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

Volume 12, Issue 6

1217 -- 1218Hsien-Da Huang, Yi-Ping Phoebe Chen. Guest Editorial for the 13th Asia Pacific Bioinformatics Conference
1219 -- 1226Liang Cheng, Jie Li, Yang Hu, Yue Jiang, Yongzhuang Liu, Yan-Shuo Chu, Zhenxing Wang, Yadong Wang. Using Semantic Association to Extend and Infer Literature-Oriented Relativity Between Terms
1227 -- 1235Nicolas Wieseke, Tom Hartmann, Matthias Bernt, Martin Middendorf. Cophylogenetic Reconciliation with ILP
1236 -- 1247Huidong Chen, Jihong Guan, Shuigeng Zhou. DPNuc: Identifying Nucleosome Positions Based on the Dirichlet Process Mixture Model
1248 -- 1254Nan Gao, Yan Zhang, Bing Feng, Jijun Tang. A Cooperative Co-Evolutionary Genetic Algorithm for Tree Scoring and Ancestral Genome Inference
1255 -- 1266Minzhu Xie, Jianxin Wang, Xin Chen. LGH: A Fast and Accurate Algorithm for Single Individual Haplotyping Based on a Two-Locus Linkage Graph
1267 -- 1274Shotaro Kumozaki, Kengo Sato, Yasubumi Sakakibara. A Machine Learning Based Approach to de novo Sequencing of Glycans from Tandem Mass Spectrometry Spectrum
1275 -- 1285Xiaojing Xie, Shuigeng Zhou, Jihong Guan. CoGI: Towards Compressing Genomes as an Image
1286 -- 1294Beichen Wang, Xiaodong Chen, Hiroshi Mamitsuka, Shanfeng Zhu. BMExpert: Mining MEDLINE for Finding Experts in Biomedical Domains Based on Language Model
1295 -- 1303Han Li, Chun Li, Jie Hu, Xiaodan Fan. A Resampling Based Clustering Algorithm for Replicated Gene Expression Data
1304 -- 1321Mohammad Shahrokh Esfahani, Edward R. Dougherty. 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
1322 -- 1332Kin-On Cheng, Paula Wu, Ngai-Fong Law, Wan-Chi Siu. Compression of Multiple DNA Sequences Using Intra-Sequence and Inter-Sequence Similarities
1333 -- 1344Le Ou-Yang, Dao-Qing Dai, Xiao-fei Zhang. Detecting Protein Complexes from Signed Protein-Protein Interaction Networks
1345 -- 1354Alexandru I. Tomescu, Travis Gagie, Alexandru Popa, Romeo Rizzi, Anna Kuosmanen, Veli Mäkinen. Explaining a Weighted DAG with Few Paths for Solving Genome-Guided Multi-Assembly
1355 -- 1364Chandrabhan Seniya, Ajay Yadav, G. J. Khan, Nand K. Sah. In-silico Studies Show Potent Inhibition of HIV-1 Reverse Transcriptase Activity by a Herbal Drug
1365 -- 1373Mariano Rubiolo, Diego H. Milone, Georgina Stegmayer. Mining Gene Regulatory Networks by Neural Modeling of Expression Time-Series
1374 -- 1384Bo Liao, Yan Jiang, Wei Liang, Lihong Peng, Li Peng, Damien Hanyurwimfura, Zejun Li, Min Chen. On Efficient Feature Ranking Methods for High-Throughput Data Analysis
1385 -- 1393Xin 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
1394 -- 1404Brijesh Kumar Sriwastava, Subhadip Basu, Ujjwal Maulik. Predicting Protein-Protein Interaction Sites with a Novel Membership Based Fuzzy SVM Classifier
1405 -- 1415Ehsan Ullah, Mark Walker, Kyongbum Lee, Soha Hassoun. PreProPath: An Uncertainty-Aware Algorithm for Identifying Predictable Profitable Pathways in Biochemical Networks
1416 -- 1428Ka Chun Wong, Chengbin Peng, Yue Li. Probabilistic Inference on Multiple Normalized Signal Profiles from Next Generation Sequencing: Transcription Factor Binding Sites
1429 -- 1439Alon Raveh, Yoram Zarai, Michael Margaliot, Tamir Tuller. Ribosome Flow Model on a Ring
1440 -- 1448Mohammadreza Sehhati, Alireza Mehri Dehnavi, Hossein Rabbani, Meraj Pourhossein. Stable Gene Signature Selection for Prediction of Breast Cancer Recurrence Using Joint Mutual Information
1449 -- 1456Hao Zhang, Xing-Yuan Wang, Xiao-Hui Lin. Synchronization of Asynchronous Switched Boolean Network
1457 -- 1463T. Sengupta, M. Bhushan, Pramod P. Wangikar. A Computational Approach Using Ratio Statistics for Identifying Housekeeping Genes from cDNA Microarray Data
1464 -- 1469Prachi Pradeep, Craig A. Struble, Terrence Neumann, Daniel S. Sem, Stephen J. Merrill. A Novel Scoring Based Distributed Protein Docking Application to Improve Enrichment
1470 -- 1478Babette Dellen, Hanno Scharr, Carme Torras. Growth Signatures of Rosette Plants from Time-Lapse Video
1479 -- 1484Torbjörn Wigren. Model Order and Identifiability of Non-Linear Biological Systems in Stable Oscillation

Volume 12, Issue 5

971 -- 972Juan Antonio Gómez Pulido, Bertil Schmidt, Wu-chun Feng. Accelerating Bioinformatics Applications via Emerging Parallel Computing Systems
973 -- 981Edward B. Fernandez, Jason R. Villarreal, Stefano Lonardi, Walid A. Najjar. FHAST: FPGA-Based Acceleration of Bowtie in Hardware
982 -- 994Jorge González-Domínguez, Lars Wienbrandt, Jan Christian Kässens, David Ellinghaus, Manfred Schimmler, Bertil Schmidt. Parallelizing Epistasis Detection in GWAS on FPGA and GPU-Accelerated Computing Systems
995 -- 1007Héctor Martínez, Joaquín Tárraga, Ignacio Medina, Sergio Barrachina, Maribel Castillo, Joaquín Dopazo, Enrique S. Quintana-Ortí. Concurrent and Accurate Short Read Mapping on Multicore Processors
1008 -- 1020Sanchit Misra, Kiran Pamnany, Srinivas Aluru. Parallel Mutual Information Based Construction of Genome-Scale Networks on the Intel®Xeon Phi™ Coprocessor
1021 -- 1033Anne Jeannin-Girardon, Pascal Ballet, Vincent Rodin. Large Scale Tissue Morphogenesis Simulation on Heterogenous Systems Based on a Flexible Biomechanical Cell Model
1034 -- 1047Yao Xin, Will X. Y. Li, Zhaorui Zhang, Ray C. C. Cheung, Dong Song, Theodore W. Berger. An Application Specific Instruction Set Processor (ASIP) for Adaptive Filters in Neural Prosthetics
1048 -- 1059Alejandro Chacón, Santiago Marco-Sola, Antonio Espinosa, Paolo Ribeca, Juan Carlos Moure. Boosting the FM-Index on the GPU: Effective Techniques to Mitigate Random Memory Access
1060 -- 1073Thuy-Diem Nguyen, Bertil Schmidt, Zejun Zheng, Chee Keong Kwoh. Efficient and Accurate OTU Clustering with GPU-Based Sequence Alignment and Dynamic Dendrogram Cutting
1074 -- 1075Shi-Hua Zhang, Luonan Chen. Guest Editorial for Special Section on ISB/TBC 2014
1076 -- 1086H. Robert Frost, Zhigang Li, Folkert W. Asselbergs, Jason H. Moore. An Independent Filter for Gene Set Testing Based on Spectral Enrichment
1087 -- 1093Dominique Chu, Anton Salykin. Evolutionary Pressures on the Yeast Transcriptome
1094 -- 1103Hao Kang, Kwang-Hyun Cho, Xiaohua Douglas Zhang, Tao Zeng, Luonan Chen. Inferring Sequential Order of Somatic Mutations during Tumorgenesis based on Markov Chain Model
1104 -- 1111Nan Meng, Raghu Machiraju, Kun Huang. Identify Critical Genes in Development with Consistent H3K4me2 Patterns across Multiple Tissues
1112 -- 1122Yu-Qing Qiu, Xue Tian, Shi-Hua Zhang. Infer Metagenomic Abundance and Reveal Homologous Genomes Based on the Structure of Taxonomy Tree
1123 -- 1136Mauro Leoncini, Manuela Montangero, Marco Pellegrini, Karina Panucia Tillan. CMStalker: A Combinatorial Tool for Composite Motif Discovery
1137 -- 1145Jan Zrimec, Ales Lapanje. Fast Prediction of DNA Melting Bubbles Using DNA Thermodynamic Stability
1146 -- 1160Shuqin Zhang, Hongyu Zhao, Michael K. Ng. Functional Module Analysis for Gene Coexpression Networks with Network Integration
1161 -- 1168Jeong-Rae Kim, Sang-Mok Choo, Hyung-Seok Choi, Kwang-Hyun Cho. Identification of Gene Networks with Time Delayed Regulation Based on Temporal Expression Profiles
1169 -- 1182Leung-Yau Lo, Kwong-Sak Leung, Kin-Hong Lee. Inferring Time-Delayed Causal Gene Network Using Time-Series Expression Data
1183 -- 1192Dimitrios Kleftogiannis, Konstantinos A. Theofilatos, Spiros Likothanassis, Seferina Mavroudi. YamiPred: A Novel Evolutionary Method for Predicting Pre-miRNAs and Selecting Relevant Features
1193 -- 1198Pietro Lovato, Alejandro Giorgetti, Manuele Bicego. A Multimodal Approach for Protein Remote Homology Detection
1199 -- 1205Jure Bordon, Miha Moskon, Nikolaj Zimic, Miha Mraz. Fuzzy Logic as a Computational Tool for Quantitative Modelling of Biological Systems with Uncertain Kinetic Data
1206 -- 1212Po-Kuei Chen, Chun-Liang Lin. Synthesis of Genetic Clock with Combinational Biologic Circuits
1213 -- 1216Emmanouil I. Athanasiadis, Marilena M. Bourdakou, George M. Spyrou. ZoomOut: Analyzing Multiple Networks as Single Nodes

Volume 12, Issue 4

726 -- 728Sarath Chandra Janga, Dongxiao Zhu, Jake Y. Chen, Mohammed J. Zaki. Knowledge Discovery Using Big Data in Biomedical Systems
729 -- 737Suvarna Vani Koneru, S. Durga Bhavani. Divide and Conquer Approach to Contact Map Overlap Problem Using 2D-Pattern Mining of Protein Contact Networks
738 -- 752Rui Henriques, Sara C. Madeira. Biclustering with Flexible Plaid Models to Unravel Interactions between Biological Processes
753 -- 760Julia E. Vogt. Unsupervised Structure Detection in Biomedical Data
761 -- 762Tetsuo Shibuya, Chuan Yi Tang, Paul Horton, Kiyoshi Asai. Guest Editorial for the 25th International Conference on Genome Informatics (GIW/ISCB-Asia 2014)
763 -- 769Omar Y. Al-Jarrah, Paul D. Yoo, Kamal Taha, Sami Muhaidat, Abdallah Shami, Nazar Zaki. Randomized Subspace Learning for Proline Cis-Trans Isomerization Prediction
770 -- 777Wing-Kin Sung, Kunihiko Sadakane, Tetsuo Shibuya, Abha Belorkar, Iana Pyrogova. An O(m, log m)-Time Algorithm for Detecting Superbubbles
778 -- 784Ho-Sik Seok, Taemin Song, Sek Won Kong, Kyu Baek Hwang. An Efficient Search Algorithm for Finding Genomic-Range Overlaps Based on the Maximum Range Length
785 -- 792Yi-Yu Hsu, Hung-Yu Kao. Curatable Named-Entity Recognition Using Semantic Relations
793 -- 794Dong Xu, Kun Huang, Jeanette Schmidt. Guest Editors Introduction to the Special Issue on Software and Databases
795 -- 798Weixing Feng, Peichao Sang, Deyuan Lian, Yansheng Dong, Fengfei Song, Meng Li, B. O. He, Fenglin Cao, Yunlong Liu. ResSeq: Enhancing Short-Read Sequencing Alignment By Rescuing Error-Containing Reads
799 -- 806Matthew W. Segar, Cynthia J. Sakofsky, Anna Malkova, Yunlong Liu. MMBIRFinder: A Tool to Detect Microhomology-Mediated Break-Induced Replication
807 -- 814Suzanne J. Matthews. Heterogeneous Compression of Large Collections of Evolutionary Trees
815 -- 822Jianxin Wang, Jiancheng Zhong, Gang Chen 0010, Min Li, Fang-Xiang Wu, Yi Pan. ClusterViz: A Cytoscape APP for Cluster Analysis of Biological Network
823 -- 824Isabel A. Nepomuceno-Chamorro, Alfonso E. Márquez Chamorro, Jesuú S. Aguilar-Ruíz. Building Transcriptional Association Networks in Cytoscape with RegNetC
825 -- 836Kamal Taha, Paul D. Yoo, Mohammed Al Zaabi. iPFPi: A System for Improving Protein Function Prediction through Cumulative Iterations
837 -- 843Davide Chicco, Marco Masseroli. Software Suite for Gene and Protein Annotation Prediction and Similarity Search
844 -- 850Yan-Ping Xiang, Ke Liu, Xian-Ying Cheng, Cheng Cheng, Fang Gong, Jian-Bo Pan, Zhi Liang Ji. Rapid Assessment of Adverse Drug Reactions by Statistical Solution of Gene Association Network
851 -- 860Shovan Barma, Bo-Wei Chen, Ka Lok Man, Jhing-Fa Wang. Quantitative Measurement of Split of the Second Heart Sound (S2)
861 -- 870Hosein M. Golshan, Reza P. R. Hasanzadeh. An Optimized LMMSE Based Method for 3D MRI Denoising
871 -- 878Blesson Varghese, Ishan Patel, Adam Barker. RBioCloud: A Light-Weight Framework for Bioconductor and R-based Jobs on the Cloud
879 -- 886Wei Zhang, Xiufen Zou. A New Method for Detecting Protein Complexes based on the Three Node Cliques
887 -- 901Zhiwen Yu, Hantao Chen, Jane You, Jiming Liu, Hau-San Wong, Guoqiang Han, Le Li. Adaptive Fuzzy Consensus Clustering Framework for Clustering Analysis of Cancer Data
902 -- 913Lei Deng, Zhigang Chen. An Integrated Framework for Functional Annotation of Protein Structural Domains
914 -- 927Mohammad R. Nezami Ranjbar, Mahlet G. Tadesse, Yue Joseph Wang, Habtom W. Ressom. Bayesian Normalization Model for Label-Free Quantitative Analysis by LC-MS
928 -- 937Muxuan Liang, Zhizhong Li, Ting Chen, Jianyang Zeng. Integrative Data Analysis of Multi-Platform Cancer Data with a Multimodal Deep Learning Approach
938 -- 950Roozbeh Dehghannasiri, Byung-Jun Yoon, Edward R. Dougherty. Optimal Experimental Design for Gene Regulatory Networks in the Presence of Uncertainty
951 -- 964Ting Chen, Ulisses Braga-Neto. Statistical Detection of Intrinsically Multivariate Predictive Genes
964 -- 970Jin-Xing Liu, Yong Xu, Chun-Hou Zheng, Heng Kong, Zhihui Lai. RPCA-Based Tumor Classification Using Gene Expression Data

Volume 12, Issue 3

499 -- 0João C. Setubal, Nalvo Almeida. TCBB Special Section on the Brazilian Symposium on Bioinformatics 2013
500 -- 506Marília D. V. Braga, Jens Stoye. Sorting Linear Genomes with Rearrangements and Indels
507 -- 519Christian Höner zu Siederdissen, Ivo L. Hofacker, Peter F. Stadler. Product Grammars for Alignment and Folding
520 -- 530David Hoksza, Daniel Svozil. Multiple 3D RNA Structure Superposition Using Neighbor Joining
531 -- 537Hyrum D. Carroll, Alex C. Williams, Anthony G. Davis, John L. Spouge. Improving Retrieval Efficacy of Homology Searches Using the False Discovery Rate
538 -- 550Adriana Birlutiu, Florence d'Alché-Buc, Tom Heskes. A Bayesian Framework for Combining Protein and Network Topology Information for Predicting Protein-Protein Interactions
551 -- 559Yinglei Song, Chunmei Liu, Zhi Wang. A Machine Learning Approach for Accurate Annotation of Noncoding RNAs
560 -- 567Tahir Mehmood, Jon Bohlin, Lars Snipen. A Partial Least Squares Based Procedure for Upstream Sequence Classification in Prokaryotes
568 -- 578Liang Dong, Bing Shi, Guangdong Tian, Yanbo Li, Bing Wang, MengChu Zhou. An Accurate de novo Algorithm for Glycan Topology Determination from Mass Spectra
579 -- 589Pei Wang, Jinhu Lu, Xinghuo Yu. Colored Noise Induced Bistable Switch in the Genetic Toggle Switch Systems
590 -- 603Sourya Bhattacharyya, Jayanta Mukherjee. COSPEDTree: COuplet Supertree by Equivalence Partitioning of Taxa Set and DAG Formation
604 -- 610Krishnasamy Gopinath, Ramaraj Jayakumararaj, Muthusamy Karthikeyan. DAPD: A Knowledgebase for Diabetes Associated Proteins
611 -- 621Dong-jun Yu, Yang Li, Jun Hu, Xi-Bei Yang, Jing-yu Yang, Hong-bin Shen. Disulfide Connectivity Prediction Based on Modelled Protein 3D Structural Information and Random Forest Regression
622 -- 631Lei Huang, Li Liao, Cathy H. Wu. Evolutionary Model Selection and Parameter Estimation for Protein-Protein Interaction Network Based on Differential Evolution Algorithm
632 -- 643Saurav Basu, Chi Liu, Gustavo Kunde Rohde. Extraction of Individual Filaments from 2D Confocal Microscopy Images of Flat Cells
644 -- 655Yen Kaow Ng, Linzhi Yin, Hirotaka Ono, Shuai Cheng Li. Finding All Longest Common Segments in Protein Structures Efficiently
656 -- 666David L. González-Álvarez, Miguel A. Vega-Rodríguez, Alvaro Rubio-Largo. Finding Patterns in Protein Sequences by Using a Hybrid Multiobjective Teaching Learning Based Optimization Algorithm
667 -- 678Tommaso Mazza, Caterina Fusilli, Chiara Saracino, Gianluigi Mazzoccoli, Francesca Tavano, Manlio Vinciguerra, Valerio Pazienza. Functional Impact of Autophagy-Related Genes on the Homeostasis and Dynamics of Pancreatic Cancer Cell Lines
679 -- 685Hong Xia, Yuanning Liu, Minghui Wang, Ao Li. Identification of Genomic Aberrations in Cancer Subclones from Heterogeneous Tumor Samples
686 -- 694Dandan Song, Jiaxing Chen, Guang Chen, Ning Li, Jin Li, Jun Fan, Dongbo Bu, Shuai Cheng Li. Parameterized BLOSUM Matrices for Protein Alignment
695 -- 704Xiaojun Ding, Jianxin Wang, Alex Zelikovsky, Xuan Guo, Minzhu Xie, Yi Pan. Searching High-Order SNP Combinations for Complex Diseases Based on Energy Distribution Difference
705 -- 711Marcelo Boareto, Jonatas Cesar, Vitor B. P. Leite, Nestor Caticha. Supervised Variational Relevance Learning, An Analytic Geometric Feature Selection with Applications to Omic Datasets
712 -- 725Chih-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

Volume 12, Issue 2

252 -- 253Feng Luo, Xintao Wu. Guest Editorial for Special Section on BIBM 2013
254 -- 261Xingpeng Jiang, Xiaohua Hu, Weiwei Xu, E. K. Park. Predicting Microbial Interactions Using Vector Autoregressive Model with Graph Regularization
262 -- 275Cen Wan, Alex Alves Freitas, João Pedro de Magalhães. Predicting the Pro-Longevity or Anti-Longevity Effect of Model Organism Genes with New Hierarchical Feature Selection Methods
276 -- 288Wei Peng, Jianxin Wang, Yingjiao Cheng, Yu Lu, Fang-Xiang Wu, Yi Pan. UDoNC: An Algorithm for Identifying Essential Proteins Based on Protein Domains and Protein-Protein Interaction Networks
289 -- 297Yongguo Mei, Adria Carbo, Stefan Hoops, Raquel Hontecillas, Josep Bassaganya-Riera. ENISI SDE: A New Web-Based Tool for Modeling Stochastic Processes
298 -- 308Bin Pang, David Schlessman, Xingyan Kuang, Nan Zhao, Daniel Shyu, Dmitry Korkin, Chi-Ren Shyu. An Integrated Approach to Sequence-Independent Local Alignment of Protein Binding Sites
309 -- 321Young-Rae Cho, Yanan Xin, Greg Speegle. P-Finder: Reconstruction of Signaling Networks from Protein-Protein Interactions and GO Annotations
322 -- 334Jong Cheol Jeong, Xue-wen Chen. A New Semantic Functional Similarity over Gene Ontology
335 -- 347Hossam M. Ashtawy, Nihar R. Mahapatra. A Comparative Assessment of Predictive Accuracies of Conventional and Machine Learning Scoring Functions for Protein-Ligand Binding Affinity Prediction
348 -- 359Lina Yang, Yuan Yan Tang, Yang Lu, Huiwu Luo. A Fractal Dimension and Wavelet Transform Based Method for Protein Sequence Similarity Analysis
360 -- 371Savas Konur, Marian Gheorghe. A Property-Driven Methodology for Formal Analysis of Synthetic Biology Systems
372 -- 383Min Li, Yu Lu, Jianxin Wang, Fang-Xiang Wu, Yi Pan. A Topology Potential-Based Method for Identifying Essential Proteins from PPI Networks
384 -- 397Qiang Yu, Hongwei Huo, Jeffrey Scott Vitter, Jun Huan, Yakov Nekrich. An Efficient Exact Algorithm for the Motif Stem Search Problem over Large Alphabets
398 -- 409Xian Zhang, Ligang Wu, Shaochun Cui. An Improved Integral Inequality to Stability Analysis of Genetic Regulatory Networks With Interval Time-Varying Delays
410 -- 421Zhenhua Li, Ying He, Limsoon Wong, Jinyan Li. Burial Level Change Defines a High Energetic Relevance for Protein Binding Interfaces
422 -- 432Gautam Dasarathy, Robert D. Nowak, Sébastien Roch. Data Requirement for Phylogenetic Inference from Multiple Loci: A New Distance Method
433 -- 444Jun Meng, Jing Zhang, Yushi Luan. Gene Selection Integrated with Biological Knowledge for Plant Stress Response Using Neighborhood System and Rough Set Theory
445 -- 454Trevor 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
455 -- 466Bingjing Cai, Haiying Wang, Huiru Zheng, Hui Wang. Identification of Protein Complexes from Tandem Affinity Purification/Mass Spectrometry Data via Biased Random Walk
467 -- 472Xueming Liu, Linqiang Pan. Identifying Driver Nodes in the Human Signaling Network Using Structural Controllability Analysis
473 -- 486Hasan M. Jamil. Improving Integration Effectiveness of ID Mapping Based Biological Record Linkage
487 -- 498W. J. R. M. Priyadarshana, Georgy Sofronov. Multiple Break-Points Detection in Array CGH Data via the Cross-Entropy Method

Volume 12, Issue 1

1 -- 0Ying Xu. Editorial from the Editor-in-Chief
2 -- 3Srinivas Aluru, Donna K. Slonim. Guest Editors' Introduction: Selected Papers from ACM-BCB 2013
4 -- 16Noah M. Daniels, Andrew Gallant, Norman Ramsey, Lenore J. Cowen. MRFy: Remote Homology Detection for Beta-Structural Proteins Using Markov Random Fields and Stochastic Search
17 -- 29Manabu Torii, Cecilia N. Arighi, Gang Li, Qinghua Wang, Cathy H. Wu, K. Vijay-Shanker. RLIMS-P 2.0: A Generalizable Rule-Based Information Extraction System for Literature Mining of Protein Phosphorylation Information
30 -- 39Kun Wang, Avinash Das, Zheng-Mei Xiong, Kan Cao, Sridhar Hannenhalli. Phenotype-Dependent Coexpression Gene Clusters: Application to Normal and Premature Ageing
40 -- 52Fazle Elahi Faisal, Han Zhao, Tijana Milenkovic. Global Network Alignment in the Context of Aging
53 -- 66Haitham Gabr, Andrei Todor, Alin Dobra, Tamer Kahveci. Reachability Analysis in Probabilistic Biological Networks
67 -- 78Yongtao Ye, David Wai-Lok Cheung, Yadong Wang, Siu-Ming Yiu, Qing Zhan, Tak Wah Lam, Hing-Fung Ting. GLProbs: Aligning Multiple Sequences Adaptively
79 -- 91Hui Li, Xiaoyi Li, Murali Ramanathan, Aidong Zhang. Prediction and Informative Risk Factor Selection of Bone Diseases
92 -- 102Michael A. DeJesus, Thomas R. Ioerger. Capturing Uncertainty by Modeling Local Transposon Insertion Frequencies Improves Discrimination of Essential Genes
103 -- 112Matt Spencer, Jesse Eickholt, Jianlin Cheng. A Deep Learning Network Approach to ab initio Protein Secondary Structure Prediction
113 -- 122Bo Liao, Xiong Li, Lijun Cai, Zhi Cao, Haowen Chen. A Hierarchical Clustering Method of Selecting Kernel SNP to Unify Informative SNP and Tag SNP
123 -- 135Shing-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
136 -- 141Ye-tian Fan, Wei Wu, Jie Yang, Wenyu Yang, Rongrong Liu. An Algorithm for Motif Discovery with Iteration on Lengths of Motifs
142 -- 154Man 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
155 -- 165Pawel Górecki, Oliver Eulenstein. Gene Tree Diameter for Deep Coalescence
166 -- 178Chao Wang, Xi Li, Peng Chen, Aili Wang, Xuehai Zhou, Hong Yu. Heterogeneous Cloud Framework for Big Data Genome Sequencing
179 -- 192Wei Peng, Jianxin Wang, Bihai Zhao, Lusheng Wang. Identification of Protein Complexes Using Weighted PageRank-Nibble Algorithm and Core-Attachment Structure
193 -- 204Nan Du, Marc R. Knecht, Mark T. Swihart, Zhenghua Tang, Tiffany R. Walsh, Aidong Zhang. Identifying Affinity Classes of Inorganic Materials Binding Sequences via a Graph-Based Model
205 -- 218Xiangyuan Zhu, Kenli Li, Ahmad Salah, Lin Shi, Keqin Li. Parallel Implementation of MAFFT on CUDA-Enabled Graphics Hardware
219 -- 233Guo-Xian Yu, Huzefa Rangwala, Carlotta Domeniconi, Guoji Zhang, Zili Zhang. Predicting Protein Function Using Multiple Kernels
234 -- 247Judith Keijsper, Tim Oosterwijk. Tractable Cases of (*, 2)-Bounded Parsimony Haplotyping