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ORCIDJournal of Computational Biology, Volume 14
Volume 14, Number 1, January 2007
- Ilan Gronau, Shlomo Moran:
Neighbor Joining Algorithms for Inferring Phylogenies via LCA Distances. 1-15 - Baharak Rastegari
, Anne Condon:
Parsing Nucleic Acid Pseudoknotted Secondary Structure: Algorithm and Applications. 16-32 - Sven Siebert, Rolf Backofen:
A Dynamic Programming Approach for Finding Common Patterns in RNAs. 33-44 - Laxmi Parida:
Gapped Permutation Pattern Discovery for Gene Order Comparisons. 45-55 - Qingwu Yang, Sing-Hoi Sze:
Path Matching and Graph Matching in Biological Networks. 56-67 - Karen Lees, Stephen J. Roberts, Pari Skamnioti, Sarah J. Gurr:
Gene Microarray Analysis Using Angular Distribution Decomposition. 68-83 - Morgan A. Bishop, Anthony J. Macula, Kayla Nimmo, Lauren Wood, Wendy K. Pogozelski, Thomas E. Renz:
Group Testing to Annihilate Pairs Applied to DNA Cross-Hybridization Elimination Using SYBR Green I. 84-96 - Nilanjan Saha, Layne T. Watson, Karen Kafadar, Naren Ramakrishnan, Alexey Onufriev, Shrinivasrao P. Mane, Cecilia Vasquez-Robinet:
Validation and Estimation of Parameters for a General Probabilistic Model of the PCR Process. 97-112
Volume 14, Number 2, March 2007
- Leming Zhou, Liliana Florea:
Designing Sensitive and Specific Spaced Seeds for Cross-Species mRNA-to-Genome Alignment. 113-130 - Pankaj K. Agarwal, Nabil H. Mustafa, Yusu Wang:
Fast Molecular Shape Matching Using Contact Maps. 131-143 - Dan Levy, Christopher Reeder, Bradford Loucas, Lynn Hlatky, Allen M. Chen, Michael Cornforth, Rainer K. Sachs:
Interpreting Chromosome Aberration Spectra. 144-155 - Daniel Stefankovic, Eric Vigoda:
Phylogeny of Mixture Models: Robustness of Maximum Likelihood and Non-Identifiable Distributions. 156-189 - Jérôme Waldispühl, Peter Clote:
Computing the Partition Function and Sampling for Saturated Secondary Structures of RNA, with Respect to the Turner Energy Model. 190-215 - Isaac Elias, Tamir Tuller:
Reconstruction of Ancestral Genomic Sequences Using Likelihood. 216-237 - Yong Kong:
Generalized Correlation Functions and Their Applications in Selection of Optimal Multiple Spaced Seeds for Homology Search. 238-254
Volume 14, Number 3, April 2007
- Haifeng Li, Anton Valouev, David C. Schwartz, Michael S. Waterman, Lei M. Li:
A Quantile Method for Sizing Optical Maps. 255-266 - Eric P. Xing, Michael I. Jordan, Roded Sharan:
Bayesian Haplotype Inference via the Dirichlet Process. 267-284 - Mary Ellen Bock, Claudio Garutti, Concettina Guerra:
Discovery of Similar Regions on Protein Surfaces. 285-299 - Laxmi Parida:
Discovering Topological Motifs Using a Compact Notation. 300-323 - Naftali Kaminski, Ziv Bar-Joseph:
A Patient-Gene Model for Temporal Expression Profiles in Clinical Studies. 324-338 - Grzegorz A. Rempala, Kenneth S. Ramos, Ted Kalbfleisch, Ivo Teneng:
Validation of a Mathematical Model of Gene Transcription in Aggregated Cellular Systems: Application to L1 Retrotransposition. 339-349 - Mariusz Lubomirski, Michael R. D'Andrea, Stanley M. Belkowski, Javier Cabrera, James M. Dixon, Dhammika Amaratunga:
A Consolidated Approach to Analyzing Data from High-Throughput Protein Microarrays with an Application to Immune Response Profiling in Humans. 350-359 - Noah A. Rosenberg:
Counting Coalescent Histories. 360-377
Volume 14, Number 4, May 2007
- Sébastien Angibaud, Guillaume Fertin, Irena Rusu, Stéphane Vialette:
A Pseudo-Boolean Framework for Computing Rearrangement Distances between Genomes with Duplicates. 379-393 - Guillaume Blin, Eric Blais, Danny Hermelin, Pierre Guillon, Mathieu Blanchette, Nadia El-Mabrouk:
Gene Maps Linearization Using Genomic Rearrangement Distances. 394-407 - Michal Ozery-Flato, Ron Shamir:
Sorting by Reciprocal Translocations via Reversals Theory. 408-422 - Wei Xu, Chunfang Zheng, David Sankoff:
Paths and Cycles in Breakpoint Graph of Random Multichromosomal Genomes. 423-435 - Zaky Adam, Monique Turmel, Claude Lemieux, David Sankoff:
Common Intervals and Symmetric Difference in a Model-Free Phylogenomics, with an Application to Streptophyte Evolution. 436-445 - Abdoulaye Baniré Diallo, Vladimir Makarenkov, Mathieu Blanchette:
Exact and Heuristic Algorithms for the Indel Maximum Likelihood Problem. 446-461 - Mathieu Lajoie, Denis Bertrand, Nadia El-Mabrouk, Olivier Gascuel:
Duplication and Inversion History of a Tandemly Repeated Genes Family. 462-478 - Damian Wójtowicz, Jerzy Tiuryn:
Evolution of Gene Families Based on Gene Duplication, Loss, Accumulated Change, and Innovation. 479-495 - Nan Song, R. D. Sedgewick, Dannie Durand:
Domain Architecture Comparison for Multidomain Homology Identification. 496-516 - Cuong Than, Derek A. Ruths, Hideki Innan, Luay Nakhleh:
Confounding Factors in HGT Detection: Statistical Error, Coalescent Effects, and Multiple Solutions. 517-535
Volume 14, Number 5, June 2007
- Alberto Apostolico:
Preface. 537-538 - Teresa M. Przytycka:
Stability of Characters and Construction of Phylogenetic Trees. 539-549 - Jim C. Huang, Quaid Morris, Brendan J. Frey:
Bayesian Inference of MicroRNA Targets from Sequence and Expression Data. 550-563 - Jinbo Xu, Feng Jiao, Bonnie Berger:
A Parameterized Algorithm for Protein Structure Alignment. 564-577 - Tsung-Han Chiang, Mehmet Serkan Apaydin, Douglas L. Brutlag, David Hsu, Jean-Claude Latombe:
Using Stochastic Roadmap Simulation to Predict Experimental Quantities in Protein Folding Kinetics: Folding Rates and Phi-Values. 578-593 - Michael Cameron, Yaniv Bernstein, Hugh E. Williams:
Clustered Sequence Representation for Fast Homology Search. 594-614 - Martin Bader, Enno Ohlebusch:
Sorting by Weighted Reversals, Transpositions, and Inverted Transpositions. 615-636 - Wei Xie, Nikolaos V. Sahinidis:
A Reduction-Based Exact Algorithm for the Contact Map Overlap Problem. 637-654 - Philipp W. Messer, Ralf Bundschuh, Martin Vingron, Peter F. Arndt:
Effects of Long-Range Correlations in DNA on Sequence Alignment Score Statistics. 655-668 - Stefanie Scheid, Rainer Spang:
Compensating for Unknown Confounders in Microarray Data Analysis Using Filtered Permutations. 669-681 - Samuel A. Andersson, Jens Lagergren:
Motif Yggdrasil: Sampling Sequence Motifs from a Tree Mixture Model. 682-697
Volume 14, Number 6, July 2007
- Alberto Apostolico:
Preface. 699-700 - Stanislav Angelov, Boulos Harb, Sampath Kannan, Sanjeev Khanna, Junhyong Kim:
Efficient Enumeration of Phylogenetically Informative Substrings. 701-723 - Nicholas D. Pattengale, Eric J. Gottlieb, Bernard M. E. Moret:
Efficiently Computing the Robinson-Foulds Metric. 724-735 - David Heckerman, Carl Myers Kadie, Jennifer Listgarten:
Leveraging Information Across HLA Alleles/Supertypes Improves Epitope Prediction. 736-746 - Mehmet Koyutürk, Wojciech Szpankowski, Ananth Grama:
Assessing Significance of Connectivity and Conservation in Protein Interaction Networks. 747-764 - Chakra Chennubhotla, Ivet Bahar:
Markov Methods for Hierarchical Coarse-Graining of Large Protein Dynamics. 765-776 - Xiaoduan Ye, Alan M. Friedman, Chris Bailey-Kellogg:
Hypergraph Model of Multi-Residue Interactions in Proteins: Sequentially-Constrained Partitioning Algorithms for Optimization of Site-Directed Protein Recombination. 777-790 - Brian Y. Chen, Viacheslav Fofanov, Drew H. Bryant, Bradley D. Dodson, David M. Kristensen, Andreas Martin Lisewski, Marek Kimmel, Olivier Lichtarge, Lydia E. Kavraki:
The MASH Pipeline for Protein Function Prediction and an Algorithm for the Geometric Refinement of 3D Motifs. 791-816 - Benny Chor, Tamir Tuller:
Biological Networks: Comparison, Conservation, and Evolution via Relative Description Length. 817-838 - Shawna L. Thomas, Xinyu Tang, Lydia Tapia, Nancy M. Amato:
Simulating Protein Motions with Rigidity Analysis. 839-855 - Ydo Wexler, Chaya Ben-Zaken Zilberstein, Michal Ziv-Ukelson:
A Study of Accessible Motifs and RNA Folding Complexity. 856-872
Volume 14, Number 7, July 2007
- Nevzat Onur Domaniç, Franco P. Preparata:
A Novel Approach to the Detection of Genomic Approximate Tandem Repeats in the Levenshtein Metric. 873-891 - Manikandan Narayanan, Richard M. Karp:
Comparing Protein Interaction Networks via a Graph Match-and-Split Algorithm. 892-907 - Isana Veksler-Lublinsky, Michal Ziv-Ukelson, Danny Barash, Klara Kedem:
A Structure-Based Flexible Search Method for Motifs in RNA. 908-926 - Réka Albert, Bhaskar DasGupta, Riccardo Dondi, Sema Kachalo, Eduardo D. Sontag, Alexander Zelikovsky, Kelly Westbrooks:
A Novel Method for Signal Transduction Network Inference from Indirect Experimental Evidence. 927-949 - Liqing Zhang, Layne T. Watson:
Note on the Computation of Critical Effective Population Sizes. 950-960 - Frank Emmert-Streib:
The Chronic Fatigue Syndrome: A Comparative Pathway Analysis. 961-972 - Mircea Andrecut, Stuart A. Kauffman:
A Physical Analogy of the Genetic Toggle Switch. 973-983 - Stefan Zeiser, Johannes Müller, Volkmar Liebscher:
Modeling the Hes1 Oscillator. 984-1000 - Manolis Christodoulakis, Geoffrey Brian Golding, Costas S. Iliopoulos, Yoan José Pinzón Ardila, William F. Smyth:
Efficient Algorithms for Counting and Reporting Segregating Sites in Genomic Sequences. 1001-1010 - Yi Y. Shi, Gerald A. Miller, Oleg Denisenko, Hong Qian, Karol Bomsztyk:
Quantitative Model for Binary Measurements of Protein-Protein Interactions. 1011-1023
Volume 14, Number 8, October 2007
- Xue Wu, Chau-Wen Tseng, Nathan Edwards:
HMMatch: Peptide Identification by Spectral Matching of Tandem Mass Spectra Using Hidden Markov Models. 1025-1043 - Zakharia M. Frenkel, Edward N. Trifonov:
Evolutionary Networks in the Formatted Protein Sequence Space. 1044-1057 - Beckett W. Sterner, Rohit Singh, Bonnie Berger:
Predicting and Annotating Catalytic Residues: An Information Theoretic Approach. 1058-1073 - Rolf Backofen, Shihyen Chen, Danny Hermelin, Gad M. Landau, Mikhail A. Roytberg, Oren Weimann, Kaizhong Zhang:
Locality and Gaps in RNA Comparison. 1074-1087 - Morgan A. Bishop, Arkadii G. D'yachkov, Anthony J. Macula, Thomas E. Renz, Vyacheslav V. Rykov:
Free Energy Gap and Statistical Thermodynamic Fidelity of DNA Codes. 1088-1104 - Koen Deforche, Ricardo Camacho, Kristel Van Laethem, Beth Shapiro, Yves Moreau, Andrew Rambaut, Anne-Mieke Vandamme, Philippe Lemey:
Estimating the Relative Contribution of dNTP Pool Imbalance and APOBEC3G/3F Editing to HIV Evolution In Vivo. 1105-1114 - Aleksandar Stojmirovic, Yi-Kuo Yu:
Information Flow in Interaction Networks. 1115-1143
Volume 14, Number 9, November 2007
- Laxmi Parida:
Statistical Significance of Large Gene Clusters. 1145-1159 - Zheng Fu, Xin Chen, Vladimir Vacic, Peng Nan, Yang Zhong, Tao Jiang:
MSOAR: A High-Throughput Ortholog Assignment System Based on Genome Rearrangement. 1160-1175 - Francis L. Martin, Matthew J. German, Ernst Wit, Thomas Fearn, Narasimhan Ragavan, Hubert M. Pollock:
Identifying Variables Responsible for Clustering in Discriminant Analysis of Data from Infrared Microspectroscopy of a Biological Sample. 1176-1184 - Hendrik Fuß, Werner Dubitzky, C. Stephen Downes, Mary Jo Kurth:
Deactivation of Src Family Kinases: Hypothesis Testing Using a Monte Carlo Sensitivity Analysis of Systems-Level Properties. 1185-1200 - Tetsuo Shibuya:
Efficient Substructure RMSD Query Algorithms. 1201-1207 - Yongxi Cheng, Ding-Zhu Du:
Efficient Constructions of Disjunct Matrices with Applications to DNA Library Screening. 1208-1216 - Achim Tresch, Tim Beißbarth, Holger Sültmann, Ruprecht Kuner, Annemarie Poustka, Andreas Buness:
Discrimination of Direct and Indirect Interactions in a Network of Regulatory Effects. 1217-1228 - Ilkka Havukkala, Stijn Vanderlooy:
On the Reliable Identification of Plant Sequences Containing a Polyadenylation Site. 1229-1245
Volume 14, Number 10, December 2007
- Dan Gusfield, Vikas Bansal, Vineet Bafna, Yun S. Song:
A Decomposition Theory for Phylogenetic Networks and Incompatible Characters. 1247-1272 - Yun S. Song, Zhihong Ding, Dan Gusfield, Charles H. Langley, Yufeng Wu:
Algorithms to Distinguish the Role of Gene-Conversion from Single-Crossover Recombination in the Derivation of SNP Sequences in Populations. 1273-1286 - Scott C. Schmidler, Joseph E. Lucas, Terrence G. Oas:
Statistical Estimation of Statistical Mechanical Models: Helix-Coil Theory and Peptide Helicity Prediction. 1287-1310 - Dongxiao Zhu, Alfred O. Hero III:
Bayesian Hierarchical Model for Large-Scale Covariance Matrix Estimation. 1311-1326 - Michael Hirsch, Stephen Swift, Xiaohui Liu:
Optimal Search Space for Clustering Gene Expression Data via Consensus. 1327-1341 - Binhai Zhu:
Protein Local Structure Alignment Under the Discrete Fréchet Distance. 1343-1351 - Magnus Åstrand, Petter Mostad, Mats Rudemo:
Improved Covariance Matrix Estimators for Weighted Analysis of Microarray Data. 1353-1367
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