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ORCIDJournal of Computational Biology, Volume 16
Volume 16, Number 1, January 2009
- Lee Aaron Newberg, Charles E. Lawrence:
Exact Calculation of Distributions on Integers, with Application to Sequence Alignment. 1-18 - Alireza Hadj Khodabakhshi, Ján Manuch, Arash Rafiey, Arvind Gupta:
Stable Structure-Approximating Inverse Protein Folding in 2D Hydrophobic-Polar-Cysteine (HPC) Model. 19-30 - Yong Kong
:
Statistical Distributions of Pyrosequencing. 31-42 - Paola Bonizzoni, Giancarlo Mauri, Graziano Pesole, Ernesto Picardi, Yuri Pirola, Raffaella Rizzi:
Detecting Alternative Gene Structures from Spliced ESTs: A Computational Approach. 43-66 - Valéria Lima Passos, Frans E. S. Tan, Bjorn Winkens, Martijn P. F. Berger:
Optimal Designs for One- and Two-Color Microarrays Using Mixed Models: A Comparative Evaluation of Their Efficiencies. 67-83 - Tamjidul Hoque, Madhu Chetty, Abdul Sattar:
Extended HP Model for Protein Structure Prediction. 85-103 - Ran Libeskind-Hadas, Michael A. Charleston:
On the Computational Complexity of the Reticulate Cophylogeny Reconstruction Problem. 105-117 - Hao Ge, Min Qian:
Boolean Network Approach to Negative Feedback Loops of the p53 Pathways: Synchronized Dynamics and Stochastic Limit Cycles. 119-132
Volume 16, Number 2, February 2009
- Henry C. M. Leung, Qian Xiang, Siu-Ming Yiu, Francis Y. L. Chin:
Predicting Protein Complexes from PPI Data: A Core-Attachment Approach. 133-144 - Xiaoning Qian, Sing-Hoi Sze, Byung-Jun Yoon:
Querying Pathways in Protein Interaction Networks Based on Hidden Markov Models. 145-157 - Fereydoun Hormozdiari, Raheleh Salari, Michael Hsing, Alexander Schönhuth, Simon K. Chan, Süleyman Cenk Sahinalp, Artem Cherkasov:
The Effect of Insertions and Deletions on Wirings in Protein-Protein Interaction Networks: A Large-Scale Study. 159-167 - Jason E. McDermott, Ronald C. Taylor, Hyunjin Yoon, Fred Heffron:
Bottlenecks and Hubs in Inferred Networks Are Important for Virulence in Salmonella typhimurium. 169-180 - Shaul Karni, Hermona Soreq, Roded Sharan:
A Network-Based Method for Predicting Disease-Causing Genes. 181-189 - Elhanan Borenstein, Marcus W. Feldman:
Topological Signatures of Species Interactions in Metabolic Networks. 191-200 - Karen Sachs, Solomon Itani, Jennifer Carlisle, Garry P. Nolan, Dana Pe'er, Douglas A. Lauffenburger:
Learning Signaling Network Structures with Sparsely Distributed Data. 201-212 - Robert Castelo, Alberto Roverato:
Reverse Engineering Molecular Regulatory Networks from Microarray Data with qp-Graphs. 213-227 - Daniel Marbach, Thomas Schaffter, Claudio Mattiussi, Dario Floreano:
Generating Realistic In Silico Gene Networks for Performance Assessment of Reverse Engineering Methods. 229-239 - Francesco Iorio, Roberto Tagliaferri, Diego di Bernardo:
Identifying Network of Drug Mode of Action by Gene Expression Profiling. 241-251 - Saket Navlakha, Michael C. Schatz, Carl Kingsford:
Revealing Biological Modules via Graph Summarization. 253-264 - Xi Chen, Lily Wang:
Integrating Biological Knowledge with Gene Expression Profiles for Survival Prediction of Cancer. 265-278 - Gal Chechik, Daphne Koller:
Timing of Gene Expression Responses to Environmental Changes. 279-290 - Balaji Veeramani, Joel S. Bader:
Metabolic Flux Correlations, Genetic Interactions, and Disease. 291-302 - Tamir Tuller, Udi Rubinstein, Dani Bar, Michael Gurevich, Eytan Ruppin, Martin Kupiec:
Higher-Order Genomic Organization of Cellular Functions in Yeast. 303-316 - Leping Li:
GADEM: A Genetic Algorithm Guided Formation of Spaced Dyads Coupled with an EM Algorithm for Motif Discovery. 317-329 - J. William Lee, Tomasz Zemojtel, Eugene I. Shakhnovich:
Systems-Level Evidence of Transcriptional Co-Regulation of Yeast Protein Complexes. 331-339 - Guo-Cheng Yuan:
Targeted Recruitment of Histone Modifications in Humans Predicted by Genomic Sequences. 341-355 - Zhen Xuan Yeo, Hock Chuan Yeo, Joan Keng Suan Yeo, Ai Li Yeo, Ye Li, Neil D. Clarke:
Inferring Transcription Factor Targets from Gene Expression Changes and Predicted Promoter Occupancy. 357-368 - Albert Erives:
Non-Homologous Structured CRMs from the Ciona Genome. 369-377 - Giovanni Russo, Mario di Bernardo:
How to Synchronize Biological Clocks. 379-393 - Boguslaw Kluge, Anna Gambin, Wojciech Niemiro:
Modeling Exopeptidase Activity from LC-MS Data. 395-406
Volume 16, Number 3, March 2009
- Ali Shojaie, George Michailidis:
Analysis of Gene Sets Based on the Underlying Regulatory Network. 407-426 - Junfeng Gu, Honglin Li, Hualiang Jiang, Xicheng Wang:
Optimizing Energy Potential for Protein Fold Recognition with Parametric Evaluation Function. 427-442 - Michelle R. Lacey, Jason Calmes:
A Sharp Error Probability Estimate for the Reconstruction of Phylogenetic Quartets by the Four-Point Method. 443-456 - Renqiang Min, Anthony J. Bonner, Jingjing Li, Zhaolei Zhang:
Learned Random-Walk Kernels and Empirical-Map Kernels for Protein Sequence Classification. 457-474 - Juliette Blanchet, Matthieu Vignes:
A Model-Based Approach to Gene Clustering with Missing Observation Reconstruction in a Markov Random Field Framework. 475-486 - Scott Grandison, Carl Roberts, Richard J. Morris:
The Application of 3D Zernike Moments for the Description of "Model-Free" Molecular Structure, Functional Motion, and Structural Reliability. 487-500 - David Soloveichik:
Robust Stochastic Chemical Reaction Networks and Bounded Tau-Leaping. 501-522
Volume 16, Number 4, April 2009
- David Dynerman, Erick Butzlaff, Julie C. Mitchell:
CUSA and CUDE: GPU-Accelerated Methods for Estimating Solvent Accessible Surface Area and Desolvation. 523-537 - Andre S. Ribeiro, Olli-Pekka Smolander, Tiina Rajala, Antti Häkkinen, Olli Yli-Harja:
Delayed Stochastic Model of Transcription at the Single Nucleotide Level. 539-553 - Andrey V. Ilatovskiy, Michael Petukhov:
Genome-Wide Search for Local DNA Segments with Anomalous GC-Content. 555-564 - Waibhav Tembe, John V. Pearson, Nils Homer, James Lowey, Edward Suh, David W. Craig:
Statistical Comparison Framework and Visualization Scheme for Ranking-Based Algorithms in High-Throughput Genome-Wide Studies. 565-577 - Aleksandar Stojmirovic, Yi-Kuo Yu:
Geometric Aspects of Biological Sequence Comparison. 579-610 - József Dombi, Attila Kertész-Farkas:
Applying Fuzzy Technologies to Equivalence Learning in Protein Classification. 611-623 - Lucinda K. Southworth, Stuart K. Kim, Art B. Owen:
Properties of Balanced Permutations. 625-638
Volume 16, Number 5, May 2009
- Yan Liu, Jaime G. Carbonell, Vanathi Gopalakrishnan, Peter Weigele:
Conditional Graphical Models for Protein Structural Motif Recognition. 639-657 - Sang-Cheol Seok, Michael Evans, Veronica J. Vieland:
Fast and Accurate Calculation of a Computationally Intensive Statistic for Mapping Disease Genes. 659-676 - Christine De Mol, Sofia Mosci, Magali Traskine, Alessandro Verri:
A Regularized Method for Selecting Nested Groups of Relevant Genes from Microarray Data. 677-690 - Zheng Rong Yang:
Predict Collagen Hydroxyproline Sites Using Support Vector Machines. 691-702 - Alexander G. Georgiev:
Interpretable Numerical Descriptors of Amino Acid Space. 703-723 - Utz-Uwe Haus, Kathrin Niermann, Klaus Truemper, Robert Weismantel:
Logic Integer Programming Models for Signaling Networks. 725-743 - Ye-In Chang, Jiun-Rung Chen, Yueh-Chi Tsai:
Mining Subspace Clusters from DNA Microarray Data Using Large Itemset Techniques. 745-768
Volume 16, Number 6, June 2009
- Alireza Hadj Khodabakhshi, Ján Manuch, Arash Rafiey, Arvind Gupta:
Inverse Protein Folding in 3D Hexagonal Prism Lattice under HPC Model. 769-802 - Ho-Lin Chen, Anne Condon, Hosna Jabbari:
An O(n5) Algorithm for MFE Prediction of Kissing Hairpins and 4-Chains in Nucleic Acids. 803-815 - Yong Kong:
Statistical Distributions of Sequencing by Synthesis with Probabilistic Nucleotide Incorporation. 817-827 - Jörn Behre, Stefan Schuster:
Modeling Signal Transduction in Enzyme Cascades with the Concept of Elementary Flux Modes. 829-844 - Niels Richard Hansen:
Statistical Models for Local Occurrences of RNA Structures. 845-858 - Filippo Geraci, Mauro Leoncini, Manuela Montangero, Marco Pellegrini, M. Elena Renda:
K-Boost: A Scalable Algorithm for High-Quality Clustering of Microarray Gene Expression Data. 859-873 - Elias August, Antonis Papachristodoulou:
A New Computational Tool for Establishing Model Parameter Identifiability. 875-885 - Correction. J. Comput. Biol. 16(6): 886 (2009)
Volume 16, Number 7, July 2009
- Xiaoqiu Huang, Martin Vingron:
Maximum Similarity: A New Formulation of Phylogenetic Reconstruction. 887-896 - Niranjan Nagarajan, Mihai Pop:
Parametric Complexity of Sequence Assembly: Theory and Applications to Next Generation Sequencing. 897-908 - Mircea Andrecut, D. Foster, H. Carteret, Stuart A. Kauffman:
Maximal Information Transfer and Behavior Diversity in Random Threshold Networks. 909-916 - Xiaodong Cai, Zhi-Min Yuan:
Stochastic Modeling and Simulation of the p53-MDM2/MDMX Loop. 917-933 - Peng Qiu, Sylvia K. Plevritis:
Simultaneous Class Discovery and Classification of Microarray Data Using Spectral Analysis. 935-944 - Yuki Kato, Tatsuya Akutsu, Hiroyuki Seki:
Dynamic Programming Algorithms and Grammatical Modeling for Protein Beta-Sheet Prediction. 945-957 - Kilian Bartholomé, Clemens Kreutz, Jens Timmer:
Estimation of Gene Induction Enables a Relevance-Based Ranking of Gene Sets. 959-967
Volume 16, Number 8, August 2009
- Special RECOMB 2008 Issue. J. Comput. Biol. 16(8): 969 (2009)
- Caroline C. Friedel, Jan Krumsiek, Ralf Zimmer:
Bootstrapping the Interactome: Unsupervised Identification of Protein Complexes in Yeast. 971-987 - Maxim Kalaev, Vineet Bafna, Roded Sharan:
Fast and Accurate Alignment of Multiple Protein Networks. 989-999 - Jason Flannick, Antal F. Novak, Chuong B. Do, Balaji S. Srinivasan, Serafim Batzoglou:
Automatic Parameter Learning for Multiple Local Network Alignment. 1001-1022 - Michael R. Mehan, Juan Nunez-Iglesias, Mrinal Kalakrishnan, Michael S. Waterman, Xianghong Jasmine Zhou:
An Integrative Network Approach to Map the Transcriptome to the Phenome. 1023-1034 - Yanxin Shi, Michael Klutstein, Itamar Simon, Tom M. Mitchell, Ziv Bar-Joseph:
A Combined Expression-Interaction Model for Inferring the Temporal Activity of Transcription Factors. 1035-1049 - Yu Zhang, Giltae Song, Tomás Vinar, Eric D. Green, Adam C. Siepel, Webb Miller:
Evolutionary History Reconstruction for Mammalian Complex Gene Clusters. 1051-1070 - John Gordon Burleigh, Mukul S. Bansal, André Wehe, Oliver Eulenstein:
Locating Large-Scale Gene Duplication Events through Reconciled Trees: Implications for Identifying Ancient Polyploidy Events in Plants. 1071-1083 - Sebastian Böcker, Katharina Jahn, Julia Mixtacki, Jens Stoye:
Computation of Median Gene Clusters. 1085-1099 - Paul Medvedev, Michael Brudno:
Maximum Likelihood Genome Assembly. 1101-1116 - Michael Sammeth:
Complete Alternative Splicing Events Are Bubbles in Splicing Graphs. 1117-1140 - Sivan Bercovici, Dan Geiger:
Inferring Ancestries Efficiently in Admixed Populations with Linkage Disequilibrium. 1141-1150 - Wei Zheng, Alan M. Friedman, Chris Bailey-Kellogg:
Algorithms for Joint Optimization of Stability and Diversity in Planning Combinatorial Libraries of Chimeric Proteins. 1151-1168 - Ritendra Datta, Marshall W. Bern:
Spectrum Fusion: Using Multiple Mass Spectra for De Novo Peptide Sequencing. 1169-1182 - Yong Fuga Li, Randy J. Arnold, Yixue Li, Predrag Radivojac, Quanhu Sheng, Haixu Tang:
A Bayesian Approach to Protein Inference Problem in Shotgun Proteomics. 1183-1193
Volume 16, Number 9, September 2009
- Mary E. Sehl, Alexander V. Alekseyenko, Kenneth Lange:
Accurate Stochastic Simulation via the Step Anticipation τ-Leaping (SAL) Algorithm. 1195-1208 - Jens Ledet Jensen:
A Note on the Linear Memory Baum-Welch Algorithm. 1209-1210 - Catherine Eng, Charu Asthana, Bertrand Aigle, Sébastien Hergalant, Jean-François Mari, Pierre Leblond:
A New Data Mining Approach for the Detection of Bacterial Promoters Combining Stochastic and Combinatorial Methods. 1211-1225 - Hanen Ben Hassen, Afif Masmoudi, Ahmed Rebai:
Inference in Signal Transduction Pathways Using EM Algorithm and an Implicit Algorithm: Incomplete Data Case. 1227-1240 - Qiang Cheng, Jie Cheng:
Sparsity Optimization Method for Multivariate Feature Screening for Gene Expression Analysis. 1241-1252 - Jin Jun, Paul Ryvkin, Edward Hemphill, Craig E. Nelson:
Duplication Mechanism and Disruptions in Flanking Regions Determine the Fate of Mammalian Gene Duplicates. 1253-1266 - Géraldine Jean, David James Sherman, Macha Nikolski:
Mining the Semantics of Genome Super-Blocks to Infer Ancestral Architectures. 1267-1284
Volume 16, Number 10, October 2009
- Craig E. Nelson, Stéphane Vialette:
RECOMB-Comparative Genomics Special Issue. J. Comput. Biol. 16(10): 1285-1286 (2009) - Sèverine Bérard, Annie Chateau, Cédric Chauve, Christophe Paul, Eric Tannier:
Computation of Perfect DCJ Rearrangement Scenarios with Linear and Circular Chromosomes. 1287-1309 - Sophia Yancopoulos, Richard Friedberg:
DCJ Path Formulation for Genome Transformations which Include Insertions, Deletions, and Duplications. 1311-1338 - Krister M. Swenson, Yu Lin, Vaibhav Rajan, Bernard M. E. Moret:
Hurdles and Sorting by Inversions: Combinatorial, Statistical, and Experimental Results. 1339-1351 - David Sankoff, Chunfang Zheng, P. Kerr Wall, Claude de Pamphilis, James H. Leebens-Mack, Victor A. Albert:
Towards Improved Reconstruction of Ancestral Gene Order in Angiosperm Phylogeny. 1353-1367 - Andrew Wei Xu:
A Fast and Exact Algorithm for the Median of Three Problem: A Graph Decomposition Approach. 1369-1381 - Melvin Zhang, Hon Wai Leong:
Gene Team Tree: A Hierarchical Representation of Gene Teams for All Gap Lengths. 1383-1398 - Jean-Philippe Doyon, Cédric Chauve, Sylvie Hamel:
Space of Gene/Species Trees Reconciliations and Parsimonious Models. 1399-1418 - Daniel R. Schrider, James C. Costello, Matthew W. Hahn:
All Human-Specific Gene Losses Are Present in the Genome as Pseudogenes. 1419-1427 - Jin Jun, Paul Ryvkin, Edward Hemphill, Ion I. Mandoiu, Craig E. Nelson:
The Birth of New Genes by RNA- and DNA-Mediated Duplication during Mammalian Evolution. 1429-1444 - Michal Ozery-Flato, Ron Shamir:
Sorting Cancer Karyotypes by Elementary Operations. 1445-1460 - Abdoulaye Baniré Diallo, Dunarel Badescu, Mathieu Blanchette, Vladimir Makarenkov:
A Whole Genome Study and Identification of Specific Carcinogenic Regions of the Human Papilloma Viruses. 1461-1473 - Denis Bertrand, Mathieu Blanchette, Nadia El-Mabrouk:
Genetic Map Refinement Using a Comparative Genomic Approach. 1475-1486 - Bernhard Haubold, Peter Pfaffelhuber, Mirjana Domazet-Loso, Thomas Wiehe:
Estimating Mutation Distances from Unaligned Genomes. 1487-1500
Volume 16, Number 11, November 2009
- Yunxia Sui, Xiaoyue Zhao, Terence P. Speed, Zhijin Wu:
Background Adjustment for DNA Microarrays Using a Database of Microarray Experiments. 1501-1515 - John P. McCrow:
Alignment of Phylogenetically Unambiguous Indels in Shewanella. 1517-1528 - Yongxi Cheng, Ding-Zhu Du, Ker-I Ko, Guohui Lin:
On the Parameterized Complexity of Pooling Design. 1529-1537 - Ming-Wei Su, Hsiu-Man Lin, Hanna S. Yuan, Woei-Chyn Chu:
Categorizing Host-Dependent RNA Viruses by Principal Component Analysis of Their Codon Usage Preferences. 1539-1547 - Fenix W. D. Huang, Wade W. J. Peng, Christian M. Reidys:
Folding 3-Noncrossing RNA Pseudoknot Structures. 1549-1575 - Matteo Comin, Concettina Guerra, Frank Dellaert:
Binding Balls: Fast Detection of Binding Sites Using a Property of Spherical Fourier Transform. 1577-1591 - Mircea Andrecut:
Parallel GPU Implementation of Iterative PCA Algorithms. 1593-1599 - Kouichi Kimura, Yutaka Suzuki, Sumio Sugano, Asako Koike:
Computation of Rank and Select Functions on Hierarchical Binary String and Its Application to Genome Mapping Problems for Short-Read DNA Sequences. 1601-1613
Volume 16, Number 12, December 2009
- Gesine Reinert, David Chew, Fengzhu Sun, Michael S. Waterman:
Alignment-Free Sequence Comparison (I): Statistics and Power. 1615-1634 - Nadia Pisanti, Henry Soldano, Mathilde Carpentier, Joël Pothier:
A Relational Extension of the Notion of Motifs: Application to the Common 3D Protein Substructures Searching Problem. 1635-1660 - Zhenqiu Liu, Ronald B. Gartenhaus, Xue-wen Chen, Charles D. Howell, Ming Tan:
Survival Prediction and Gene Identification with Penalized Global AUC Maximization. 1661-1670 - Huixiao Hong, Qilong Hong, Roger Perkins, Leming M. Shi, Hong Fang, Zhenqiang Su, Yvonne P. Dragan, James C. Fuscoe, Weida Tong:
The Accurate Prediction of Protein Family from Amino Acid Sequence by Measuring Features of Sequence Fragments. 1671-1688 - Li-Yeh Chuang, Cheng-Huei Yang, Cheng-Hong Yang:
Tabu Search and Binary Particle Swarm Optimization for Feature Selection Using Microarray Data. 1689-1703 - Andrei S. Rodin, Anatoliy Litvinenko, Kathy Klos, Alanna C. Morrison, Trevor Woodage, Josef Coresh, Eric Boerwinkle:
Use of Wrapper Algorithms Coupled with a Random Forests Classifier for Variable Selection in Large-Scale Genomic Association Studies. 1705-1718 - Yi He, Changjun Chen, Yi Xiao:
United-Residue (UNRES) Langevin Dynamics Simulations of trpzip2 Folding. 1719-1730 - Li-Ching Wu, Jorng-Tzong Horng, Yong-An Chen:
A Computation to Integrate the Analysis of Genetic Variations Occurring within Regulatory Elements and Their Possible Effects. 1731-1747
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