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IEEE/ACM Transactions on Computational Biology and Bioinformatics, Volume 12
Volume 12, Number 1, January - February 2015
- Ying Xu:
Editorial from the Editor-in-Chief. 1 - Srinivas Aluru, Donna K. Slonim
:
Guest Editors' Introduction: Selected Papers from ACM-BCB 2013. 2-3 - Noah M. Daniels, Andrew Gallant, Norman Ramsey, Lenore J. Cowen:
MRFy: Remote Homology Detection for Beta-Structural Proteins Using Markov Random Fields and Stochastic Search. 4-16 - Manabu Torii
RLIMS-P 2.0: A Generalizable Rule-Based Information Extraction System for Literature Mining of Protein Phosphorylation Information. 17-29 - Kun Wang, Avinash Das Sahu, Zheng-Mei Xiong, Kan Cao, Sridhar Hannenhalli:
Phenotype-Dependent Coexpression Gene Clusters: Application to Normal and Premature Ageing. 30-39 - Fazle Elahi Faisal, Han Zhao, Tijana Milenkovic:
Global Network Alignment in the Context of Aging. 40-52 - Haitham Gabr, Andrei Todor, Alin Dobra
Reachability Analysis in Probabilistic Biological Networks. 53-66 - Yongtao Ye
GLProbs: Aligning Multiple Sequences Adaptively. 67-78 - Hui Li, Xiaoyi Li, Murali Ramanathan, Aidong Zhang:
Prediction and Informative Risk Factor Selection of Bone Diseases. 79-91 - Michael A. DeJesus
Capturing Uncertainty by Modeling Local Transposon Insertion Frequencies Improves Discrimination of Essential Genes. 92-102 - Matt Spencer, Jesse Eickholt, Jianlin Cheng
A Deep Learning Network Approach to ab initio Protein Secondary Structure Prediction. 103-112 - Bo Liao, Xiong Li, Lijun Cai, Zhi Cao, Haowen Chen:
A Hierarchical Clustering Method of Selecting Kernel SNP to Unify Informative SNP and Tag SNP. 113-122 - Shing-Chow Chan, Li Zhang, Ho-Chun Wu, Kai Man Tsui:
A Maximum A Posteriori Probability and Time-Varying Approach for Inferring Gene Regulatory Networks from Time Course Gene Microarray Data. 123-135 - Yetian Fan
An Algorithm for Motif Discovery with Iteration on Lengths of Motifs. 136-141 - Man Hon Wong, Ho-Yin Antonio Sze-To, Leung-Yau Peter Lo, Tak-Ming Cyrus Chan, Kwong-Sak Leung:
Discovering Binding Cores in Protein-DNA Binding Using Association Rule Mining with Statistical Measures. 142-154 - Pawel Górecki
Gene Tree Diameter for Deep Coalescence. 155-165 - Chao Wang, Xi Li, Peng Chen, Aili Wang, Xuehai Zhou, Hong Yu
Heterogeneous Cloud Framework for Big Data Genome Sequencing. 166-178 - Wei Peng, Jianxin Wang, Bihai Zhao, Lusheng Wang
Identification of Protein Complexes Using Weighted PageRank-Nibble Algorithm and Core-Attachment Structure. 179-192 - Nan Du, Marc R. Knecht, Mark T. Swihart
Identifying Affinity Classes of Inorganic Materials Binding Sequences via a Graph-Based Model. 193-204 - Xiangyuan Zhu, Kenli Li, Ahmad Salah
Parallel Implementation of MAFFT on CUDA-Enabled Graphics Hardware. 205-218 - Guo-Xian Yu, Huzefa Rangwala, Carlotta Domeniconi, Guoji Zhang, Zili Zhang:
Predicting Protein Function Using Multiple Kernels. 219-233 - Judith Keijsper, Tim Oosterwijk
Tractable Cases of (*, 2)-Bounded Parsimony Haplotyping. 234-247
Volume 12, Number 2, March - April 2015
- Feng Luo, Xintao Wu
Guest Editorial for Special Section on BIBM 2013. 252-253 - Xingpeng Jiang
Predicting Microbial Interactions Using Vector Autoregressive Model with Graph Regularization. 254-261 - Cen Wan
Predicting the Pro-Longevity or Anti-Longevity Effect of Model Organism Genes with New Hierarchical Feature Selection Methods. 262-275 - Wei Peng, Jianxin Wang, Yingjiao Cheng, Yu Lu, Fang-Xiang Wu
UDoNC: An Algorithm for Identifying Essential Proteins Based on Protein Domains and Protein-Protein Interaction Networks. 276-288 - Yongguo Mei, Adria Carbo, Stefan Hoops, Raquel Hontecillas, Josep Bassaganya-Riera:
ENISI SDE: A New Web-Based Tool for Modeling Stochastic Processes. 289-297 - Bin Pang, David Schlessman, Xingyan Kuang, Nan Zhao
An Integrated Approach to Sequence-Independent Local Alignment of Protein Binding Sites. 298-308 - Young-Rae Cho
P-Finder: Reconstruction of Signaling Networks from Protein-Protein Interactions and GO Annotations. 309-321 - Jong Cheol Jeong, Xue-wen Chen:
A New Semantic Functional Similarity over Gene Ontology. 322-334 - Hossam M. Ashtawy, Nihar R. Mahapatra:
A Comparative Assessment of Predictive Accuracies of Conventional and Machine Learning Scoring Functions for Protein-Ligand Binding Affinity Prediction. 335-347 - Lina Yang, Yuan Yan Tang, Yang Lu, Huiwu Luo:
A Fractal Dimension and Wavelet Transform Based Method for Protein Sequence Similarity Analysis. 348-359 - Savas Konur, Marian Gheorghe
A Property-Driven Methodology for Formal Analysis of Synthetic Biology Systems. 360-371 - Min Li, Yu Lu, Jianxin Wang, Fang-Xiang Wu
A Topology Potential-Based Method for Identifying Essential Proteins from PPI Networks. 372-383 - Qiang Yu, Hongwei Huo
An Efficient Exact Algorithm for the Motif Stem Search Problem over Large Alphabets. 384-397 - Xian Zhang
An Improved Integral Inequality to Stability Analysis of Genetic Regulatory Networks With Interval Time-Varying Delays. 398-409 - Zhenhua Li
Burial Level Change Defines a High Energetic Relevance for Protein Binding Interfaces. 410-421 - Gautam Dasarathy
Data Requirement for Phylogenetic Inference from Multiple Loci: A New Distance Method. 422-432 - Jun Meng, Jing Zhang, Yushi Luan:
Gene Selection Integrated with Biological Knowledge for Plant Stress Response Using Neighborhood System and Rough Set Theory. 433-444 - Trevor Cickovski, Tiffany Flor, Galen Irving-Sachs, Philip Novikov, James Parda, Giri Narasimhan
GPUDePiCt: A Parallel Implementation of a Clustering Algorithm for Computing Degenerate Primers on Graphics Processing Units. 445-454 - Bingjing Cai, Haiying Wang
Identification of Protein Complexes from Tandem Affinity Purification/Mass Spectrometry Data via Biased Random Walk. 455-466 - Xueming Liu, Linqiang Pan
Identifying Driver Nodes in the Human Signaling Network Using Structural Controllability Analysis. 467-472 - Hasan M. Jamil
Improving Integration Effectiveness of ID Mapping Based Biological Record Linkage. 473-486 - W. J. R. M. Priyadarshana
Multiple Break-Points Detection in Array CGH Data via the Cross-Entropy Method. 487-498
Volume 12, Number 3, May - June 2015
- João C. Setubal
TCBB Special Section on the Brazilian Symposium on Bioinformatics 2013. 499 - Marília D. V. Braga, Jens Stoye
Sorting Linear Genomes with Rearrangements and Indels. 500-506 - Christian Höner zu Siederdissen
Product Grammars for Alignment and Folding. 507-519 - David Hoksza
Multiple 3D RNA Structure Superposition Using Neighbor Joining. 520-530 - Hyrum D. Carroll, Alex C. Williams, Anthony G. Davis, John L. Spouge:
Improving Retrieval Efficacy of Homology Searches Using the False Discovery Rate. 531-537 - Adriana Birlutiu
A Bayesian Framework for Combining Protein and Network Topology Information for Predicting Protein-Protein Interactions. 538-550 - Yinglei Song, Chunmei Liu, Zhi Wang:
A Machine Learning Approach for Accurate Annotation of Noncoding RNAs. 551-559 - Tahir Mehmood
A Partial Least Squares Based Procedure for Upstream Sequence Classification in Prokaryotes. 560-567 - Liang Dong
An Accurate de novo Algorithm for Glycan Topology Determination from Mass Spectra. 568-578 - Pei Wang
Colored Noise Induced Bistable Switch in the Genetic Toggle Switch Systems. 579-589 - Sourya Bhattacharyya
COSPEDTree: COuplet Supertree by Equivalence Partitioning of Taxa Set and DAG Formation. 590-603 - Krishnasamy Gopinath
DAPD: A Knowledgebase for Diabetes Associated Proteins. 604-610 - Dong-Jun Yu, Yang Li, Jun Hu, Xibei Yang, Jing-Yu Yang, Hong-Bin Shen:
Disulfide Connectivity Prediction Based on Modelled Protein 3D Structural Information and Random Forest Regression. 611-621 - Lei Huang, Li Liao, Cathy H. Wu
Evolutionary Model Selection and Parameter Estimation for Protein-Protein Interaction Network Based on Differential Evolution Algorithm. 622-631 - Saurav Basu, Chi Liu, Gustavo Kunde Rohde:
Extraction of Individual Filaments from 2D Confocal Microscopy Images of Flat Cells. 632-643 - Yen Kaow Ng
Finding All Longest Common Segments in Protein Structures Efficiently. 644-655 - David L. González-Álvarez, Miguel A. Vega-Rodríguez
Finding Patterns in Protein Sequences by Using a Hybrid Multiobjective Teaching Learning Based Optimization Algorithm. 656-666 - Tommaso Mazza
Functional Impact of Autophagy-Related Genes on the Homeostasis and Dynamics of Pancreatic Cancer Cell Lines. 667-678 - Hong Xia, Yuanning Liu, Minghui Wang, Ao Li:
Identification of Genomic Aberrations in Cancer Subclones from Heterogeneous Tumor Samples. 679-685 - Dandan Song, Jiaxing Chen
Parameterized BLOSUM Matrices for Protein Alignment. 686-694 - Xiaojun Ding, Jianxin Wang, Alex Zelikovsky
Searching High-Order SNP Combinations for Complex Diseases Based on Energy Distribution Difference. 695-704 - Marcelo Boareto
Supervised Variational Relevance Learning, An Analytic Geometric Feature Selection with Applications to Omic Datasets. 705-711 - Chih-Yuan Hsu, Zhen-Ming Pan, Rei-Hsing Hu, Chih-Chun Chang, Hsiao-Chun Cheng, Che Lin, Bor-Sen Chen:
Systematic Biological Filter Design with a Desired I/O Filtering Response Based on Promoter-RBS Libraries. 712-725
Volume 12, Number 4, July - August 2015
- Sarath Chandra Janga
Knowledge Discovery Using Big Data in Biomedical Systems. 726-728 - K. Suvarna Vani
Divide and Conquer Approach to Contact Map Overlap Problem Using 2D-Pattern Mining of Protein Contact Networks. 729-737 - Rui Henriques
Biclustering with Flexible Plaid Models to Unravel Interactions between Biological Processes. 738-752 - Julia E. Vogt
Unsupervised Structure Detection in Biomedical Data. 753-760 - Tetsuo Shibuya, Chuan Yi Tang, Paul Horton, Kiyoshi Asai:
Guest Editorial for the 25th International Conference on Genome Informatics (GIW/ISCB-Asia 2014). 761-762 - Omar Y. Al-Jarrah, Paul D. Yoo
Randomized Subspace Learning for Proline Cis-Trans Isomerization Prediction. 763-769 - Wing-Kin Sung
An O(m, log m)-Time Algorithm for Detecting Superbubbles. 770-777 - Ho-Sik Seok
An Efficient Search Algorithm for Finding Genomic-Range Overlaps Based on the Maximum Range Length. 778-784 - Yi-Yu Hsu, Hung-Yu Kao:
Curatable Named-Entity Recognition Using Semantic Relations. 785-792 - Dong Xu, Kun Huang, Jeanette Schmidt:
Guest Editors Introduction to the Special Issue on Software and Databases. 793-794 - Weixing Feng
ResSeq: Enhancing Short-Read Sequencing Alignment By Rescuing Error-Containing Reads. 795-798 - Matthew W. Segar
MMBIRFinder: A Tool to Detect Microhomology-Mediated Break-Induced Replication. 799-806 - Suzanne J. Matthews
Heterogeneous Compression of Large Collections of Evolutionary Trees. 807-814 - Jianxin Wang, Jiancheng Zhong, Gang Chen, Min Li, Fang-Xiang Wu
ClusterViz: A Cytoscape APP for Cluster Analysis of Biological Network. 815-822 - Isabel A. Nepomuceno-Chamorro
Building Transcriptional Association Networks in Cytoscape with RegNetC. 823-824 - Kamal Taha
iPFPi: A System for Improving Protein Function Prediction through Cumulative Iterations. 825-836 - Davide Chicco
Software Suite for Gene and Protein Annotation Prediction and Similarity Search. 837-843 - Yanping Xiang, Ke Liu, Xian-Ying Cheng, Cheng Cheng, Fang Gong, Jian-Bo Pan
Rapid Assessment of Adverse Drug Reactions by Statistical Solution of Gene Association Network. 844-850 - Shovan Barma
Quantitative Measurement of Split of the Second Heart Sound (S2). 851-860 - Hosein M. Golshan, Reza P. R. Hasanzadeh
An Optimized LMMSE Based Method for 3D MRI Denoising. 861-870 - Blesson Varghese, Ishan Patel, Adam Barker:
RBioCloud: A Light-Weight Framework for Bioconductor and R-based Jobs on the Cloud. 871-878 - Wei Zhang, Xiufen Zou:
A New Method for Detecting Protein Complexes based on the Three Node Cliques. 879-886 - Zhiwen Yu, Hantao Chen, Jane You
Adaptive Fuzzy Consensus Clustering Framework for Clustering Analysis of Cancer Data. 887-901 - Lei Deng, Zhigang Chen:
An Integrated Framework for Functional Annotation of Protein Structural Domains. 902-913 - Mohammad R. Nezami Ranjbar, Mahlet G. Tadesse, Yue Joseph Wang, Habtom W. Ressom:
Bayesian Normalization Model for Label-Free Quantitative Analysis by LC-MS. 914-927 - Muxuan Liang
Integrative Data Analysis of Multi-Platform Cancer Data with a Multimodal Deep Learning Approach. 928-937 - Roozbeh Dehghannasiri
Optimal Experimental Design for Gene Regulatory Networks in the Presence of Uncertainty. 938-950 - Ting Chen, Ulisses M. Braga-Neto:
Statistical Detection of Intrinsically Multivariate Predictive Genes. 951-964 - Jin-Xing Liu
RPCA-Based Tumor Classification Using Gene Expression Data. 964-970
Volume 12, Number 5, September - October 2015
- Juan Antonio Gómez Pulido
Accelerating Bioinformatics Applications via Emerging Parallel Computing Systems. 971-972 - Edward B. Fernandez, Jason R. Villarreal, Stefano Lonardi
FHAST: FPGA-Based Acceleration of Bowtie in Hardware. 973-981 - Jorge González-Domínguez
Parallelizing Epistasis Detection in GWAS on FPGA and GPU-Accelerated Computing Systems. 982-994 - Héctor Martínez
Concurrent and Accurate Short Read Mapping on Multicore Processors. 995-1007 - Sanchit Misra, Kiran Pamnany, Srinivas Aluru:
Parallel Mutual Information Based Construction of Genome-Scale Networks on the Intel®Xeon Phi™ Coprocessor. 1008-1020 - Anne Jeannin-Girardon, Pascal Ballet, Vincent Rodin:
Large Scale Tissue Morphogenesis Simulation on Heterogenous Systems Based on a Flexible Biomechanical Cell Model. 1021-1033 - Yao Xin, Will X. Y. Li, Zhaorui Zhang
An Application Specific Instruction Set Processor (ASIP) for Adaptive Filters in Neural Prosthetics. 1034-1047 - Alejandro Chacón
Boosting the FM-Index on the GPU: Effective Techniques to Mitigate Random Memory Access. 1048-1059 - Thuy-Diem Nguyen, Bertil Schmidt
Efficient and Accurate OTU Clustering with GPU-Based Sequence Alignment and Dynamic Dendrogram Cutting. 1060-1073 - Shi-Hua Zhang, Luonan Chen:
Guest Editorial for Special Section on ISB/TBC 2014. 1074-1075 - H. Robert Frost, Zhigang Li, Folkert W. Asselbergs
An Independent Filter for Gene Set Testing Based on Spectral Enrichment. 1076-1086 - Dominique F. Chu, Anton Salykin:
Evolutionary Pressures on the Yeast Transcriptome. 1087-1093 - Hao Kang, Kwang-Hyun Cho, Xiaohua Douglas Zhang
Inferring Sequential Order of Somatic Mutations during Tumorgenesis based on Markov Chain Model. 1094-1103 - Nan Meng, Raghu Machiraju, Kun Huang:
Identify Critical Genes in Development with Consistent H3K4me2 Patterns across Multiple Tissues. 1104-1111 - Yu-Qing Qiu, Xue Tian, Shi-Hua Zhang:
Infer Metagenomic Abundance and Reveal Homologous Genomes Based on the Structure of Taxonomy Tree. 1112-1122 - Mauro Leoncini, Manuela Montangero
CMStalker: A Combinatorial Tool for Composite Motif Discovery. 1123-1136 - Jan Zrimec
Fast Prediction of DNA Melting Bubbles Using DNA Thermodynamic Stability. 1137-1145 - Shuqin Zhang
Functional Module Analysis for Gene Coexpression Networks with Network Integration. 1146-1160 - Jeong-Rae Kim
Identification of Gene Networks with Time Delayed Regulation Based on Temporal Expression Profiles. 1161-1168 - Leung-Yau Lo, Kwong-Sak Leung, Kin-Hong Lee:
Inferring Time-Delayed Causal Gene Network Using Time-Series Expression Data. 1169-1182 - Dimitrios Kleftogiannis
YamiPred: A Novel Evolutionary Method for Predicting Pre-miRNAs and Selecting Relevant Features. 1183-1192 - Pietro Lovato, Alejandro Giorgetti
A Multimodal Approach for Protein Remote Homology Detection. 1193-1198 - Jure Bordon, Miha Moskon
Fuzzy Logic as a Computational Tool for Quantitative Modelling of Biological Systems with Uncertain Kinetic Data. 1199-1205 - Po-Kuei Chen, Chun-Liang Lin:
Synthesis of Genetic Clock with Combinational Biologic Circuits. 1206-1212 - Emmanouil I. Athanasiadis
ZoomOut: Analyzing Multiple Networks as Single Nodes. 1213-1216
Volume 12, Number 6, November - December 2015
- Hsien-Da Huang, Yi-Ping Phoebe Chen
Guest Editorial for the 13th Asia Pacific Bioinformatics Conference. 1217-1218 - Liang Cheng
Using Semantic Association to Extend and Infer Literature-Oriented Relativity Between Terms. 1219-1226 - Nicolas Wieseke, Tom Hartmann
Cophylogenetic Reconciliation with ILP. 1227-1235 - Huidong Chen
DPNuc: Identifying Nucleosome Positions Based on the Dirichlet Process Mixture Model. 1236-1247 - Nan Gao, Yan Zhang, Bing Feng, Jijun Tang:
A Cooperative Co-Evolutionary Genetic Algorithm for Tree Scoring and Ancestral Genome Inference. 1248-1254 - Minzhu Xie, Jianxin Wang, Xin Chen:
LGH: A Fast and Accurate Algorithm for Single Individual Haplotyping Based on a Two-Locus Linkage Graph. 1255-1266 - Shotaro Kumozaki, Kengo Sato
A Machine Learning Based Approach to de novo Sequencing of Glycans from Tandem Mass Spectrometry Spectrum. 1267-1274 - Xiaojing Xie, Shuigeng Zhou, Jihong Guan:
CoGI: Towards Compressing Genomes as an Image. 1275-1285 - Beichen Wang, Xiaodong Chen, Hiroshi Mamitsuka
BMExpert: Mining MEDLINE for Finding Experts in Biomedical Domains Based on Language Model. 1286-1294 - Han Li, Chun Li, Jie Hu, Xiaodan Fan
A Resampling Based Clustering Algorithm for Replicated Gene Expression Data. 1295-1303 - Mohammad Shahrokh Esfahani
An Optimization-Based Framework for the Transformation of Incomplete Biological Knowledge into a Probabilistic Structure and Its Application to the Utilization of Gene/Protein Signaling Pathways in Discrete Phenotype Classification. 1304-1321 - Kin-On Cheng, Paula Wu, Ngai-Fong Law, Wan-Chi Siu:
Compression of Multiple DNA Sequences Using Intra-Sequence and Inter-Sequence Similarities. 1322-1332 - Le Ou-Yang, Dao-Qing Dai, Xiao-Fei Zhang:
Detecting Protein Complexes from Signed Protein-Protein Interaction Networks. 1333-1344 - Alexandru I. Tomescu
Explaining a Weighted DAG with Few Paths for Solving Genome-Guided Multi-Assembly. 1345-1354 - Chandrabhan Seniya
In-silico Studies Show Potent Inhibition of HIV-1 Reverse Transcriptase Activity by a Herbal Drug. 1355-1364 - Mariano Rubiolo, Diego H. Milone
Mining Gene Regulatory Networks by Neural Modeling of Expression Time-Series. 1365-1373 - Bo Liao, Yan Jiang, Wei Liang
On Efficient Feature Ranking Methods for High-Throughput Data Analysis. 1374-1384 - Xin Ma, Jing Guo, Ke Xiao, Xiao Sun:
PRBP: Prediction of RNA-Binding Proteins Using a Random Forest Algorithm Combined with an RNA-Binding Residue Predictor. 1385-1393 - Brijesh Kumar Sriwastava, Subhadip Basu, Ujjwal Maulik:
Predicting Protein-Protein Interaction Sites with a Novel Membership Based Fuzzy SVM Classifier. 1394-1404 - Ehsan Ullah, Mark Walker
PreProPath: An Uncertainty-Aware Algorithm for Identifying Predictable Profitable Pathways in Biochemical Networks. 1405-1415 - Ka-Chun Wong
Probabilistic Inference on Multiple Normalized Signal Profiles from Next Generation Sequencing: Transcription Factor Binding Sites. 1416-1428 - Alon Raveh, Yoram Zarai, Michael Margaliot
Ribosome Flow Model on a Ring. 1429-1439 - Mohammadreza Sehhati
Stable Gene Signature Selection for Prediction of Breast Cancer Recurrence Using Joint Mutual Information. 1440-1448 - Hao Zhang, Xing-Yuan Wang, Xiaohui Lin:
Synchronization of Asynchronous Switched Boolean Network. 1449-1456 - T. Sengupta, M. Bhushan, Pramod P. Wangikar:
A Computational Approach Using Ratio Statistics for Identifying Housekeeping Genes from cDNA Microarray Data. 1457-1463 - Prachi Pradeep
A Novel Scoring Based Distributed Protein Docking Application to Improve Enrichment. 1464-1469 - Babette Dellen, Hanno Scharr
Growth Signatures of Rosette Plants from Time-Lapse Video. 1470-1478 - Torbjörn Wigren
Model Order and Identifiability of Non-Linear Biological Systems in Stable Oscillation. 1479-1484
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