Table of Contents

• Integrative analysis of methylation and gene expression data in TCGAYihua Liu, Peng Qiu. 1-4 [doi]
• Hierarchical Bayesian methods for integration of various types of genomics dataElizabeth M. Jennings, Jeffrey S. Morris, Raymond J. Carroll, Ganiraju Manyam, Veerabhadran Baladandayuthapani. 5-8 [doi]
• Anticancer drug sensitivity analysis: An integrated approach applied to Erlotinib sensitivity prediction in the CCLE databaseRanadip Pal, Noah Berlow, Saad Haider. 9-12 [doi]
• Integration of multiple data sources for identifying functional modules using Bayesian networkJinlian Wang, Hongyan Yuan, Mahlet G. Tadesse, Habtom W. Ressom. 13-17 [doi]
• Integrating multi-platform genomic data using hierarchical Bayesian relevance vector machinesSanvesh Srivastava, Wenyi Wang, Pascal O. Zinn, Rivka R. Colen, Veerabhadran Baladandayuthapani. 18-21 [doi]
• Integration of imaging and systems biology to study treatment of medulloblastomaSean S. Wang, Olga C. Rodriguez, Ye Tian, Shaozhen Ye, Emanual F. Petricoin, Chris Albanese. 22-25 [doi]
• Fast DNA barcode generating algorithm using Radix Coding methodAmir Nikooienejad, Richard Metz, Byung-Jun Yoon, Charles D. Johnson. 26-30 [doi]
• Design of short barcodes for next generation sequencing of DNA and RNASteffen Schober, Katharina Mir, Klaus Neuhaus, Martin Bossert. 31-34 [doi]
• A message passing algorithm for reference-guided sequence assembly from high-throughput sequencing dataXiaohu Shen, Haris Vikalo. 35-37 [doi]
• A comparative study of methods for detecting small somatic variants in disease-normal paired next generation sequencing dataQingguo Wang, Zhongming Zhao. 38-41 [doi]
• A Bayesian model for SNP discovery based on next-generation sequencing dataYanxun Xu, Xiaofeng Zheng, Yuan Yuan, Marcos R. Estecio, Jean-Pierre Issa, Yuan Ji, Shoudan Liang. 42-45 [doi]
• Utilizing RNA-Seq data for cancer network inferenceYing Cai, Bernard Fendler, Gurinder S. Atwal. 46-49 [doi]
• Optimal therapeutic methods with random-length response in probabilistic boolean networksMohammadmahdi R. Yousefi, Aniruddha Datta, Edward R. Dougherty. 50-53 [doi]
• A new phenotypically constrained control policy in boolean networks based on basins of attractionXiaoning Qian. 54-57 [doi]
• Combination therapy design for targeted therapeutics from a drug-protein interaction perspectiveSaad Haider, Noah Berlow, Ranadip Pal, Lara E. Davis, Charles Keller. 58-61 [doi]
• Genome-wide meta-regression of gene-environment interactionXiaoxiao Xu, Gang Shi, Arye Nehorai. 62-65 [doi]
• Feature ranking based on synergy networks to identify prognostic markers in DPT-1Amin Ahmadi-Adl, Xiaoning Qian, Ping Xu, Kendra Vehik, Jeffrey P. Krischer. 66-69 [doi]
• Improving the flexibility of RNA-Seq data analysis pipelinesJohn H. Phan, Po-Yen Wu, May D. Wang. 70-73 [doi]
• Accurate identification of significant aberrations in contaminated cancer genomeXuchu Hou, Guoqiang Yu, Xiguo Yuan, Bai Zhang, Ie-Ming Shih, Zhen Zhang, Robert Clarke, Subha Madhavan. 74-77 [doi]
• A comparison of periodicity profile methods for sequence analysisManas Bellani, Julien Epps, Gavin A. Huttley. 78-81 [doi]
• NMF based approach for finding recurrent aberrations in DNA copy number dataMohammed Elhenawy, Guoqiang Yu. 82-85 [doi]
• MiB: A comparative assembly processing pipelineBilal Wajid, Erchin Serpedin, Mohamed N. Nounou, Hazem N. Nounou. 86-89 [doi]
• OBGene: Optimal barcode generator for NGS experimentsEsmaeil Atashpaz-Gargari, Mohammad Shahrokh Esfahani, Richard Metz, Charles D. Johnson. 90-94 [doi]
• Determining the relative prevalence of different subpopulations in heterogeneous cancer tissueAnwoy Kumar Mohanty, Aniruddha Datta, Jijayanagaram Venkatraj. 95-96 [doi]
• Detection and clustering of palindrome in genome sequences by DCT-II methodAhsan Zaigam Rizvi, C. Bhattacharya. 97-98 [doi]
• Cell type specific analysis of human transcriptome dataXiaoxiao Xu, Arye Nehorai, Joseph Dougherty. 99-100 [doi]
• Comprehensive analyses of tumor suppressor genes in protein-protein interaction networks: A topological perspectiveMin Zhao, Jingchun Sun, Zhongming Zhao. 101-102 [doi]
• An investigation of clinical outcome prediction from integrative genomic profiles in ovarian cancerLin Zhang 0015, Hui Liu, Tzu-Hung Hsiao, Yidong Chen, Yufei Huang. 103-106 [doi]
• Detection of short exons in DNA sequences using complex wavelet transform of structural featuresIvo Provaznik, Vladimira Kubicova, Helena Skutkova, Jiri Nedved, Ewaryst Tkacz, Petr Babula, René Kizek. 107-110 [doi]
• Multiclass cancer-microarray classification algorithm with pair-against-all redundancyMattia Bosio, Pau Bellot Pujalte, Philippe Salembier, Albert Oliveras-Vergés. 111-112 [doi]
• Sparse Bayesian graphical models for RPPA time course dataRiten Mitra, Peter Müller, Yuan Ji, Gordon B. Mills, Yiling Lu. 113-117 [doi]
• A new algorithm for predicting competing endogenous rnasMario Flores, Yufei Huang. 118-121 [doi]
• Logistic principal component analysis for rare variants in gene-environment interaction analysisMeng Lu, Hye-Seung Lee, David Hadley, Jianhua Z. Huang, Xiaoning Qian. 122-125 [doi]
• A non-parametric approach for estimating stromal contamination in cancer samplesMohammed Elhenawy, Xuchu Hou, Guoqiang Yu. 126-129 [doi]
• Latent feature decompositions for integrative analysis of diverse high-throughput genomic dataKarl B. Gregory, Kevin R. Coombes, Amin Momin, Luc Girard, Lauren A. Byers, Steven Lin, Michael Peyton, John V. Heymach, John D. Minna, Veerabhadran Baladandayuthapani. 130-134 [doi]
• A Bayesian graphical model for integrative analysis of TCGA dataYanxun Xu, Jie Zhang, Yuan Yuan, Riten Mitra, Peter Müller, Yuan Ji. 135-138 [doi]
• Network-based methods to identify highly discriminating subsets of biomarkersSeyed Javad Sajjadi, Xiaoning Qian, Bo Zeng. 139-142 [doi]
• Information theoretic feature selection for high dimensional metagenomic dataGregory Ditzler, Gail Rosen, Robi Polikar. 143-146 [doi]
• Finding robust pathway markers for cancer classificationNavadon Khunlertgit, Byung-Jun Yoon. 147-150 [doi]
• A statistical test for intrinsically multivariate predictive genesTing Chen, Ulisses Braga-Neto. 151-154 [doi]
• Identification of functional genomic regions with copy number alteration in liver cancerTzu-Hung Hsiao, Hung-I Harry Chen, Yidong Chen. 155-158 [doi]
• Inferring gene functions from metabolic reactionsGünhan Gülsoy, Tamer Kahveci. 159-163 [doi]
• Optimal Bayesian classification and its application to gene regulatory networksLori A. Dalton, Edward R. Dougherty. 164-167 [doi]
• Inferring weighted and directed gene interaction networks from gene expression data using the phi-mixing coefficientNitin K. Singh, Mehmet Eren Ahsen, Shiva Mankala, M. Vidyasagar, Michael A. White. 168-171 [doi]
• Inference of time-varying gene networks using constrained and smoothed Kalman filteringGhulam Rasool, Nidhal Bouaynaya. 172-175 [doi]
• Determining gene function in boolean networks using boolean satisfiabilityPey-Chang Kent Lin, Sunil P. Khatri. 176-179 [doi]
• External control of probabilistic boolean networks using inhomogeneous Markov chainsTimothy M. Josserand. 180-182 [doi]
• Toward exhaustive gating of flow cytometry dataPeng Qiu. 183-186 [doi]
• Normalization of LC-MS data using Gaussian processMohammad R. Nezami Ranjbar, Mahlet G. Tadesse, Yue Joseph Wang, Habtom W. Ressom. 187-190 [doi]
• Robust MS serum sample classification in proteomics by the use of inverse problemsPascal Szacherski, Jean-François Giovannelli, Laurent Gerfault, Audrey Giremus, Pierre Grangeat. 191-194 [doi]
• Variability assessment of LC-MS experiments and its application to experimental design and difference detectionYi Zhao, Tsung-Heng Tsai, Cristina Di Poto, Lewis K. Pannell, Mahlet G. Tadesse, Habtom W. Ressom. 195-198 [doi]
• An SILAC quantification algorithm for LC-FTMSJian Cui, Xuepo Ma, Xiaolin Zhang, William Haskins, Jiangiu (Michelle) Zhang. 199-202 [doi]
• An evaluation for merging signaling pathways by using protein-protein interaction dataXiaogang Wu, Jake Y. Chen. 203-206 [doi]