Volume 7, Number 1-2, February/April 2000
- Gesine Reinert, Sophie Schbath, Michael S. Waterman:
Probabilistic and Statistical Properties of Words: An Overview.
1-46
- Sophie Schbath, Nathalie Bossard, Simon Tavaré:
The Effect of Nonhomogeneous Clone Length Distribution on the Progress of an STS Mapping Project.
47-57
- Vineet Bafna, Sridhar Hannenhalli, Ken Rice, Lisa Vawter:
Ligand-Receptor Pairing Via Tree Comparison.
59-70
- Alberto Apostolico, Mary Ellen Bock, Stefano Lonardi, Xuyan Xu:
Efficient Detection of Unusual Words.
71-94
- Tommi Jaakkola, Mark Diekhans, David Haussler:
A Discriminative Framework for Detecting Remote Protein Homologies.
95-114
- Dirk Drasdo, Terence Hwa, Michael Lässig:
Scaling Laws and Similarity Detection in Sequence Alignment with Gaps.
115-141
- Dai Wang, Cheng Zhao, Rong Cheng, Fengzhu Sun:
Estimation of the Mutation Rate During Error-prone Polymerase Chain Reaction.
143-158
- Gráinne McGuire, Frank Wright, Michael J. Prentice:
A Bayesian Model for Detecting Past Recombination Events in DNA Multiple Alignments.
159-170
- Martin Fekete, Ivo L. Hofacker, Peter F. Stadler:
Prediction of RNA Base Pairing Probabilities on Massively Parallel Computers.
171-182
- Igor N. Berezovsky, Natalia G. Esipova, Vladimir G. Tumanyan:
Hierarchy of Regions of Amino Acid Sequence with Respect to Their Role in the Protein Spatial Structure.
183-192
- Sophie Schbath:
An Overview on the Distribution of Word Counts in Markov Chains.
193-201
- Zheng Zhang, Scott Schwartz, Lukas Wagner, Webb Miller:
A Greedy Algorithm for Aligning DNA Sequences.
203-214
- Vasily Ramensky, Vsevolod Makeev, Mikhail A. Roytberg, Vladimir G. Tumanyan:
DNA Segmentation Through the Bayesian Approach.
215-231
- Scott C. Schmidler, Jun S. Liu, Douglas L. Brutlag:
Bayesian Segmentation of Protein Secondary Structure.
233-248
- François Rodolphe, Catherine Mathé:
Translation Conditional Models for Protein Coding Sequences.
249-260
- Gaston H. Gonnet, Chantal Korostensky, Steven A. Benner:
Evaluation Measures of Multiple Sequence Alignments.
261-276
- Vincent Moulton, Michael Zuker, Mike A. Steel, Robin Pointon, David Penny:
Metrics on RNA Secondary Structures.
277-292
- Piotr Berman, Zheng Zhang, Yuri I. Wolf, Eugene V. Koonin, Webb Miller:
Winnowing Sequences from a Database Search.
293-302
- Richard M. Karp, Ron Shamir:
Algorithms for Optical Mapping.
303-316
- Edward C. Thayer, Chris Bystroff, David Baker:
Detection of Protein Coding Sequences Using a Mixture Model for Local Protein Amino Acid Sequence.
317-327
Volume 7, Number 3-4, August 2000
Selected Papers from RECOMB 2000
- Ron Shamir:
Preface: Special RECOMB 2000 Issue.
329-330
- Tatsuya Akutsu, Satoru Miyano, Satoru Kuhara:
Algorithms for Identifying Boolean Networks and Related Biological Networks Based on Matrix Multiplication and Fingerprint Function.
331-343
- Laurent Marsan, Marie-France Sagot:
Algorithms for Extracting Structured Motifs Using a Suffix Tree with an Application to Promoter and Regulatory Site Consensus Identification.
345-362
- Y. Zenmei Ohkubo, Gordon M. Crippen:
Potential Energy Function for Continuous State Models of Globular Proteins.
363-379
- Alberto Apostolico, Gill Bejerano:
Optimal Amnesic Probabilistic Automata or How to Learn and Classify Proteins in Linear Time and Space.
381-393
- Steffen Heber, Jens Stoye, Marcus Frohme, Jörg D. Hoheisel, Martin Vingron:
Contig Selection in Physical Mapping.
395-408
- Rune B. Lyngsø, Christian N. S. Pedersen:
RNA Pseudoknot Prediction in Energy-Based Models.
409-427
- Kevin Chen, Dannie Durand, Martin Farach-Colton:
NOTUNG: A Program for Dating Gene Duplications and Optimizing Gene Family Trees.
429-447
- Ying Xu, Dong Xu, Oakley H. Crawford, J. Ralph Einstein:
A Computational Method for NMR-Constrained Protein Threading.
449-467
- Jon M. Sorenson, Teresa Head-Gordon:
Matching Simulation and Experiment: A New Simplified Model for Simulating Protein Folding.
469-481
- Alexander Zien, Ralf Zimmer, Thomas Lengauer:
A Simple Iterative Approach to Parameter Optimization.
483-501
- Amir Ben-Dor, Richard M. Karp, Benno Schwikowski, Zohar Yakhini:
Universal DNA Tag Systems: A Combinatorial Design Scheme.
503-519
- David Sankoff, David Bryant, Mélanie Deneault, B. Franz Lang, Gertraud Burger:
Early Eukaryote Evolution Based on Mitochondrial Gene Order Breakpoints.
521-535
- Christopher Bailey-Kellogg, Alik Widge, John J. Kelley, Marcelo J. Berardi, John H. Bushweller, Bruce Randall Donald:
The NOESY Jigsaw: Automated Protein Secondary Structure and Main-Chain Assignment from Sparse, Unassigned NMR Data.
537-558
- Amir Ben-Dor, Laurakay Bruhn, Nir Friedman, Iftach Nachman, Michèl Schummer, Zohar Yakhini:
Tissue Classification with Gene Expression Profiles.
559-583
- Reece Hart, Ajay K. Royyuru, Gustavo Stolovitzky, Andrea Califano:
Systematic and Fully Automated Identification of Protein Sequence Patterns.
585-600
- Nir Friedman, Michal Linial, Iftach Nachman, Dana Pe'er:
Using Bayesian Networks to Analyze Expression Data.
601-620
- Franco P. Preparata, Eli Upfal:
Sequencing-by-Hybridization at the Information-Theory Bound: An Optimal Algorithm.
621-630
- Abstracts from TIGR's Fourth Annual Conference on Computational Genomics November 16-19, 2000, Baltimore, MD.
631-651
Volume 7, Number 5, October 2000
- Martin Lermen, Knut Reinert:
The Practical Use of the A* Algorithm for Exact Multiple Sequence Alignment.
655-671
- Ognyan Stoyanov, Alexander Kister, Israel Gelfand, Casimir A. Kulikowski, Cyrus Chothia:
Geometric Invariant Core for the CL and CH1 Domains of Immunoglobulin Molecules.
673-684
- Ingvar Eidhammer, Inge Jonassen, William R. Taylor:
Structure Comparison and Structure Patterns.
685-716
- Simon Cawley, Terence P. Speed:
DNA Sequencing with Transposons.
717-729
- Vladimir Makarenkov, Bruno Leclerc:
Comparison of Additive Trees Using Circular Orders.
731-744
- Richard M. Karp, Itsik Pe'er, Ron Shamir:
An Algorithm Combining Discrete and Continuous Methods for Optical Mapping.
745-760
Volume 7, Number 6, December 2000
- Tobias Müller, Martin Vingron:
Modeling Amino Acid Replacement.
761-776
- Pavel A. Pevzner, Vlado Dancík, Chris L. Tang:
Mutation-Tolerant Protein Identification by Mass Spectrometry.
777-787
- Richard Desper, Feng Jiang, Olli-P. Kallioniemi, Holger Moch, Christos H. Papadimitriou, Alejandro A. Schäffer:
Distance-Based Reconstruction of Tree Models for Oncogenesis.
789-803
- Trey Ideker, Vesteinn Thorsson, Andrew F. Siegel, Leroy E. Hood:
Testing for Differentially-Expressed Genes by Maximum-Likelihood Analysis of Microarray Data.
805-817
- M. Kathleen Kerr, Mitchell Martin, Gary A. Churchill:
Analysis of Variance for Gene Expression Microarray Data.
819-837
- Dirk Faulhammer, Richard J. Lipton, Laura F. Landweber:
Fidelity of Enzymatic Ligation for DNA Computing.
839-848
- I. Saira Mian, Inna Dubchak:
Representing and Reasoning about Protein Families Using Generative and Discriminative Methods.
849-862
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