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Articles

Grammar String: a Novel ncRNA Secondary Structure Representation p. 2
Rujira Achawanantakun, Seyedeh Shohreh Takyar, Yanni Sun

Hierarchical Boosting for Gene Function Prediction p. 14
Noor Alaydie, Chandan K. Reddy, Farshad Fotouhi

Modeling Perturbations Using Gene Networks p. 26
Nirmalya Bandyopadhyay, Manas Somaiya, Tamer Kahveci, Sanjay Ranka

A Genome Compression Algorithm Supporting Manipulation p. 38
Lenwood S. Heath, Ao-ping Hou, Huadong Xia, Liqing Zhang

Modeling of Hysteresis in a Mammalian Gene Regulatory Network p. 50
J. Hu, K. R. Qin, C. Xiang, T. H. Lee

RNAv: Non-Coding RNA Secondary Structure Variation Search via Graph Homomorphism p. 56
Zhibin Huang, Russell L. Malmberg, Mohammad Mohebbi, Liming Cai

Temporal Graphical Models for Cross-Species Gene Regulatory Network Discovery p. 70
Yan Liu, Alexandru Niculescu-Mizil, Aurelie Lozano, Yong Lu

Classification of Large Microarray Data Sets Using Fast Random Forest Construction p. 82
E. A. Manilich, Z. M. Ozsoyoglu, V. Trubachev, T. Radivoyevitch

Comparing Multiple Protein Binding Profiles in ChIP-seq Experiments p. 92
Hatice Gulcin Ozer, Jiejun Wu, Yi-Wen Huang, Jeffrey Parvin, Tim Huang, Kun Huang

Optimization of Therapeutic Proteins to Delete T-Cell Epitopes While Maintaining Beneficial Residue Interactions p. 100
Andrew S. Parker, Karl E. Griswold, Chris Bailey-Kellogg

Algorithmic Strategies for Estimating the Amount of Reticulation From a Collection of Gene Trees p. 114
H. J. Park, G. Jin, L. Nakhleh

Novel Gene Discovery in the Human Malaria Parasite using Nucleosome Positioning Data p. 124
N. Pokhriyal, N. Ponts, E. Y. Harris, K. G. Le Roch, S. Lonardi

Generating Executable Models From Signaling Network Connectivity and Semi-Quantitative Proteomic Measurements p. 136
Derek Ruths, Luay Nakhleh

Analyzing Modular RNA Structure Reveals Low Global Structural Entropy in MicroRNA Sequence p. 146
Timothy I. Shaw, Amir Manzour, Yingfeng Wang, Russell L. Malmberg, Liming Cai

Kernel-Based Gene Regulatory Network Inference p. 156
Yi Shi, Yuhong Guo, Guohui Lin, Dale Schuurmans

Accurate Identification of Ortholog Groups Among Multiple Genomes p. 166
Guanqun Shi, Meng-Chih Peng, Tao Jiang

Lex-SVM: Exploring the Potential of Exon Expression Profiling for Disease Classification p. 180
Xiongying Yuan, Yi Zhao, Changning Liu, Dongbo Bu

Inferring Haplotypes from Genotypes on a Pedigree with Mutations, Genotyping Errors and Missing Alleles p. 192
Wei-Bung Wang, Tao Jiang

Approximating Conserved Regions of Protein Structures p. 204
Yi Wei, Mingfu Shao, Jishuang Yang, Chao Wang, Shuai Cheng Li, Dongbo Bu