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ORCIDJournal of Computational Biology, Volume 12
Volume 12, Number 1, Februar 2005
- Andrei S. Rodin, Thomas H. Mosley Jr., Andrew G. Clark
, Charles F. Sing, Eric Boerwinkle:
Mining Genetic Epidemiology Data with Bayesian Networks Application to APOE Gene Variation and Plasma Lipid Levels. 1-11 - Golan Yona, Klara Kedem:
The URMS-RMS Hybrid Algorithm for Fast and Sensitive Local Protein Structure Alignment. 12-32 - Elodie Nédélec, Thomas Moncion, Elisabeth Gassiat, Bruno Bossard, Guillemette Duchateau-Nguyen, Alain Denise, Michel Termier:
A Pairwise Alignment Algorithm Which Favors Clusters of Blocks. 33-47 - Jason W. Zwolak, John J. Tyson, Layne T. Watson:
Parameter Estimation for a Mathematical Model of the Cell Cycle in Frog Eggs. 48-63 - Konstantinos Blekas, Dimitrios I. Fotiadis, Aristidis Likas:
Motif-Based Protein Sequence Classification Using Neural Networks. 64-82 - Peter Clote:
An Efficient Algorithm to Compute the Landscape of Locally Optimal RNA Secondary Structures with Respect to the NussinovJacobson Energy Model. 83-101 - Ying Chih Lin, Chin Lung Lu, Hwan-You Chang, Chuan Yi Tang:
An Efficient Algorithm for Sorting by Block-Interchanges and Its Application to the Evolution of Vibrio Species. 102-112
Volume 12, Number 2, March 2005
- Joël R. Pradines, Victor Farutin, Steve Rowley, Vlado Dancík:
Analyzing Protein Lists with Large Networks: Edge-Count Probabilities in Random Graphs with Given Expected Degrees. 113-128 - Zhi-Zhong Chen, Guohui Lin, Romeo Rizzi, Jianjun Wen, Dong Xu, Ying Xu, Tao Jiang:
More Reliable Protein NMR Peak Assignment via Improved 2-Interval Scheduling. 129-146 - Yun S. Song, Jotun Hein:
Constructing Minimal Ancestral Recombination Graphs. 147-169 - Lei M. Li, Henry Horng-Shing Lu:
Explore Biological Pathways from Noisy Array Data by Directed Acyclic Boolean Networks. 170-185 - Asger Hobolth, Jens Ledet Jensen:
Applications of Hidden Markov Models for Characterization of Homologous DNA Sequences with a Common Gene. 186-203 - Bernd Sturmfels, Seth Sullivant:
Toric Ideals of Phylogenetic Invariants. 204-228 - Biao Xing, Mark J. van der Laan:
A Statistical Method for Constructing Transcriptional Regulatory Networks Using Gene Expression and Sequence Data. 229-246 - Yuval Nov, Lawrence M. Wein:
Modeling and Analysis of Protein Design under Resource Constraints. 247-282
Volume 12, Number 3, April 2005
- Michael C. Wendl:
Probabilistic Assessment of Clone Overlaps in DNA Fingerprint Mapping via a Priori Models. 283-297 - Yuting Jia, T. Gregory Dewey:
A Random Polymer Model of the Statistical Significance of Structure Alignment. 298-313 - Libi Hertzberg, Or Zuk, Gad Getz, Eytan Domany:
Finding Motifs in Promoter Regions. 314-330 - Ming-Ying Leung, Kwok Pui Choi, Aihua Xia, Louis H. Y. Chen:
Nonrandom Clusters of Palindromes in Herpesvirus Genomes. 331-354 - Michael Wagner, Rafal Adamczak, Aleksey A. Porollo, Jaroslaw Meller:
Linear Regression Models for Solvent Accessibility Prediction in Proteins. 355-369 - Lang Li, Huidong Shi, Constantin T. Yiannoutsos, Tim Hui-Ming Huang, Kenneth P. Nephew:
Epigenetic Hypothesis Tests for Methylation and Acetylation in a Triple Microarray System. 370-390
Volume 12, Number 4, May 2005
- Dabao Zhang, Martin T. Wells, Christine D. Smart, William E. Fry:
Bayesian Normalization and Identification for Differential Gene Expression Data. 391-406 - Ross Lippert:
Space-Efficient Whole Genome Comparisons with BurrowsWheeler Transforms. 407-415 - Uri Keich:
sFFT: A Faster Accurate Computation of the p-Value of the Entropy Score. 416-430 - Chaim Linhart, Ron Shamir:
The Degenerate Primer Design Problem: Theory and Applications. 431-456 - Bernd Sturmfels, Seth Sullivant:
Toric Ideals of Phylogenetic Invariants. 457-481 - Stan Pounds, Cheng Cheng:
Statistical Development and Evaluation of Microarray Gene Expression Data Filters. 482-495
Volume 12, Number 5, June 2005
- Ian M. Dew, Brian Walenz, Granger G. Sutton:
A Tool for Analyzing Mate Pairs in Assemblies (TAMPA). 497-513 - Roded Sharan, Jens Gramm, Zohar Yakhini, Amir Ben-Dor:
Multiplexing Schemes for Generic SNP Genotyping Assays. 514-533 - Daniel P. Berrar, Brian Sturgeon, Ian Bradbury, C. Stephen Downes, Werner Dubitzky:
Survival Trees for Analyzing Clinical Outcome in Lung Adenocarcinomas Based on Gene Expression Profiles: Identification of Neogenin and Diacylglycerol Kinase Expression as Critical Factors. 534-544 - Manuel Dehnert, Rainer Plaumann, Werner E. Helm, Marc-Thorsten Hütt:
Genome Phylogeny Based on Short-Range Correlations in DNA Sequences. 545-553 - Martijn J. Schuemie, Jan A. Kors, Barend Mons:
Word Sense Disambiguation in the Biomedical Domain: An Overview. 554-565
Volume 12, Number 6, July 2005
- Dan Gusfield:
Preface: Special RECOMB 2004 Issue. 567-568 - Chris Bailey-Kellogg, Sheetal Chainraj, Gopal Pandurangan:
A Random Graph Approach to NMR Sequential Assignment. 569-583 - Niko Beerenwinkel, Jörg Rahnenführer, Martin Däumer, Daniel Hoffmann, Rolf Kaiser, Joachim Selbig, Thomas Lengauer:
Learning Multiple Evolutionary Pathways from Cross-Sectional Data. 584-598 - Sourav Chatterji, Lior Pachter:
Large Multiple Organism Gene Finding by Collapsed Gibbs Sampling. 599-608 - Michael A. Erdmann:
Protein Similarity from Knot Theory: Geometric Convolution and Line Weavings. 609-637 - Xin He, Michael H. Goldwasser:
Identifying Conserved Gene Clusters in the Presence of Homology Families. 638-656 - Jun Huan, Deepak Bandyopadhyay, Wei Wang, Jack Snoeyink, Jan F. Prins, Alexander Tropsha:
Comparing Graph Representations of Protein Structure for Mining Family-Specific Residue-Based Packing Motifs. 657-671 - Henry C. M. Leung, Francis Y. L. Chin, Siu-Ming Yiu, Ronald Rosenfeld, Wai Wan Tsang:
Finding Motifs with Insufficient Number of Strong Binding Sites. 686-701 - Haifeng Li, Tao Jiang:
A Class of Edit Kernels for SVMs to Predict Translation Initiation Sites in Eukaryotic mRNAs. 702-718 - Jing Li, Tao Jiang:
Computing the Minimum Recombinant Haplotype Configuration from Incomplete Genotype Data on a Pedigree by Integer Linear Programming. 719-739 - Ryan H. Lilien, Brian W. Stevens, Amy C. Anderson, Bruce Randall Donald:
A Novel Ensemble-Based Scoring and Search Algorithm for Protein Redesign and Its Application to Modify the Substrate Specificity of the Gramicidin Synthetase A Phenylalanine Adenylation Enzyme. 740-761 - Ross A. Lippert, Xiaoyue Zhao, Liliana Florea, Clark M. Mobarry, Sorin Istrail:
Finding Anchors for Genomic Sequence Comparison. 762-776 - Matthew Menke, Jonathan King, Bonnie Berger, Lenore Cowen:
Wrap-and-Pack: A New Paradigm for Beta Structural Motif Recognition with Application to Recognizing Beta Trefoils. 777-795 - Luay Nakhleh, Tandy J. Warnow, C. Randal Linder, Katherine St. John:
Reconstructing Reticulate Evolution in SpeciesTheory and Practice. 796-811 - David Sankoff, Phil Trinh:
Chromosomal Breakpoint Reuse in Genome Sequence Rearrangement. 812-821 - Eran Segal, Roded Sharan:
A Discriminative Model for Identifying Spatial cis-Regulatory Modules. 822-834 - Roded Sharan, Trey Ideker, Brian P. Kelley, Ron Shamir, Richard M. Karp:
Identification of Protein Complexes by Comparative Analysis of Yeast and Bacterial Protein Interaction Data. 835-846 - Yanni Sun, Jeremy Buhler:
Designing Multiple Simultaneous Seeds for DNA Similarity Search. 847-861 - Xinyu Tang, Bonnie Kirkpatrick, Shawna L. Thomas, Guang Song, Nancy M. Amato:
Using Motion Planning to Study RNA Folding Kinetics. 862-881 - Zhijin Wu, Rafael A. Irizarry:
Stochastic Models Inspired by Hybridization Theory for Short Oligonucleotide Arrays. 882-893 - Xiaoyue Zhao, Haiyan Huang, Terence P. Speed:
Finding Short DNA Motifs Using Permuted Markov Models. 894-906
Volume 12, Number 7, September 2005
- Alexis J. Battle, Eran Segal, Daphne Koller:
Probabilistic Discovery of Overlapping Cellular Processes and Their Regulation. 909-927 - Ydo Wexler, Zohar Yakhini, Yechezkel Kashi, Dan Geiger:
Finding Approximate Tandem Repeats in Genomic Sequences. 928-942 - Ross A. Lippert, Clark M. Mobarry, Brian Walenz:
A Space-Efficient Construction of the Burrows-Wheeler Transform for Genomic Data. 943-951 - Jun Xie, Nak-Kyeong Kim:
Bayesian Models and Markov Chain Monte Carlo Methods for Protein Motifs with the Secondary Characteristics. 952-970 - Jian Liu, Ming Li:
Finding Cancer Biomarkers from Mass Spectrometry Data by Decision Lists. 971-979 - Itai Sharon, Aaron Birkland, Kuan Y. Chang, Ran El-Yaniv, Golan Yona:
Correcting BLAST e-Values for Low-Complexity Segments. 980-1003 - Robert F. Tichy, Stephan G. Wagner:
Extremal Problems for Topological Indices in Combinatorial Chemistry. 1004-1013 - Menachem Kaufman, David Blokh, Naomi Zurgil, Yana Shafran, Mordechai Deutsch:
A Cluster Pattern Algorithm for the Analysis of Multiparametric Cell Assays. 1014-1028 - Dongxiao Zhu, Alfred O. Hero III, Zhaohui S. Qin, Anand Swaroop:
High Throughput Screening of Co-Expressed Gene Pairs with Controlled False Discovery Rate (FDR) and Minimum Acceptable Strength (MAS). 1029-1045
Volume 12, Number 8, October 2005
- Sheng Zhao, Russell D. Fernald:
Comprehensive Algorithm for Quantitative Real-Time Polymerase Chain Reaction. 1047-1064 - Michele Morgante, Alberto Policriti, Nicola Vitacolonna, Andrea Zuccolo:
Structured Motifs Search. 1065-1082 - Rose Hoberman, David Sankoff, Dannie Durand:
The Statistical Analysis of Spatially Clustered Genes under the Maximum Gap Criterion. 1083-1102 - Albert C.-C. Yang, Ary L. Goldberger, Chung-Kang Peng:
Genomic Classification Using an Information-Based Similarity Index: Application to the SARS Coronavirus. 1103-1116 - Sanguthevar Rajasekaran, Sudha Balla, Chun-Hsi Huang:
Exact Algorithms for Planted Motif Problems. 1117-1128 - Arkadii G. D'yachkov, Frank K. Hwang, Anthony J. Macula, Pavel A. Vilenkin, Chih-Wen Weng:
A Construction of Pooling Designs with Some Happy Surprises. 1129-1136
Volume 12, Number 9, November 2005
- Franco P. Preparata, Louxin Zhang, Kwok Pui Choi:
Quick, Practical Selection of Effective Seeds for Homology Search. 1137-1152 - Changchuan Yin, Stephen S.-T. Yau:
A Fourier Characteristic of Coding Sequences: Origins and a Non-Fourier Approximation. 1153-1165 - Ole F. Christensen, Asger Hobolth, Jens Ledet Jensen:
Pseudo-Likelihood Analysis of Codon Substitution Models with Neighbor-Dependent Rates. 1166-1182 - Noah A. Rosenberg:
Algorithms for Selecting Informative Marker Panels for Population Assignment. 1183-1201 - Chu-Wen Yang, Chin-Fu Hsiao, Chen-Kung Chou:
Evaluation of Experimental Designs for Two-Color cDNA Microarrays. 1202-1220 - Zeyar Aung, Kian-Lee Tan:
Automatic 3D Protein Structure Classification without Structural Alignment. 1221-1241
Volume 12, Number 10, December 2005
- Gad Kimmel, Ron Shamir:
A Block-Free Hidden Markov Model for Genotypes and Its Application to Disease Association. 1243-1260 - Yao-Ting Huang, Kun-Mao Chao, Ting Chen:
An Approximation Algorithm for Haplotype Inference by Maximum Parsimony. 1261-1274 - Daniel M. Dunlavy, Dianne P. O'Leary, Dmitri Klimov, D. Thirumalai:
HOPE: A Homotopy Optimization Method for Protein Structure Prediction. 1275-1288 - Gad M. Landau, Laxmi Parida, Oren Weimann:
Gene Proximity Analysis across Whole Genomes via PQ Trees1. 1289-1306 - Wolfram Liebermeister:
Predicting Physiological Concentrations of Metabolites from Their Molecular Structure. 1307-1315 - Silvio C. E. Tosatto:
The Victor/FRST Function for Model Quality Estimation. 1316-1327 - Arvind Gupta, Ján Manuch, Ladislav Stacho:
Structure-Approximating Inverse Protein Folding Problem in the 2D HP Model. 1328-1345
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