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ORCIDJournal 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 A. 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 - Susanta Tewari, Jonathan P. 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 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
- 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 V. 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 S. 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 S. 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
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