| Evolution of Regulatory Systems in Bacteria (Invited Keynote Talk) / Mikhail S. Gelfand ; Alexei E. Kazakov ; Yuri D. Korostelev ; Olga N. Laikova ; Andrei A. Mironov ; Alexandra B. Rakhmaninova ; Dmitry A. Ravcheev ; Dmitry A. Rodionov ; Alexei G. Vitreschak |
| Integrating Multiple-Platform Expression Data through Gene Set Features / Matěj Holec ; Filip Železný ; Jiří Kléma ; Jakub Tolar |
| Practical Quality Assessment of Microarray Data by Simulation of Differential Gene Expression / Brian E. Howard ; Beate Sick ; Steffen Heber |
| Mean Square Residue Biclustering with Missing Data and Row Inversions / Stefan Gremalschi ; Gulsah Altun ; Irina Astrovskaya ; Alexander Zelikovsky |
| Using Gene Expression Modeling to Determine Biological Relevance of Putative Regulatory Networks / Peter Larsen ; Yang Dai |
| Querying Protein-Protein Interaction Networks / Guillaume Blin ; Florian Sikora ; Stéphane Vialette |
| Integrative Approach for Combining TNF α-NF κB Mathematical Model to a Protein Interaction Connectivity Map / Mahesh Visvanathan ; Bernhard Pfeifer ; Christian Baumgartner ; Bernhard Tilg ; Gerald Henry Lushington |
| Hierarchical Organization of Functional Modules in Weighted Protein Interaction Networks Using Clustering Coefficient / Min Li ; Jianxin Wang ; Jianer Chen ; Yi Pan |
| Bioinformatics Challenges in Translational Research (Invited Keynote Talk) / Nicholas F. Tsinoremas |
| Untangling Tanglegrams: Comparing Trees by Their Drawings / Balaji Venkatachalam ; Jim Apple ; Katherine St. John ; Dan Gusfield |
| An Experimental Analysis of Consensus Tree Algorithms for Large-Scale Tree Collections / Seung-Jin Sul ; Tiffani L. Williams |
| Counting Faces in Split Networks / Lichen Bao ; Sergey Bereg |
| Relationship between Amino Acids Sequences and Protein Structures: Folding Patterns and Sequence Patterns / Alexander Kister |
| Improved Algorithms for Parsing ESLTAGs: A Grammatical Model Suitable for RNA Pseudoknots / Sanguthevar Rajasekaran ; Sahar Al Seesi ; Reda Ammar |
| Efficient Algorithms for Self Assembling Triangular and Other Nano Structures / Vamsi Kundeti |
| Motif Construction from High-Throughput SELEX Data (Invited Keynote Talk) / Esko Ukkonen |
| Rearrangement Phylogeny of Genomes in Contig Form / Adriana Muñoz ; David Sankoff |
| Prediction of Contiguous Regions in the Amniote Ancestral Genome / Aïda Ouangraoua ; Frédéric Boyer ; Andrew McPherson ; Éric Tannier ; Cedric Chauve |
| Pure Parsimony Xor Haplotyping / Paola Bonizzoni ; Gianluca Della Vedova ; Riccardo Dondi ; Yuri Pirola ; Romeo Rizzi |
| A Decomposition of the Pure Parsimony Haplotyping Problem / Allen Holder ; Thomas Langley |
| Exact Computation of Coalescent Likelihood under the Infinite Sites Model / Yufeng Wu |
| Imputation-Based Local Ancestry Inference in Admixed Populations / Bogdan Paşaniuc ; Justin Kennedy ; Ion M&acaron;ndoiu |
| Interpreting Population Sequencing Data (Invited Keynote Talk) / Shamil R. Sunyaev |
| Modeling and Visualizing Heterogeneity of Spatial Patterns of Protein-DNA Interaction from High-Density Chromatin Precipitation Mapping Data / Juntao Li ; Fajrian Yunus ; Zhu Lei ; Majid Eshaghi ; Jianhua Liu ; R. Krishna Murthy Karuturi |
| A Linear-Time Algorithm for Analyzing Array CGH Data Using Log Ratio Triangulation / Matthew Hayes ; Jing Li |
| Mining of cis-Regulatory Motifs Associated with Tissue-Specific Alternative Splicing / Jihye Kim ; Sihui Zhao |
| Analysis of Cis-Regulatory Motifs in Cassette Exons by Incorporating Exon Skipping Rates |
| A Class of Evolution-Based Kernels for Protein Homology Analysis: A Generalization of the PAM Model / Valentina Sulimova ; Vadim Mottl ; Boris Mirkin ; Ilya Muchnik ; Casimir Kulikowski |
| Irreplaceable Amino Acids and Reduced Alphabets in Short-Term and Directed Protein Evolution / Miguel A. Jiménez-Montaño ; Matthew He |
| A One-Class Classification Approach for Protein Sequences and Structures / András Bánhalmi ; Róbert Busa-Fekete ; Balázs Kégl |
| Prediction and Classification of Real and Pseudo MicroRNA Precursors via Data Fuzzification and Fuzzy Decision Trees / Na'el Abu-halaweh ; Robert Harrison |
| Author Index |
| Evolution of Regulatory Systems in Bacteria (Invited Keynote Talk) / Mikhail S. Gelfand ; Alexei E. Kazakov ; Yuri D. Korostelev ; Olga N. Laikova ; Andrei A. Mironov ; Alexandra B. Rakhmaninova ; Dmitry A. Ravcheev ; Dmitry A. Rodionov ; Alexei G. Vitreschak |
| Integrating Multiple-Platform Expression Data through Gene Set Features / Matěj Holec ; Filip Železný ; Jiří Kléma ; Jakub Tolar |
| Practical Quality Assessment of Microarray Data by Simulation of Differential Gene Expression / Brian E. Howard ; Beate Sick ; Steffen Heber |
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