Volume 9, Number 1, 2012
Daniel DeBlasio, Jocelyne Bruand, Shaojie Zhang: A Memory Efficient Method for Structure-Based RNA Multiple Alignment. 1-11- Yuri Pirola, Paola Bonizzoni, Tao Jiang: An Efficient Algorithm for Haplotype Inference on Pedigrees with Recombinations and Mutations. 12-25
- Jean-Philippe Doyon, Sylvie Hamel, Cedric Chauve: An Efficient Method for Exploring the Space of Gene Tree/Species Tree Reconciliations in a Probabilistic Framework. 26-39
- Chong Wang, Peter Beyerlein, Heike Pospisil, Antje Krause, Chris D. Nugent, Werner Dubitzky: An Efficient Method for Modeling Kinetic Behavior of Channel Proteins in Cardiomyocytes. 40-51
- Bane V. Vasic, Vida Ravanmehr, Anantha Raman Krishnan: An Information Theoretic Approach to Constructing Robust Boolean Gene Regulatory Networks. 52-65
- Piraveenan Mahendra, Mikhail Prokopenko, Albert Y. Zomaya: Assortative Mixing in Directed Biological Networks. 66-78
- Raymond H. Chan, Tony H. Chan, Hau Man Yeung, Roger Wei Wang: Composition Vector Method Based on Maximum Entropy Principle for Sequence Comparison. 79-87
- José Ramón Quevedo, Antonio Bahamonde, Miguel Pérez-Enciso, Oscar Luaces: Disease Liability Prediction from Large Scale Genotyping Data Using Classifiers with a Reject Option. 88-97
- Ying-Xin Li, Shuiwang Ji, Sudhir Kumar, Jieping Ye, Zhi-Hua Zhou: Drosophila Gene Expression Pattern Annotation through Multi-Instance Multi-Label Learning. 98-112
- David R. Paoletti, Dan E. Krane, Travis E. Doom, Michael L. Raymer: Inferring the Number of Contributors to Mixed DNA Profiles. 113-122
- Xiaoning Qian, Edward R. Dougherty: Intervention in Gene Regulatory Networks via Phenotypically Constrained Control Policies Based on Long-Run Behavior. 123-136
- Shanika Kuruppu, Bryan Beresford-Smith, Thomas C. Conway, Justin Zobel: Iterative Dictionary Construction for Compression of Large DNA Data Sets. 137-149
- Damian Bogdanowicz, Krzysztof Giaro: Matching Split Distance for Unrooted Binary Phylogenetic Trees. 150-160
- Thomas K. F. Wong, Y. S. Chiu, Tak Wah Lam, Siu-Ming Yiu: Memory Efficient Algorithms for Structural Alignment of RNAs with Pseudoknots. 161-168
- Arthur W. Mahoney, Gregory J. Podgorski, Nicholas S. Flann: Multiobjective Optimization Based-Approach for Discovering Novel Cancer Therapies. 169-184
- Jianyong Sun, Jonathan M. Garibaldi, Charlie Hodgman: Parameter Estimation Using Metaheuristics in Systems Biology: A Comprehensive Review. 185-202
- Andrea Passerini, Marco Lippi, Paolo Frasconi: Predicting Metal-Binding Sites from Protein Sequence. 203-213
- Shahid H. Bokhari, Laura W. Pomeroy, Daniel Janies: Reassortment Networks and the Evolution of Pandemic H1N1 Swine-Origin Influenza. 214-227
- Lingyu Ma, Marco Reisert, Hans Burkhardt: RENNSH: A Novel ά-Helix Identification Approach for Intermediate Resolution Electron Density Maps. 228-239
- Shuai Cheng Li, Dongbo Bu, Ming Li: Residues with Similar Hexagon Neighborhoods Share Similar Side-Chain Conformations. 240-248
- Hong Sun, Ahmet Sacan, Hakan Ferhatosmanoglu, Yusu Wang: Smolign: A Spatial Motifs-Based Protein Multiple Structural Alignment Method. 249-261
- Lei Yu, Yue Han, Michael E. Berens: Stable Gene Selection from Microarray Data via Sample Weighting. 262-272
- Maria Luisa Bonet, Simone Linz, Katherine St. John: The Complexity of Finding Multiple Solutions to Betweenness and Quartet Compatibility. 273-285
- Yang Xiang, Philip R. O. Payne, Kun Huang: Transactional Database Transformation and Its Application in Prioritizing Human Disease Genes. 294-304
- Kyle H. Ambert, Aaron M. Cohen: k-Information Gain Scaled Nearest Neighbors: A Novel Approach to Classifying Protein-Protein Interaction-Related Documents. 305-310
- Yun Xu, Da Teng, YiMing Lei: MinePhos: A Literature Mining System for Protein Phoshphorylation Information Extraction. 311-315
Volume 9, Number 2, March - April 2012
- Nianyin Zeng, Zidong Wang, Yurong Li, Min Du, Xiaohui Liu: A Hybrid EKF and Switching PSO Algorithm for Joint State and Parameter Estimation of Lateral Flow Immunoassay Models. 321-329
- Biing-Feng Wang, Chung-Chin Kuo, Shang-Ju Liu, Chien-Hsin Lin: A New Efficient Algorithm for the Gene-Team Problem on General Sequences. 330-344
- Sascha Steinbiss, Stefan Kurtz: A New Efficient Data Structure for Storage and Retrieval of Multiple Biosequences. 345-357
- Kyriakos Kentzoglanakis, Matthew Poole: A Swarm Intelligence Framework for Reconstructing Gene Networks: Searching for Biologically Plausible Architectures. 358-371
- Zhi-Zhong Chen, Lusheng Wang: Algorithms for Reticulate Networks of Multiple Phylogenetic Trees. 372-384
- Sandro Andreotti, Gunnar W. Klau, Knut Reinert: Antilope - A Lagrangian Relaxation Approach to the de novo Peptide Sequencing Problem. 385-394
- Andreas Spillner, Binh T. Nguyen, Vincent Moulton: Constructing and Drawing Regular Planar Split Networks. 395-407
- Selim Mimaroglu, Emin Aksehirli: DICLENS: Divisive Clustering Ensemble with Automatic Cluster Number. 408-420
- M. Oguzhan Külekci, Jeffrey Scott Vitter, Bojian Xu: Efficient Maximal Repeat Finding Using the Burrows-Wheeler Transform and Wavelet Tree. 421-429
- Daifeng Wang, Mia K. Markey, Claus O. Wilke, Ari Arapostathis: Eigen-Genomic System Dynamic-Pattern Analysis (ESDA): Modeling mRNA Degradation and Self-Regulation. 430-437
- Lipi R. Acharya, Thair Judeh, Zhansheng Duan, Michael Rabbat, Dongxiao Zhu: GSGS: A Computational Approach to Reconstruct Signaling Pathway Structures from Gene Sets. 438-450
- Ola ElBakry, M. Omair Ahmad, M. N. S. Swamy: Identification of Differentially Expressed Genes for Time-Course Microarray Data Based on Modified RM ANOVA. 451-466
- Loris Nanni, Alessandra Lumini, Dinesh Gupta, Aarti Garg: Identifying Bacterial Virulent Proteins by Fusing a Set of Classifiers Based on Variants of Chou's Pseudo Amino Acid Composition and on Evolutionary Information. 467-475
- Yi-Ming Cheng, Srinivasa Murthy Gopal, Sean M. Law, Michael Feig: Molecular Dynamics Trajectory Compression with a Coarse-Grained Model. 476-486
- Martin Hopfensitz, Christoph Müssel, Christian Wawra, Markus Maucher, Michael Kühl, Heiko Neumann, Hans A. Kestler: Multiscale Binarization of Gene Expression Data for Reconstructing Boolean Networks. 487-498
- Wenji Ma, Yong Yang, Zhi-Zhong Chen, Lusheng Wang: Mutation Region Detection for Closely Related Individuals without a Known Pedigree. 499-510
- Aleksandar Poleksic: On Complexity of Protein Structure Alignment Problem under Distance Constraint. 511-516
- Biing-Feng Wang: Output-Sensitive Algorithms for Finding the Nested Common Intervals of Two General Sequences. 548-559
- Qinghua Huang, Dacheng Tao, Xuelong Li, Alan Liew: Parallelized Evolutionary Learning for Detection of Biclusters in Gene Expression Data. 560-570
- Ioannis Karafyllidis: Quantum Gate Circuit Model of Signal Integration in Bacterial Quorum Sensing. 571-579
- Shu-Ling Wang, Yi-Hai Zhu, Wei Jia, De-Shuang Huang: Robust Classification Method of Tumor Subtype by Using Correlation Filters. 580-591
- Barbara Di Camillo, Marco Falda, Gianna Toffolo, Claudio Cobelli: SimBioNeT: A Simulator of Biological Network Topology. 592-600
- Ulavappa B. Angadi, M. Venkatesulu: Structural SCOP Superfamily Level Classification Using Unsupervised Machine Learning. 601-608
- Yongwook Yoon, Gary Geunbae Lee: Subcellular Localization Prediction through Boosting Association Rules. 609-618
- Chien-Hao Su, Tse-Yi Wang, Ming-Tsung Hsu, Francis Cheng-Hsuan Weng, Cheng-Yan Kao, Daryi Wang, Huai-Kuang Tsai: The Impact of Normalization and Phylogenetic Information on Estimating the Distance for Metagenomes. 619-628
- Zeny Z. Feng, Xiaojian Yang, Sanjeena Subedi, Paul D. McNicholas: The LASSO and Sparse Least Squares Regression Methods for SNP Selection in Predicting Quantitative Traits. 629-636
Volume 9, Number 3, May - June 2012
- Tommaso Mazza: High Performance Computational Systems Biology. 641-642
- Mark Burkitt, Dawn C. Walker, Daniela M. Romano, Alireza Fazeli: Constructing Complex 3D Biological Environments from Medical Imaging Using High Performance Computing. 643-654
- Lorenzo Dematté: Smoldyn on Graphics Processing Units: Massively Parallel Brownian Dynamics Simulations. 655-667
- Vincenzo Belcastro, Francesco Gregoretti, Velia Siciliano, Michele Santoro, Giovanni D'Angelo, Gennaro Oliva, Diego di Bernardo: Reverse Engineering and Analysis of Genome-Wide Gene Regulatory Networks from Gene Expression Profiles Using High-Performance Computing. 668-678
- Alhadi Bustamam, Kevin Burrage, Nicholas A. Hamilton: Fast Parallel Markov Clustering in Bioinformatics Using Massively Parallel Computing on GPU with CUDA and ELLPACK-R Sparse Format. 679-692
- Jiri Barnat, Lubos Brim, Adam Krejci, Adam Streck, David Safránek, Martin Vejnar, Tomas Vejpustek: On Parameter Synthesis by Parallel Model Checking. 693-705
- Georgina Stegmayer, Diego H. Milone, Laura Kamenetzky, Mariana G. Lopez, Fernando Carrari: A Biologically Inspired Validity Measure for Comparison of Clustering Methods over Metabolic Data Sets. 706-716
- Clara Pizzuti, Simona E. Rombo: A Coclustering Approach for Mining Large Protein-Protein Interaction Networks. 717-730
- Petros Kountouris, Michalis Agathocleous, Vasilis J. Promponas, Georgia Christodoulou, Simos Hadjicostas, Vassilis Vassiliades, Chris Christodoulou: A Comparative Study on Filtering Protein Secondary Structure Prediction. 731-739
- Xiao-Fei Zhang, Dao-Qing Dai: A Framework for Incorporating Functional Interrelationships into Protein Function Prediction Algorithms. 740-753
- Alok Sharma, Seiya Imoto, Satoru Miyano: A Top-r Feature Selection Algorithm for Microarray Gene Expression Data. 754-764
- Shuai Cheng Li, Dongbo Bu, Ming Li: Clustering 100, 000 Protein Structure Decoys in Minutes. 765-773
- Yanni Sun, Jeremy Buhler, Cheng Yuan: Designing Filters for Fast-Known NcRNA Identification. 774-787
- Milos Krejnik, Jirí Kléma: Empirical Evidence of the Applicability of Functional Clustering through Gene Expression Classification. 788-798
- Giuliano Armano, Filippo Ledda: Exploiting Intrastructure Information for Secondary Structure Prediction with Multifaceted Pipelines. 799-808
- Oliver Serang, William Stafford Noble: Faster Mass Spectrometry-Based Protein Inference: Junction Trees Are More Efficient than Sampling and Marginalization by Enumeration. 809-817
- Hong Huang, Hailiang Feng: Gene Classification Using Parameter-Free Semi-Supervised Manifold Learning. 818-827
- Peter Jarvis, Jeremy G. Sumner: Markov Invariants for Phylogenetic Rate Matrices Derived from Embedded Submodels. 828-836
- Cheng-Hong Yang, Yu-Huei Cheng, Cheng-Huei Yang, Li-Yeh Chuang: Mutagenic Primer Design for Mismatch PCR-RFLP SNP Genotyping Using a Genetic Algorithm. 837-845
- Mindaugas Norkus, Damien Fay, Mary J. Murphy, Frank Barry, Gearóid Ó Laighin, Liam Kilmartin: On the Application of Active Learning and Gaussian Processes in Postcryopreservation Cell Membrane Integrity Experiments. 846-856
- Xiao-Fei Zhang, Dao-Qing Dai, Xiao-Xin Li: Protein Complexes Discovery Based on Protein-Protein Interaction Data via a Regularized Sparse Generative Network Model. 857-870
- Yong Zhang, Peng Li, Garng M. Huang: Quantifying Dynamic Stability of Genetic Memory Circuits. 871-884
- Eugen Czeizler, Andrzej Mizera, Elena Czeizler, Ralph-Johan Back, John E. Eriksson, Ion Petre: Quantitative Analysis of the Self-Assembly Strategies of Intermediate Filaments from Tetrameric Vimentin. 885-898
- Michael Mooney, Beth Wilmot, The Bipolar Genome Study, Shannon K. McWeeney: The GA and the GWAS: Using Genetic Algorithms to Search for Multilocus Associations. 899-910
- Tommaso Mazza, Paolo Ballarini, Rosita Guido, Davide Prandi: The Relevance of Topology in Parallel Simulation of Biological Networks. 911-923
- Debarka Sengupta, Ujjwal Maulik, Sanghamitra Bandyopadhyay: Weighted Markov Chain Based Aggregation of Biomolecule Orderings. 924-933
- Italo Zoppis, Erica Gianazza, Massimiliano Borsani, Clizia Chinello, Veronica Mainini, Carmen Galbusera, Carlo Ferrarese, Gloria Galimberti, Alessandro Sorbi, Barbara Borroni, Fulvio Magni, Marco Antoniotti, Giancarlo Mauri: Mutual Information Optimization for Mass Spectra Data Alignment. 934-939
- Denise Fagundes-Lima, Gerald Weber: Comment on "SCS: Signal, Context, and Structure Features for Genome-Wide Human Promoter Recognition". 940-941
Volume 9, Number 4, July - August 2012
- Luonan Chen, Michael K. Ng: Guest Editorial: Bioinformatics and Computational Systems Biology. 945-946
- Yinyin Yuan, Christina Curtis, Carlos Caldas, Florian Markowetz: A Sparse Regulatory Network of Copy-Number Driven Gene Expression Reveals Putative Breast Cancer Oncogenes. 947-954
- Li-Zhi Liu, Fang-Xiang Wu, Wen-Jun Zhang: Inference of Biological S-System Using the Separable Estimation Method and the Genetic Algorithm. 955-965
- Shuichi Kawano, Teppei Shimamura, Atsushi Niida, Seiya Imoto, Rui Yamaguchi, Masao Nagasaki, Ryo Yoshida, Cristin G. Print, Satoru Miyano: Identifying Gene Pathways Associated with Cancer Characteristics via Sparse Statistical Methods. 966-972
- Haseong Kim, Erol Gelenbe: Stochastic Gene Expression Modeling with Hill Function for Switch-Like Gene Responses. 973-979
- Xin Chen, Xiaohua Hu, Tze Yee Lim, Xiajiong Shen, E. K. Park, Gail L. Rosen: Exploiting the Functional and Taxonomic Structure of Genomic Data by Probabilistic Topic Modeling. 980-991
- Alvaro J. González, Li Liao, Cathy H. Wu: Predicting Ligand Binding Residues and Functional Sites Using Multipositional Correlations with Graph Theoretic Clustering and Kernel CCA. 992-1001
- Jianer Chen, Alexander Zelikovsky: Guest Editors' Introduction to the Special Section on Bioinformatics Research and Applications. 1002-1003
- Ruchi Chaudhary, J. Gordon Burleigh, David Fernández-Baca: Fast Local Search for Unrooted Robinson-Foulds Supertrees. 1004-1013
- Yu Lin, Vaibhav Rajan, Bernard M. E. Moret: A Metric for Phylogenetic Trees Based on Matching. 1014-1022
- Krister M. Swenson, Eric Chen, Nicholas D. Pattengale, David Sankoff: The Kernel of Maximum Agreement Subtrees. 1023-1031
- Xiuwei Zhang, Bernard M. E. Moret: Refining Regulatory Networks through Phylogenetic Transfer of Information. 1032-1045
- Luqman Hodgkinson, Richard M. Karp: Algorithms to Detect Multiprotein Modularity Conserved during Evolution. 1046-1058
- Jonathan Q. Jiang, Lisa J. McQuay: Predicting Protein Function by Multi-Label Correlated Semi-Supervised Learning. 1059-1069
- Jianxin Wang, Min Li, Huan Wang, Yi Pan: Identification of Essential Proteins Based on Edge Clustering Coefficient. 1070-1080
- Woo-Hyuk Jang, Suk Hoon Jung, Dong-Soo Han: A Computational Model for Predicting Protein Interactions Based on Multidomain Collaboration. 1081-1090
- Ickwon Choi, Michael W. Kattan, Brian J. Wells, Changhong Yu: A Hybrid Approach to Survival Model Building Using Integration of Clinical and Molecular Information in Censored Data. 1091-1105
- Cosmin Lazar, Jonatan Taminau, Stijn Meganck, David Steenhoff, Alain Coletta, Colin Molter, Virginie de Schaetzen, Robin Duque, Hugues Bersini, Ann Nowé: A Survey on Filter Techniques for Feature Selection in Gene Expression Microarray Analysis. 1106-1119
- Claudio Felicioli, Roberto Marangoni: BpMatch: An Efficient Algorithm for a Segmental Analysis of Genomic Sequences. 1120-1127
- Stephen J. Willson: CSD Homomorphisms between Phylogenetic Networks. 1128-1138
- Soumi Sengupta, Sanghamitra Bandyopadhyay: De Novo Design of Potential RecA Inhibitors Using MultiObjective Optimization. 1139-1154
- Peng Chen, Limsoon Wong, Jinyan Li: Detection of Outlier Residues for Improving Interface Prediction in Protein Heterocomplexes. 1155-1165
- Georgina Mirceva, Ivana Cingovska, Zoran Dimov, Danco Davcev: Efficient Approaches for Retrieving Protein Tertiary Structures. 1166-1179
- Nicoletta De Francesco, Giuseppe Lettieri, Luca Martini: Efficient Genotype Elimination via Adaptive Allele Consolidation. 1180-1189
- Yijia Zhang, Hongfei Lin, Zhihao Yang, Jian Wang, Yanpeng Li: Hash Subgraph Pairwise Kernel for Protein-Protein Interaction Extraction. 1190-1202
- Amina Noor, Erchin Serpedin, Mohamed N. Nounou, Hazem N. Nounou: Inferring Gene Regulatory Networks via Nonlinear State-Space Models and Exploiting Sparsity. 1203-1211
- Chao Yang, Zengyou He, Can Yang, Weichuan Yu: Peptide Reranking with Protein-Peptide Correspondence and Precursor Peak Intensity Information. 1212-1219
- Haitao Jiang, Chunfang Zheng, David Sankoff, Binhai Zhu: Scaffold Filling under the Breakpoint and Related Distances. 1220-1229
- Ranadip Pal, Sonal Bhattacharya: Transient Dynamics of Reduced-Order Models of Genetic Regulatory Networks. 1230-1244
- Jose Salavert Torres, Ignacio Blanquer Espert, Andres Tomas Dominguez, Vicente Hernández, Ignacio Medina, Joaquín Tárraga, Joaquín Dopazo: Using GPUs for the Exact Alignment of Short-Read Genetic Sequences by Means of the Burrows-Wheeler Transform. 1245-1256
- Shaohong Zhang, Hau-San Wong, Ying Shen, Dongqing Xie: A New Unsupervised Feature Ranking Method for Gene Expression Data Based on Consensus Affinity. 1257-1263
Volume 9, Number 5, September - October 2012
- Yi-Ping Phoebe Chen: Guest Editorial: Application and Development of Bioinformatics. 1265
- Stephanus Daniel Handoko, Xuchang Ouyang, Chinh Tran To Su, Chee Keong Kwoh, Yew-Soon Ong: QuickVina: Accelerating AutoDock Vina Using Gradient-Based Heuristics for Global Optimization. 1266-1272
- Pengyi Yang, Jie Ma, Penghao Wang, Yunping Zhu, Bing Bing Zhou, Jean Yee Hwa Yang: Improving X!Tandem on Peptide Identification from Mass Spectrometry by Self-Boosted Percolator. 1273-1280
- Lin Wan, Fengzhu Sun: CEDER: Accurate Detection of Differentially Expressed Genes by Combining Significance of Exons Using RNA-Seq. 1281-1292
- Richard Röttger, Ulrich Rückert, Jan Taubert, Jan Baumbach: How Little Do We Actually Know? On the Size of Gene Regulatory Networks. 1293-1300
- Hossam M. Ashtawy, Nihar R. Mahapatra: A Comparative Assessment of Ranking Accuracies of Conventional and Machine-Learning-Based Scoring Functions for Protein-Ligand Binding Affinity Prediction. 1301-1313
- François Fages, Sylvain Soliman: Guest Editors' Introduction to the Special Section on Computational Methods in Systems Biology. 1314-1315
- Jimmy Omony, Astrid R. Mach-Aigner, Leo H. de Graaff, Gerrit van Straten, Anton J. B. van Boxtel: Evaluation of Design Strategies for Time Course Experiments in Genetic Networks: Case Study of the XlnR Regulon in Aspergillus niger. 1316-1325
- Eugen Czeizler, Vladimir Rogojin, Ion Petre: The Phosphorylation of the Heat Shock Factor as a Modulator for the Heat Shock Response. 1326-1337
- Hannes Klarner, Heike Siebert, Alexander Bockmayr: Time Series Dependent Analysis of Unparametrized Thomas Networks. 1338-1351
- Sucheendra K. Palaniappan, S. Akshay, Bing Liu, Blaise Genest, P. S. Thiagarajan: A Hybrid Factored Frontier Algorithm for Dynamic Bayesian Networks with a Biopathways Application. 1352-1365
- Nicola Paoletti, Pietro Liò, Emanuela Merelli, Marco Viceconti: Multilevel Computational Modeling and Quantitative Analysis of Bone Remodeling. 1366-1378
- Blaise Hanczar, Avner Bar-Hen: A New Measure of Classifier Performance for Gene Expression Data. 1379-1386
- Uday Kamath, Jack Compton, Rezarta Islamaj Dogan, Kenneth A. De Jong, Amarda Shehu: An Evolutionary Algorithm Approach for Feature Generation from Sequence Data and Its Application to DNA Splice Site Prediction. 1387-1398
- Nadeem Ansari, Riyue Bao, Calin Voichita, Sorin Draghici: Detecting Phenotype-Specific Interactions between Biological Processes from Microarray Data and Annotations. 1399-1409
- Tatsuya Akutsu, Sven Kosub, Avraham A. Melkman, Takeyuki Tamura: Finding a Periodic Attractor of a Boolean Network. 1410-1421
- Herbert Pang, Stephen L. George, Ken Hui, Tiejun Tong: Gene Selection Using Iterative Feature Elimination Random Forests for Survival Outcomes. 1422-1431
- Bilge Karaçali: Hierarchical Motif Vectors for Prediction of Functional Sites in Amino Acid Sequences Using Quasi-Supervised Learning. 1432-1441
- Pablo H. Hennings-Yeomans, Gregory F. Cooper: Improving the Prediction of Clinical Outcomes from Genomic Data Using Multiresolution Analysis. 1442-1450
- Nicolas Bonnel, Pierre-Francois Marteau: LNA: Fast Protein Structural Comparison Using a Laplacian Characterization of Tertiary Structure. 1451-1458
- Francesco Sambo, Marco Antonio Montes de Oca, Barbara Di Camillo, Gianna Toffolo, Thomas Stützle: MORE: Mixed Optimization for Reverse Engineering - An Application to Modeling Biological Networks Response via Sparse Systems of Nonlinear Differential Equations. 1459-1471
- Neil Jacklin, Zhi Ding, Wei Chen, Chunqi Chang: Noniterative Convex Optimization Methods for Network Component Analysis. 1472-1481
- Silvana Badaloni, Barbara Di Camillo, Francesco Sambo: Qualitative Reasoning for Biological Network Inference from Systematic Perturbation Experiments. 1482-1491
- John C. Hawkins, Hongbo Zhu, Joan Teyra, M. Teresa Pisabarro: Reduced False Positives in PDZ Binding Prediction Using Sequence and Structural Descriptors. 1492-1503
- Jianyong Sun, Jonathan M. Garibaldi, Kim Kenobi: Robust Bayesian Clustering for Replicated Gene Expression Data. 1504-1514
- Zhi-Zhong Chen, Fei Deng, Lusheng Wang: Simultaneous Identification of Duplications, Losses, and Lateral Gene Transfers. 1515-1528
- Shaini Joseph, Shreyas Karnik, Pravin Nilawe, Vaidyanathan K. Jayaraman, Susan Idicula-Thomas: ClassAMP: A Prediction Tool for Classification of Antimicrobial Peptides. 1535-1538
- Mohamed N. Nounou, Hazem N. Nounou, Nader Meskin, Aniruddha Datta, Edward R. Dougherty: Multiscale Denoising of Biological Data: A Comparative Analysis. 1539-1545
Volume 9, Number 6, November - December 2012
- Marie-France Sagot: EIC Editorial. 1553-1557
- James H. Degnan, Noah A. Rosenberg, Tanja Stadler: A Characterization of the Set of Species Trees that Produce Anomalous Ranked Gene Trees. 1558-1568
- Yang Tang, Zidong Wang, Huijun Gao, Stephen Swift, Jürgen Kurths: A Constrained Evolutionary Computation Method for Detecting Controlling Regions of Cortical Networks. 1569-1581
- Yuri Pirola, Gianluca Della Vedova, Stefano Biffani, Alessandra Stella, Paola Bonizzoni: A Fast and Practical Approach to Genotype Phasing and Imputation on a Pedigree with Erroneous and Incomplete Information. 1582-1594
- Nabila Kazmi, M. A. Hossain, Roger M. Phillips: A Hybrid Cellular Automaton Model of Solid Tumor Growth and Bioreductive Drug Transport. 1595-1606
- Alessandro Abate, Stéphane Vincent, Roel Dobbe, Alberto Silletti, Neal Master, Jeffrey D. Axelrod, Claire J. Tomlin: A Mathematical Model to Study the Dynamics of Epithelial Cellular Networks. 1607-1620
- Gizem Çavuslar, Bülent Çatay, Mehmet Serkan Apaydin: A Tabu Search Approach for the NMR Protein Structure-Based Assignment Problem. 1621-1628
- Christopher Ma, Thomas K. F. Wong, Tak Wah Lam, Wing-Kai Hon, Kunihiko Sadakane, Siu-Ming Yiu: An Efficient Alignment Algorithm for Searching Simple Pseudoknots over Long Genomic Sequence. 1629-1638
- Ibrahim Burak Özyurt: Automatic Identification and Classification of Noun Argument Structures in Biomedical Literature. 1639-1648
- Meng-Yun Wu, Dao-Qing Dai, Yu Shi, Hong Yan, Xiao-Fei Zhang: Biomarker Identification and Cancer Classification Based on Microarray Data Using Laplace Naive Bayes Model with Mean Shrinkage. 1649-1662
- Ozan Irsoy, Olcay Taner Yildiz, Ethem Alpaydin: Design and Analysis of Classifier Learning Experiments in Bioinformatics: Survey and Case Studies. 1663-1675
- Wendy Ashlock, Suprakash Datta: Distinguishing Endogenous Retroviral LTRs from SINE Elements Using Features Extracted from Evolved Side Effect Machines. 1676-1689
- Richard Tzong-Han Tsai: Improving Protein-Protein Interaction Pair Ranking with an Integrated Global Association Score. 1690-1695
- Seyedsasan Hashemikhabir, Eyüp Serdar Ayaz, Yusuf Kavurucu, Tolga Can, Tamer Kahveci: Large-Scale Signaling Network Reconstruction. 1696-1708
- Khachik Sargsyan, Cosmin Safta, Bert J. Debusschere, Habib N. Najm: Multiparameter Spectral Representation of Noise-Induced Competence in Bacillus Subtilis. 1709-1723
- Michael Margaliot, Tamir Tuller: On the Steady-State Distribution in the Homogeneous Ribosome Flow Model. 1724-1736
- Tobias Marschall, Inke Herms, Hans-Michael Kaltenbach, Sven Rahmann: Probabilistic Arithmetic Automata and Their Applications. 1737-1750
- Zhiwen Yu, Le Li, Jane You, Hau-San Wong, Guoqiang Han: SC³: Triple Spectral Clustering-Based Consensus Clustering Framework for Class Discovery from Cancer Gene Expression Profiles. 1751-1765
- Xin Ma, Jing Guo, Hongde Liu, Jianming Xie, Xiao Sun: Sequence-Based Prediction of DNA-Binding Residues in Proteins with Conservation and Correlation Information. 1766-1775
- Jianxin Wang, Yuannan Huang, Fang-Xiang Wu, Yi Pan: Symmetry Compression Method for Discovering Network Motifs. 1776-1789
- Mohammad Shafkat Amin, Russell L. Finley Jr., Hasan M. Jamil: Top-k Similar Graph Matching Using TraM in Biological Networks. 1790-1804
- Zachary Dwight, Robert Palais, Carl T. Wittwer: uAnalyze: Web-Based High-Resolution DNA Melting Analysis with Comparison to Thermodynamic Predictions. 1805-1811
- Matteo Re, Marco Mesiti, Giorgio Valentini: A Fast Ranking Algorithm for Predicting Gene Functions in Biomolecular Networks. 1812-1818
- Hazem N. Nounou, Mohamed N. Nounou, Nader Meskin, Aniruddha Datta, Edward R. Dougherty: Fuzzy Intervention in Biological Phenomena. 1819-1825
- Manuele Bicego, Pietro Lovato, Alessandro Perina, Marianna Fasoli, Massimo Delledonne, Mario Pezzotti, Annalisa Polverari, Vittorio Murino: Investigating Topic Models' Capabilities in Expression Microarray Data Classification. 1831-1836
- Elena Grassi, Federico Di Gregorio, Ivan Molineris: KungFQ: A Simple and Powerful Approach to Compress fastq Files. 1837-1842
- Dániel Györffy, Péter Závodszky, András Szilágyi: "Pull Moves" for Rectangular Lattice Polymer Models Are Not Fully Reversible. 1847-1849
- Ricardo J. G. B. Campello, Davoud Moulavi, Jörg Sander: A Simpler and More Accurate AUTO-HDS Framework for Clustering and Visualization of Biological Data. 1850-1852
- Stephanus Daniel Handoko, Xuchang Ouyang, Chinh Tran To Su, Chee Keong Kwoh, Yew-Soon Ong: Erratum to "QuickVina: Accelerating AutoDock Vina Using Gradient-Based Heuristics for Global Optimization". 1853
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