Journal: IEEE/ACM Trans. Comput. Biology Bioinform.

Volume 9, Issue 6

1553 -- 1557Marie-France Sagot. EIC Editorial
1558 -- 1568James H. Degnan, Noah A. Rosenberg, Tanja Stadler. A Characterization of the Set of Species Trees that Produce Anomalous Ranked Gene Trees
1569 -- 1581Yang Tang, Zidong Wang, Huijun Gao, Stephen Swift, Jürgen Kurths. A Constrained Evolutionary Computation Method for Detecting Controlling Regions of Cortical Networks
1582 -- 1594Yuri 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
1595 -- 1606Nabila Kazmi, M. Alamgir Hossain, Roger M. Phillips. A Hybrid Cellular Automaton Model of Solid Tumor Growth and Bioreductive Drug Transport
1607 -- 1620Alessandro 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
1621 -- 1628Gizem Çavuslar, Bülent Çatay, Mehmet Serkan Apaydin. A Tabu Search Approach for the NMR Protein Structure-Based Assignment Problem
1629 -- 1638Christopher 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
1639 -- 1648Ibrahim Burak Özyurt. Automatic Identification and Classification of Noun Argument Structures in Biomedical Literature
1649 -- 1662Meng-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
1663 -- 1675Ozan Irsoy, Olcay Taner Yildiz, Ethem Alpaydin. Design and Analysis of Classifier Learning Experiments in Bioinformatics: Survey and Case Studies
1676 -- 1689Wendy Ashlock, Suprakash Datta. Distinguishing Endogenous Retroviral LTRs from SINE Elements Using Features Extracted from Evolved Side Effect Machines
1690 -- 1695Richard Tzong-Han Tsai. Improving Protein-Protein Interaction Pair Ranking with an Integrated Global Association Score
1696 -- 1708Seyedsasan Hashemikhabir, Eyüp Serdar Ayaz, Yusuf Kavurucu, Tolga Can, Tamer Kahveci. Large-Scale Signaling Network Reconstruction
1709 -- 1723Khachik Sargsyan, Cosmin Safta, Bert J. Debusschere, Habib N. Najm. Multiparameter Spectral Representation of Noise-Induced Competence in Bacillus Subtilis
1724 -- 1736Michael Margaliot, Tamir Tuller. On the Steady-State Distribution in the Homogeneous Ribosome Flow Model
1737 -- 1750Tobias Marschall, Inke Herms, Hans-Michael Kaltenbach, Sven Rahmann. Probabilistic Arithmetic Automata and Their Applications
1751 -- 1765Zhiwen 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
1766 -- 1775Xin Ma, Jing Guo, Hongde Liu, Jianming Xie, Xiao Sun. Sequence-Based Prediction of DNA-Binding Residues in Proteins with Conservation and Correlation Information
1776 -- 1789Jianxin Wang, Yuannan Huang, Fang-Xiang Wu, Yi Pan. Symmetry Compression Method for Discovering Network Motifs
1790 -- 1804Mohammad Shafkat Amin, Russell L. Finley Jr., Hasan M. Jamil. Top-k Similar Graph Matching Using TraM in Biological Networks
1805 -- 1811Zachary Dwight, Robert Palais, Carl T. Wittwer. uAnalyze: Web-Based High-Resolution DNA Melting Analysis with Comparison to Thermodynamic Predictions
1812 -- 1818Matteo Re, Marco Mesiti, Giorgio Valentini. A Fast Ranking Algorithm for Predicting Gene Functions in Biomolecular Networks
1819 -- 1825Hazem N. Nounou, Mohamed N. Nounou, Nader Meskin, Aniruddha Datta, Edward R. Dougherty. Fuzzy Intervention in Biological Phenomena
1826 -- 1830George Papadakis, Electra Gizeli. In Silico Search of DNA Drugs Targeting Oncogenes
1831 -- 1836Manuele Bicego, Pietro Lovato, Alessandro Perina, Marianna Fasoli, Massimo Delledonne, Mario Pezzotti, Annalisa Polverari, Vittorio Murino. Investigating Topic Models' Capabilities in Expression Microarray Data Classification
1837 -- 1842Elena Grassi, Federico Di Gregorio, Ivan Molineris. KungFQ: A Simple and Powerful Approach to Compress fastq Files
1843 -- 1846Christina Boucher, Mohamed Omar. On the Hardness of Counting and Sampling Center Strings
1847 -- 1849Dániel Györffy, Péter Závodszky, András Szilágyi. "Pull Moves" for Rectangular Lattice Polymer Models Are Not Fully Reversible
1850 -- 1852Ricardo J. G. B. Campello, Davoud Moulavi, Jörg Sander. A Simpler and More Accurate AUTO-HDS Framework for Clustering and Visualization of Biological Data
1853 -- 0Stephanus 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"

Volume 9, Issue 5

1265 -- 0Yi-Ping Phoebe Chen. Guest Editorial: Application and Development of Bioinformatics
1266 -- 1272Stephanus 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
1273 -- 1280Pengyi 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
1281 -- 1292Lin Wan, Fengzhu Sun. CEDER: Accurate Detection of Differentially Expressed Genes by Combining Significance of Exons Using RNA-Seq
1293 -- 1300Richard Röttger, Ulrich Rückert, Jan Taubert, Jan Baumbach. How Little Do We Actually Know? On the Size of Gene Regulatory Networks
1301 -- 1313Hossam 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
1314 -- 1315François Fages, Sylvain Soliman. Guest Editors' Introduction to the Special Section on Computational Methods in Systems Biology
1316 -- 1325Jimmy 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
1326 -- 1337Eugen Czeizler, Vladimir Rogojin, Ion Petre. The Phosphorylation of the Heat Shock Factor as a Modulator for the Heat Shock Response
1338 -- 1351Hannes Klarner, Heike Siebert, Alexander Bockmayr. Time Series Dependent Analysis of Unparametrized Thomas Networks
1352 -- 1365Sucheendra K. Palaniappan, S. Akshay, Bing Liu 0013, Blaise Genest, P. S. Thiagarajan. A Hybrid Factored Frontier Algorithm for Dynamic Bayesian Networks with a Biopathways Application
1366 -- 1378Nicola Paoletti, Pietro Liò, Emanuela Merelli, Marco Viceconti. Multilevel Computational Modeling and Quantitative Analysis of Bone Remodeling
1379 -- 1386Blaise Hanczar, Avner Bar-Hen. A New Measure of Classifier Performance for Gene Expression Data
1387 -- 1398Uday 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
1399 -- 1409Nadeem Ansari, Riyue Bao, Calin Voichita, Sorin Draghici. Detecting Phenotype-Specific Interactions between Biological Processes from Microarray Data and Annotations
1410 -- 1421Tatsuya Akutsu, Sven Kosub, Avraham A. Melkman, Takeyuki Tamura. Finding a Periodic Attractor of a Boolean Network
1422 -- 1431Herbert Pang, Stephen L. George, Ken Hui, Tiejun Tong. Gene Selection Using Iterative Feature Elimination Random Forests for Survival Outcomes
1432 -- 1441Bilge Karaçali. Hierarchical Motif Vectors for Prediction of Functional Sites in Amino Acid Sequences Using Quasi-Supervised Learning
1442 -- 1450Pablo H. Hennings-Yeomans, Gregory F. Cooper. Improving the Prediction of Clinical Outcomes from Genomic Data Using Multiresolution Analysis
1451 -- 1458Nicolas Bonnel, Pierre-Francois Marteau. LNA: Fast Protein Structural Comparison Using a Laplacian Characterization of Tertiary Structure
1459 -- 1471Francesco 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
1472 -- 1481Neil Jacklin, Zhi Ding, Wei Chen, Chunqi Chang. Noniterative Convex Optimization Methods for Network Component Analysis
1482 -- 1491Silvana Badaloni, Barbara Di Camillo, Francesco Sambo. Qualitative Reasoning for Biological Network Inference from Systematic Perturbation Experiments
1492 -- 1503John C. Hawkins, Hongbo Zhu, Joan Teyra, M. Teresa Pisabarro. Reduced False Positives in PDZ Binding Prediction Using Sequence and Structural Descriptors
1504 -- 1514Jianyong Sun, Jonathan M. Garibaldi, Kim Kenobi. Robust Bayesian Clustering for Replicated Gene Expression Data
1515 -- 1528Zhi-Zhong Chen, Fei Deng, Lusheng Wang. Simultaneous Identification of Duplications, Losses, and Lateral Gene Transfers
1529 -- 1534Bo Liao, Xiong Li, Wen Zhu, Zhi Cao. A Novel Method to Select Informative SNPs and Their Application in Genetic Association Studies
1535 -- 1538Shaini Joseph, Shreyas Karnik, Pravin Nilawe, Vaidyanathan K. Jayaraman, Susan Idicula-Thomas. ClassAMP: A Prediction Tool for Classification of Antimicrobial Peptides
1539 -- 1545Mohamed N. Nounou, Hazem N. Nounou, Nader Meskin, Aniruddha Datta, Edward R. Dougherty. Multiscale Denoising of Biological Data: A Comparative Analysis
1545 -- 1552Michael Margaliot, Tamir Tuller. Stability Analysis of the Ribosome Flow Model

Volume 9, Issue 4

945 -- 946Luonan Chen, Michael K. Ng. Guest Editorial: Bioinformatics and Computational Systems Biology
947 -- 954Yinyin Yuan, Christina Curtis, Carlos Caldas, Florian Markowetz. A Sparse Regulatory Network of Copy-Number Driven Gene Expression Reveals Putative Breast Cancer Oncogenes
955 -- 965Li-Zhi Liu, Fang-Xiang Wu, Wen-Jun Zhang. Inference of Biological S-System Using the Separable Estimation Method and the Genetic Algorithm
966 -- 972Shuichi 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
973 -- 979Haseong Kim, Erol Gelenbe. Stochastic Gene Expression Modeling with Hill Function for Switch-Like Gene Responses
980 -- 991Xin 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
992 -- 1001Alvaro J. González, Li Liao, Cathy H. Wu. Predicting Ligand Binding Residues and Functional Sites Using Multipositional Correlations with Graph Theoretic Clustering and Kernel CCA
1002 -- 1003Jianer Chen, Alexander Zelikovsky. Guest Editors' Introduction to the Special Section on Bioinformatics Research and Applications
1004 -- 1013Ruchi Chaudhary, J. Gordon Burleigh, David Fernández-Baca. Fast Local Search for Unrooted Robinson-Foulds Supertrees
1014 -- 1022Yu Lin, Vaibhav Rajan, Bernard M. E. Moret. A Metric for Phylogenetic Trees Based on Matching
1023 -- 1031Krister M. Swenson, Eric Chen, Nicholas D. Pattengale, David Sankoff. The Kernel of Maximum Agreement Subtrees
1032 -- 1045Xiuwei Zhang, Bernard M. E. Moret. Refining Regulatory Networks through Phylogenetic Transfer of Information
1046 -- 1058Luqman Hodgkinson, Richard M. Karp. Algorithms to Detect Multiprotein Modularity Conserved during Evolution
1059 -- 1069Jonathan Q. Jiang, Lisa J. McQuay. Predicting Protein Function by Multi-Label Correlated Semi-Supervised Learning
1070 -- 1080Jianxin Wang, Min Li, Huan Wang, Yi Pan. Identification of Essential Proteins Based on Edge Clustering Coefficient
1081 -- 1090Woo-Hyuk Jang, Suk Hoon Jung, Dong-Soo Han. A Computational Model for Predicting Protein Interactions Based on Multidomain Collaboration
1091 -- 1105Ickwon 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
1106 -- 1119Cosmin 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
1120 -- 1127Claudio Felicioli, Roberto Marangoni. BpMatch: An Efficient Algorithm for a Segmental Analysis of Genomic Sequences
1128 -- 1138Stephen J. Willson. CSD Homomorphisms between Phylogenetic Networks
1139 -- 1154Soumi Sengupta, Sanghamitra Bandyopadhyay. De Novo Design of Potential RecA Inhibitors Using MultiObjective Optimization
1155 -- 1165Peng Chen 0001, Limsoon Wong, Jinyan Li. Detection of Outlier Residues for Improving Interface Prediction in Protein Heterocomplexes
1166 -- 1179Georgina Mirceva, Ivana Cingovska, Zoran Dimov, Danco Davcev. Efficient Approaches for Retrieving Protein Tertiary Structures
1180 -- 1189Nicoletta De Francesco, Giuseppe Lettieri, Luca Martini. Efficient Genotype Elimination via Adaptive Allele Consolidation
1190 -- 1202Yijia Zhang, Hongfei Lin, Zhihao Yang, Jian Wang, Yanpeng Li. Hash Subgraph Pairwise Kernel for Protein-Protein Interaction Extraction
1203 -- 1211Amina Noor, Erchin Serpedin, Mohamed N. Nounou, Hazem N. Nounou. Inferring Gene Regulatory Networks via Nonlinear State-Space Models and Exploiting Sparsity
1212 -- 1219Chao Yang, Zengyou He, Can Yang, Weichuan Yu. Peptide Reranking with Protein-Peptide Correspondence and Precursor Peak Intensity Information
1220 -- 1229Haitao Jiang, Chunfang Zheng, David Sankoff, Binhai Zhu. Scaffold Filling under the Breakpoint and Related Distances
1230 -- 1244Ranadip Pal, Sonal Bhattacharya. Transient Dynamics of Reduced-Order Models of Genetic Regulatory Networks
1245 -- 1256Jose 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
1257 -- 1263Shaohong Zhang, Hau-San Wong, Ying Shen, Dongqing Xie. A New Unsupervised Feature Ranking Method for Gene Expression Data Based on Consensus Affinity

Volume 9, Issue 3

641 -- 642Tommaso Mazza. High Performance Computational Systems Biology
643 -- 654Mark Burkitt, Dawn C. Walker, Daniela M. Romano, Alireza Fazeli. Constructing Complex 3D Biological Environments from Medical Imaging Using High Performance Computing
655 -- 667Lorenzo Dematté. Smoldyn on Graphics Processing Units: Massively Parallel Brownian Dynamics Simulations
668 -- 678Vincenzo 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
679 -- 692Alhadi 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
693 -- 705Jiri Barnat, Lubos Brim, Adam Krejci, Adam Streck, David Safránek, Martin Vejnar, Tomas Vejpustek. On Parameter Synthesis by Parallel Model Checking
706 -- 716Georgina 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
717 -- 730Clara Pizzuti, Simona E. Rombo. A Coclustering Approach for Mining Large Protein-Protein Interaction Networks
731 -- 739Petros Kountouris, Michalis Agathocleous, Vasilis J. Promponas, Georgia Christodoulou, Simos Hadjicostas, Vassilis Vassiliades, Chris Christodoulou. A Comparative Study on Filtering Protein Secondary Structure Prediction
740 -- 753Xiao-fei Zhang, Dao-Qing Dai. A Framework for Incorporating Functional Interrelationships into Protein Function Prediction Algorithms
754 -- 764Alok Sharma, Seiya Imoto, Satoru Miyano. A Top-r Feature Selection Algorithm for Microarray Gene Expression Data
765 -- 773Shuai Cheng Li, Dongbo Bu, Ming Li. Clustering 100, 000 Protein Structure Decoys in Minutes
774 -- 787Yanni Sun, Jeremy Buhler, Cheng Yuan. Designing Filters for Fast-Known NcRNA Identification
788 -- 798Milos Krejnik, Jirí Kléma. Empirical Evidence of the Applicability of Functional Clustering through Gene Expression Classification
799 -- 808Giuliano Armano, Filippo Ledda. Exploiting Intrastructure Information for Secondary Structure Prediction with Multifaceted Pipelines
809 -- 817Oliver Serang, William Stafford Noble. Faster Mass Spectrometry-Based Protein Inference: Junction Trees Are More Efficient than Sampling and Marginalization by Enumeration
818 -- 827Hong Huang, Hailiang Feng. Gene Classification Using Parameter-Free Semi-Supervised Manifold Learning
828 -- 836Peter Jarvis, Jeremy G. Sumner. Markov Invariants for Phylogenetic Rate Matrices Derived from Embedded Submodels
837 -- 845Cheng-Hong Yang, Yu-Huei Cheng, Cheng-Huei Yang, Li-Yeh Chuang. Mutagenic Primer Design for Mismatch PCR-RFLP SNP Genotyping Using a Genetic Algorithm
846 -- 856Mindaugas 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
857 -- 870Xiao-fei Zhang, Dao-Qing Dai, Xiao-Xin Li. Protein Complexes Discovery Based on Protein-Protein Interaction Data via a Regularized Sparse Generative Network Model
871 -- 884Yong Zhang, Peng Li, Garng M. Huang. Quantifying Dynamic Stability of Genetic Memory Circuits
885 -- 898Eugen 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
899 -- 910Michael Mooney, Beth Wilmot, The Bipolar Genome Study, Shannon K. McWeeney. The GA and the GWAS: Using Genetic Algorithms to Search for Multilocus Associations
911 -- 923Tommaso Mazza, Paolo Ballarini, Rosita Guido, Davide Prandi. The Relevance of Topology in Parallel Simulation of Biological Networks
924 -- 933Debarka Sengupta, Ujjwal Maulik, Sanghamitra Bandyopadhyay. Weighted Markov Chain Based Aggregation of Biomolecule Orderings
934 -- 939Italo 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
940 -- 941Denise Fagundes-Lima, Gerald Weber. Comment on "SCS: Signal, Context, and Structure Features for Genome-Wide Human Promoter Recognition"

Volume 9, Issue 2

321 -- 329Nianyin 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
330 -- 344Biing-Feng Wang, Chung-Chin Kuo, Shang-Ju Liu, Chien-Hsin Lin. A New Efficient Algorithm for the Gene-Team Problem on General Sequences
345 -- 357Sascha Steinbiss, Stefan Kurtz. A New Efficient Data Structure for Storage and Retrieval of Multiple Biosequences
358 -- 371Kyriakos Kentzoglanakis, Matthew Poole. A Swarm Intelligence Framework for Reconstructing Gene Networks: Searching for Biologically Plausible Architectures
372 -- 384Zhi-Zhong Chen, Lusheng Wang. Algorithms for Reticulate Networks of Multiple Phylogenetic Trees
385 -- 394Sandro Andreotti, Gunnar W. Klau, Knut Reinert. Antilope - A Lagrangian Relaxation Approach to the de novo Peptide Sequencing Problem
395 -- 407Andreas Spillner 0001, Binh T. Nguyen, Vincent Moulton. Constructing and Drawing Regular Planar Split Networks
408 -- 420Selim Mimaroglu, Emin Aksehirli. DICLENS: Divisive Clustering Ensemble with Automatic Cluster Number
421 -- 429M. Oguzhan Külekci, Jeffrey Scott Vitter, Bojian Xu. Efficient Maximal Repeat Finding Using the Burrows-Wheeler Transform and Wavelet Tree
430 -- 437Daifeng Wang, Mia K. Markey, Claus O. Wilke, Ari Arapostathis. Eigen-Genomic System Dynamic-Pattern Analysis (ESDA): Modeling mRNA Degradation and Self-Regulation
438 -- 450Lipi R. Acharya, Thair Judeh, Zhansheng Duan, Michael Rabbat, Dongxiao Zhu. GSGS: A Computational Approach to Reconstruct Signaling Pathway Structures from Gene Sets
451 -- 466Ola ElBakry, M. Omair Ahmad, M. N. S. Swamy. Identification of Differentially Expressed Genes for Time-Course Microarray Data Based on Modified RM ANOVA
467 -- 475Loris 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
476 -- 486Yi-Ming Cheng, Srinivasa Murthy Gopal, Sean M. Law, Michael Feig. Molecular Dynamics Trajectory Compression with a Coarse-Grained Model
487 -- 498Martin Hopfensitz, Christoph Müssel, Christian Wawra, Markus Maucher, Michael Kühl, Heiko Neumann, Hans A. Kestler. Multiscale Binarization of Gene Expression Data for Reconstructing Boolean Networks
499 -- 510Wenji Ma, Yong Yang, Zhi-Zhong Chen, Lusheng Wang. Mutation Region Detection for Closely Related Individuals without a Known Pedigree
511 -- 516Aleksandar Poleksic. On Complexity of Protein Structure Alignment Problem under Distance Constraint
517 -- 534Steven Kelk, Celine Scornavacca, Leo van Iersel. On the Elusiveness of Clusters
535 -- 547Paul Phipps, Sergey Bereg. Optimizing Phylogenetic Networks for Circular Split Systems
548 -- 559Biing-Feng Wang. Output-Sensitive Algorithms for Finding the Nested Common Intervals of Two General Sequences
560 -- 570Qinghua Huang, Dacheng Tao, Xuelong Li, Alan Liew. Parallelized Evolutionary Learning for Detection of Biclusters in Gene Expression Data
571 -- 579Ioannis Karafyllidis. Quantum Gate Circuit Model of Signal Integration in Bacterial Quorum Sensing
580 -- 591Shu-Ling Wang, Yi-Hai Zhu, Wei Jia, De-Shuang Huang. Robust Classification Method of Tumor Subtype by Using Correlation Filters
592 -- 600Barbara Di Camillo, Marco Falda, Gianna Toffolo, Claudio Cobelli. SimBioNeT: A Simulator of Biological Network Topology
601 -- 608Ulavappa B. Angadi, M. Venkatesulu. Structural SCOP Superfamily Level Classification Using Unsupervised Machine Learning
609 -- 618Yongwook Yoon, Gary Geunbae Lee. Subcellular Localization Prediction through Boosting Association Rules
619 -- 628Chien-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
629 -- 636Zeny Z. Feng, Xiaojian Yang, Sanjeena Subedi, Paul D. McNicholas. The LASSO and Sparse Least Squares Regression Methods for SNP Selection in Predicting Quantitative Traits

Volume 9, Issue 1

1 -- 11Daniel DeBlasio, Jocelyne Bruand, Shaojie Zhang. A Memory Efficient Method for Structure-Based RNA Multiple Alignment
12 -- 25Yuri Pirola, Paola Bonizzoni, Tao Jiang. An Efficient Algorithm for Haplotype Inference on Pedigrees with Recombinations and Mutations
26 -- 39Jean-Philippe Doyon, Sylvie Hamel, Cedric Chauve. An Efficient Method for Exploring the Space of Gene Tree/Species Tree Reconciliations in a Probabilistic Framework
40 -- 51Chong Wang, Peter Beyerlein, Heike Pospisil, Antje Krause, Chris D. Nugent, Werner Dubitzky. An Efficient Method for Modeling Kinetic Behavior of Channel Proteins in Cardiomyocytes
52 -- 65Bane V. Vasic, Vida Ravanmehr, Anantha Raman Krishnan. An Information Theoretic Approach to Constructing Robust Boolean Gene Regulatory Networks
66 -- 78Piraveenan Mahendra, Mikhail Prokopenko, Albert Y. Zomaya. Assortative Mixing in Directed Biological Networks
79 -- 87Raymond H. Chan, Tony H. Chan, Hau Man Yeung, Roger Wei Wang. Composition Vector Method Based on Maximum Entropy Principle for Sequence Comparison
88 -- 97José Ramón Quevedo, Antonio Bahamonde, Miguel Pérez-Enciso, Oscar Luaces. Disease Liability Prediction from Large Scale Genotyping Data Using Classifiers with a Reject Option
98 -- 112Ying-Xin Li, Shuiwang Ji, Sudhir Kumar, Jieping Ye, Zhi-Hua Zhou. Drosophila Gene Expression Pattern Annotation through Multi-Instance Multi-Label Learning
113 -- 122David R. Paoletti, Dan E. Krane, Travis E. Doom, Michael L. Raymer. Inferring the Number of Contributors to Mixed DNA Profiles
123 -- 136Xiaoning Qian, Edward R. Dougherty. Intervention in Gene Regulatory Networks via Phenotypically Constrained Control Policies Based on Long-Run Behavior
137 -- 149Shanika Kuruppu, Bryan Beresford-Smith, Thomas C. Conway, Justin Zobel. Iterative Dictionary Construction for Compression of Large DNA Data Sets
150 -- 160Damian Bogdanowicz, Krzysztof Giaro. Matching Split Distance for Unrooted Binary Phylogenetic Trees
161 -- 168Thomas K. F. Wong, Y. S. Chiu, Tak Wah Lam, Siu-Ming Yiu. Memory Efficient Algorithms for Structural Alignment of RNAs with Pseudoknots
169 -- 184Arthur W. Mahoney, Gregory J. Podgorski, Nicholas S. Flann. Multiobjective Optimization Based-Approach for Discovering Novel Cancer Therapies
185 -- 202Jianyong Sun, Jonathan M. Garibaldi, Charlie Hodgman. Parameter Estimation Using Metaheuristics in Systems Biology: A Comprehensive Review
203 -- 213Andrea Passerini, Marco Lippi, Paolo Frasconi. Predicting Metal-Binding Sites from Protein Sequence
214 -- 227Shahid H. Bokhari, Laura W. Pomeroy, Daniel Janies. Reassortment Networks and the Evolution of Pandemic H1N1 Swine-Origin Influenza
228 -- 239Lingyu Ma, Marco Reisert, Hans Burkhardt. RENNSH: A Novel ά-Helix Identification Approach for Intermediate Resolution Electron Density Maps
240 -- 248Shuai Cheng Li, Dongbo Bu, Ming Li. Residues with Similar Hexagon Neighborhoods Share Similar Side-Chain Conformations
249 -- 261Hong Sun, Ahmet Sacan, Hakan Ferhatosmanoglu, Yusu Wang. Smolign: A Spatial Motifs-Based Protein Multiple Structural Alignment Method
262 -- 272Lei Yu, Yue Han, Michael E. Berens. Stable Gene Selection from Microarray Data via Sample Weighting
273 -- 285Maria Luisa Bonet, Simone Linz, Katherine St. John. The Complexity of Finding Multiple Solutions to Betweenness and Quartet Compatibility
294 -- 304Yang Xiang, Philip R. O. Payne, Kun Huang. Transactional Database Transformation and Its Application in Prioritizing Human Disease Genes
305 -- 310Kyle H. Ambert, Aaron M. Cohen. k-Information Gain Scaled Nearest Neighbors: A Novel Approach to Classifying Protein-Protein Interaction-Related Documents
311 -- 315Yun Xu, Da Teng, Yiming Lei. MinePhos: A Literature Mining System for Protein Phoshphorylation Information Extraction