Volume 6, Number 1, February 2008

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  Narayanan Raghupathy, Rose Hoberman, Dannie Durand: Two Plus Two Does not Equal Three: Statistical Tests for Multiple genome Comparison. 1-22
• 
  Andrew Wei Xu: The Distribution of Distances between Randomly Constructed genomes: Generating Function, Expectation, Variance and Limits. 23-36
• 
  Martin Stig Stissing, Thomas Mailund, Christian N. S. Pedersen, Gerth Stølting Brodal, Rolf Fagerberg: Computing the All-Pairs Quartet Distance on a Set of Evolutionary Trees. 37-50
• 
  Minghui Jiang, Ying Xu, Binhai Zhu: Protein Structure-structure Alignment with Discrete FrÉchet Distance. 51-64
• 
  V. Choi, Y. Huang, Vy Lam, D. Potter, Reinhard C. Laubenbacher, Karen Duca: Using Formal Concept Analysis for microarray Data Comparison. 65-75
• 
  Baozhen Shan, Bin Ma, Kaizhong Zhang, Gilles Lajoie: Complexities and Algorithms for Glycan Sequencing Using Tandem Mass Spectrometry. 77-91
• 
  Ján Manuch, Daya Ram Gaur: Fitting protein Chains to cubic Lattice is NP-Complete. 93-106
• 
  Yury V. Bukhman, Moyez Dharsee, Rob M. Ewing, Peter Chu, Thodoros Topaloglou, Thierry Le Bihan, Theo Goh, Henry Duewel, Ian I. Stewart, Jacek R. Wisniewski, Nancy F. Ng: Design and Analysis of Quantitative Differential Proteomics Investigations Using LC-MS Technology. 107-123
• 
  S. Tewari, Jonathan Arnold, Suchendra M. Bhandarkar: Likelihood of a Particular Order of Genetic Markers and the Construction of Genetic Maps. 125-162
• 
  Xijiang Miao, Peter J. Waddell, Homayoun Valafar: Tali: Local Alignment of protein Structures Using Backbone Torsion Angles. 163-181
• 
  Yonggang Lu, Jing He, Charlie E. M. Strauss: Deriving Topology and Sequence Alignment for the Helix Skeleton in Low-Resolution protein Density Maps. 183-201
• 
  Cao D. Nguyen, Michael Mannino, Katheleen J. Gardiner, Krzysztof J. Cios: CLusFCM: an Algorithm for Predicting protein Functions Using homologies and protein Interactions. 203-222
• 
  Jianwen Fang, Yinghua Dong, Todd D. Williams, Gerald H. Lushington: Feature Selection in Validating Mass Spectrometry Database Search Results. 223-240
• 
  Jing Li, Tao Jiang: A Survey on Haplotyping Algorithms for Tightly Linked Markers. 241-259

Volume 6, Number 2, April 2008

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  Ao Yuan, Wenqing He: Semiparametric Clustering Method for microarray Data Analysis. 261-282
• 
  Feng Cui, Robert L. Jernigan, Zhijun Wu: Knowledge-Based versus experimentally Acquired Distance and Angle Constraints for NMR Structure Refinement. 283-300
• 
  Lev Klebanov, Xing Qiu, Andrei Yakovlev: Testing Differential Expression in Nonoverlapping gene Pairs: a New Perspective for the Empirical Bayes Method. 301-316
• 
  José Osorio y Fortéa, Éric Prina, Thierry Lang, Geneviève Milon, Clarisse Davory, Jean-Yves Coppée, Béatrice Regnault: Affygcqc: a Web-Based Interface to Detect Outlying GeneChips with Extreme studentized Deviate Tests. 317-334
• 
  Aleksandar Poleksic, Mark A. Fienup, Joseph F. Danzer, Derek A. Debe: A Different Look at the Quality of Modeled Three-Dimensional protein Structures. 335-345
• 
  Sheng Wang, Wei-Mou Zheng: ClEPaps: Fast Pair Alignment of protein Structures Based on conformational Letters. 347-366
• 
  Mario Huerta, Juan Cedano, Enrique Querol: Analysis of Nonlinear Relations between Expression Profiles by the Principal Curves of Oriented-Points Approach. 367-386
• 
  Zoi I. Litou, Pantelis G. Bagos, Konstantinos D. Tsirigos, Theodore D. Liakopoulos, Stavros J. Hamodrakas: Prediction of Cell Wall Sorting Signals in Gram-Positive bacteria with a Hidden Markov Model: Application to Complete genomes. 387-401
• 
  Rafal Pokrzywa: New Method for yeast Identification Using Burrows-wheeler Transform. 403-413

Volume 6, Number 3, June 2008

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  Zeyar Aung, Soon-Heng Tan, See-Kiong Ng, Kian-Lee Tan: Ppiclust: Efficient Clustering of 3D protein-protein Interaction Interfaces. 415-433
• 
  Hon Nian Chua, Kang Ning, Wing-Kin Sung, Hon Wai Leong, Limsoon Wong: Using Indirect protein-protein Interactions for protein Complex Prediction. 435-466
• 
  Kang Ning, Nan Ye, Hon Wai Leong: On Preprocessing and Antisymmetry in de novo peptide Sequencing: Improving Efficiency and Accuracy. 467-492
• 
  Arvind Rao, Alfred O. Hero III, David J. States, James Douglas Engel: Using Directed Information to Build Biologically Relevant Influence Networks. 493-519
• 
  Zefeng Zhang, Hao Lin, Ming Li: Mango: Multiple Alignment with n Gapped Oligos. 521-541
• 
  Adriano Velasque Werhli, Dirk Husmeier: Gene Regulatory Network Reconstruction by Bayesian Integration of Prior Knowledge and/or Different Experimental Conditions. 543-572
• 
  Zheng Fu, Tao Jiang: Clustering of Main orthologs for Multiple genomes. 573-584
• 
  Kyle Ellrott, Jun-tao Guo, Victor Olman, Ying Xu: Improving the Performance of protein Threading Using Insertion/Deletion Frequency Arrays. 585-602
• 
  Yonghui Wu, Lan Liu, Timothy J. Close, Stefano Lonardi: Deconvoluting BAC-Gene Relationships Using a Physical Map. 603-622
• 
  Sérgio A. de Carvalho, Sven Rahmann: Better GeneChip microarray Layouts by Combining Probe Placement and Embedding. 623-641

Volume 6, Number 4, August 2008

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  Andrei G. Yakovlev, Tatiana A. Shkuropatova, Lyudmila G. Vasilieva, Anatoli Ya. Shkuropatov, Vladimir A. Shuvalov: Wave Packet Motions Coupled to electron Transfer in Reaction Centers of Chloroflexus Aurantiacus. 643-666
• 
  Oxana V. Galzitskaya, Natalya S. Bogatyreva, Dmitry N. Ivankov: Compactness Determines protein Folding Type. 667-680
• 
  Oxana V. Galzitskaya: Search for Folding Initiation Sites from amino acid Sequence. 681-691
• 
  Alexei V. Finkelstein, Michael Y. Lobanov, Nikita V. Dovidchenko, Natalya S. Bogatyreva: Many-Atom van der Waals Interactions lead to Direction-Sensitive Interactions of covalent bonds. 693-707
• 
  Kirill Alexandrov, Boris Sobolev, Dmitry Filimonov, Vladimir Poroikov: Recognition of protein Function Using the Local Similarity. 709-725
• 
  Tatiana Tatarinova, John Bouck, Alan Schumitzky: Kullback-Leibler Markov Chain Monte Carlo - a New Algorithm for Finite Mixture Analysis and its Application to Gene Expression Data. 727-746
• 
  Daisuke Tominaga, Katsuhisa Horimoto: Judgment Algorithm for Periodicity of Time Series Data Based on Bayesian Information Criterion. 747-757
• 
  Alexander Y. Panchin, Sergei A. Spirin, Sergey A. Lukyanov, Yuri B. Lebedev, Yuri V. Panchin: Human Trash ESTs - Sequences from cDNA Collection that are not Aligned to genome Assembly. 759-773
• 
  Evgeniy Aksianov, Olga Zanegina, Alexander Grishin, Sergei A. Spirin, Anna Karyagina, Andrei Alexeevski: Conserved water molecules in X-Ray Structures Highlight the Role of water in intramolecular and intermolecular Interactions. 775-788
• 
  Zhengwei Zhu, Andrey Tovchigrechko, Tatiana Baronova, Ying Gao, Dominique Douguet, Nicholas O'Toole, Ilya A. Vakser: Large-Scale Structural Modeling of protein complexes at Low Resolution. 789-810
• 
  Alexander E. Ivliev, Marina G. Sergeeva: Orthofocus: Program for Identification of orthologs in Multiple genomes in Family-Focused Studies. 811-824
• 
  Jonas Gamalielsson, Björn Olsson: Gene Ontology-Based Semantic Alignment of Biological Pathways by Evolutionary Search. 825-842
• 
  Kirill Peskov, Igor Goryanin, Oleg V. Demin: Kinetic Model of phosphofructokinase-1 from Escherichia coli. 843-867
• 
  Natalia Sinitsina, Igor Orshansky, Olga Sokolova: Actin-Binding proteins: How to Reveal the conformational Changes. 869-884

Volume 6, Number 5, October 2008

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  Igor F. Tsigelny, Jerry Greenberg, Valentina Kouznetsova, Sanjay K. Nigam: Modeling of glycerol-3-phosphate transporter suggests a Potential 'Tilt' Mechanism involved in its Function. 885-904
• 
  Eli Kaminuma, Hiroshi Masuya, Ikuo Miura, Hiromi Motegi, Kenzi R. Takahasi, Miki Nakazawa, Minami Matsui, Yoichi Gondo, Tetsuo Noda, Toshihiko Shiroishi, Shigeharu Wakana, Tetsuro Toyoda: Objective Evaluation Measures of Genetic Marker Selection in Large-Scale SNP genotyping. 905-917
• 
  Tamara B. Sipes, Susan M. Freier: Prediction of antisense oligonucleotide Efficacy Using Aggregate motifs. 919-932
• 
  Kirill Peskov, Igor Goryanin, Klaus Prank, Frank Tobin, Oleg V. Demin: Kinetic Modeling of ACE operon Genetic Regulation in Escherichia coli. 933-959
• 
  André Fujita, João Ricardo Sato, Humberto Miguel Garay-Malpartida, Mari Cleide Sogayar, Carlos Eduardo Ferreira, Satoru Miyano: Modeling Nonlinear Gene Regulatory Networks from Time Series Gene Expression Data. 961-979
• 
  Xiu-Feng Wan, Mufit Ozden, Guohui Lin: Ubiquitous Reassortments in influenza a viruses. 981-999
• 
  Alberto J. M. Martin, Davide Baù, Alessandro Vullo, Ian Walsh, Gianluca Pollastri: Long-Range Information and Physicality Constraints Improve predicted protein Contact Maps. 1001-1020
• 
  Thomas K. F. Wong, Tak Wah Lam, Wanling Yang, Siu-Ming Yiu: Finding Alternative Splicing Patterns with Strong Support from expressed Sequences on Individual exons/introns. 1021-1033
• 
  Nikita V. Dovidchenko, Natalya S. Bogatyreva, Oxana V. Galzitskaya: Prediction of Loop Regions in protein Sequence. 1035-1047

Volume 6, Number 6, December 2008

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  Yonghui Wu, Stefano Lonardi: A Linear-Time Algorithm for Predicting Functional Annotations from PPI Networks. 1049-1065
• 
  Matteo Comin, Concettina Guerra, Giuseppe Zanotti: Mining Overrepresented 3D Patterns of Secondary Structures in proteins. 1067-1087
• 
  Ying Liu, Wenyuan Li: Visualizing microarray Data for Biomarker Discovery by Matrix Reordering and Replicator Dynamics. 1089-1113
• 
  Thanh Phuong Nguyen, Tu Bao Ho: An Integrative Domain-Based Approach to Predicting protein-protein Interactions. 1115-1132
• 
  Koki Tsukamoto, Tatsuya Yoshikawa, Yuichiro Hourai, Kazuhiko Fukui, Yutaka Akiyama: Development of an Affinity Evaluation and Prediction System by Using the Shape complementarity Characteristic between proteins. 1133-1156
• 
  Dominic Rose, Julian Jöris, Jörg Hackermüller, Kristin Reiche, Qiang Li, Peter F. Stadler: Duplicated RNA genes in teleost Fish genomes. 1157-1175
• 
  Nadezhda Sazonova, E. James Harner: Haplotype Inference and Block Partitioning in Mixed Population Samples. 1177-1192
• 
  Mihailo Kaplarevic, Alison E. Murray, Stephen C. Cary, Guang R. Gao: Engenius - Environmental genome Informational Utility System. 1193-1211

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