Annals of the New York Academy of Sciences

Preface
pp. ix-xii(4)

Ranking Genes by Their Co-expression to Subsets of Pathway Members
pp. 1-13(13)
Authors: Adler, Priit; Peterson, Hedi; Agius, Phaedra; Reimand, Jüri; Vilo, Jaak

Creating Reference Datasets for Systems Biology Applications Using Text Mining
pp. 14-28(15)
Authors: Krallinger, Martin; Rojas, Ana María; Valencia, Alfonso

The Condition-Dependent Transcriptional Network in Escherichia coli
pp. 29-35(7)
Authors: Lemmens, Karen; De Bie, Tijl; Dhollander, Thomas; Monsieurs, Pieter; De Moor, Bart; Collado-Vides, Julio; Engelen, Kristof; Marchal, Kathleen

Reverse-Engineering Transcriptional Modules from Gene Expression Data
pp. 36-43(8)
Authors: Michoel, Tom; De Smet, Riet; Joshi, Anagha; Marchal, Kathleen; Van de Peer, Yves

Specification of Spatial Relationships in Directed Graphs of Cell Signaling Networks
pp. 44-56(13)
Authors: Lipshtat, Azi; Neves, Susana R.; Iyengar, Ravi

Uncovering Metabolic Objectives Pursued by Changes of Enzyme Levels
pp. 57-70(14)
Authors: Hoffmann, Sabrina; Holzhütter, Hermann-Georg

Modeling of Gene Regulatory Network Dynamics Using Threshold Logic
pp. 71-81(11)
Authors: Gowda, Tejaswi; Vrudhula, Sarma; Kim, Seungchan

Global Robustness and Identifiability of Random, Scale-Free, and Small-World Networks
pp. 82-92(11)
Authors: Gong, Yunchen; Zhang, Zhaolei

The Five-Gene-Network Data Analysis with Local Causal Discovery Algorithm Using Causal Bayesian Networks
pp. 93-101(9)
Authors: Yoo, Changwon; Brilz, Erik M.

Combining Multiple Results of a Reverse-Engineering Algorithm: Application to the DREAM Five-Gene Network Challenge
pp. 102-113(12)
Authors: Marbach, Daniel; Mattiussi, Claudio; Floreano, Dario

Network Inference by Combining Biologically Motivated Regulatory Constraints with Penalized Regression
pp. 114-124(11)
Authors: Parisi, Fabio; Koeppl, Heinz; Naef, Felix

A Gene Network Simulator to Assess Reverse Engineering Algorithms
pp. 125-142(18)
Authors: Di Camillo, Barbara; Toffolo, Gianna; Cobelli, Claudio

A Network Inference Workflow Applied to Virulence-Related Processes in Salmonella typhimurium
pp. 143-158(16)
Authors: Taylor, Ronald C.; Singhal, Mudita; Weller, Jennifer; Khoshnevis, Saeed; Shi, Liang; McDermott, Jason

Lessons from the DREAM2 Challenges: A Community Effort to Assess Biological Network Inference
pp. 159-195(37)
Authors: Stolovitzky, Gustavo; Prill, Robert J.; Califano, Andrea

DREAM2 Challenge: Integrated Multi-Array Supervised Learning Algorithm for BCL6 Transcriptional Targets Prediction
pp. 196-204(9)
Authors: Lee, W.H.; Narang, V.; Xu, H.; Lin, F.; Chin, K.C.; Sung, W.K.

A Data Integration Framework for Prediction of Transcription Factor Targets: A BCL6 Case Study
pp. 205-214(10)
Authors: Nykter, Matti; Lähdesmäki, Harri; Rust, Alistair; Thorsson, Vesteinn; Shmulevich, Ilya

Inferring Direct Regulatory Targets of a Transcription Factor in the DREAM2 Challenge
pp. 215-223(9)
Authors: Vega, Vinsensius B.; Woo, Xing Yi; Hamidi, Habib; Yeo, Hock Chuan; Yeo, Zhen Xuan; Bourque, Guillaume; Clarke, Neil D.

A Probabilistic Graph-Theoretic Approach to Integrate Multiple Predictions for the Protein-Protein Subnetwork Prediction Challenge
pp. 224-233(10)
Authors: Chua, Hon Nian; Hugo, Willy; Liu, Guimei; Li, Xiaoli; Wong, Limsoon; Ng, See-Kiong

Replaying the Evolutionary Tape: Biomimetic Reverse Engineering of Gene Networks
pp. 234-245(12)
Authors: Marbach, Daniel; Mattiussi, Claudio; Floreano, Dario

Inferring Gene Networks: Dream or Nightmare?: Part 1: Challenges 1 and 3
pp. 246-256(11)
Authors: Baralla, Angela; Mentzen, Wieslawa I.; de la Fuente, Alberto

NIRest: A Tool for Gene Network and Mode of Action Inference
pp. 257-264(8)
Authors: Lauria, Mario; Iorio, Francesco; di Bernardo, Diego

Reverse Engineering of Gene Networks with LASSO and Nonlinear Basis Functions
pp. 265-275(11)
Authors: Gustafsson, Mika; Hörnquist, Michael; Lundström, Jesper; Björkegren, Johan; Tegnér, Jesper

Prediction of Pairwise Gene Interaction Using Threshold Logic
pp. 276-286(11)
Authors: Gowda, Tejaswi; Vrudhula, Sarma; Kim, Seungchan

Inferring Gene Networks: Dream or Nightmare?: Part 2: Challenges 4 and 5
pp. 287-301(15)
Authors: Scheinine, Alan; Mentzen, Wieslawa I.; Fotia, Giorgio; Pieroni, Enrico; Maggio, Fabio; Mancosu, Gianmaria; de la Fuente, Alberto

Inference of Regulatory Gene Interactions from Expression Data Using Three-Way Mutual Information
pp. 302-313(12)
Authors: Watkinson, John; Liang, Kuo-ching; Wang, Xiadong; Zheng, Tian; Anastassiou, Dimitris

Index of Contributors
pp. 315-316(2)