Journal of Bioinformatics and Computational Biology, Volume 2

Volume 2, Number 1, March 2004

• Foreword. 3-20
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• Tomoyuki Yamada, Shinichi Morishita:
  Computing Highly Specific and Noise-tolerant Oligomers Efficiently. 21-46
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• S. Liang, Manoj Pratim Samanta, B. A. Biegel:
  Cwinnower Algorithm for Finding Fuzzy DNA Motifs. 47-60
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• Werner G. Krebs, Philip E. Bourne:
  Statistical and Visual Morph Movie Analysis of Crystallographic Mutant Selection Bias in Protein Mutation Resource Data. 61-76
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• Seiya Imoto, Tomoyuki Higuchi, Takao Goto, Kousuke Tashiro, Satoru Kuhara, Satoru Miyano:
  Combining Microarrays and Biological Knowledge for Estimating Gene Networks via Bayesian Networks. 77-98
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• Orhan Çamoglu, Tamer Kahveci, Ambuj K. Singh:
  Index-based Similarity Search for Protein Structure Databases. 99-126
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• Eric P. Xing, Wei Wu, Michael I. Jordan, Richard M. Karp:
  Logos: a Modular Bayesian Model for de Novo Motif Detection. 127-154
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• Robert L. Grossman, Pavan Kasturi, Donald Hamelberg, Bing Liu:
  An Empirical Study of the Universal Chemical Key Algorithm for Assigning Unique Keys to Chemical Compounds. 155-172
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• Dan Gusfield, Satish Eddhu, Charles H. Langley:
  Optimal, Efficient Reconstruction of Phylogenetic Networks with Constrained Recombination. 173-214
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• Tolga Can, Yuan-Fang Wang:
  Protein Structure Alignment and Fast Similarity Search Using Local Shape Signatures. 215-239
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Volume 2, Number 2, June 2004

• Nadia El-Mabrouk:
  Deriving Haplotypes through Recombination and Gene Conversion Pathways. 241-256
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• Louigi Addario-Berry, Benny Chor, Michael T. Hallett, Jens Lagergren, Alessandro Panconesi, Todd Wareham:
  Ancestral Maximum Likelihood of Evolutionary Trees Is Hard. 257-272
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• Hideo Bannai, Shunsuke Inenaga, Ayumi Shinohara, Masayuki Takeda, Satoru Miyano:
  Efficiently Finding Regulatory Elements Using Correlation with Gene Expression. 273-288
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• Jan T. Kim, Jan E. Gewehr, Thomas Martinetz:
  Binding Matrix: a Novel Approach for Binding Site Recognition. 289-308
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• Sumie Kitamura-Abe, Hitomi Itoh, Takanori Washio, Akihiro Tsutsumi, Masaru Tomita:
  Characterization of the Splice Sites in Gt-ag and Gc-ag Introns in Higher Eukaryotes Using Full-length Cdnas. 309-332
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• Wei-Mou Zheng:
  Clustering of Amino Acids for Protein Secondary Structure Prediction. 333-342
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• Xin Liu, Li-Mei Zhang, Wei-Mou Zheng:
  Prediction of Protein Secondary Structure Based on Residue Pairs. 343-352
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• Zheng-Qing Ouyang, Huaiqiu Zhu, Jin Wang, Zhen-Su She:
  Multivariate Entropy Distance Method for Prokaryotic Gene Identification. 353-374
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• Zoé Lacroix, Louiqa Raschid, Barbara A. Eckman:
  Techniques for Optimization of Queries on Integrated Biological Resources. 375-412
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• William Krivan:
  Searching for Transcription Factor Binding Site Clusters: How True Are True Positives? 413-416
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Volume 2, Number 3, September 2004

• Ming Li, Bin Ma, Derek Kisman, John Tromp:
  Patternhunter Ii: Highly Sensitive and Fast Homology Search. 417-440
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• Sun-Chong Wang:
  Reconstructing Genetic Networks from Time Ordered Gene Expression Data Using Bayesian Method with Global Search Algorithm. 441-458
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• Alain Guénoche:
  Supersequences of Masks for Oligo-chips. 459-470
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• Luigi Palopoli, Giorgio Terracina:
  Coopps: a System for the Cooperative Prediction of Protein Structures. 471-496
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• Yoshiharu Hayashi, Mime Kobayashi, Katsuyoshi Sakaguchi, Nao Iwata, Masaki Kobayashi, Yo Kikuchi, Yoshimasa Takahashi:
  Protein Classification Using Comparative Molecular Interaction Profile Analysis System. 497-510
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• Zheng Rong Yang, Emily A. Berry:
  Reduced Bio-basis Function Neural Networks for Protease Cleavage Site Prediction. 511-532
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• Yukihiro Maki, Yoriko Takahashi, Yuji Arikawa, Shoji Watanabe, Ken Aoshima, Yukihiro Eguchi, Takanori Ueda, Sachiyo Aburatani, Satoru Kuhara, Masahiro Okamoto:
  An Integrated Comprehensive Workbench for Inferring Genetic Networks: voyagene. 533-550
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• Jung-jae Kim, Jong C. Park:
  Bioie: Retargetable Information Extraction and Ontological Annotation of Biological Interactions from the Literature. 551-568
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• Kee Yew Wong, Yin Choy Chuan, Amit Aggarwal, Lawrence Tham, Waiming Kong, Patrick Tan:
  Identifying Patterns of Dna for Tumor Diagnosis Using Capillary Electrophoresis-amplified Fragment Length Polymorphism (ce-aflp) Screening. 569-588
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• Dag G. Ahrén, Christos A. Ouzounis:
  Robustness of Metabolic Map Reconstruction. 589-593
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Volume 2, Number 4, December 2004

• Gong-Xin Yu:
  Ruleminer: a Knowledge System for Supporting High-throughput Protein Function Annotations. 595-618
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• Simon Hardy, Pierre N. Robillard:
  Modeling and Simulation of Molecular Biology Systems Using Petri Nets: Modeling Goals of Various Approaches. 619-638
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• Youlian Pan, Jeffrey D. Pylatuik, Junjun Ouyang, A. Fazel Famili, Pierre R. Fobert:
  Discovery of Functional Genes for Systemic Acquired Resistance in arabidopsis Thaliana through Integrated Data Mining. 639-656
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• Süleyman Cenk Sahinalp, Evan E. Eichler, Paul W. Goldberg, Petra Berenbrink, Tom Friedetzky, Funda Ergün:
  Identifying Uniformly Mutated Segments within Repeats. 657-668
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• Masato Inoue, Shin-ichi Nishimura, Gen Hori, Hiroyuki Nakahara, Michiko Saito, Yoshihiro Yoshihara, Shun-ichi Amari:
  Improved Parameter Estimation for Variance-stabilizing Transformation of Gene-expression Microarray Data. 669-680
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• Rolf Backofen, Sebastian Will:
  Local Sequence-structure Motifs in Rna. 681-698
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• Jieping Ye, Ravi Janardan, Songtao Liu:
  Pairwise Protein Structure Alignment Based on an Orientation-independent Backbone Representation. 699-718
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• Arun Siddharth Konagurthu, James C. Whisstock, Peter J. Stuckey:
  Progressive Multiple Alignment Using Sequence Triplet Optimizations and Three-residue Exchange Costs. 719-746
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• Xiang Wan, Theodore Tegos, Guohui Lin:
  Histogram-based Scoring Schemes for Protein Nmr Resonance Assignment. 747-764
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• Guillaume Bourque, David Sankoff:
  Improving Gene Network Inference by Comparing Expression Time-series across Species, Developmental Stages or Tissues. 765-784
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• X.-M. Zhu, L. Yin, L. Hood, P. Ao:
  Robustness, Stability and Efficiency of Phage lambda Genetic Switch: Dynamical Structure Analysis. 785-818
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• Daniel G. Brown, Ming Li, Bin Ma:
  A Tutorial of Recent Developments in the Seeding of Local Alignment. 819-842
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