Journal of Bioinformatics and Computational Biology, Volume 5

Volume 5, Number 1, February 2007

• Troy Hawkins, Daisuke Kihara:
  Function Prediction of uncharacterized proteins. 1-30
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• Olli Haavisto, Heikki Hyötyniemi, Christophe Roos:
  State Space Modeling of yeast gene Expression Dynamics. 31-46
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• Chengpeng Bi:
  Seam: a Stochastic EM-Type Algorithm for Motif-Finding in Biopolymer Sequences. 47-77
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• Erik Andries, Thomas Hagstrom, Susan R. Atlas, Cheryl Willman:
  Regularization Strategies for Hyperplane Classifiers: Application to Cancer Classification with gene Expression Data. 79-104
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• Markus T. Friberg:
  Prediction of transcription Factor Binding Sites Using CHIP-Chip and Phylogenetic footprinting Data. 105-116
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• Jakkarin Suksawatchon, Chidchanok Lursinsap, Mikael Bodén:
  Computing the Reversal Distance between genomes in the Presence of Multi-gene Families via Binary Integer Programming. 117-133
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• Shailza Singh, B. K. Malik, D. K. Sharma:
  Metabolic Pathway Analysis of S. Pneumoniae: an in silico Approach towards Drug-Design. 135-153
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• Vassily A. Lyubetsky, Sergey A. Pirogov, Lev I. Rubanov, Alexander Seliverstov:
  Modeling Classic Attenuation Regulation of gene Expression in bacteria. 155-180
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Volume 5, Number 2a, April 2007

• Yufeng Wu, Dan Gusfield:
  Efficient Computation of Minimum Recombination with genotypes (not Haplotypes). 181-200
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• S. Tewari, Suchendra M. Bhandarkar, Jonathan Arnold:
  Design and Analysis of an Efficient Recursive Linking Algorithm for Constructing Likelihood Based Genetic Maps for a Large Number of Markers. 201-250
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• Wenyuan Li, Yanxiong Peng, Hung-Chung Huang, Ying Liu:
  Biomarker Discovery and Visualization in gene Expression Data with Efficient Generalized Matrix Approximations. 251-279
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• Xu Han, Wing-Kin Sung, Lin Feng:
  Identifying differentially expressed genes in Time-Course microarray Experiment without Replicate. 281-296
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• Chungong Yu, Yu Lin, Shiwei Sun, Jinjin Cai, Jingfen Zhang, Dongbo Bu, Zhuo Zhang, Runsheng Chen:
  An Iterative Algorithm to Quantify Factors Influencing peptide Fragmentation during Tandem Mass Spectrometry. 297-311
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• Xiang Wan, Guohui Lin:
  Gasa: a Graph-Based Automated NMR Backbone Resonance Sequential Assignment Program. 313-333
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• Kevin W. Deronne, George Karypis:
  Effective Optimization Algorithms for Fragment-Assembly Based protein Structure Prediction. 335-352
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• Brian Y. Chen, Drew H. Bryant, Viacheslav Fofanov, David M. Kristensen, Amanda E. Cruess, Marek Kimmel, Olivier Lichtarge, Lydia E. Kavraki:
  Cavity Scaling: Automated Refinement of Cavity-Aware motifs in protein Function Prediction. 353-382
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• Jake Yue Chen, Zhong Yan, Changyu Shen, Dawn P. G. Fitzpatrick, Mu Wang:
  A Systems Biology Approach to the Study of cisplatin Drug Resistance in Ovarian cancers. 383-405
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• Gregory Pennington, Charles A. Smith, Stanley Shackney, Russell Schwartz:
  Reconstructing Tumor phylogenies from Heterogeneous Single-Cell Data. 407-427
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Volume 5, Number 2b, April 2007

• Andrey Y. Sivachenko, Anton Yuryev, Nikolai Daraselia, Ilya Mazo:
  Molecular Networks in microarray Analysis. 429-456
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• Ralf Hofestädt:
  Extended Backus-Systems for the Representation and Specification of the genome. 457-466
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• Eric Mjolsness:
  On Cooperative Quasi-Equilibrium Models of transcriptional Regulation. 467-490
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• Konstantin V. Gunbin, Leonid V. Omelyanchuk, Vladislav V. Kogai, Stanislav I. Fadeev, Nikolay A. Kolchanov:
  Model of the reception of Hedgehog morphogen concentration Gradient: Comparison with an Extended Range of Experimental Data. 491-506
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• Tamara M. Khlebodarova, Nina V. Tikunova, Alla V. Kachko, Irina L. Stepanenko, Nikolay L. Podkolodny, Nikolay A. Kolchanov:
  Application of Bioinformatics Resources for Genosensor Design. 507-520
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• Vitali A. Likhoshvai, Alexander V. Ratushny:
  Generalized Hill Function Method for Modeling Molecular Processes. 521-531
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• Irina I. Abnizova, Klaudia Walter, Rene te Boekhorst, G. Elgar, Walter R. Gilks:
  Statistical Information Characterization of conserved Non-Coding Elements in vertebrates. 533-547
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• Maria N. Tutukina, Konstantin S. Shavkunov, Irina S. Masulis, Olga N. Ozoline:
  Intragenic PROMOTOR-Like Sites in the genome of Escherichia coli Discovery and Functional Implication. 549-560
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• Stefan Posch, Jan Grau, Andre Gohr, Irad E. Ben-Gal, Alexander E. Kel, Ivo Grosse:
  Recognition of cis-Regulatory Elements with Vombat. 561-577
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• Alexis S. Ivanov, Oksana V. Gnedenko, Andrey A. Molnar, Yury V. Mezentsev, Andrey Lisitsa, Alexander I. Archakov:
  Protein-protein Interactions as New Targets for Drug Design: Virtual and Experimental Approaches. 579-592
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• Elena L. Mishchenko, Kirill D. Bezmaternykh, Vitali A. Likhoshvai, Alexander V. Ratushny, Tamara M. Khlebodarova, Natalia Yu. Sournina, Vladimir A. Ivanisenko, Nikolay A. Kolchanov:
  Mathematical Model for Suppression of Subgenomic Hepatitis C Virus RNA Replication in Cell Culture. 593-609
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• Anton A. Polyansky, Pavel E. Volynsky, Roman G. Efremov:
  Computer Simulations of Membrane-Lytic peptides: Perspectives in Drug Design. 611-626
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• Daniel Mateus, Jean-Pierre Gallois, Jean-Paul Comet, Pascale Le Gall:
  Symbolic Modeling of Genetic Regulatory Networks. 627-640
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• Ilya R. Akberdin, Evgeniy A. Ozonov, Victoria V. Mironova, Nadezda A. Omelyanchuk, Vitali A. Likhoshvai, Dmytry N. Gorpinchenko, Nikolay A. Kolchanov:
  A Cellular Automaton to Model the Development of Primary Shoot Meristems of Arabidopsis thaliana. 641-650
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Volume 5, Number 3, June 2007

• Patrick C. H. Ma, Keith C. C. Chan:
  An Effective Data Mining Technique for Reconstructing gene Regulatory Networks from Time Series Expression Data. 651-668
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• Takashi Kaburagi, Daigo Muramatsu, Takashi Matsumoto:
  Transmembrane Structure Predictions with Hydropathy Index/charge Two-Dimensional Trajectories of Stochastic Dynamical Systems. 669-692
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• Petras J. Kundrotas, Paulina Georgieva, Alexandra Shosheva, Petya Christova, Emil Alexov:
  Assessing the Quality of the Homology-Modeled 3D Structures from electrostatic Standpoint: Test on bacterial nucleoside monophosphate kinase Families. 693-715
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• Eleazar Eskin, Sagi Snir:
  Incorporating homologues into Sequence Embeddings for protein Analysis. 717-738
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• Cao Nguyen, Katheleen J. Gardiner, Krzysztof J. Cios:
  A Hidden Markov Model for Predicting protein Interfaces. 739-753
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• Virginia González-Vélez, Horacio González-Vélez:
  Parallel Stochastic Simulation of Macroscopic calcium currents. 755-772
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• Peter von Rohr, Markus T. Friberg, Haja N. Kadarmideen:
  Prediction of transcription Factor Binding Sites Using genetical genomics Methods. 773-793
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• Minzhu Xie, Jianer Chen, Jianxin Wang:
  Research on Parameterized Algorithms of the Individual Haplotyping Problem. 795-816
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Volume 5, Number 4, August 2007

• Guojun Li, Jizhu Lu, Victor Olman, Ying Xu:
  Prediction of cis-Regulatory Elements: from High-Information Content Analysis to Motif Identification. 817-838
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• Rogier J. P. van Berlo, Lodewyk F. A. Wessels, Dick de Ridder, Marcel J. T. Reinders:
  Protein Complex Prediction Using an Integrative Bioinformatics Approach. 839-864
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• Taesung Park, Kiwoong Kim, Sung-Gon Yi, Jin Hyuk Kim, Yong-Sung Lee, Seungyeoun Lee:
  Spot Intensity Ratio Statistics in Two-Channel microarray Experiments. 865-873
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• Aixiang Jiang, Wei Pan, Liming C. Milbauer, Yu Shyr, Robert P. Hebbel:
  A Practical Question Based on Cross-Platform microarray Data Normalization: are Boec More Like Large Vessel or microvascular Endothelial Cells or Neither of Them? 875-893
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• Meng Piao Tan, James R. Broach, Christodoulos A. Floudas:
  Evaluation of Normalization and Pre-Clustering Issues in a Novel Clustering Approach: Global Optimum Search with Enhanced Positioning. 895-913
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• Eric Sakk:
  On the Computation of Molecular Surface Correlations for protein docking Using Fourier Techniques. 915-935
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• Qi Fu, Elizabeth Bent, James Borneman, Marek Chrobak, Neal E. Young:
  Algorithmic Approaches to Selecting Control Clones in DNA Array Hybridization Experiments. 937-961
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• Xing Qiu, Andrei Yakovlev:
  Comments on Probabilistic Models Behind the Concept of False Discovery Rate. 963-975
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• Beatriz Stransky, Junior Barrera, Lucila Ohno-Machado, Sandro J. de Souza:
  Modeling Cancer: Integration of "omics" Information in Dynamic Systems. 977-986
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• Avner Bar-Hen, Kyung In Kim, Mark A. van de Wiel:
  Some Comments on False Discovery Rate. 987-990
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Volume 5, Number 5, October 2007

• Ekaterina O. Ermakova, Ramil N. Nurtdinov, Mikhail S. Gelfand:
  Overlapping Alternative donor splice Sites in the Human genome. 991-1004
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• Elena Tsiporkova, Veselka Boeva:
  Two-Pass Imputation Algorithm for Missing Value Estimation in gene Expression Time Series. 1005-1022
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• Wayne G. Fisher, Kevin P. Rosenblatt, David A. Fishman, Gordon R. Whiteley, Alvydas Mikulskis, Scott A. Kuzdzal, Mary F. Lopez, Niclas Chiang Tan, Dwight C. German, Harold R. Garner:
  A Robust Biomarker Discovery Pipeline for High-Performance Mass Spectrometry Data. 1023-1045
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• Tsutomu Matsunaga, Masaaki Muramatsu:
  Disease-Related Concept Mining by Knowledge-Based Two-Dimensional gene Mapping. 1047-1067
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• Manuele Bicego, Franco Dellaglio, Giovanna E. Felis:
  Multimodal Phylogeny for Taxonomy: Integrating Information from nucleotide and amino acid Sequences. 1069-1085
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• Zheng Fu, Tao Jiang:
  Computing the Breakpoint Distance between Partially Ordered genomes. 1087-1101
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• Yasubumi Sakakibara, Kris Popendorf, Nana Ogawa, Kiyoshi Asai, Kengo Sato:
  Stem Kernels for RNA Sequence Analyses. 1103-1122
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• James T. L. Mah, K. S. Chia:
  A Gentle Introduction to SNP Analysis: Resources and Tools. 1123-1138
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• Lev Klebanov, Galina Glazko, Peter Salzman, Andrei Yakovlev, Yuanhui Xiao:
  A Multivariate Extension of the gene Set Enrichment Analysis. 1139-1153
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Volume 5, Number 6, December 2007

• Brian O'Leary, Steven G. Davis, Michael F. Smith, Bartley Brown, Mathew B. Kemp, Hakeem Almabrazi, Jason A. Grundstad, Thomas Burns, Vladimir Leontiev, Jeaneen Andorf, Abbot F. Clark, Val C. Sheffield, Thomas L. Casavant, Todd E. Scheetz, Edwin M. Stone, Terry A. Braun:
  Transcript Annotation Prioritization and Screening System (TRApss) for Mutation Screening. 1155-1172
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• Hiroshi Masuya, Sumi Yoshikawa, Naohiko Heida, Tetsuro Toyoda, Shigeharu Wakana, Toshihiko Shiroishi:
  Phenosite: a Web Database Integrating the mouse phenotyping Platform and the Experimental Procedures in mice. 1173-1191
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• Chi-Ren Shyu, Jaturon Harnsomburana, Jason Green, Adrian S. Barb, Toni Kazic, Mary Schaeffer, Edward H. Coe:
  Searching and Mining Visually Observed Phenotypes of maize Mutants. 1193-1213
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• Yum Lina Yip, Nathalie Lachenal, Violaine Pillet, Anne-Lise Veuthey:
  Retrieving Mutation-Specific Information for Human proteins in UniProt/Swiss-PROT knowledgebase. 1215-1231
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• J. Gregory Caporaso, William A. Baumgartner Jr., David A. Randolph, K. Bretonnel Cohen, Lawrence Hunter:
  Rapid Pattern Development for Concept Recognition Systems: Application to Point mutations. 1233-1259
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• Muge Erdogmus, Osman Ugur Sezerman:
  Application of Automatic Mutation-gene Pair Extraction to Diseases. 1261-1275
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• Roman Klinger, Christoph M. Friedrich, Heinz-Theodor Mevissen, Juliane Fluck, Martin Hofmann-Apitius, Laura Inés Furlong, Ferran Sanz:
  Identifying gene-Specific Variations in Biomedical Text. 1277-1296
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• Catherine L. Worth, G. Richard J. Bickerton, Adrian Schreyer, Julia R. Forman, Tammy M. K. Cheng, Semin Lee, Sungsam Gong, David F. Burke, Tom L. Blundell:
  A Structural Bioinformatics Approach to the Analysis of nonsynonymous Single nucleotide polymorphisms (nsSNPS) and their Relation to Disease. 1297-1318
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• Kanagasabai Rajaraman, Khar Heng Choo, Shoba Ranganathan, Christopher J. O. Baker:
  A Workflow for Mutation Extraction and Structure Annotation. 1319-1337
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• René Witte, Christopher J. O. Baker:
  Towards a Systematic Evaluation of protein Mutation Extraction Systems. 1339-1359
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