Annals of the New York Academy of Sciences

Cover image for Vol. 1158 The Challenges of Systems Biology Community Efforts to Harness Biological Complexity

March 2009

Volume 1158 The Challenges of Systems Biology Community Efforts to Harness Biological Complexity

Pages ix–xii, 1–316

  1. Preface

    1. Top of page
    2. Preface
    3. Part I. Selected Papers from the ENFIN-DREAM Joint Conference
    4. Part I. Selected Papers from the DREAM2 Conference
    5. Part II. Best Performer Papers from the DREAM2 Challenges
    6. Index of Contributors
    1. Preface (pages ix–xii)

      Gustavo Stolovitzky, Pascal Kahlem and Andrea Califano

      Article first published online: 30 MAR 2009 | DOI: 10.1111/j.1749-6632.2009.04470.x

  2. Part I. Selected Papers from the ENFIN-DREAM Joint Conference

    1. Top of page
    2. Preface
    3. Part I. Selected Papers from the ENFIN-DREAM Joint Conference
    4. Part I. Selected Papers from the DREAM2 Conference
    5. Part II. Best Performer Papers from the DREAM2 Challenges
    6. Index of Contributors
    1. Ranking Genes by Their Co-expression to Subsets of Pathway Members (pages 1–13)

      Priit Adler, Hedi Peterson, Phaedra Agius, Jüri Reimand and Jaak Vilo

      Article first published online: 30 MAR 2009 | DOI: 10.1111/j.1749-6632.2008.03747.x

    2. Creating Reference Datasets for Systems Biology Applications Using Text Mining (pages 14–28)

      Martin Krallinger, Ana María Rojas and Alfonso Valencia

      Article first published online: 30 MAR 2009 | DOI: 10.1111/j.1749-6632.2008.03750.x

  3. Part I. Selected Papers from the DREAM2 Conference

    1. Top of page
    2. Preface
    3. Part I. Selected Papers from the ENFIN-DREAM Joint Conference
    4. Part I. Selected Papers from the DREAM2 Conference
    5. Part II. Best Performer Papers from the DREAM2 Challenges
    6. Index of Contributors
    1. Transcriptional Modules and Regulatory Networks

      The Condition-Dependent Transcriptional Network in Escherichia coli (pages 29–35)

      Karen Lemmens, Tijl De Bie, Thomas Dhollander, Pieter Monsieurs, Bart De Moor, Julio Collado-Vides, Kristof Engelen and Kathleen Marchal

      Article first published online: 30 MAR 2009 | DOI: 10.1111/j.1749-6632.2008.03746.x

    2. Reverse-Engineering Transcriptional Modules from Gene Expression Data (pages 36–43)

      Tom Michoel, Riet De Smet, Anagha Joshi, Kathleen Marchal and Yves Van de Peer

      Article first published online: 30 MAR 2009 | DOI: 10.1111/j.1749-6632.2008.03943.x

    3. Signaling and Metabolic Networks

      Specification of Spatial Relationships in Directed Graphs of Cell Signaling Networks (pages 44–56)

      Azi Lipshtat, Susana R. Neves and Ravi Iyengar

      Article first published online: 30 MAR 2009 | DOI: 10.1111/j.1749-6632.2008.03748.x

    4. Uncovering Metabolic Objectives Pursued by Changes of Enzyme Levels (pages 57–70)

      Sabrina Hoffmann and Hermann-Georg Holzhütter

      Article first published online: 30 MAR 2009 | DOI: 10.1111/j.1749-6632.2008.03753.x

    5. Biological Network Models

      Modeling of Gene Regulatory Network Dynamics Using Threshold Logic (pages 71–81)

      Tejaswi Gowda, Sarma Vrudhula and Seungchan Kim

      Article first published online: 30 MAR 2009 | DOI: 10.1111/j.1749-6632.2008.03754.x

    6. Reverse Engineering Algorithms

    7. Computation Tools for Reverse Engineering

      A Gene Network Simulator to Assess Reverse Engineering Algorithms (pages 125–142)

      Barbara Di Camillo, Gianna Toffolo and Claudio Cobelli

      Article first published online: 30 MAR 2009 | DOI: 10.1111/j.1749-6632.2008.03756.x

    8. A Network Inference Workflow Applied to Virulence-Related Processes in Salmonella typhimurium (pages 143–158)

      Ronald C. Taylor, Mudita Singhal, Jennifer Weller, Saeed Khoshnevis, Liang Shi and Jason McDermott

      Article first published online: 30 MAR 2009 | DOI: 10.1111/j.1749-6632.2008.03762.x

  4. Part II. Best Performer Papers from the DREAM2 Challenges

    1. Top of page
    2. Preface
    3. Part I. Selected Papers from the ENFIN-DREAM Joint Conference
    4. Part I. Selected Papers from the DREAM2 Conference
    5. Part II. Best Performer Papers from the DREAM2 Challenges
    6. Index of Contributors
    1. Overview of the DREAM2 Challenges

      Lessons from the DREAM2 Challenges : A Community Effort to Assess Biological Network Inference (pages 159–195)

      Gustavo Stolovitzky, Robert J. Prill and Andrea Califano

      Article first published online: 30 MAR 2009 | DOI: 10.1111/j.1749-6632.2009.04497.x

    2. The BCL6 Target Discovery Challenge Best Performer Papers

    3. A Data Integration Framework for Prediction of Transcription Factor Targets : A BCL6 Case Study (pages 205–214)

      Matti Nykter, Harri Lähdesmäki, Alistair Rust, Vesteinn Thorsson and Ilya Shmulevich

      Article first published online: 30 MAR 2009 | DOI: 10.1111/j.1749-6632.2008.03758.x

    4. Inferring Direct Regulatory Targets of a Transcription Factor in the DREAM2 Challenge (pages 215–223)

      Vinsensius B. Vega, Xing Yi Woo, Habib Hamidi, Hock Chuan Yeo, Zhen Xuan Yeo, Guillaume Bourque and Neil D. Clarke

      Article first published online: 30 MAR 2009 | DOI: 10.1111/j.1749-6632.2008.03759.x

    5. The Protein-Protein Interaction Challenge Best Performer Paper

      A Probabilistic Graph-Theoretic Approach to Integrate Multiple Predictions for the Protein–Protein Subnetwork Prediction Challenge (pages 224–233)

      Hon Nian Chua, Willy Hugo, Guimei Liu, Xiaoli Li, Limsoon Wong and See-Kiong Ng

      Article first published online: 30 MAR 2009 | DOI: 10.1111/j.1749-6632.2008.03760.x

    6. The Five Gene Network Challenges Best Performer Papers

      Replaying the Evolutionary Tape: Biomimetic Reverse Engineering of Gene Networks (pages 234–245)

      Daniel Marbach, Claudio Mattiussi and Dario Floreano

      Article first published online: 30 MAR 2009 | DOI: 10.1111/j.1749-6632.2008.03944.x

    7. Inferring Gene Networks: Dream or Nightmare? : Part 1: Challenges 1 and 3 (pages 246–256)

      Angela Baralla, Wieslawa I. Mentzen and Alberto De La Fuente

      Article first published online: 30 MAR 2009 | DOI: 10.1111/j.1749-6632.2008.04099.x

    8. The in Silico Network Challenges Best Performer Papers

      NIRest: A Tool for Gene Network and Mode of Action Inference (pages 257–264)

      Mario Lauria, Francesco Iorio and Diego Di Bernardo

      Article first published online: 30 MAR 2009 | DOI: 10.1111/j.1749-6632.2008.03761.x

    9. Reverse Engineering of Gene Networks with LASSO and Nonlinear Basis Functions (pages 265–275)

      Mika Gustafsson, Michael Hörnquist, Jesper Lundström, Johan Björkegren and Jesper Tegnér

      Article first published online: 30 MAR 2009 | DOI: 10.1111/j.1749-6632.2008.03764.x

    10. Prediction of Pairwise Gene Interaction Using Threshold Logic (pages 276–286)

      Tejaswi Gowda, Sarma Vrudhula and Seungchan Kim

      Article first published online: 30 MAR 2009 | DOI: 10.1111/j.1749-6632.2008.03763.x

    11. Inferring Gene Networks: Dream or Nightmare? : Part 2: Challenges 4 and 5 (pages 287–301)

      Alan Scheinine, Wieslawa I. Mentzen, Giorgio Fotia, Enrico Pieroni, Fabio Maggio, Gianmaria Mancosu and Alberto De La Fuente

      Article first published online: 30 MAR 2009 | DOI: 10.1111/j.1749-6632.2008.04100.x

    12. The Genome Scale Challenge Best Performer Paper

      Inference of Regulatory Gene Interactions from Expression Data Using Three-Way Mutual Information (pages 302–313)

      John Watkinson, Kuo-ching Liang, Xiadong Wang, Tian Zheng and Dimitris Anastassiou

      Article first published online: 30 MAR 2009 | DOI: 10.1111/j.1749-6632.2008.03757.x

  5. Index of Contributors

    1. Top of page
    2. Preface
    3. Part I. Selected Papers from the ENFIN-DREAM Joint Conference
    4. Part I. Selected Papers from the DREAM2 Conference
    5. Part II. Best Performer Papers from the DREAM2 Challenges
    6. Index of Contributors
    1. Index of Contributors (pages 315–316)

      Article first published online: 30 MAR 2009 | DOI: 10.1111/j.1749-6632.2009.04613.x

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