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Preface p. 1

Committees p. 3

Referees p. 5

Genomics and Genetics

MSOAR 2.0: Incorporating tandem duplications into ortholog assignment based on genome rearrangement p. 13
Guanqun Shi, Liqing Zhang, Tao Jiang

Characteristic restriction endonuclease cut order for classification and identification of fungal sequences p. 25
Rajib Sengupta, Dhundy Bastola, Hesham Ali

Ranking genes by relevance to a disease p. 37
Shivani Agarwal, Shiladitya Sengupta

A general graphical framework for detecting copy number variations p. 47
Xiao-Lin Yin, Jing Li

Combinatorial reconstruction of half-sibling groups p. 59
Saad I. Sheikh, Tanya Y. Berger-Wolf, Ashfaq A, Khokhar, Isabel C. Caballero, Mary V. Ashley, Wanpracha Chaovalitwongse, Bhaskar DasGupta

Structural Bioinformatics

A mesoscopic model for molecular dynamics studies of RNA nanostructures p. 71
Maxim Paly, Roderick Melnick, Bruce Shapiro

A set-cover-based approach for inexact graph matching p. 81
M. Mongiovi, R. Di Natale, R. Guigno, A. Pulvirenti, A. Ferro, R. Sharan

Modeling and inference of sequence-structure specificity p. 91
Hetunandan Kamisetty, Ghosh Bornika, Chris Bailey-Kellogg, Christopher J. Langmead

A systematic study of homologous protein structures with insertions/deletions p. 103
RyangGuk Kim, Jon McCafferty, Jun-tao Guo

Transcriptomics and Proteomics

Peptide identification using both spectrum libraries and protein databases p. 117
Marshall Bern

Understanding distal transcriptional regulation from sequence, expression and interactome perspectives p. 127
Arvind Rao, David J. States, Alfred O. Hero, James D. Engel

A close-to optimum bi-clustering algorithm for microarray gene expression data p. 139
Guojun Li, Qin Ma, Bingqiang Liu, Haibao Tang, Andrew H. Paterson, Ying Xu

Nonnegative least square - a new look into SAGE data p. 151
Erliang Zeng, Mitsunori Ogihara

Biological Pathways and Networks

Conditional pathway integration p. 165
Alexandra Skolozub, Ofer Sarig, Ron Y. Pinter

A pathway approach to align regulatory-metabolic networks p. 177
Y. Li, J. J. Bot, M. J. Reinders, D. De Ridder

Managing and querying mammalian metabolic networks: a metabolism query language and its query processing p. 189
Ali Cakmak, Gultekin Ozsoyoglu, Richard W. Hanson

Generalized queries and Bayesian statistical model checking in dynamic Bayesian networks: application to personalized medicine p. 201
Christopher J. Langmead

Computational modeling of pathway dynamics for detecting drug effects: paradoxical effects of LYS303511 on TRAIL-induced apoptosis p. 213
Yuan Shi, Simi M. Varghese, Sinong Huang, Jacob White, Shazib Pervaiz, Lisa Tucker-Kellogg

Functions and Interactions

Prediction of Gene Ontology terms using methods for structured output spaces p. 227
Artem Sokolov, Asa Ben-Hur

Characterizing the space of interatomic distance distribution functions consistent with solution scattering data p. 239
Paritosh A. Kavathekar, Bruce A. Craig, Alan M. Friedman, Christopher Bailey-Kellogg, Devin J. Balkcom

Improved small molecule activity determination via centroid nearest neighbors classification p. 251
Phuong Dao, Farhad Hormozdiari, Hossein Jowhari, S. C. Sahinalp, Kendall Byler, Artem Cherkasov, Zehra Cataltepe

Author Index p. 269