Journal of Computational Biology, Volume 15 (original) (raw)

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Volume 15, Number 1, January 2008

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    Franck Picard, Jean-Jacques Daudin, Michel Koskas, Sophie Schbath, Stéphane Robin:
    Assessing the Exceptionality of Network Motifs. 1-20
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    Mircea Andrecut, Stuart A. Kauffman:
    On the Sparse Reconstruction of Gene Networks. 21-30
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    W. A. Lorenz, Yann Ponty, Peter Clote:
    Asymptotics of RNA Shapes. 31-63
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    Rosemarie Swanson, Ioannis Kagiampakis, Jerry W. Tsai:
    An Information Measure of the Quality of Protein Secondary Structure Prediction. 65-79
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    Dumitru Brinza, Alexander Zelikovsky:
    Design and Validation of Methods Searching for Risk Factors in Genotype Case-Control Studies. 81-90
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    Sagi Snir, Tandy J. Warnow, Satish Rao:
    Short Quartet Puzzling: A New Quartet-Based Phylogeny Reconstruction Algorithm. 91-103
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    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

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    Xiaoqiu Huang:
    Sequence Alignment with an Appropriate Substitution Matrix. 129-138
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    Hosna Jabbari, Anne Condon, Shelly Zhao:
    Novel and Efficient RNA Secondary Structure Prediction Using Hierarchical Folding. 139-163
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    Ramu Anandakrishnan, Alexey Onufriev:
    Analysis of Basic Clustering Algorithms for Numerical Estimation of Statistical Averages in Biomolecules. 165-184
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    Jutta Gebert, Susanne Motameny, Ulrich Faigle, Christian V. Forst, Rainer Schrader:
    Identifying Genes of Gene Regulatory Networks Using Formal Concept Analysis. 185-194
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    Yongxi Cheng, Ding-Zhu Du:
    New Constructions of One- and Two-Stage Pooling Designs. 195-205
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    Guzmán Santafé, José Antonio Lozano, Pedro Larrañaga:
    Inference of Population Structure Using Genetic Markers and a Bayesian Model Averaging Approach for Clustering. 207-220
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    Thomas Stolte, Volker Hösel, Johannes Müller, Michael R. Speicher:
    Modeling Clonal Expansion from M-FISH Experiments. 221-230

Volume 15, Number 3, April 2008

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    George Nicola, Colin A. Smith, Ruben Abagyan:
    New Method for the Assessment of All Drug-Like Pockets Across a Structural Genome. 231-240
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    Jing Li:
    Prioritize and Select SNPs for Association Studies with Multi-Stage Designs. 241-257
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    Utz-Uwe Haus, Steffen Klamt, Tamon Stephen:
    Computing Knock-Out Strategies in Metabolic Networks. 259-268
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    Adeniyi J. Adewale, Irina Dinu, John D. Potter, Qi Liu, Yutaka Yasui:
    Pathway Analysis of Microarray Data via Regression. 269-277
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    Jing Wu, Jun Xie:
    Computation-Based Discovery of Cis-Regulatory Modules by Hidden Markov Model. 279-290
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    Mikael Bodén, Rohan D. Teasdale:
    Determining Nucleolar Association from Sequence by Leveraging Protein-Protein Interactions. 291-304
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    Raya Khanin, Veronica Vinciotti:
    Computational Modeling of Post-Transcriptional Gene Regulation by MicroRNAs. 305-316
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    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

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    Enno Ohlebusch, Stefan Kurtz:
    Space Efficient Computation of Rare Maximal Exact Matches between Multiple Sequences. 357-377
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    Valery Polyanovsky, Mikhail A. Roytberg, Vladimir G. Tumanyan:
    Reconstruction of Genuine Pair-Wise Sequence Alignment. 379-391
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    Vladimir Filkov, Nameeta Y. Shah:
    A Simple Model of the Modular Structure of Transcriptional Regulation in Yeast. 393-405
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    Jonathan M. Keith, Peter Adams, Stuart Stephen, John S. Mattick:
    Delineating Slowly and Rapidly Evolving Fractions of the Drosophila Genome. 407-430
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    Patrick C. H. Ma, Keith C. C. Chan:
    UPSEC: An Algorithm for Classifying Unaligned Protein Sequences into Functional Families. 431-443
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    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
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    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

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    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
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    Buhm Han, Banu Dost, Vineet Bafna, Shaojie Zhang:
    Structural Alignment of Pseudoknotted RNA. 489-504
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    Zhiyu Zhao, Bin Fu, Francisco J. Alanis, Christopher M. Summa:
    Feedback Algorithm and Web-Server for Protein Structure Alignment. 505-524
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    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
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    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

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    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
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    Torsten Blum, Oliver Kohlbacher:
    Using Atom Mapping Rules for an Improved Detection of Relevant Routes in Weighted Metabolic Networks. 565-576
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    Anne Kupczok, Arndt von Haeseler, Steffen Klaere:
    An Exact Algorithm for the Geodesic Distance between Phylogenetic Trees. 577-591
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    Xu Ling, Xin He, Dong Xin, Jiawei Han:
    Efficiently Identifying Max-Gap Clusters in Pairwise Genome Comparison. 593-609
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    David L. Gold, Bani K. Mallick, Kevin R. Coombes:
    Real-Time Gene Expression: Statistical Challenges in Design and Inference. 611-623
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    Andrew K. C. Wong, Wai-Ho Au, Keith C. C. Chan:
    Discovering High-Order Patterns of Gene Expression Levels. 625-637
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    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

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    Terry Speed:
    Preface. 653-653
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    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
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    Yufeng Wu:
    Association Mapping of Complex Diseases with Ancestral Recombination Graphs: Models and Efficient Algorithms. 667-684
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    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
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    Marshall W. Bern, David Goldberg:
    Improved Ranking Functions for Protein and Modification-Site Identifications. 705-719
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    Ydo Wexler, Dan Geiger:
    Variational Upper and Lower Bounds for Probabilistic Graphical Models. 721-735
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    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
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    Hetunandan Kamisetty, Eric P. Xing, Christopher James Langmead:
    Free Energy Estimates of All-Atom Protein Structures Using Generalized Belief Propagation. 755-766
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    Yue Lu, Sing-Hoi Sze:
    Multiple Sequence Alignment Based on Profile Alignment of Intermediate Sequences. 767-777
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    Hiroyuki Kuwahara, Chris J. Myers:
    Production-Passage-Time Approximation: A New Approximation Method to Accelerate the Simulation Process of Enzymatic Reactions. 779-792
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    Michal Ozery-Flato, Ron Shamir:
    Sorting Genomes with Centromeres by Translocations. 793-812
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    Anshul Nigham, David Hsu:
    Protein Conformational Flexibility Analysis with Noisy Data. 813-828
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    T. M. Murali, Corban G. Rivera:
    Network Legos: Building Blocks of Cellular Wiring Diagrams. 829-844
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    Antonio Piccolboni:
    Multivariate Segmentation in the Analysis of Transcription Tiling Array Data. 845-856
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    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
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    Chun-Nam John Yu, Thorsten Joachims, Ron Elber, Jaroslaw Pillardy:
    Support Vector Training of Protein Alignment Models. 867-880
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    Wah-Heng Lee, Wing-Kin Sung:
    RB-Finder: An Improved Distance-Based Sliding Window Method to Detect Recombination Breakpoints. 881-898
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    Chen Yanover, Ora Schueler-Furman, Yair Weiss:
    Minimizing and Learning Energy Functions for Side-Chain Prediction. 899-911
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    Banu Dost, Tomer Shlomi, Nitin Gupta, Eytan Ruppin, Vineet Bafna, Roded Sharan:
    QNet: A Tool for Querying Protein Interaction Networks. 913-925
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    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

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    Glenn Tesler, Dannie Durand:
    Preface. 943-946
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    Chunfang Zheng, Qian Zhu, David Sankoff:
    Descendants of Whole Genome Duplication within Gene Order Phylogeny. 947-964
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    Ai Xia, Maria V. Sharakhova, Igor V. Sharakhov:
    Reconstructing Ancestral Autosomal Arrangements in the Anopheles gambiae Complex. 965-980
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    Benjamin Vernot, Maureen Stolzer, Aiton Goldman, Dannie Durand:
    Reconciliation with Non-Binary Species Trees. 981-1006
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    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
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    Simon Gog, Martin Bader:
    Fast Algorithms for Transforming Back and Forth between a Signed Permutation and Its Equivalent Simple Permutation. 1029-1041
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    Cédric Chauve, Jean-Philippe Doyon, Nadia El-Mabrouk:
    Gene Family Evolution by Duplication, Speciation, and Loss. 1043-1062
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    Denis Bertrand, Mathieu Lajoie, Nadia El-Mabrouk:
    Inferring Ancestral Gene Orders for a Family of Tandemly Arrayed Genes. 1063-1077
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    William Arndt, Jijun Tang:
    Improving Reversal Median Computation Using Commuting Reversals and Cycle Information. 1079-1092
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    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
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    Max A. Alekseyev:
    Multi-Break Rearrangements and Breakpoint Re-Uses: From Circular to Linear Genomes. 1117-1131
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    Correction. 1132

Volume 15, Number 9, November 2008

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    Laxmi Parida, Marta Melé, Francesc Calafell, Jaume Bertranpetit:
    Estimating the Ancestral Recombinations Graph (ARG) as Compatible Networks of SNP Patterns. 1133-1153
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    Justin Kennedy, Ion I. Mandoiu, Bogdan Pasaniuc:
    Genotype Error Detection Using Hidden Markov Models of Haplotype Diversity. 1155-1171
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    Mircea Andrecut, Sui Huang, Stuart A. Kauffman:
    Heuristic Approach to Sparse Approximation of Gene Regulatory Networks. 1173-1186
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    Lee Aaron Newberg:
    Significance of Gapped Sequence Alignments. 1187-1194
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    Hillary S. W. Han, Christian M. Reidys:
    Pseudoknot RNA Structures with Arc-Length >= 4. 1195-1208
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    Kanti V. Mardia, Vysaul B. Nyirongo:
    Simulating Virtual Protein Calpha Traces with Applications. 1209-1220
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    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

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    Xianyang Jiang, Dominique Lavenier, Stephen S.-T. Yau:
    Coding Region Prediction Based on a Universal DNA Sequence Representation Method. 1237-1256
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    Gang Ma, Christian M. Reidys:
    Canonical RNA Pseudoknot Structures. 1257-1273
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    Jing Xiao, Lusheng Wang, Xiaowen Liu, Tao Jiang:
    An Efficient Voting Algorithm for Finding Additive Biclusters with Random Background. 1275-1293
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    Jialiang Yang, Louxin Zhang:
    Run Probabilities of Seed-Like Patterns and Identifying Good Transition Seeds. 1295-1313
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    Antonio Lijoi, Ramsés H. Mena, Igor Prünster:
    A Bayesian Nonparametric Approach for Comparing Clustering Structures in EST Libraries. 1315-1327
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    Miranda van Uitert, Wouter Meuleman, Lodewyk F. A. Wessels:
    Biclustering Sparse Binary Genomic Data. 1329-1345
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    Man-Hung Eric Tang, Anders Krogh, Ole Winther:
    BayesMD: Flexible Biological Modeling for Motif Discovery. 1347-1363
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    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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