinen P, Mezlini AM, Molparia B, Pirinen M, Saarela J, Samwald M, Stoven V, Tang H, Tang J, Torkamani A, Vert JP, Wang B, Wang T, Wennerberg K, Wineinger NE, Xiao G, Xie Y, Yeung R, Zhan X, Zhao C; Members of the Rheumatoid Arthritis Challenge Consortium; Greenberg J, Kremer J, Michaud K, Barton A, Coenen M, Mariette X, Miceli C, Shadick N, Weinblatt M, de Vries N, Tak PP, Gerlag D, Huizinga TWJ, Kurreeman F, Allaart CF, Louis Bridges S Jr, Criswell L, Moreland L, Klareskog L, Saevarsdottir S, Padyukov L, Gregersen PK, Friend S, Plenge R, Stolovitzky G, Oliva B, Guan Y, Mangravite LM. Sieberts SK, et al. Among authors: hoff b. Nat Commun. 2016 Aug 23;7:12460. doi: 10.1038/ncomms12460. Nat Commun. 2016. PMID: 27549343 Free PMC article.
Stratification of amyotrophic lateral sclerosis patients: a crowdsourcing approach.
Kueffner R, Zach N, Bronfeld M, Norel R, Atassi N, Balagurusamy V, Di Camillo B, Chio A, Cudkowicz M, Dillenberger D, Garcia-Garcia J, Hardiman O, Hoff B, Knight J, Leitner ML, Li G, Mangravite L, Norman T, Wang L; ALS Stratification Consortium; Xiao J, Fang WC, Peng J, Yang C, Chang HJ, Stolovitzky G. Kueffner R, et al. Among authors: hoff b. Sci Rep. 2019 Jan 24;9(1):690. doi: 10.1038/s41598-018-36873-4. Sci Rep. 2019. PMID: 30679616 Free PMC article.
Evaluation of Combined Artificial Intelligence and Radiologist Assessment to Interpret Screening Mammograms.
Schaffter T, Buist DSM, Lee CI, Nikulin Y, Ribli D, Guan Y, Lotter W, Jie Z, Du H, Wang S, Feng J, Feng M, Kim HE, Albiol F, Albiol A, Morrell S, Wojna Z, Ahsen ME, Asif U, Jimeno Yepes A, Yohanandan S, Rabinovici-Cohen S, Yi D, Hoff B, Yu T, Chaibub Neto E, Rubin DL, Lindholm P, Margolies LR, McBride RB, Rothstein JH, Sieh W, Ben-Ari R, Harrer S, Trister A, Friend S, Norman T, Sahiner B, Strand F, Guinney J, Stolovitzky G; and the DM DREAM Consortium; Mackey L, Cahoon J, Shen L, Sohn JH, Trivedi H, Shen Y, Buturovic L, Pereira JC, Cardoso JS, Castro E, Kalleberg KT, Pelka O, Nedjar I, Geras KJ, Nensa F, Goan E, Koitka S, Caballero L, Cox DD, Krishnaswamy P, Pandey G, Friedrich CM, Perrin D, Fookes C, Shi B, Cardoso Negrie G, Kawczynski M, Cho K, Khoo CS, Lo JY, Sorensen AG, Jung H. Schaffter T, et al. Among authors: hoff b. JAMA Netw Open. 2020 Mar 2;3(3):e200265. doi: 10.1001/jamanetworkopen.2020.0265. JAMA Netw Open. 2020. PMID: 32119094 Free PMC article.
DREAMTools: a Python package for scoring collaborative challenges.
Cokelaer T, Bansal M, Bare C, Bilal E, Bot BM, Chaibub Neto E, Eduati F, de la Fuente A, Gönen M, Hill SM, Hoff B, Karr JR, Küffner R, Menden MP, Meyer P, Norel R, Pratap A, Prill RJ, Weirauch MT, Costello JC, Stolovitzky G, Saez-Rodriguez J. Cokelaer T, et al. Among authors: hoff b. F1000Res. 2015 Oct 9;4:1030. doi: 10.12688/f1000research.7118.2. eCollection 2015. F1000Res. 2015. PMID: 27134723 Free PMC article.
Erratum: Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis.
Sieberts SK, Zhu F, García-García J, Stahl E, Pratap A, Pandey G, Pappas D, Aguilar D, Anton B, Bonet J, Eksi R, Fornés O, Guney E, Li H, Marín MA, Panwar B, Planas-Iglesias J, Poglayen D, Cui J, Falcao AO, Suver C, Hoff B, Balagurusamy VSK, Dillenberger D, Neto EC, Norman T, Aittokallio T, Ammad-Ud-Din M, Azencott CA, Bellón V, Boeva V, Bunte K, Chheda H, Cheng L, Corander J, Dumontier M, Goldenberg A, Gopalacharyulu P, Hajiloo M, Hidru D, Jaiswal A, Kaski S, Khalfaoui B, Khan SA, Kramer ER, Marttinen P, Mezlini AM, Molparia B, Pirinen M, Saarela J, Samwald M, Stoven V, Tang H, Tang J, Torkamani A, Vert JP, Wang B, Wang T, Wennerberg K, Wineinger NE, Xiao G, Xie Y, Yeung R, Zhan X, Zhao C; Members of the Rheumatoid Arthritis Challenge Consortium; Greenberg J, Kremer J, Michaud K, Barton A, Coenen M, Mariette X, Miceli C, Shadick N, Weinblatt M, de Vries N, Tak PP, Gerlag D, Huizinga TWJ, Kurreeman F, Allaart CF, Bridges SL Jr, Criswell L, Moreland L, Klareskog L, Saevarsdottir S, Padyukov L, Gregersen PK, Friend S, Plenge R, Stolovitzky G, Oliva B, Guan Y, Mangravite LM. Sieberts SK, et al. Among authors: hoff b. Nat Commun. 2016 Oct 10;7:13205. doi: 10.1038/ncomms13205. Nat Commun. 2016. PMID: 27721464 Free PMC article. No abstract available.
237 results