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Preface p. v

Committees p. vii

Referees p. ix

Proteomics

A max-flow based approach to the identification of protein complexes using protein interaction and microarray data p. 51
Jianxing Feng, Rui Jiang, Tao Jiang

MSDASH: Mass spectrometry database and search p. 63
Zhan Wu, Gilles Lajoie, Bin Ma

Estimating support for protein-protein interaction data with applications to function prediction p. 73
Erliang Zeng, Chris Ding, Giri Narasimhan, Stephen Holbrook

GaborLocal: peak detection in mass spectrum by Gabor filters and Guassian local maxima p. 85
Nha Nguyen, Heng Huang, Soontorn Oraintara, An Vo

Structural Bioinformatics

Optimizing Bayes error for protein structure model selection by stability mutagenesis p. 99
Xiaoduan Ye, Alan Friedman, Chris Bailey-Kellogg

Feedback algorithm and web-server for protein structure alignment p. 109
Zhiyu Zhao, Bin Fu, Francisco J. Alanis, Christopher M. Summa

Predicting flexible length linear B-cell epitopes p. 121
Yasser EL-Manzalawy, Drena Dobbs, Vasant Honavar

Fast and accurate multi-class protein fold recognition with spatial sample kernels p. 133
Pavel Kuksa, Pai-Hsi Huang, Vladimir Pavlovic

Designing secondary structure profiles for fast ncRNA identification p. 145
Yanni Sun, Jeremy Buhler

Matching of structural motifs using hashing on residue labels and geometric filtering for protein function prediction p. 157
Mark Moll, Lydia E. Kavraki

A Hausdorff-based NOE assignment algorithm using protein backbone determined from residual dipolar couplings and rotamer patterns p. 169
Jianyang Zeng, Cittaranjan Tripathy, Pei Zhou, Bruce R. Donald

Iterative non-sequential protein structural alignment p. 183
Saeed Salem, Mohammed J. Zaki

Combining sequence and structural profiles for protein solvent accessibility prediction p. 195
Rajkumar Bondugula, Dong Xu

Extensive exploration of conformational space improves rosetta results for short protein domains p. 203
Yaohang Li, Andrew J. Bordner, Yuan Tian, Xiuping Tao, Andrey A. Gorin

Improving homology models for protein-ligand binding sites p. 211
Chris Kauffman, Huzefa Rangwala, George Karypis

Pathways, Networks, and Biological Systems

Using relative importance methods to model high-throughput gene perturbation screens p. 225
Jin Ying, Naren Ramakrishnan, Lenwood S. Heath, Richard F. Helm

Consistent alignment of metabolic pathways without abstraction p. 237
Ferhat Ay, Tamer Kahveci, Valerie de Crécy-Lagard

Detecting pathways transcriptionally correlated with clinical parameters p. 249
Igor Ulitsky, Ron Shamir

Computational Genomics

The effect of massive gene loss following whole genome duplication on the algorithmic reconstruction of the ancestral Populus diploid p. 261
Chunfang Zheng, P. Kerr Wall, Jim Leebens-Mack, Victor A. Albert, Claude dePamphilis, David Sankoff

Error tolerant sibship reconstruction in wild populations p. 273
Saad I. Sheikh, Tanya Y. Berger-Wolf, Mary V. Ashley, Isabel C. Caballero, Wanpracha Chaovalitwongse, Bhaskar DasGupta

On the accurate construction of consensus genetic maps p. 285
Yonghui Wu, Timothy J. Close, Stefano Lonardi

Efficient haplotype inference from pedigrees with missing data using linear systems with disjoint-set data structures p. 297
Xin Li, Jing Li

Computational Methods

Knowledge representation and data mining for biological imaging p. 311
Wamiq M. Ahmed

Fast multisegment alignments for temporal expression profiles p. 315
Adam A. Smith, Mark Craven

Graph wavelet alignment kernels for drug virtual screening p. 327
Aaron Smalter, Jun Huan, Gerald Lushington

Author Index p. 339