Journal of Bioinformatics and Computational Biology, Volume 7

Volume 7, Number 1, February 2009

• Nitin Bhardwaj, Hui Lu:
  Co-Expression among Constituents of a Motif in the protein-protein Interaction Network. 1-17
  
• Guojun Li, Dongsheng Che, Ying Xu:
  A Universal operon Predictor for prokaryotic genomes. 19-38
  
• Gao Shan, Wei-Mou Zheng:
  Counting of oligomers in Sequences Generated by Markov Chains for DNA Motif Discovery. 39-54
  
• Miguel M. F. Bugalho, Arlindo L. Oliveira:
  Constant Time Clash Detection in protein Folding. 55-74
  
• Sung-Gon Yi, Yoon-Jeong Joo, Taesung Park:
  Rank-Based Clustering Analysis for the Time-Course microarray Data. 75-91
  
• Pratap R. Patnaik:
  Transient Response Analysis of the eukaryotic Chemosensory System to Intra-Cellular Fluctuations. 93-105
  
• Jialiang Wu, Eberhard Voit:
  Hybrid Modeling in Biochemical Systems Theory by Means of Functional Petri Nets. 107-134
  
• Vinhthuy Phan, E. Olusegun George, Quynh T. Tran, Shirlean Goodwin, Sridevi Bodreddigari, Thomas R. Sutter:
  Analyzing microarray Data with Transitive Directed Acyclic Graphs. 135-156
  
• Shihong Mao, Charles Wang, Guozhu Dong:
  Evaluation of Inter-Laboratory and Cross-Platform concordance of DNA microarrays through Discriminating genes and Classifier transferability. 157-173
  
• Ao Yuan, Guanjie Chen, Charles Rotimi:
  Genetic Network Analysis by Quasi-Bayesian Method. 175-192
  
• Pierre R. Bushel:
  Clustering of Gene Expression Data and End-Point Measurements by Simulated Annealing. 193-215
  
• Lin Gao, Peng-Gang Sun, Jia Song:
  Clustering Algorithms for Detecting Functional Modules in protein Interaction Networks. 217-242
  
• Kumar Selvarajoo, Masaru Tomita, Masa Tsuchiya:
  Can Complex Cellular Processes be Governed by Simple Linear Rules? 243-268
  

Volume 7, Number 2, April 2009

• Johannes Aßfalg, Jing Gong, Hans-Peter Kriegel, Alexey Pryakhin, Tiandi Wei, Arthur Zimek:
  Supervised Ensembles of Prediction Methods for Subcellular Localization. 269-285
  
• Mohamed Ibrahim Abouelhoda, Robert Giegerich, Behshad Behzadi, Jean-Marc Steyaert:
  Alignment of Minisatellite Maps Based on Run-Length Encoding Scheme. 287-308
  
• Xing-Ming Zhao, Rui-Sheng Wang, Luonan Chen, Kazuyuki Aihara:
  Automatic Modeling of Signaling Pathways by Network Flow Model. 309-322
  
• Christopher James Langmead, Sumit Kumar Jha:
  Symbolic Approaches for Finding Control Strategies in Boolean Networks. 323-338
  
• Satish Tadepalli, Naren Ramakrishnan, Layne T. Watson, Bud Mishra, Richard F. Helm:
  Simultaneously Segmenting Multiple Gene Expression Time Courses by Analyzing Cluster Dynamics. 339-356
  
• Robert Warren, David Sankoff:
  Genome Halving with Double Cut and Join. 357-371
  
• Huei-Hun Tseng, Zasha Weinberg, Jeremy Gore, Ronald R. Breaker, Walter L. Ruzzo:
  Finding Non-Coding RNAs through genome-Scale Clustering. 373-388
  

Volume 7, Number 3, June 2009

• Ferhat Ay, Tamer Kahveci, Valérie de Crécy-Lagard:
  A Fast and Accurate Algorithm for Comparative Analysis of metabolic Pathways. 389-428
  
• En Cheng, Brendan Elliott, Z. Meral Özsoyoglu:
  Efficient Computation of Kinship and Identity Coefficients on Large Pedigrees. 429-453
  
• Yuzhen Ye, Haixu Tang:
  An Orfome Assembly Approach to Metagenomics Sequences Analysis. 455-471
  
• Aaron M. Smalter, Jun Huan, Gerald H. Lushington:
  Graph Wavelet Alignment Kernels for Drug Virtual Screening. 473-497
  
• Chunfang Zheng, P. Kerr Wall, James Leebens-Mack, Claude de Pamphilis, Victor A. Albert, David Sankoff:
  Gene Loss under Neighborhood Selection Following Whole genome Duplication and the Reconstruction of the Ancestral Populus genome. 499-520
  
• Xin Li, Jing Li:
  An Almost Linear Time Algorithm for a General Haplotype Solution on Tree Pedigrees with no Recombination and its Extensions. 521-545
  
• Nha Nguyen, Heng Huang, Soontorn Oraintara, An P. N. Vo:
  Peak Detection in Mass Spectrometry by Gabor Filters and Envelope Analysis. 547-569
  
• Saeed Salem, Mohammed J. Zaki, Christopher Bystroff:
  Iterative Non-Sequential protein Structural Alignment. 571-596
  

Volume 7, Number 4, August 2009

• Leo van Iersel, Steven Kelk, Matthias Mnich:
  Uniqueness, Intractability and Exact Algorithms: Reflections on Level-k Phylogenetic Networks. 597-623
  
• Sagi Snir, Tamir Tuller:
  The Net-HMM Approach: Phylogenetic Network Inference by Combining Maximum Likelihood and Hidden Markov Models. 625-644
  
• Xin Chen:
  Curve-Based Clustering of Time Course Gene Expression Data Using Self-Organizing Maps. 645-661
  
• André Fujita, João Ricardo Sato, Marcos Angelo Almeida Demasi, Mari Cleide Sogayar, Carlos Eduardo Ferreira, Satoru Miyano:
  Comparing Pearson, Spearman and Hoeffding's d Measure for Gene Expression Association Analysis. 663-684
  
• Enrico Capobianco:
  Aliasing in Gene Feature Detection by Projective Methods. 685-700
  
• Henry Chi-Ming Leung, Man-Hung Siu, Siu-Ming Yiu, Francis Yuk-Lun Chin, Ken Wing-Kin Sung:
  Clustering-Based Approach for Predicting Motif Pairs from protein Interaction Data. 701-716
  
• Haseong Kim, Jae K. Lee, Taesung Park:
  Inference of Large-Scale Gene Regulatory Networks Using Regression-Based Network Approach. 717-735
  
• Daniil Golod, Daniel G. Brown:
  A Tutorial of Techniques for Improving Standard Hidden Markov Model Algorithms. 737-754
  

Volume 7, Number 5, October 2009

• Zaixin Lu, Zhiyu Zhao, Sergio Garcia, Krishnakumar Krishnaswamy, Bin Fu:
  Search Similar protein Structures with Classification, Sequence and 3D alignments. 755-771
  
• Peng Chen, Chunmei Liu, Legand L. Burge III, Mahmood Mohammad, William M. Southerland, Clay Gloster:
  Protein fold Classification with Genetic Algorithms and Feature Selection. 773-788
  
• Xin Gao, Jinbo Xu, Shuai Cheng Li, Ming Li:
  Predicting Local Quality of a Sequence-Structure Alignment. 789-810
  
• Alexander Bujotzek, Marcus Weber:
  Efficient Simulation of ligand-receptor Binding Processes Using the Conformation Dynamics Approach. 811-831
  
• Christine Sinoquet:
  Iterative Two-Pass Algorithm for Missing Data Imputation in SNP Arrays. 833-852
  
• Anirban Mukhopadhyay, Ujjwal Maulik, Sanghamitra Bandyopadhyay:
  A Novel Coherence Measure for Discovering Scaling Biclusters from Gene Expression Data. 853-868
  
• Peter Clote, Evangelos Kranakis, Danny Krizanc, Bruno Salvy:
  Asymptotics of Canonical and Saturated RNA Secondary Structures. 869-893
  
• Anthony Almudevar:
  A Note on the Calculation of n-Statistics. 895-903
  

Volume 7, Number 6, December 2009

• Weiqi Wang, Yanbo J. Wang, René Bañares-Alcántara, Frans Coenen, Zhanfeng Cui:
  Analysis of Mesenchymal Stem Cell Differentiation in vitro Using Classification Association Rule Mining. 905-930
  
• Gábor Iván, Zoltan Szabadka, Vince Grolmusz:
  On the Asymmetry of the Residue Compositions of the Binding Sites on protein Surfaces. 931-938
  
• Tuan S. Nguyen, Javier Rojo:
  Dimension Reduction of microarray Gene Expression Data: the Accelerated Failure Time Model. 939-954
  
• Jingjing Li, Martin Renqiang Min, Anthony J. Bonner, Zhaolei Zhang:
  A Probabilistic Framework to Improve microRNA Target Prediction by Incorporating Proteomics Data. 955-972
  
• Chuan Hock Koh, Sharene Lin, Gregory Jedd, Limsoon Wong:
  Sirius PSB: a Generic System for Analysis of Biological Sequences. 973-990
  
• Yuri Matsuzaki, Yusuke Matsuzaki, Toshiyuki Sato, Yutaka Akiyama:
  In silico Screening of protein-protein Interactions with All-to-All Rigid docking and Clustering: an Application to Pathway Analysis. 991-1012
  
• Graham J. Hickman, Charlie Hodgman:
  Inference of Gene Regulatory Networks Using Boolean-Network Inference Methods. 1013-1029
  
• William Krivan, Darrick Carter:
  Exploring the protein Landscape in Ramachandran Space: IT's not Just PSI-phi. 1031-1037
  

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