https://biorxiv.org This feed contains articles for bioRxiv Channel "DREAM" bioRxiv https://biorxiv.org https://biorxiv.org/cgi/content/short/082495v1?rss=1" Keller, A. Gerkin, R. C. Guan, Y. Dhurandhar, A. Turu, G. Szalai, B. Mainland, J. D. Ihara, Y. Yu, C. W. Wolfinger, R. Vens, C. Schietgat, L. De Grave, K. Norel, R. DREAM Olfaction Prediction Challenge Consortium, Stolovitzky, G. Cecchi, G. Vosshall, L. B. Meyer, P. 2016-10-21 doi:10.1101/082495 Cold Spring Harbor Laboratory Press 2016-10-21 https://biorxiv.org/cgi/content/short/265553v1?rss=1" Choobdar, S. Ahsen, M. E. Crawford, J. Tomasoni, M. Lamparter, D. Lin, J. Hescott, B. Hu, X. Mercer, J. Natoli, T. Narayan, R. The DREAM Module Identification Challenge Consortium, Subramanian, A. Stolovitzky, G. Kutalik, Z. Lage, K. Slonim, D. K. Saez-Rodriguez, J. Cowen, L. J. Bergmann, S. Marbach, D. 2018-02-15 doi:10.1101/265553 Cold Spring Harbor Laboratory Press 2018-02-15 https://biorxiv.org/cgi/content/short/200451v1?rss=1" 60% of drug combinations synergy was reproducibly predicted with an accuracy matching biological replicate experiments, however 20% of drug combinations were poorly predicted by all methods. Genomic rationale for synergy predictions were identified, including antagonism unique to combined PIK3CB/D inhibition with the ADAM17 inhibitor where synergy is seen with other PI3K pathway inhibitors. All data, methods and code are freely available as a resource to the community. ]]> Menden, M. P. Wang, D. Guan, Y. Mason, M. Szalai, B. Bulusu, K. C. Yu, T. Kang, J. Jeon, M. Wolfinger, R. Nguyen, T. Zaslavskiy, M. AstraZeneca-Sanger Drug Combination DREAM Consorti, Jang, I. S. Ghazoui, Z. Ahsen, M. E. Vogel, R. Chaibub Neto, E. Norman, T. Tang, E. K. Garnett, M. J. Di Veroli, G. Fawell, S. Stolovitzky, G. Guinney, J. Dry, J. R. Saez-Rodriguez, J. 2017-10-09 doi:10.1101/200451 Cold Spring Harbor Laboratory Press 2017-10-09 https://biorxiv.org/cgi/content/short/224733v1?rss=1" Lee, A. Y.-W. Ewing, A. D. Ellrott, K. Hu, Y. Houlahan, K. E. Bare, J. C. Espiritu, S. M. G. Huang, V. Dang, K. Chong, Z. Caloian, C. Yamaguchi, T. N. ICGC-TCGA DREAM Somatic Mutation Calling Challenge, Kellen, M. R. Chen, K. Norman, T. C. Friend, S. H. Guinney, J. Stolovitzky, G. Haussler, D. Margolin, A. A. Stuart, J. M. Boutros, P. C. 2017-11-25 doi:10.1101/224733 Cold Spring Harbor Laboratory Press 2017-11-25 https://biorxiv.org/cgi/content/short/311696v1?rss=1" Fourati, S. Talla, A. Mahmoudian, M. Burkhart, J. G. Klen, R. Henao, R. Aydin, Z. Yeung, K. Y. Ahsen, M. E. Almugbel, R. Jahandideh, S. Liang, X. Nordling, T. E. M. Shiga, M. Stanescu, A. Vogel, R. The Respiratory Viral DREAM Challenge Consortium, Pandey, G. Chiu, C. McClain, M. T. Woods, C. W. Ginsburg, G. S. Elo, L. L. Tsalik, E. L. Mangravite, L. M. Sieberts, S. K. 2018-04-30 doi:10.1101/311696 Cold Spring Harbor Laboratory Press 2018-04-30 https://biorxiv.org/cgi/content/short/087809v1?rss=1" Seyednasrollah, F. Koestler, D. C. Wang, T. Piccolo, S. R. Vega, R. Greiner, R. Fuchs, C. Gofer, E. Kumar, L. Wolfinger, R. D. Kanigel Winner, K. Bare, C. Neto, E. C. Yu, T. Shen, L. Abdallah, K. Norman, T. Stolovitzky, G. PCC-DREAM Community, Soule, H. Sweeney, C. J. Ryan, C. J. Scher, H. I. Sartor, O. Elo, L. L. Zhou, F. L. Guinney, J. Costello, J. C. 2016-11-15 doi:10.1101/087809 Cold Spring Harbor Laboratory Press 2016-11-15 https://biorxiv.org/cgi/content/short/796029v1?rss=1" Tanevski, J. Nguyen, T. Truong, B. Karaiskos, N. Ahsen, M. E. Zhang, X. Shu, C. Hu, Y. Pham, H. V. V. Li, X. Le, T. D. Tarca, A. 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. Glaab, E. Krause, R. Banda, P. Stolovitzky, G. Rajewsky, N. Saez-Rodriguez, J. Meyer, P. 2019-10-10 doi:10.1101/796029 Cold Spring Harbor Laboratory Press 2019-10-10 https://biorxiv.org/cgi/content/short/294231v1?rss=1" 10,000 patients from completed ALS clinical trials and 1479 patients from community-based patient registers. Challenge participants used machine learning and clustering techniques to predict ALS progression and survival. By developing new approaches, the best performing teams were able to predict disease outcomes better than currently available methods. At the same time, the integration of clustering components across methods led to the emergence of distinct consensus clusters, separating patients into four consistent groups, each with its unique predictors for classification. This analysis reveals for the first time the potential of a crowdsourcing approach to uncover covert patient sub-populations, and to accelerate disease understanding and therapeutic development. ]]> 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, M. L. Li, G. Mangravite, L. Norman, T. Wang, L. The ALS Stratification Consortium, Xiao, J. Fang, W.-C. Peng, J. Stolovitzky, G. 2018-04-05 doi:10.1101/294231 Cold Spring Harbor Laboratory Press 2018-04-05 https://biorxiv.org/cgi/content/short/737122v1?rss=1" Mason, M. J. Schinke, C. Eng, C. Towfic, F. Gruber, F. Dervan, A. White, B. S. Pratapa, A. Guan, Y. Chen, H. Cui, Y. Li, B. Yu, T. Chaibub Neto, E. Mavrommatis, K. Ortiz, M. Lyzogubov, V. Bisht, K. Dai, H. Y. Schmitz, F. Flynt, E. Rozelle, D. Danziger, S. A. Ratushny, A. Dalton, W. S. Goldschmidt, H. Avet-Loiseau, H. Samur, M. Hayete, B. Sonneveld, P. Shain, K. H. Munshi, N. Auclair, D. Hose, D. Morgan, G. Trotter, M. Bassett, D. Goeke, J. Walker, B. A. Thakurta, A. Guinney, J. A. 2019-08-22 doi:10.1101/737122 Cold Spring Harbor Laboratory Press 2019-08-22 https://biorxiv.org/cgi/content/short/856922v1?rss=1" Ford, C. T. Janies, D. A. 2019-11-27 doi:10.1101/856922 Cold Spring Harbor Laboratory Press 2019-11-27 https://biorxiv.org/cgi/content/short/204370v1?rss=1" Sendorek, D. H. Caloian, C. Ellrott, K. Bare, J. C. Yamaguchi, T. N. Ewing, A. D. Houlahan, K. E. Norman, T. C. Margolin, A. A. Stuart, J. M. Boutros, P. C. 2017-10-17 doi:10.1101/204370 Cold Spring Harbor Laboratory Press 2017-10-17 https://biorxiv.org/cgi/content/short/254839v1?rss=1" Cooper, C. I. Yao, D. Sendorek, D. H. Yamaguchi, T. N. P'ng, C. Houlahan, K. E. Caloian, C. Fraser, M. SMC-DNA Challenge Participants, Ellrott, K. Margolin, A. A. Bristow, R. G. Stuart, J. M. Boutros, P. C. 2018-01-28 doi:10.1101/254839 Cold Spring Harbor Laboratory Press 2018-01-28 https://biorxiv.org/cgi/content/short/243568v1?rss=1" Aben, N. de Ruiter, J. Bosdriesz, E. Kim, Y. Bounova, G. Vis, D. Wessels, L. Michaut, M. 2018-01-05 doi:10.1101/243568 Cold Spring Harbor Laboratory Press 2018-01-05 https://biorxiv.org/cgi/content/short/2019.12.31.891812v1?rss=1" Cichonska, A. Ravikumar, B. Allaway, R. J. Park, S. Wan, F. Isayev, O. Li, S. Mason, M. J. Lamb, A. Tanoli, Z.-u.-R. Jeon, M. Kim, S. Popova, M. Zeng, J. Dang, K. Koytiger, G. Kang, J. Wells, C. I. Willson, T. M. The IDG-DREAM Drug-Kinase Binding Prediction Challenge Consortium, Oprea, T. I. Schlessinger, A. Drewry, D. H. Stolovitzky, G. A. Wennerberg, K. Guinney, J. Aittokallio, T. 2020-01-07 doi:10.1101/2019.12.31.891812 Cold Spring Harbor Laboratory Press 2020-01-07 https://biorxiv.org/cgi/content/short/2020.01.13.904722v1?rss=1" Sieberts, S. K. Schaff, J. Duda, M. Pataki, B. A. Sun, M. Snyder, P. Daneault, J.-F. Parisi, F. Costante, G. Rubin, U. Banda, P. Chae, Y. Neto, E. C. Dorsey, R. Aydın, Z. Chen, A. Elo, L. L. Espino, C. Glaab, E. Goan, E. Golabchi, F. N. Görmez, Y. Jaakkola, M. K. Jonnagaddala, J. KLEn, R. Li, D. McDaniel, C. Perrin, D. Rad, N. M. Rainaldi, E. Sapienza, S. Schwab, P. Shokhirev, N. Venäläinen, M. S. Vergara-Diaz, G. Zhang, Y. Parkinson's Disease Digital Biomarker Challenge Consortium, Wang, Y. Guan, Y. Brunner, D. Bonato, P. Mangravite, L. M. Omberg 2020-01-16 doi:10.1101/2020.01.13.904722 Cold Spring Harbor Laboratory Press 2020-01-16 https://biorxiv.org/cgi/content/short/2020.06.05.130971v1?rss=1" Tarca, A. Pataki, B. A. Romero, R. Sirota, M. Guan, Y. Kutum, R. Gomez-Lopez, N. Done, B. Bhatti, G. Yu, T. Andreoletti, G. Chaiworapongsa, T. Consortium, T. D. P. B. P. C. Hassan, S. S. Hsu, C.-D. Aghaeepour, N. Stolovitzky, G. A. Csabai, I. Costello, J. C. 2020-06-06 doi:10.1101/2020.06.05.130971 Cold Spring Harbor Laboratory Press 2020-06-06 https://biorxiv.org/cgi/content/short/2020.12.21.423514v1?rss=1" Douglass, E. F. Allaway, R. J. Szalai, B. Wang, W. Tian, T. Fernandez, A. Realubit, R. Karan, C. Zheng, S. Pessia, A. Tanoli, Z. Jafari, M. Wan, F. Li, S. Xiong, Y. Duran-Frigola, M. Bertoni, M. Badia-i-Mompel, P. Mateo, L. Guitart-Pla, O. Chung, V. DREAM CTD-squared Pancancer Drug Activity Challenge Consortium, Tang, J. Zeng, J. Aloy, P. Saez-Rodriguez, J. Guinney, J. Gerhard, D. S. Califano, A. 2020-12-22 doi:10.1101/2020.12.21.423514 Cold Spring Harbor Laboratory Press 2020-12-22 https://biorxiv.org/cgi/content/short/2021.02.15.430538v1?rss=1" Xiong, Z. Jeon, M. Allaway, R. J. Kang, J. Park, D. Lee, J. Jeon, H. Ko, M. Jiang, H. Zheng, M. Tan, A. C. Guo, X. The Multi-Targeting Drug DREAM Challenge Community, Dang, K. K. Tropsha, A. Hecht, C. Das, T. K. Carlson, H. A. Abagyan, R. Guinney, J. Schlessinger, A. Cagan, R. 2021-02-17 doi:10.1101/2021.02.15.430538 Cold Spring Harbor Laboratory Press 2021-02-17 https://biorxiv.org/cgi/content/short/2020.05.09.086397v1?rss=1" Pham, V. V. H. Li, X. Truong, B. Nguyen, T. Liu, L. Li, J. Le, T. 2020-05-10 doi:10.1101/2020.05.09.086397 Cold Spring Harbor Laboratory Press 2020-05-10 https://biorxiv.org/cgi/content/short/2021.03.23.436603v1?rss=1" View larger version (24K): org.highwire.dtl.DTLVardef@a95337org.highwire.dtl.DTLVardef@966d5aorg.highwire.dtl.DTLVardef@1e55b18org.highwire.dtl.DTLVardef@bfb5d7_HPS_FORMAT_FIGEXP M_FIG C_FIG Key pointsO_LIOver 80 million single-cell multiplexed measurements across 67 cell lines, 54 conditions and 10 time points to benchmark predictive models of single cell signaling C_LIO_LI73 approaches from 27 teams for predicting response to kinase inhibitors on single cell level, and dynamic response from unperturbed basal omics data C_LIO_LIPredictions of single marker models correlate with measurements with a correlation coefficient of 0.76 C_LIO_LITop models of whole signaling response models perform almost as well as a biological replicate C_LIO_LICell-line specific variation in dynamics can be predicted from basal omics C_LI ]]> Gabor, A. Tognetti, M. Driessen, A. Tanevski, J. Guo, B. Cao, W. Shen, H. Yu, T. Chung, V. Single Cell Signaling in Breast Cancer DREAM Consortium, Bodenmiller, B. Saez-Rodriguez, J. 2021-03-23 doi:10.1101/2021.03.23.436603 Cold Spring Harbor Laboratory Press 2021-03-23 https://biorxiv.org/cgi/content/short/2020.07.21.214205v1?rss=1" ma, w. Kim, S. Chowdhury, S. li, z. YANG, M. Yoo, S. Petralia, F. Jacobsen, J. Li, J. J. Ge, X. Li, K. Yu, T. Edwards, N. J. Payne, S. Boutros, P. C. Rodriguez, H. Stolovitzky, G. A. Kang, J. Fenyo, D. Saez, J. Wang, P. 2020-07-22 doi:10.1101/2020.07.21.214205 Cold Spring Harbor Laboratory Press 2020-07-22 https://biorxiv.org/cgi/content/short/310425v1?rss=1" Boutros, P. C. Salcedo, A. Tarabichi, M. Espiritu, S. M. G. Deshwar, A. G. David, M. Wilson, N. M. Dentro, S. Wintersinger, J. A. Liu, L. Y. Ko, M. Sivanandan, S. Zhang, H. Zhu, K. Yang, T.-H. Chilton, J. M. Buchanan, A. Lalansingh, C. M. P'ng, C. Anghel, C. V. Umar, I. Lo, B. Simpson, J. T. Stuart, J. M. Anastassiou, D. Guan, Y. Ewing, A. Ellrott, K. Wedge, D. C. Morris, Q. D. Van Loo, P. DREAM SMC-Het Participants, 2018-04-28 doi:10.1101/310425 Cold Spring Harbor Laboratory Press 2018-04-28