Journal of Computational Biology, Volume 11

Volume 11, Number 1, February 2004

• Haiyan Huang, Ming-Chih J. Kao, Xianghong Jasmine Zhou, Jun S. Liu, Wing Hung Wong:
  Determination of Local Statistical Significance of Patterns in Markov Sequences with Application to Promoter Element Identification. 1-14
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• Alberto Apostolico, Laxmi Parida:
  Incremental Paradigms of Motif Discovery. 15-25
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• Alberto Caprara, Robert D. Carr, Sorin Istrail, Giuseppe Lancia, Brian Walenz:
  1001 Optimal PDB Structure Alignments: Integer Programming Methods for Finding the Maximum Contact Map Overlap. 27-52
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• Andreas Wagner:
  Reconstructing Pathways in Large Genetic Networks from Genetic Perturbations. 53-60
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• Peter A. Spiro, Natasa Macura:
  A Local Alignment Metric for Accelerating Biosequence Database Search. 61-82
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• Maxim Shatsky, Ruth Nussinov, Haim J. Wolfson:
  FlexProt: Alignment of Flexible Protein Structures Without a Predefinition of Hinge Regions. 83-106
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• Leo Wang-Kit Cheung:
  Use of Runs Statistics for Pattern Recognition in Genomic DNA Sequences. 107-124
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• Myong-Hee Sung, Richard Simon:
  Genomewide Conserved Epitope Profiles of HIV-1 Predicted by Biophysical Properties of MHC Binding Peptides. 125-145
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• Xiaobo Zhou, Xiaodong Wang, Edward R. Dougherty, Daniel Russ, Edward Suh:
  Gene Clustering Based on Clusterwide Mutual Information. 147-161
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• Ryszard W. Adamiak, Jacek Blazewicz, Piotr Formanowicz, Zofia Gdaniec, Marta Kasprzak, Mariusz Popenda, Marta Szachniuk:
  An Algorithm for an Automatic NOE Pathways Analysis of 2D NMR Spectra of RNA Duplexes. 163-179
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• Markus Wistrand, Erik L. L. Sonnhammer:
  Transition Priors for Protein Hidden Markov Models: An Empirical Study towards Maximum Discrimination. 181-193
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• Vladimir Makarenkov, Pierre Legendre:
  From a Phylogenetic Tree to a Reticulated Network. 195-212
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Volume 11, Number 2/3, March 2004

• Wentian Li, Fengzhu Sun, Ivo Grosse:
  Extreme Value Distribution Based Gene Selection Criteria for Discriminant Microarray Data Analysis Using Logistic Regression. 215-226
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• Balaji Krishnapuram, Lawrence Carin, Alexander J. Hartemink:
  Joint Classifier and Feature Optimization for Comprehensive Cancer Diagnosis Using Gene Expression Data. 227-242
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• Chen-Hsiang Yeang, Trey Ideker, Tommi Jaakkola:
  Physical Network Models. 243-262
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• Maáyan Fishelson, Dan Geiger:
  Optimizing Exact Genetic Linkage Computations. 263-275
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• Christopher James Langmead, Anthony K. Yan, Ryan H. Lilien, Lincong Wang, Bruce Randall Donald:
  A Polynomial-Time Nuclear Vector Replacement Algorithm for Automated NMR Resonance Assignments. 277-298
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• Itay Lotan, Fabian Schwarzer:
  Approximation of Protein Structure for Fast Similarity Measures. 299-317
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• Manolis Kellis, Nick Patterson, Bruce Birren, Bonnie Berger, Eric S. Lander:
  Methods in Comparative Genomics: Genome Correspondence, Gene Identification and Regulatory Motif Discovery. 319-355
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• Amos Tanay, Ron Shamir:
  Multilevel Modeling and Inference of Transcription Regulation. 357-375
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• Gene W. Yeo, Christopher B. Burge:
  Maximum Entropy Modeling of Short Sequence Motifs with Applications to RNA Splicing Signals. 377-394
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• Krishna M. Roskin, Mark Diekhans, David Haussler:
  Score Functions for Determining Regional Conservation in Two-Species Local Alignments. 395-411
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• Adam C. Siepel, David Haussler:
  Combining Phylogenetic and Hidden Markov Models in Biosequence Analysis. 413-428
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• Andrew B. Kahng, Ion I. Mandoiu, Pavel A. Pevzner, Sherief Reda, Alexander Zelikovsky:
  Scalable Heuristics for Design of DNA Probe Arrays. 429-447
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• Tatsuya Akutsu:
  Efficient Extraction of Mapping Rules of Atoms from Enzymatic Reaction Data. 449-462
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• Minghua Deng, Ting Chen, Fengzhu Sun:
  An Integrated Probabilistic Model for Functional Prediction of Proteins. 463-475
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• Amir Ben-Dor, Tzvika Hartman, Richard M. Karp, Benno Schwikowski, Roded Sharan, Zohar Yakhini:
  Towards Optimally Multiplexed Applications of Universal Arrays. 476-492
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• Gideon Greenspan, Dan Geiger:
  Model-Based Inference of Haplotype Block Variation. 493-504
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• Lei M. Li, Jong Hyun Kim, Michael S. Waterman:
  Haplotype Reconstruction from SNP Alignment. 505-516
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Volume 11, Number 4, August 2004

• Craig J. Benham, Chengpeng Bi:
  The Analysis of Stress-Induced Duplex Destabilization in Long Genomic DNA Sequences. 519-543
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• Kevin A. Janes, Jason R. Kelly, Suzanne Gaudet, John G. Albeck, Peter K. Sorger, Douglas A. Lauffenburger:
  Cue-Signal-Response Analysis of TNF-Induced Apoptosis by Partial Least Squares Regression of Dynamic Multivariate Data. 544-561
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• Rongling Wu, Chang-Xing Ma, George Casella:
  A Mixed Polyploid Model for Linkage Analysis in Outcrossing Tetraploids Using a Pseudo-Test Backcross Design. 562-580
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• Paul Helman, Robert Veroff, Susan R. Atlas, Cheryl Willman:
  A Bayesian Network Classification Methodology for Gene Expression Data. 581-615
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• Hilary S. Booth, John H. Maindonald, Susan R. Wilson, Jill E. Gready:
  An Efficient Z-Score Algorithm for Assessing Sequence Alignments. 616-625
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• Dan Levy, Mariel Vázquez, Michael Cornforth, Bradford Loucas, Rainer K. Sachs, Javier Arsuaga:
  Comparing DNA Damage-Processing Pathways by Computer Analysis of Chromosome Painting Data. 626-641
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• Jason Ku, Xiao-Jiang Feng, Herschel Rabitz:
  Closed-Loop Learning Control of Bio-Networks. 642-659
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• Ciprian Doru Giurcaneanu, Ioan Tabus, Jaakko Astola, Juha Ollila, Mauno Vihinen:
  Fast Iterative Gene Clustering Based on Information Theoretic Criteria for Selecting the Cluster Structure. 660-682
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• Lin Zhihua, Wu Yuzhang, Zhu Bo, Ni Bing, Wang Li:
  Toward the Quantitative Prediction of T-Cell Epitopes: QSAR Studies on Peptides Having Affinity with the Class I MHC Molecular HLA-A_*0201. 683-694
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• Tracy L. Bergemann, R. J. Laws, Filemon Quiaoit, Lue Ping Zhao:
  A Statistically Driven Approach for Image Segmentation and Signal Extraction in cDNA Microarrays. 695-713
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• Sue-Jane Wang, James J. Chen:
  Sample Size for Identifying Differentially Expressed Genes in Microarray Experiments. 714-726
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• Nicolas Galtier, Alain Jean-Marie:
  Markov-Modulated Markov Chains and the Covarion Process of Molecular Evolution. 727-733
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• Michael Roberts, Brian R. Hunt, James A. Yorke, Randall A. Bolanos, Arthur L. Delcher:
  A Preprocessor for Shotgun Assembly of Large Genomes. 734-752
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• Franco P. Preparata, John S. Oliver:
  DNA Sequencing by Hybridization Using Semi-Degenerate Bases. 753-765
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• Piotr Berman, Paul Bertone, Bhaskar DasGupta, Mark Gerstein, Ming-Yang Kao, Michael Snyder:
  Fast Optimal Genome Tiling with Applications to Microarray Design and Homology Search. 766-785
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Volume 11, Number 5, October 2004

• Yuting Jia, T. Gregory Dewey, Ilya N. Shindyalov, Philip E. Bourne:
  A New Scoring Function and Associated Statistical Significance for Structure Alignment by CE. 787-799
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• Hagit Shatkay, Jason Miller, Clark M. Mobarry, Michael Flanigan, Shibu Yooseph, Granger G. Sutton:
  ThurGood: Evaluating Assembly-to-Assembly Mapping. 800-811
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• Joseph S. Oliveira, Janet B. Jones-Oliveira, David A. Dixon, Colin G. Bailey, Dean W. Gull:
  Hyperdigraph-Theoretic Analysis of the EGFR Signaling Network: Initial Steps Leading to GTP: Ras Complex Formation. 812-842
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• Andreas Heger, Michael Lappe, Liisa Holm:
  Accurate Detection of Very Sparse Sequence Motifs. 843-857
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• Vineet Bafna, Dan Gusfield, Sridhar Hannenhalli, Shibu Yooseph:
  A Note on Efficient Computation of Haplotypes via Perfect Phylogeny. 858-866
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• Gill Bejerano, Nir Friedman, Naftali Tishby:
  Efficient Exact p-Value Computation for Small Sample, Sparse, and Surprising Categorical Data. 867-886
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• Andres Figueroa, James Borneman, Tao Jiang:
  Clustering Binary Fingerprint Vectors with Missing Values for DNA Array Data Analysis. 887-901
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• Itay Lotan, Fabian Schwarzer, Dan Halperin, Jean-Claude Latombe:
  Algorithm and Data Structures for Efficient Energy Maintenance during Monte Carlo Simulation of Proteins. 902-932
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• Can Alkan, Evan E. Eichler, Jeffrey A. Bailey, Süleyman Cenk Sahinalp, Eray Tüzün:
  The Role of Unequal Crossover in Alpha-Satellite DNA Evolution: A Computational Analysis. 933-944
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• Kaleigh Smith, Michael T. Hallett:
  Towards Quality Control for DNA Microarrays. 945-970
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• Stephen D. Bay, Lonnie Chrisman, Andrew Pohorille, Jeff Shrager:
  Temporal Aggregation Bias and Inference of Causal Regulatory Networks. 971-985
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• Jieping Ye, Ravi Janardan:
  Approximate Multiple Protein Structure Alignment Using the Sum-of-Pairs Distance. 986-1000
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• Miklós Csürös, Aleksandar Milosavljevic:
  Pooled Genomic Indexing (PGI): Analysis and Design of Experiments. 1001-1021
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Volume 11, Number 6, Decamber 2004

• Grégory Nuel:
  LD-SPatt: Large Deviations Statistics for Patterns on Markov Chains. 1023-1033
  Electronic Edition (link) BibTeX
• Irit Gat-Viks, Amos Tanay, Ron Shamir:
  Modeling and Analysis of Heterogeneous Regulation in Biological Networks. 1034-1049
  Electronic Edition (link) BibTeX
• Revital Eres, Gad M. Landau, Laxmi Parida:
  Permutation Pattern Discovery in Biosequences. 1050-1060
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• Matteo Comin, Concettina Guerra, Giuseppe Zanotti:
  PROuST: A Comparison Method of Three-Dimensional Structures of Proteins Using Indexing Techniques. 1061-1072
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• Chiranjib Bhattacharyya, L. R. Grate, Michael I. Jordan, Laurent El Ghaoui, I. Saira Mian:
  Robust Sparse Hyperplane Classifiers: Application to Uncertain Molecular Profiling Data. 1073-1089
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• P. Chiappetta, M. C. Roubaud, Bruno Torrésani:
  Blind Source Separation and the Analysis of Microarray Data. 1090-1109
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• Sebastian Böcker:
  Sequencing from Compomers: Using Mass Spectrometry for DNA de novo Sequencing of 200+ nt. 1110-1134
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• Mathäus Dejori, Martin Stetter:
  Identifying Interventional and Pathogenic Mechanisms by Generative Inverse Modeling of Gene Expression Profiles. 1135-1148
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• Ahmet Palazoglu, Attila Gürsoy, Yaman Arkun, Burak Erman:
  Folding Dynamics of Proteins from Denatured to Native State: Principal Component Analysis. 1149-1168
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• Danny Barash:
  Spectral Decomposition for the Search and Analysis of RNA Secondary Structure. 1169-1174
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• Nanxiang Ge, Charles B. Epstein:
  An Empirical Bayesian Significance Test of cDNA Library Data. 1175-1188
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• Darrell Conklin:
  Recognition of the Helical Cytokine Fold. 1189-1200
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