1. Preface

   • Ying Xu
   • Ming Li
   • Tao Jiang

   OriginalPaper 20 January 2010 Pages: 1 - 2

2. New Generations: Sequencing Machines and Their Computational Challenges

   • David C. Schwartz
   • Michael S. Waterman

   Survey 20 January 2010 Pages: 3 - 9

3. Issues in the Reconstruction of Gene Order Evolution

   • David Sankoff
   • Chunfang Zheng
   • Qian Zhu

   Regular Paper 20 January 2010 Pages: 10 - 25

4. Challenges in Understanding Genome-Wide DNA Methylation

   • Michael Q. Zhang
   • Andrew D. Smith

   Survey 20 January 2010 Pages: 26 - 34

5. Genome-Wide Analysis of Epigenetic Modifications

   • Shoudan Liang

   Survey 20 January 2010 Pages: 35 - 41

6. Some Algorithmic Challenges in Genome-Wide Ortholog Assignment

   • Tao Jiang

   Survey 20 January 2010 Pages: 42 - 52

7. Computational Challenges in Deciphering Genomic Structures of Bacteria

   • Ying Xu

   Survey 20 January 2010 Pages: 53 - 70

8. Metagenomics: Facts and Artifacts, and Computational Challenges

   • John C. Wooley
   • Yuzhen Ye

   Survey 20 January 2010 Pages: 71 - 81

9. Understanding the “Horizontal Dimension” of Molecular Evolution to Annotate, Classify, and Discover Proteins with Functional Domains

   • Gloria Rendon
   • Mao-Feng Ger
   • Eric Jakobsson

   Survey 20 January 2010 Pages: 82 - 94

10. Can We Determine a Protein Structure Quickly?

    • Ming Li

    Survey 20 January 2010 Pages: 95 - 106

11. Challenges in Computational Analysis of Mass Spectrometry Data for Proteomics

    • Bin Ma

    Survey 20 January 2010 Pages: 107 - 123

12. Protein Interactome Analysis for Countering Pathogen Drug Resistance

    • Limsoon Wong
    • Guimei Liu

    Survey 20 January 2010 Pages: 124 - 130

13. Network-Based Predictions and Simulations by Biological State Space Models: Search for Drug Mode of Action

    • Rui Yamaguchi
    • Seiya Imoto
    • Satoru Miyano

    Survey 20 January 2010 Pages: 131 - 153

14. Computational Cellular Dynamics Based on the Chemical Master Equation: A Challenge for Understanding Complexity

    • Jie Liang
    • Hong Qian

    Survey 20 January 2010 Pages: 154 - 168

15. New Challenges for Biological Text-Mining in the Next Decade

    • Hong-Jie Dai
    • Yen-Ching Chang
    • Wen-Lian Hsu

    Regular Paper 20 January 2010 Pages: 169 - 179