Lessons from the DREAM2 Challenges: A Community Effort to Assess Biological Network Inference von Stolovitzky, Gustavo, Prill, Robert J., Califano, Andrea

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Statistical Analysis of MPSS Measurements: Application to the Study of LPS-Activated Macrophage Gene Expression von Stolovitzky, G. A., Kundaje, A., Held, G. A., Duggar, K. H., Haudenschild, C. D., Zhou, D., Vasicek, T. J., Smith, K. D., Aderem, A., Roach, J. C., Cantor, Charles R.

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Gene expression profiling of B cell chronic lymphocytic leukemia reveals a homogeneous phenotype related to memory B cells von Klein, U, Tu, Y, Stolovitzky, G A, Mattioli, M, Cattoretti, G, Husson, H, Freedman, A, Inghirami, G, Cro, L, Baldini, L, Neri, A, Califano, A, Dalla-Favera, R

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Inference of Regulatory Gene Interactions from Expression Data Using Three-Way Mutual Information von Watkinson, John, Liang, Kuo-ching, Wang, Xiadong, Zheng, Tian, Anastassiou, Dimitris

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Transcriptional Analysis of the B Cell Germinal Center Reaction von Klein, Ulf, Tu, Yuhai, Stolovitzky, Gustavo A., Keller, Jeffrey L., Haddad, Joseph, Miljkovic, Vladan, Cattoretti, Giorgio, Califano, Andrea, Dalla-Favera, Riccardo

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A Gene Network Simulator to Assess Reverse Engineering Algorithms von Di Camillo, Barbara, Toffolo, Gianna, Cobelli, Claudio

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Reverse Engineering of Gene Networks with LASSO and Nonlinear Basis Functions von Gustafsson, Mika, Hörnquist, Michael, Lundström, Jesper, Björkegren, Johan, Tegnér, Jesper

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Combining Multiple Results of a Reverse-Engineering Algorithm: Application to the DREAM Five-Gene Network Challenge von Marbach, Daniel, Mattiussi, Claudio, Floreano, Dario

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Replaying the Evolutionary Tape: Biomimetic Reverse Engineering of Gene Networks von Marbach, Daniel, Mattiussi, Claudio, Floreano, Dario

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Inferring Gene Networks: Dream or Nightmare?: Part 1: Challenges 1 and 3 von Baralla, Angela, Mentzen, Wieslawa I., De La Fuente, Alberto

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Inferring Gene Networks: Dream or Nightmare?: Part 2: Challenges 4 and 5 von Scheinine, Alan, Mentzen, Wieslawa I., Fotia, Giorgio, Pieroni, Enrico, Maggio, Fabio, Mancosu, Gianmaria, De La Fuente, Alberto

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Global Robustness and Identifiability of Random, Scale-Free, and Small-World Networks von Gong, Yunchen, Zhang, Zhaolei

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Creating Reference Datasets for Systems Biology Applications Using Text Mining von Krallinger, Martin, Rojas, Ana María, Valencia, Alfonso

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The Five-Gene-Network Data Analysis with Local Causal Discovery Algorithm Using Causal Bayesian Networks von Yoo, Changwon, Brilz, Erik M.

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Ranking Genes by Their Co-expression to Subsets of Pathway Members von Adler, Priit, Peterson, Hedi, Agius, Phaedra, Reimand, Jüri, Vilo, Jaak

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NIRest: A Tool for Gene Network and Mode of Action Inference von Lauria, Mario, Iorio, Francesco, Di Bernardo, Diego

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A Probabilistic Graph-Theoretic Approach to Integrate Multiple Predictions for the Protein-Protein Subnetwork Prediction Challenge von Chua, Hon Nian, Hugo, Willy, Liu, Guimei, Li, Xiaoli, Wong, Limsoon, Ng, See-Kiong

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Uncovering Metabolic Objectives Pursued by Changes of Enzyme Levels von Hoffmann, Sabrina, Holzhütter, Hermann-Georg

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Reverse-Engineering Transcriptional Modules from Gene Expression Data von Michoel, Tom, De Smet, Riet, Joshi, Anagha, Marchal, Kathleen, Van de Peer, Yves

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A Network Inference Workflow Applied to Virulence-Related Processes in Salmonella typhimurium von Taylor, Ronald C., Singhal, Mudita, Weller, Jennifer, Khoshnevis, Saeed, Shi, Liang, McDermott, Jason

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