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ORCIDJournal of Bioinformatics and Computational Biology, Volume 2
Volume 2, Number 1, March 2004
- Foreword. 3-20
- Tomoyuki Yamada, Shinichi Morishita
:
Computing Highly Specific and Noise-tolerant Oligomers Efficiently. 21-46 - S. Liang, Manoj Pratim Samanta, B. A. Biegel:
Cwinnower Algorithm for Finding Fuzzy DNA Motifs. 47-60 - Werner G. Krebs, Philip E. Bourne:
Statistical and Visual Morph Movie Analysis of Crystallographic Mutant Selection Bias in Protein Mutation Resource Data. 61-76 - 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 - Orhan Çamoglu, Tamer Kahveci, Ambuj K. Singh:
Index-based Similarity Search for Protein Structure Databases. 99-126 - Eric P. Xing, Wei Wu, Michael I. Jordan, Richard M. Karp:
Logos: a Modular Bayesian Model for de Novo Motif Detection. 127-154 - 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 - Dan Gusfield, Satish Eddhu, Charles H. Langley:
Optimal, Efficient Reconstruction of Phylogenetic Networks with Constrained Recombination. 173-214 - Tolga Can, Yuan-Fang Wang:
Protein Structure Alignment and Fast Similarity Search Using Local Shape Signatures. 215-239
Volume 2, Number 2, June 2004
- Nadia El-Mabrouk:
Deriving Haplotypes through Recombination and Gene Conversion Pathways. 241-256 - Louigi Addario-Berry, Benny Chor, Michael T. Hallett, Jens Lagergren, Alessandro Panconesi, Todd Wareham:
Ancestral Maximum Likelihood of Evolutionary Trees Is Hard. 257-272 - Hideo Bannai, Shunsuke Inenaga, Ayumi Shinohara, Masayuki Takeda, Satoru Miyano:
Efficiently Finding Regulatory Elements Using Correlation with Gene Expression. 273-288 - Jan T. Kim, Jan E. Gewehr, Thomas Martinetz:
Binding Matrix: a Novel Approach for Binding Site Recognition. 289-308 - 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 - Wei-Mou Zheng:
Clustering of Amino Acids for Protein Secondary Structure Prediction. 333-342 - Xin Liu, Li-Mei Zhang, Wei-Mou Zheng:
Prediction of Protein Secondary Structure Based on Residue Pairs. 343-352 - Zheng-Qing Ouyang, Huaiqiu Zhu, Jin Wang, Zhen-Su She:
Multivariate Entropy Distance Method for Prokaryotic Gene Identification. 353-374 - Zoé Lacroix, Louiqa Raschid, Barbara A. Eckman:
Techniques for Optimization of Queries on Integrated Biological Resources. 375-412 - William Krivan:
Searching for Transcription Factor Binding Site Clusters: How True Are True Positives? 413-416
Volume 2, Number 3, September 2004
- Ming Li, Bin Ma, Derek Kisman, John Tromp:
Patternhunter Ii: Highly Sensitive and Fast Homology Search. 417-440 - Sun-Chong Wang:
Reconstructing Genetic Networks from Time Ordered Gene Expression Data Using Bayesian Method with Global Search Algorithm. 441-458 - Alain Guénoche:
Supersequences of Masks for Oligo-chips. 459-470 - Luigi Palopoli, Giorgio Terracina:
Coopps: a System for the Cooperative Prediction of Protein Structures. 471-496 - 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 - Zheng Rong Yang, Emily A. Berry:
Reduced Bio-basis Function Neural Networks for Protease Cleavage Site Prediction. 511-532 - 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 - Jung-Jae Kim, Jong-Chan Park:
Bioie: Retargetable Information Extraction and Ontological Annotation of Biological Interactions from the Literature. 551-568 - 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 - Dag G. Ahrén, Christos A. Ouzounis:
Robustness of Metabolic Map Reconstruction. 589-593
Volume 2, Number 4, December 2004
- Gong-Xin Yu:
Ruleminer: a Knowledge System for Supporting High-throughput Protein Function Annotations. 595-618 - Simon Hardy, Pierre N. Robillard:
Modeling and Simulation of Molecular Biology Systems Using Petri Nets: Modeling Goals of Various Approaches. 619-638 - 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 - Süleyman Cenk Sahinalp, Evan E. Eichler, Paul W. Goldberg, Petra Berenbrink, Tom Friedetzky, Funda Ergün:
Identifying Uniformly Mutated Segments within Repeats. 657-668 - 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 - Rolf Backofen, Sebastian Will:
Local Sequence-structure Motifs in Rna. 681-698 - Jieping Ye, Ravi Janardan, Songtao Liu:
Pairwise Protein Structure Alignment Based on an Orientation-independent Backbone Representation. 699-718 - Arun Siddharth Konagurthu, James C. Whisstock, Peter J. Stuckey:
Progressive Multiple Alignment Using Sequence Triplet Optimizations and Three-residue Exchange Costs. 719-746 - Xiang Wan, Theodore Tegos, Guohui Lin:
Histogram-based Scoring Schemes for Protein Nmr Resonance Assignment. 747-764 - Guillaume Bourque, David Sankoff:
Improving Gene Network Inference by Comparing Expression Time-series across Species, Developmental Stages or Tissues. 765-784 - Xiaomei Zhu, Lan Yin, Leroy Hood, Ping Ao:
Robustness, Stability and Efficiency of Phage lambda Genetic Switch: Dynamical Structure Analysis. 785-818 - Daniel G. Brown, Ming Li, Bin Ma:
A Tutorial of Recent Developments in the Seeding of Local Alignment. 819-842
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