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    Journal: J. Bioinformatics and Computational Biology

    Volume 7, Issue 6

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

    Volume 7, Issue 5

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

    Volume 7, Issue 4

    597 -- 623Leo van Iersel, Steven Kelk, Matthias Mnich. Uniqueness, Intractability and Exact Algorithms: Reflections on Level-k Phylogenetic Networks
    625 -- 644Sagi Snir, Tamir Tuller. The Net-HMM Approach: Phylogenetic Network Inference by Combining Maximum Likelihood and Hidden Markov Models
    645 -- 661Xin Chen. Curve-Based Clustering of Time Course Gene Expression Data Using Self-Organizing Maps
    663 -- 684André 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
    685 -- 700Enrico Capobianco. Aliasing in Gene Feature Detection by Projective Methods
    701 -- 716Henry 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
    717 -- 735Haseong Kim, Jae K. Lee, Taesung Park. Inference of Large-Scale Gene Regulatory Networks Using Regression-Based Network Approach
    737 -- 754Daniil Golod, Daniel G. Brown. A Tutorial of Techniques for Improving Standard Hidden Markov Model Algorithms

    Volume 7, Issue 3

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

    Volume 7, Issue 2

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

    Volume 7, Issue 1

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