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 Apostolico, Laxmi Parida:
Incremental Paradigms of Motif Discovery.
15-25
- 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
- Vladimir Makarenkov, Pierre Legendre:
From a Phylogenetic Tree to a Reticulated Network.
195-212
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
- Chen-Hsiang Yeang, Trey Ideker, Tommi Jaakkola:
Physical Network Models.
243-262
- Maáyan Fishelson, Dan Geiger:
Optimizing Exact Genetic Linkage Computations.
263-275
- 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
- Amos Tanay, Ron Shamir:
Multilevel Modeling and Inference of Transcription Regulation.
357-375
- 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
- Gideon Greenspan, Dan Geiger:
Model-Based Inference of Haplotype Block Variation.
493-504
- Lei M. Li, Jong Hyun Kim, Michael S. Waterman:
Haplotype Reconstruction from SNP Alignment.
505-516
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
- Jason Ku, Xiao-Jiang Feng, Herschel Rabitz:
Closed-Loop Learning Control of Bio-Networks.
642-659
- 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
- Kaleigh Smith, Michael T. Hallett:
Towards Quality Control for DNA Microarrays.
945-970
- 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
- Revital Eres, Gad M. Landau, Laxmi Parida:
Permutation Pattern Discovery in Biosequences.
1050-1060
- 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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