Table of Contents

• Computational analysis and modelling of intra-host adaptation of hepatitis C virus: The role of immune cross-reactivity of HCV quasispeciesPavel Skums, David S. Campo, Zoya Dimitrova, Leonid Bunimovich, Yuri Khudyakov. 1 [doi]
• Workshop: Reconstructing the organization of cancer genomesLayla Oesper, Benjamin J. Raphael. 1 [doi]
• Multicore and GPU algorithms for nussinov RNA foldingJunjie Li, Sanjay Ranka, Sartaj Sahni. 1-2 [doi]
• Optimizing pooling strategies for the massive next-generation sequencing of viral samplesPavel Skums, Olga Glebova, Alex Zelikovsky, Ion I. Mandoiu, Yuri Khudyakov. 1 [doi]
• Hepatitis C virus genetic association to rate of liver fibrosis progressionJames Lara, Yuri Khudyakov, F. Xavier Lopez-Labrador, Fernando González-Candelas, Marina Berenguer. 1 [doi]
• FAC-PIN: Fast agglomerative clustering method for functional modules and protein complex identification in PINsMohammad Shamsur Rahman, Alioune Ngom. 1-6 [doi]
• Poster: Clustering-based approach for constructing reliable radiation hybrid framework mapsRaed I. Seetan, Anne M. Denton, Omar Al Azzam, Ajay Kumar, Muhammad Javed Iqbal, Shahryar F. Kianian. 1 [doi]
• Probing of viral diversity by global haplotype predictionArmin Töpfer, Francesca Di Giallonardo, Karin J. Metzner, Huldrych F. Günthard, Niko Beerenwinkel. 1 [doi]
• Using triangulation to include target structure improves drug resistance prediction accuracyRobert W. Harrison, Xiaxia Yu, Irene T. Weber. 1 [doi]
• Rigidity and flexibility of protein-nucleic acid complexesEmily Flynn, Filip Jagodzinski, Sharon Pamela Santana, Ileana Streinu. 1-6 [doi]
• Scalable heuristics for clustering biological graphsInna Rytsareva, Ananth Kalyanaraman, Kishori M. Konwar, Steven J. Hallam. 1-6 [doi]
• Large-scale metagenomic clustering via quasi clique enumeration and read assignment ambiguity resolutionSrinivas Aluru. 1 [doi]
• Differential gene expression analysis using coexpression and RNA-Seq dataEi-Wen Yang, Thomas Girke, Tao Jiang. 1 [doi]
• An unsupervised learning approach to assembly validationIrena Lanc, Scott J. Emrich. 1-2 [doi]
• Comparing analysis engines for generated micro-patterned, actin imagesJason M. Kinser, Stephen J. Lockett, Thomas Turbyville, Karlyne M. Reilly, John Beutler. 1-5 [doi]
• Extraction of gene regulatory networks from biological literatureKarthik Tangirala, Doina Caragea. 1-6 [doi]
• Triangulation heuristics for maximum character compatibilityRob Gysel, Dan Gusfield, Kristian Stevens. 1-2 [doi]
• Poster: User-centered query expansion model for health disparities researchSanghoon Lee, Saeid Belkasim. 1 [doi]
• Monte-Carlo Regression algorithm for isoform frequency estimation from RNA-Seq dataAdrian Caciula, Alex Zelikovsky, Serghei Mangul, James Lindsay, Ion I. Mandoiu. 1 [doi]
• Systematic analysis of global features and model building for recognition of antimicrobial peptidesElena G. Randou, Daniel Veltri, Amarda Shehu. 1-6 [doi]
• kGEM: An EM-based algorithm for local reconstruction of viral quasispeciesAlexander Artyomenko, Nicholas Mancuso, Alex Zelikovsky, Pavel Skums, Ion I. Mandoiu. 1 [doi]
• A randomized algorithm for aligning DNA sequences to reference genomesNam S. Vo, Quang Tran, Nobal Niraula, Vinhthuy Phan. 1-6 [doi]
• Predicting bacterial functional traits from whole genome sequences using random forestWei Zhang, Erliang Zeng, Scott J. Emrich, Joshua Livermore, Dan Liu, Stuart E. Jones. 1-2 [doi]
• Mutational robustness of hepatitis C virus intra-host variantsDavid S. Campo, Zoya Dimitrova, Pavel Skums, Yuri Khudyakov. 1 [doi]
• Towards whole transcriptome deconvolution using single-cell dataJames Lindsay, Craig E. Nelson, Ion I. Mandoiu. 1 [doi]
• Efficient algorithms for sequence assemblySanguthevar Rajasekaran, Subrata Saha. 1 [doi]
• An improved statistics-based backbone torsion potential energy for protein loop structure modelingIonel Rata, Kyle Wessells, Yaohang Li. 1-6 [doi]
• A deterministic-stochastic crossover algorithm for simulation of complex biochemical systemsGuoxing Fu, Amit Sabnis, Robert W. Harrison. 1-7 [doi]
• HIV drug resistance prediction using multiple regressionXiaxia Yu, Robert W. Harrison, Irene T. Weber. 1-2 [doi]
• Parallel analysis of large graph-structured data in genomics and proteomicsKamesh Madduri. 1 [doi]
• Practical software for big genomics dataBen Langmead. 1 [doi]
• Computational prediction of hinge axes in proteinsRittika Shamsuddin, Milka Doktorova, Sheila Jaswal, Audrey Lee-St. John, Kathryn McMenimen. 1-2 [doi]
• Poster: Auto-reduction of features for containing communication costs in a distributed privacy-preserving clinical decision support systemGeorge Mathew, Zoran Obradovic. 1 [doi]
• PMS6MC: A multicore algorithm for motif discoveryShibdas Bandyopadhyay, Sartaj Sahni, Sanguthevar Rajasekaran. 1-5 [doi]
• Extracting association rules from liver cancer data using the FP-growth algorithmFabiola M. R. Pinheiro, Mu-Hsing Kuo, Alex Thomo, Jeff Barnett. 1 [doi]
• Reference assisted nucleic acid sequence reconstruction from mass spectrometry dataGabriel Ilie, Alex Zelikovsky, Ion I. Mandoiu. 1 [doi]
• Poster: Quantification of correlations between sleep spindles in EEG for patients with sleep apneaRafael Toledo F. de Souza, José Luiz Rybarczyk Filho, Ney Lemke, Suzana V. Schonwald, Emerson L. de Santa-Helena, Gunther J. L. Gerhardt. 1 [doi]
• Template-based prediction of protein 8-state secondary structuresAshraf Yaseen, Yaohang Li. 1-2 [doi]
• POSTER: "Pseudomonas fluorescens Strain NCIMB 11764, a unique bacterium with cyanide adaptation features"Claudia Vilo, Daniel Kunz, Xiang Gao, Qunfeng Dong. 1 [doi]
• Transcriptome assembly and quantification from Ion Torrent RNA-Seq dataSerghei Mangul, Sahar Al Seesi, Ion I. Mandoiu, Adrian Caciula, Alex Zelikovsky, Dumitru Brinza. 1 [doi]
• Workflow-driven programming paradigms for distributed analysis of biological big dataIlkay Altintas. 1 [doi]
• Higher-order representations of protein structure spaceKevin Molloy, M. Jennifer Van, Daniel Barbara, Amarda Shehu. 1-2 [doi]
• Identifying significant mutations in large cohorts of cancer genomesFabio Vandin, Eli Upfal, Benjamin J. Raphael. 1 [doi]
• Estimation of viral population structure from amplicon-based readsNicholas Mancuso, Alexander Artyomenko, Alex Zelikovsky, Pavel Skums, Ion I. Mandoiu. 1 [doi]
• st International Workshop on Big Data in Life SciencesAnanth Kalyanaraman, Jaroslaw Zola. 1 [doi]
• Space-efficient read indexing and retrieval based on compressed de Bruijn graphsMeznah Almutairy, Jordan A. Fish, C. Titus Brown. 1 [doi]
• A memory-efficient algorithm to obtain splicing graphs and de novo expression estimates from de Bruijn graphs of RNA-seq dataSing-Hoi Sze, Aaron M. Tarone. 1 [doi]
• Deep sequencing of ribosomal footprints for studying genome-wide mRNA translation in plantsKaren Merchante, Qiwen Hu, Anna N. Stepanova, Jose M. Alonso, Steffen Heber. 1 [doi]
• An SVM-based approach for genotyping deletions and insertions with population sequence readsChong Chu, Jin Zhang, Yufeng Wu. 1 [doi]
• Memory efficient assembly of human genomeFarhad Hormozdiari, Eleazar Eskin. 1 [doi]