Challenges of Systems Biology

Gustavo Stolovitzky is the editor of The Challenges of Systems Biology: Community Efforts to Harness Biological Complexity, Volume 1158, published by Wiley. Pascal Kahlem is the editor of The Challenges of Systems Biology: Community Efforts to Harness Biological Complexity, Volume 1158, published by Wiley.

• Preface: Gustavo Stolovitzky, Pascal Kahlem, and Andrea Califano Part I: Selected Papers from the ENFIN-DREAM Joint Conference1. Ranking genes by their co-expression to subsets of pathway members: Priit Adler, Hedi Peterson, Phaedra Agius, Jüri Reimand, and Jaak Vilo2. Creating reference datasets for Systems Biology applications using text mining: Martin Krallinger, Ana Maria Rojas, and Alfonso Valencia Selected Papers from the DREAM2 Conference Transcriptional Modules and Regulatory Networks3. Condition-dependent combinatorial regulation in Escherichia coli: Karen Lemmens, Tijl De Bie, Thomas Dhollander, Pieter Monsieurs, Bart De Moor, Julio Collado-Vides, Kristof Engelen, and Kathleen Marchal4. Reverse-engineering transcriptional modules from gene expression data: Tom Michoel, Riet De Smet , Anagha Joshi, Kathleen Marchal and Yves Van de Peer Signaling and Metabolic Networks5. Specification of spatial relationships in directed graphs of cell signaling networks:  Azi Lipshtat, Susana R. Neves, and Ravi Iyengar6. Uncovering metabolic objectives pursued by changes of enzyme levels:Sabrina Hoffmann and Hermann-Georg Holzhütter. Biological Network Models7. Modeling of Gene Regulatory Network Dynamics Using Threshold Logic: Tejaswi Gowda, Sarma Vrudhula, and Seungchan Kim8. Global robustness and identifiability of random, scale-free and small-world networks: Yunchen Gong and Zhaolei Zhang Reverse Engineering Algorithms9. DREAM Project: The five-gene-network data analysis with Local Causal Discovery Algorithm using Causal Bayesian networks: Changwon Yoo and Erik Brilz10. Combining multiple results of a network reverse engineering algorithm: Daniel Marbach, Claudio Mattiussi, and Dario Floreano11. Network inference by combining biologically motivated regulatory constraints with penalized regression: Fabio Parisi, Heinz Koeppl, and Felix Naef.Computation Tools for Reverse Engineering12. A Gene Network Simulator to Assess Reverse Engineering Algorithms: Barbara Di Camillo, Gianna Toffolo, and Claudio Cobelli13. A Network Inference Workflow Applied to Virulence-related Processes in Salmonella typhimurium: Ronald C. Taylor, Mudita Singhal, Jennifer Weller, Saeed Khoshnevis, Liang Shi, and Jason McDermottPart II: Best Performer Papers from the DREAM2 ChallengesOverview of the DREAM2 Challenges14. Lessons from the DREAM2 Challenges: a community effort to assess biological network inference: Gustavo Stolovitzky, Robert J. Prill, and Andrea Califano The BCL6 Target Discovery Challenge Best Performer Papers15. DREAM2 Challenge: Integrated Multi-Array Supervised Learning Algorithm for BCL-6 Transcriptional Targets Prediction:  W.H. Lee, V. Narang, H. Xu, F. Lin, K.C. Chin, W.K. Sung16. A data integration framework for prediction of transcription factor targets: a BCL6 case study: Matti Nykter, Harri Lähdesmäki, Alistair Rust, Vesteinn Thorsson, and Ilya Shmulevich17. Inferring direct regulatory targets of a transcription factor in the DREAM2 Challenge: Vinsensius B. Vega, Xing Yi Woo, Habib Hamidi, Hock Chuan Yeo, Zhen Xuan Yeo, Guillaume Bourque, and Neil D. Clarke The Protein–Protein Interaction Challenge Best Performer Paper18. A Probabilistic Graph-theoretic Approach to Integrate Multiple Predictions for the Protein-Protein Subnetwork Prediction Challenge: Chua Hon Nian, Hugo Willy, Liu Guimei, Li Xiaoli, Wong Limsoon, Ng See-Kiong The Five Gene Network Challenges Best Performer Papers19. Replaying the Evolutionary Tape: Biomimetic Reverse Engineering of Gene Networks: Daniel Marbach, Claudio Mattiussi, and Dario Floreano20. Inferring Gene Networks: Dream or nightmare? Part 1: Challenges 1 and 3: Angela Baralla, Wieslawa Mentzen, Alberto de la FuenteThe in Silico Network Challenges Best Performer Papers21. NIRest: a tool for gene network and mode of action inference: Mario Lauria, Francesco Iorioa, and Diego di Bernardo22. Reverse Engineering of Gene Networks with LASSO and Non-Linear Basis Functions: Mika Gustafsson, Michael Hörnquist, Jesper Lundström, Johan Björkegren, and Jesper Tegnér23. Prediction of Pair-wise Gene Interaction Using Threshold Logic: Tejaswi Gowda, Sarma Vrudhul, and Seungchan Kim24. Inferring Gene Networks: Dream or nightmare? Part 2: Challenges 4 and 5: Alan Scheinine, Wieslawa Mentzen, E. Pieroni, F. Maggio, G. Mancosu, and Alberto de la Fuente The Genome Scale Challenge Best Performer Paper25.  Inference of regulatory gene interactions from expression data using three-way mutual information: John Watkinson, Kuo-ching Liang, Xiaodong Wang, Tian Zheng and Dimitris AnastassiouIndex of Contributors