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ORCIDIEEE/ACM Transactions on Computational Biology and Bioinformatics, Volume 9
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, Cédric 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 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 G. 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 - Steven Kelk, Céline Scornavacca, Leo van Iersel:
On the Elusiveness of Clusters. 517-534 - Paul Phipps, Sergey Bereg:
Optimizing Phylogenetic Networks for Circular Split Systems. 535-547 - 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 Wee-Chung 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 D. 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, 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 C. H. 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 - José Salavert Torres, Ignacio Blanquer Espert, Andrés Tomás 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 - Bo Liao, Xiong Li, Wen Zhu, Zhi Cao:
A Novel Method to Select Informative SNPs and Their Application in Genetic Association Studies. 1529-1534 - 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 - Michael Margaliot, Tamir Tuller:
Stability Analysis of the Ribosome Flow Model. 1545-1552
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. Alamgir 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 - George Papadakis, Electra Gizeli:
In Silico Search of DNA Drugs Targeting Oncogenes. 1826-1830 - 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 - Christina Boucher, Mohamed Omar:
On the Hardness of Counting and Sampling Center Strings. 1843-1846 - 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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