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- 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
- Andreas Wagner: Reconstructing Pathways in Large Genetic Networks from Genetic Perturbations. 53-60
- Peter A. Spiro, Natasa Macura: A Local Alignment Metric for Accelerating Biosequence Database Search. 61-82
- Maxim Shatsky, Ruth Nussinov, Haim J. Wolfson: FlexProt: Alignment of Flexible Protein Structures Without a Predefinition of Hinge Regions. 83-106
- Leo Wang-Kit Cheung: Use of Runs Statistics for Pattern Recognition in Genomic DNA Sequences. 107-124
- Myong-Hee Sung, Richard Simon: Genomewide Conserved Epitope Profiles of HIV-1 Predicted by Biophysical Properties of MHC Binding Peptides. 125-145
- Xiaobo Zhou, Xiaodong Wang, Edward R. Dougherty, Daniel Russ, Edward Suh: Gene Clustering Based on Clusterwide Mutual Information. 147-161
- 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
- Markus Wistrand, Erik L. L. Sonnhammer: Transition Priors for Protein Hidden Markov Models: An Empirical Study towards Maximum Discrimination. 181-193
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
- Balaji Krishnapuram, Lawrence Carin, Alexander J. Hartemink: Joint Classifier and Feature Optimization for Comprehensive Cancer Diagnosis Using Gene Expression Data. 227-242
- 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
- Itay Lotan, Fabian Schwarzer: Approximation of Protein Structure for Fast Similarity Measures. 299-317
- 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
- Gene W. Yeo, Christopher B. Burge: Maximum Entropy Modeling of Short Sequence Motifs with Applications to RNA Splicing Signals. 377-394
- Krishna M. Roskin, Mark Diekhans, David Haussler: Score Functions for Determining Regional Conservation in Two-Species Local Alignments. 395-411
- Adam C. Siepel, David Haussler: Combining Phylogenetic and Hidden Markov Models in Biosequence Analysis. 413-428
- Andrew B. Kahng, Ion I. Mandoiu, Pavel A. Pevzner, Sherief Reda, Alexander Zelikovsky: Scalable Heuristics for Design of DNA Probe Arrays. 429-447
- Tatsuya Akutsu: Efficient Extraction of Mapping Rules of Atoms from Enzymatic Reaction Data. 449-462
- Minghua Deng, Ting Chen, Fengzhu Sun: An Integrated Probabilistic Model for Functional Prediction of Proteins. 463-475
- Amir Ben-Dor, Tzvika Hartman, Richard M. Karp, Benno Schwikowski, Roded Sharan, Zohar Yakhini: Towards Optimally Multiplexed Applications of Universal Arrays. 476-492
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
- 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
- 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
- Paul Helman, Robert Veroff, Susan R. Atlas, Cheryl Willman: A Bayesian Network Classification Methodology for Gene Expression Data. 581-615
- Hilary S. Booth, John H. Maindonald, Susan R. Wilson, Jill E. Gready: An Efficient Z-Score Algorithm for Assessing Sequence Alignments. 616-625
- 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
- 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
- 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
- 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
- Sue-Jane Wang, James J. Chen: Sample Size for Identifying Differentially Expressed Genes in Microarray Experiments. 714-726
- Nicolas Galtier, Alain Jean-Marie: Markov-Modulated Markov Chains and the Covarion Process of Molecular Evolution. 727-733
- Michael Roberts, Brian R. Hunt, James A. Yorke, Randall A. Bolanos, Arthur L. Delcher: A Preprocessor for Shotgun Assembly of Large Genomes. 734-752
- Franco P. Preparata, John S. Oliver: DNA Sequencing by Hybridization Using Semi-Degenerate Bases. 753-765
- 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
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
- Hagit Shatkay, Jason R. Miller, Clark M. Mobarry, Michael Flanigan, Shibu Yooseph, Granger G. Sutton: ThurGood: Evaluating Assembly-to-Assembly Mapping. 800-811
- 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
- Andreas Heger, Michael Lappe, Liisa Holm: Accurate Detection of Very Sparse Sequence Motifs. 843-857
- Vineet Bafna, Dan Gusfield, Sridhar Hannenhalli, Shibu Yooseph: A Note on Efficient Computation of Haplotypes via Perfect Phylogeny. 858-866
- Gill Bejerano, Nir Friedman, Naftali Tishby: Efficient Exact p-Value Computation for Small Sample, Sparse, and Surprising Categorical Data. 867-886
- Andres Figueroa, James Borneman, Tao Jiang: Clustering Binary Fingerprint Vectors with Missing Values for DNA Array Data Analysis. 887-901
- 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
- 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
- Stephen D. Bay, Lonnie Chrisman, Andrew Pohorille, Jeff Shrager: Temporal Aggregation Bias and Inference of Causal Regulatory Networks. 971-985
- Jieping Ye, Ravi Janardan: Approximate Multiple Protein Structure Alignment Using the Sum-of-Pairs Distance. 986-1000
- Miklós Csürös, Aleksandar Milosavljevic: Pooled Genomic Indexing (PGI): Analysis and Design of Experiments. 1001-1021
Volume 11, Number 6, Decamber 2004
- Grégory Nuel: LD-SPatt: Large Deviations Statistics for Patterns on Markov Chains. 1023-1033
- Irit Gat-Viks, Amos Tanay, Ron Shamir: Modeling and Analysis of Heterogeneous Regulation in Biological Networks. 1034-1049
- Matteo Comin, Concettina Guerra, Giuseppe Zanotti: PROuST: A Comparison Method of Three-Dimensional Structures of Proteins Using Indexing Techniques. 1061-1072
- 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
- P. Chiappetta, M. C. Roubaud, Bruno Torrésani: Blind Source Separation and the Analysis of Microarray Data. 1090-1109
- Sebastian Böcker: Sequencing from Compomers: Using Mass Spectrometry for DNA de novo Sequencing of 200+ nt. 1110-1134
- Mathäus Dejori, Martin Stetter: Identifying Interventional and Pathogenic Mechanisms by Generative Inverse Modeling of Gene Expression Profiles. 1135-1148
- Ahmet Palazoglu, Attila Gürsoy, Yaman Arkun, Burak Erman: Folding Dynamics of Proteins from Denatured to Native State: Principal Component Analysis. 1149-1168
- Danny Barash: Spectral Decomposition for the Search and Analysis of RNA Secondary Structure. 1169-1174
- Nanxiang Ge, Charles B. Epstein: An Empirical Bayesian Significance Test of cDNA Library Data. 1175-1188
- Darrell Conklin: Recognition of the Helical Cytokine Fold. 1189-1200
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last updated on 2013-06-17T203624 by the dblp team