Journal of Bioinformatics and Computational Biology, Volume 6

Volume 6, Number 1, February 2008

• 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

• 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

• 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 V. 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, Jr., Sven Rahmann:
  Better GeneChip microarray Layouts by Combining Probe Placement and Embedding. 623-641
  

Volume 6, Number 4, August 2008

• 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 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

• 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

• 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