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ORCIDJournal of Computational Biology, Volume 7
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 S. 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 J. 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
- 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 C. 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 M. 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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