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ORCIDJournal of Computational Biology, Volume 15
Volume 15, Number 1, January 2008
- Franck Picard
, Jean-Jacques Daudin, Michel Koskas, Sophie Schbath, Stéphane Robin:
Assessing the Exceptionality of Network Motifs. 1-20 - Mircea Andrecut, Stuart A. Kauffman:
On the Sparse Reconstruction of Gene Networks. 21-30 - W. A. Lorenz, Yann Ponty, Peter Clote:
Asymptotics of RNA Shapes. 31-63 - Rosemarie Swanson, Ioannis Kagiampakis, Jerry W. Tsai:
An Information Measure of the Quality of Protein Secondary Structure Prediction. 65-79 - Dumitru Brinza, Alexander Zelikovsky:
Design and Validation of Methods Searching for Risk Factors in Genotype Case-Control Studies. 81-90 - Sagi Snir, Tandy J. Warnow, Satish Rao:
Short Quartet Puzzling: A New Quartet-Based Phylogeny Reconstruction Algorithm. 91-103 - Caroline Bidot, F. Gruy, C.-S. Haudin, F. El Hentati, B. Guy, C. Lambert:
Mathematical Modeling of T-Cell Activation Kinetic. 105-128
Volume 15, Number 2, March 2008
- Xiaoqiu Huang:
Sequence Alignment with an Appropriate Substitution Matrix. 129-138 - Hosna Jabbari, Anne Condon, Shelly Zhao:
Novel and Efficient RNA Secondary Structure Prediction Using Hierarchical Folding. 139-163 - Ramu Anandakrishnan, Alexey Onufriev:
Analysis of Basic Clustering Algorithms for Numerical Estimation of Statistical Averages in Biomolecules. 165-184 - Jutta Gebert, Susanne Motameny, Ulrich Faigle, Christian V. Forst, Rainer Schrader:
Identifying Genes of Gene Regulatory Networks Using Formal Concept Analysis. 185-194 - Yongxi Cheng, Ding-Zhu Du:
New Constructions of One- and Two-Stage Pooling Designs. 195-205 - Guzmán Santafé, José Antonio Lozano, Pedro Larrañaga:
Inference of Population Structure Using Genetic Markers and a Bayesian Model Averaging Approach for Clustering. 207-220 - Thomas Stolte, Volker Hösel, Johannes Müller, Michael R. Speicher:
Modeling Clonal Expansion from M-FISH Experiments. 221-230
Volume 15, Number 3, April 2008
- George Nicola, Colin A. Smith, Ruben Abagyan:
New Method for the Assessment of All Drug-Like Pockets Across a Structural Genome. 231-240 - Jing Li:
Prioritize and Select SNPs for Association Studies with Multi-Stage Designs. 241-257 - Utz-Uwe Haus, Steffen Klamt, Tamon Stephen:
Computing Knock-Out Strategies in Metabolic Networks. 259-268 - Adeniyi J. Adewale, Irina Dinu, John D. Potter, Qi Liu, Yutaka Yasui:
Pathway Analysis of Microarray Data via Regression. 269-277 - Jing Wu, Jun Xie:
Computation-Based Discovery of Cis-Regulatory Modules by Hidden Markov Model. 279-290 - Mikael Bodén, Rohan D. Teasdale:
Determining Nucleolar Association from Sequence by Leveraging Protein-Protein Interactions. 291-304 - Raya Khanin, Veronica Vinciotti:
Computational Modeling of Post-Transcriptional Gene Regulation by MicroRNAs. 305-316 - James O. Wrabl, Nick V. Grishin:
Statistics of Random Protein Superpositions: p-Values for Pairwise Structure Alignment. 317-355
Volume 15, Number 4, May 2008
- Enno Ohlebusch, Stefan Kurtz:
Space Efficient Computation of Rare Maximal Exact Matches between Multiple Sequences. 357-377 - Valery Polyanovsky, Mikhail A. Roytberg, Vladimir G. Tumanyan:
Reconstruction of Genuine Pair-Wise Sequence Alignment. 379-391 - Vladimir Filkov, Nameeta Y. Shah:
A Simple Model of the Modular Structure of Transcriptional Regulation in Yeast. 393-405 - Jonathan M. Keith, Peter Adams, Stuart Stephen, John S. Mattick:
Delineating Slowly and Rapidly Evolving Fractions of the Drosophila Genome. 407-430 - Patrick C. H. Ma, Keith C. C. Chan:
UPSEC: An Algorithm for Classifying Unaligned Protein Sequences into Functional Families. 431-443 - Olga Tcheremenskaia, Alessandro Giuliani, Maurizio Tomasi:
PROFALIGN Algorithm Identifies the Regions Containing Folding Determinants by Scoring Pairs of Hydrophobic Profiles of Remotely Related Proteins. 445-455 - Jian Feng, Daniel Q. Naiman, Bret Cooper:
Combined Dynamic Arrays for Storing and Searching Semi-Ordered Tandem Mass Spectrometry Data. 457-468
Volume 15, Number 5, June 2008
- Huy Hoang Do, Kwok Pui Choi, Franco P. Preparata, Wing-Kin Sung, Louxin Zhang:
Spectrum-Based De Novo Repeat Detection in Genomic Sequences. 469-488 - Buhm Han, Banu Dost, Vineet Bafna, Shaojie Zhang:
Structural Alignment of Pseudoknotted RNA. 489-504 - Zhiyu Zhao, Bin Fu, Francisco J. Alanis, Christopher M. Summa:
Feedback Algorithm and Web-Server for Protein Structure Alignment. 505-524 - Anthony J. Macula, Alexander Schliep, Morgan A. Bishop, Thomas E. Renz:
New, Improved, and Practical k-Stem Sequence Similarity Measures for Probe Design. 525-534 - Zhixiang Chen, Bin Fu, Robert T. Schweller, Boting Yang, Zhiyu Zhao, Binhai Zhu:
Linear Time Probabilistic Algorithms for the Singular Haplotype Reconstruction Problem from SNP Fragments. 535-546
Volume 15, Number 6, July 2008
- Utz J. Pape, Sven Rahmann, Fengzhu Sun, Martin Vingron:
Compound Poisson Approximation of the Number of Occurrences of a Position Frequency Matrix (PFM) on Both Strands. 547-564 - Torsten Blum, Oliver Kohlbacher:
Using Atom Mapping Rules for an Improved Detection of Relevant Routes in Weighted Metabolic Networks. 565-576 - Anne Kupczok, Arndt von Haeseler, Steffen Klaere:
An Exact Algorithm for the Geodesic Distance between Phylogenetic Trees. 577-591 - Xu Ling, Xin He, Dong Xin, Jiawei Han:
Efficiently Identifying Max-Gap Clusters in Pairwise Genome Comparison. 593-609 - David L. Gold, Bani K. Mallick, Kevin R. Coombes:
Real-Time Gene Expression: Statistical Challenges in Design and Inference. 611-623 - Andrew K. C. Wong, Wai-Ho Au, Keith C. C. Chan:
Discovering High-Order Patterns of Gene Expression Levels. 625-637 - Katharina T. Huber, Martin Lott, Vincent Moulton, Andreas Spillner:
The Complexity of Deriving Multi-Labeled Trees from Bipartitions. 639-651
Volume 15, Number 7, September 2008
- Terry Speed:
Preface. 653-653 - Anthony A. Philippakis, Aaron M. Qureshi, Michael F. Berger, Martha L. Bulyk:
Design of Compact, Universal DNA Microarrays for Protein Binding Microarray Experiments. 655-665 - Yufeng Wu:
Association Mapping of Complex Diseases with Ancestral Recombination Graphs: Models and Efficient Algorithms. 667-684 - Ole Schulz-Trieglaff, Rene Hussong, Clemens Gröpl, Andreas Leinenbach, Andreas Hildebrandt, Christian G. Huber, Knut Reinert:
Computational Quantification of Peptides from LC-MS Data. 685-704 - Marshall W. Bern, David Goldberg:
Improved Ranking Functions for Protein and Modification-Site Identifications. 705-719 - Ydo Wexler, Dan Geiger:
Variational Upper and Lower Bounds for Probabilistic Graphical Models. 721-735 - Dina Schneidman-Duhovny, Oranit Dror, Yuval Inbar, Ruth Nussinov, Haim J. Wolfson:
Deterministic Pharmacophore Detection via Multiple Flexible Alignment of Drug-Like Molecules. 737-754 - Hetunandan Kamisetty, Eric P. Xing, Christopher James Langmead:
Free Energy Estimates of All-Atom Protein Structures Using Generalized Belief Propagation. 755-766 - Yue Lu, Sing-Hoi Sze:
Multiple Sequence Alignment Based on Profile Alignment of Intermediate Sequences. 767-777 - Hiroyuki Kuwahara, Chris J. Myers:
Production-Passage-Time Approximation: A New Approximation Method to Accelerate the Simulation Process of Enzymatic Reactions. 779-792 - Michal Ozery-Flato, Ron Shamir:
Sorting Genomes with Centromeres by Translocations. 793-812 - Anshul Nigham, David Hsu:
Protein Conformational Flexibility Analysis with Noisy Data. 813-828 - T. M. Murali, Corban G. Rivera:
Network Legos: Building Blocks of Cellular Wiring Diagrams. 829-844 - Antonio Piccolboni:
Multivariate Segmentation in the Analysis of Transcription Tiling Array Data. 845-856 - Wenyi Wang, Benilton S. Carvalho, Nathaniel D. Miller, Jonathan Pevsner, Aravinda Chakravarti, Rafael A. Irizarry:
Estimating Genome-Wide Copy Number Using Allele-Specific Mixture Models. 857-866 - Chun-Nam John Yu, Thorsten Joachims, Ron Elber, Jaroslaw Pillardy:
Support Vector Training of Protein Alignment Models. 867-880 - Wah-Heng Lee, Wing-Kin Sung:
RB-Finder: An Improved Distance-Based Sliding Window Method to Detect Recombination Breakpoints. 881-898 - Chen Yanover, Ora Schueler-Furman, Yair Weiss:
Minimizing and Learning Energy Functions for Side-Chain Prediction. 899-911 - Banu Dost, Tomer Shlomi, Nitin Gupta, Eytan Ruppin, Vineet Bafna, Roded Sharan:
QNet: A Tool for Querying Protein Interaction Networks. 913-925 - Noah Zaitlen, Manuel Reyes-Gomez, David Heckerman, Nebojsa Jojic:
Shift-Invariant Adaptive Double Threading: Learning MHC II-Peptide Binding. 927-942
Volume 15, Number 8, October 2008
- Glenn Tesler, Dannie Durand:
Preface. 943-946 - Chunfang Zheng, Qian Zhu, David Sankoff:
Descendants of Whole Genome Duplication within Gene Order Phylogeny. 947-964 - Ai Xia, Maria V. Sharakhova, Igor V. Sharakhov:
Reconstructing Ancestral Autosomal Arrangements in the Anopheles gambiae Complex. 965-980 - Benjamin Vernot, Maureen Stolzer, Aiton Goldman, Dannie Durand:
Reconciliation with Non-Binary Species Trees. 981-1006 - Jian Ma, Aakrosh Ratan, Brian J. Raney, Bernard B. Suh, Louxin Zhang, Webb Miller, David Haussler:
DUPCAR: Reconstructing Contiguous Ancestral Regions with Duplications. 1007-1027 - Simon Gog, Martin Bader:
Fast Algorithms for Transforming Back and Forth between a Signed Permutation and Its Equivalent Simple Permutation. 1029-1041 - Cédric Chauve, Jean-Philippe Doyon, Nadia El-Mabrouk:
Gene Family Evolution by Duplication, Speciation, and Loss. 1043-1062 - Denis Bertrand, Mathieu Lajoie, Nadia El-Mabrouk:
Inferring Ancestral Gene Orders for a Family of Tandemly Arrayed Genes. 1063-1077 - William Arndt, Jijun Tang:
Improving Reversal Median Computation Using Commuting Reversals and Cycle Information. 1079-1092 - Sébastien Angibaud, Guillaume Fertin, Irena Rusu, Annelyse Thévenin, Stéphane Vialette:
Efficient Tools for Computing the Number of Breakpoints and the Number of Adjacencies between Two Genomes with Duplicate Genes. 1093-1115 - Max A. Alekseyev:
Multi-Break Rearrangements and Breakpoint Re-Uses: From Circular to Linear Genomes. 1117-1131 - Correction. 1132
Volume 15, Number 9, November 2008
- Laxmi Parida, Marta Melé, Francesc Calafell, Jaume Bertranpetit:
Estimating the Ancestral Recombinations Graph (ARG) as Compatible Networks of SNP Patterns. 1133-1153 - Justin Kennedy, Ion I. Mandoiu, Bogdan Pasaniuc:
Genotype Error Detection Using Hidden Markov Models of Haplotype Diversity. 1155-1171 - Mircea Andrecut, Sui Huang, Stuart A. Kauffman:
Heuristic Approach to Sparse Approximation of Gene Regulatory Networks. 1173-1186 - Lee Aaron Newberg:
Significance of Gapped Sequence Alignments. 1187-1194 - Hillary S. W. Han, Christian M. Reidys:
Pseudoknot RNA Structures with Arc-Length >= 4. 1195-1208 - Kanti V. Mardia, Vysaul B. Nyirongo:
Simulating Virtual Protein Calpha Traces with Applications. 1209-1220 - María Elena Díaz, Guillermo Ayala, Teresa León, Roberto Zoncu, Derek Toomre:
Analyzing Protein-Protein Spatial-Temporal Dependencies from Image Sequences Using Fuzzy Temporal Random Sets. 1221-1236
Volume 15, Number 10, December 2008
- Xianyang Jiang, Dominique Lavenier, Stephen S.-T. Yau:
Coding Region Prediction Based on a Universal DNA Sequence Representation Method. 1237-1256 - Gang Ma, Christian M. Reidys:
Canonical RNA Pseudoknot Structures. 1257-1273 - Jing Xiao, Lusheng Wang, Xiaowen Liu, Tao Jiang:
An Efficient Voting Algorithm for Finding Additive Biclusters with Random Background. 1275-1293 - Jialiang Yang, Louxin Zhang:
Run Probabilities of Seed-Like Patterns and Identifying Good Transition Seeds. 1295-1313 - Antonio Lijoi, Ramsés H. Mena, Igor Prünster:
A Bayesian Nonparametric Approach for Comparing Clustering Structures in EST Libraries. 1315-1327 - Miranda van Uitert, Wouter Meuleman, Lodewyk F. A. Wessels:
Biclustering Sparse Binary Genomic Data. 1329-1345 - Man-Hung Eric Tang, Anders Krogh, Ole Winther:
BayesMD: Flexible Biological Modeling for Motif Discovery. 1347-1363 - Riccardo Porreca, Samuel Drulhe, Hidde de Jong, Giancarlo Ferrari-Trecate:
Structural Identification of Piecewise-Linear Models of Genetic Regulatory Networks. 1365-1380
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