作者
Steven M Hill, Laura M Heiser, Thomas Cokelaer, Michael Unger, Nicole K Nesser, Daniel E Carlin, Yang Zhang, Artem Sokolov, Evan O Paull, Chris K Wong, Kiley Graim, Adrian Bivol, Haizhou Wang, Fan Zhu, Bahman Afsari, Ludmila V Danilova, Alexander V Favorov, Wai Shing Lee, Dane Taylor, Chenyue W Hu, Byron L Long, David P Noren, Alexander J Bisberg, Rami Al-Ouran, Bernat Anton, Tomasz Arodz, Omid Askari Sichani, Neda Bagheri, Noah Berlow, Anwesha Bohler, Jaume Bonet, Richard Bonneau, Gungor Budak, Razvan Bunescu, Mehmet Caglar, Binghuang Cai, Chunhui Cai, Azzurra Carlon, Lujia Chen, Mark F Ciaccio, Gregory Cooper, Chad J Creighton, Alberto de la Fuente, Barbara Di Camillo, Joyeeta Dutta-Moscato, Kevin Emmett, Chris Evelo, Mohammad-Kasim H Fassia, Elana J Fertig, Justin D Finkle, Francesca Finotello, Stephen Friend, Xi Gao, Jean Gao, Javier Garcia-Garcia, Samik Ghosh, Alberto Giaretta, Joe W Gray, Ruth Großeholz, Yuanfang Guan, Justin Guinney, Christoph Hafemeister, Oliver Hahn, Saad Haider, Takeshi Hase, Jay Hodgson, Bruce Hoff, Chih Hao Hsu, Ying Hu, Xun Huang, Mahdi Jalili, Xia Jiang, Tim Kacprowski, Lars Kaderali, Mingon Kang, Venkateshan Kannan, Michael Kellen, Kaito Kikuchi, Dong-Chul Kim, Hiroaki Kitano, Bettina Knapp, George Komatsoulis, Heinz Koeppl, Andreas Krämer, Miron Bartosz Kursa, Martina Kutmon, Yichao Li, Xiaoyu Liang, Zhaoqi Liu, Yu Liu, Songjian Lu, Xinghua Lu, Marco Manfrini, Marta RA Matos, Daoud Meerzaman, Gordon B Mills, Wenwen Min, Sach Mukherjee, Christian Lorenz Müller, Richard E Neapolitan, Thea Norman, Baldo Oliva, Stephen Obol Opiyo, Ranadip Pal, Aljoscha Palinkas, Joan Planas-Iglesias, Daniel Poglayen, Amina A Qutub, Julio Saez-Rodriguez, Francesco Sambo, Tiziana Sanavia, Ali Sharifi-Zarchi, Janusz Slawek, Mingzhou Song, Paul T Spellman, Adam Streck, Gustavo Stolovitzky, Sonja Strunz, Joshua M Stuart, Jesper Tegnér, Kirste Thobe, Gianna Maria Toffolo, Emanuele Trifoglio, Qian Wan, Lonnie Welch, Jia J Wu, Albert Y Xue, Ryota Yamanaka, Chunhua Yan, Sakellarios Zairis, Michael Zengerling, Hector Zenil, Shihua Zhang, Zhike Zi, HPN-DREAM Consortium
发表日期
2016/4
期刊
Nature methods
卷号
13
期号
4
页码范围
310
出版商
Nature Publishing Group
简介
It remains unclear whether causal, rather than merely correlational, relationships in molecular networks can be inferred in complex biological settings. Here we describe the HPN-DREAM network inference challenge, which focused on learning causal influences in signaling networks. We used phosphoprotein data from cancer cell lines as well as in silico data from a nonlinear dynamical model. Using the phosphoprotein data, we scored more than 2,000 networks submitted by challenge participants. The networks spanned 32 biological contexts and were scored in terms of causal validity with respect to unseen interventional data. A number of approaches were effective, and incorporating known biology was generally advantageous. Additional sub-challenges considered time-course prediction and visualization. Our results suggest that learning causal relationships may be feasible in complex settings such as …
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SM Hill, LM Heiser, T Cokelaer, M Unger, NK Nesser… - Nature methods, 2016