Table of Contents

• PReach: Reachability in Probabilistic Signaling NetworksHaitham Gabr, Andrei Todor, Helia Zandi, Alin Dobra, Tamer Kahveci. 3 [doi]
• MoTeX: A word-based HPC tool for MoTif eXtractionSolon P. Pissis, Alexandros Stamatakis, Pavlos Pavlidis. 13 [doi]
• Global Network Alignment In The Context Of AgingTijana Milenkovic, Han Zhao, Fazle Elahi Faisal. 23 [doi]
• Haplotype-based prediction of gene alleles using pedigrees and SNP genotypesYuri Pirola, Gianluca Della Vedova, Paola Bonizzoni, Alessandra Stella, Filippo Biscarini. 33 [doi]
• A Semi-Supervised Learning Approach to Integrated Salient Risk Features for Bone DiseasesHui Li, Xiaoyi Li, Murali Ramanathan, Aidong Zhang. 42 [doi]
• Color distribution can accelerate network alignmentMd Mahmudul Hasan, Tamer Kahveci. 52 [doi]
• TCGA Toolbox: an Open Web App Framework for Distributing Big Data Analysis Pipelines for Cancer GenomicsDavid E. Robbins, Alexander Grüneberg, Helena F. Deus, Murat M. Tanik, Jonas S. Almeida. 62 [doi]
• A Study of Temporal Action Sequencing During Consumption of a MealRaul I. Ramos-Garcia, Adam W. Hoover. 68 [doi]
• Binary Response Models for Recognition of Antimicrobial PeptidesElena G. Randou, Daniel Veltri, Amarda Shehu. 76 [doi]
• Quantitative Early Detection of Diabetic FootViktor Chekh, Shuang (Sean) Luan, Mark Burge, Cesar Carranza, Peter Soliz, Elizabeth McGrew, E. Simon Barriga. 86 [doi]
• Reconstructing transcriptional regulatory networks by probabilistic network component analysisJinghua Gu, Jianhua Xuan, Xiao Wang, Ayesha N. Shajahan, Leena Hilakivi-Clarke, Robert Clarke. 96 [doi]
• Protein Structure Refinement by Iterative Fragment ExchangeDebswapna Bhattacharya, Jianlin Cheng. 106 [doi]
• MarkovBin: An Algorithm to Cluster Metagenomic Reads Using a Mixture Modeling of Hierarchical DistributionsTin Chi Nguyen, Dongxiao Zhu. 115 [doi]
• Detecting various types of differential splicing events using RNA-Seq dataNan Deng, Dongxiao Zhu. 124 [doi]
• MRFy: Remote Homology Detection for Beta-Structural Proteins Using Markov Random Fields and Stochastic SearchNoah M. Daniels, Andrew Gallant, Norman Ramsey, Lenore J. Cowen. 133 [doi]
• Improving discrimination of essential genes by modeling local insertion frequencies in transposon mutagenesis dataMichael A. DeJesus, Thomas R. Ioerger. 144 [doi]
• GLProbs: Aligning multiple sequences adaptivelyYongtao Ye, David W. Cheung, Yadong Wang, Siu-Ming Yiu, Qing Zhan, Tak Wah Lam, Hing-Fung Ting. 152 [doi]
• PERGA: A Paired-End Read Guided De Novo Assembler for Extending Contigs Using SVM ApproachXiao Zhu, Henry C. M. Leung, Francis Y. L. Chin, Siu-Ming Yiu, Guangri Quan, Bo Liu, Yadong Wang. 161 [doi]
• Simultaneous determination of subunit and complex structures of symmetric homo-oligomers from ambiguous NMR dataHimanshu Chandola, Bruce Randall Donald, Chris Bailey-Kellogg. 171 [doi]
• Greedy Randomized Search Procedure to Sort Genomes using Symmetric, Almost-Symmetric and Unitary InversionsUlisses Dias, Christian Baudet, Zanoni Dias. 181 [doi]
• A generalized sparse regression model with adjustment of pedigree structure for variant detection from next generation sequencing dataShaolong Cao, Huaizhen Qin, Hong-Wen Deng, Yu-Ping Wang. 191 [doi]
• Text Mining of Protein Phosphorylation Information Using a Generalizable Rule-Based ApproachManabu Torii, Cecilia N. Arighi, Qinghua Wang, Cathy H. Wu, K. Vijay-Shanker. 201 [doi]
• Decomposing Biochemical Networks Into Elementary Flux Modes Using Graph TraversalEhsan Ullah, Calvin Hopkins, Shuchin Aeron, Soha Hassoun. 211 [doi]
• PathCase-MAW: An Online Metabolic Network Analysis WorkbenchA. Ercument Cicek, Xinjian Qi, Ali Cakmak, Stephen R. Johnson, Xu Han, Sami Alshalwi, Gultekin Özsoyoglu. 219 [doi]
• Flexible RNA design under structure and sequence constraints using formal languagesYu Zhou, Yann Ponty, Stéphane Vialette, Jérôme Waldispühl, Yi Zhang, Alain Denise. 229 [doi]
• The TREC Medical Records TrackEllen M. Voorhees. 239 [doi]
• SpliceGrapherXT: From Splice Graphs to Transcripts Using RNA-SeqMark F. Rogers, Christina Boucher, Asa Ben-Hur. 247 [doi]
• Classifying Immunophenotypes With Templates From Flow CytometryAriful Azad, Arif M. Khan, Bartek Rajwa, Saumyadipta Pyne, Alex Pothen. 256 [doi]
• An Ensemble Model for Mobile Device based Arrhythmia DetectionKang Li, Suxin Guo, Jing Gao, Aidong Zhang. 266 [doi]
• Classifying Proteins by Amino Acid Variations of Sequential PatternsEn-Shiun Annie Lee, Andrew K. C. Wong. 276 [doi]
• PRASE: PageRank-based Active Subnetwork ExtractionAyat Hatem, Kamer Kaya, Ümit V. Çatalyürek. 286 [doi]
• Evaluation of Label Dependency for the Prediction of HLA GenesVanja Paunic, Michael Steinbach, Abeer Madbouly, Vipin Kumar. 296 [doi]
• Topological properties of chromosome conformation graphs reflect spatial proximities within chromatinHao Wang, Geet Duggal, Robert Patro, Michelle Girvan, Sridhar Hannenhalli, Carl Kingsford. 306 [doi]
• Improving phosphopeptide identification in shotgun proteomics by supervised filtering of peptide-spectrum matchesSujun Li, Randy J. Arnold, Haixu Tang, Predrag Radivojac. 316 [doi]
• Performance Model Selection for Learning-based Biological Image Analysis on a ClusterJie Zhou, Anthony Brunson, John Winans, Kirk L. Duffin, Nicholas T. Karonis. 324 [doi]
• An Ensemble Topic Model for Sharing Healthcare Data and Predicting Disease RiskAndrew K. Rider, Nitesh V. Chawla. 333 [doi]
• Masher: Mapping Long(er) Reads with Hash-based Genome Indexing on GPUsAnas Abu-Doleh, Erik Saule, Kamer Kaya, Ümit V. Çatalyürek. 341 [doi]
• Suffix-Tree Based Error Correction of NGS Reads Using Multiple Manifestations of an ErrorDaniel M. Savel, Thomas LaFramboise, Ananth Grama, Mehmet Koyutürk. 351 [doi]
• Genomic Sequence Fragment Identification using Quasi-AlignmentAnurag Nagar, Michael Hahsler. 359 [doi]
• Measuring Relatedness Between Scientific Entities in Annotation DatasetsGuillermo Palma, Maria-Esther Vidal, Eric Haag, Louiqa Raschid, Andreas Thor. 367 [doi]
• Identification of gene clusters with phenotype-dependent expression with application to normal and premature ageingKun Wang, Avinash Das, Zheng-Mei Xiong, Kan Cao, Sridhar Hannenhalli. 377 [doi]
• Meta-analysis of Genomic and Proteomic Features to Predict Synthetic Lethality of Yeast and Human CancerMin Wu, Xuejuan Li, Fan Zhang, Xiaoli Li, Chee Keong Kwoh, Jie Zheng. 384 [doi]
• Temporal Relation Identification and Classification in Clinical NotesJennifer D'Souza, Vincent Ng. 392 [doi]
• GapsMis: flexible sequence alignment with a bounded number of gapsCarl Barton, Tomás Flouri, Costas S. Iliopoulos, Solon P. Pissis. 402 [doi]
• An Image-Text Approach for Extracting Experimental Evidence of Protein-Protein Interactions in the Biomedical LiteratureLuis D. Lopez, Jingyi Yu, Cecilia N. Arighi, Manabu Torii, K. Vijay-Shanker, Hongzhan Huang, Cathy H. Wu. 412 [doi]
• An Island-Based Approach for Differential Expression AnalysisAbdallah Eteleeb, Robert M. Flight, Benjamin J. Harrison, Jeffrey C. Petruska, Eric C. Rouchka. 419 [doi]
• Multi-Objective Stochastic Search for Sampling Local Minima in the Protein Energy SurfaceBrian S. Olson, Amarda Shehu. 430 [doi]
• Identifying protein complexes in AP-MS data with negative evidence via soft Markov clusteringYu-Keng Shih, Srinivasan Parthasarathy. 440 [doi]
• Stable Feature Selection with Minimal Independent Dominating SetsLe Shu, Tianyang Ma, Longin Jan Latecki. 450 [doi]
• Designing Autocorrelated GenesRukhsana Yeasmin, Jesmin Jahan Tithi, Jeffrey Chen, Steven Skiena. 458 [doi]
• Cloud4SNP: Distributed Analysis of SNP Microarray Data on the CloudGiuseppe Agapito, Mario Cannataro, Pietro Hiram Guzzi, Fabrizio Marozzo, Domenico Talia, Paolo Trunfio. 468 [doi]
• Application of a MAX-CUT Heuristic to the Contig Orientation Problem in Genome AssemblyPaul Bodily, Mark J. Clement, Quinn Snell, Jared C. Price, Stanley Fujimoto, Nozomu Okuda. 476 [doi]
• Visual Analytics to Optimize Patient-Population Evidence Delivery for Personalized CareKetan K. Mane, Phillips Owen, Charles Schmitt, Kirk C. Wilhelmsen, Kenneth Gersing, Ricardo Pietrobon, Igor Akushevich. 484 [doi]
• A Confidence Measure for Model Fitting with X-Ray Crystallography DataYang Lei, Ramgopal R. Mettu. 489 [doi]
• Heuristics for the Sorting by Length-Weighted Inversion ProblemThiago da Silva Arruda, Ulisses Dias, Zanoni Dias. 498 [doi]
• glu-RNA: aliGn highLy strUctured ncRNAs using only sequence similarityPrapaporn Techa-angkoon, Yanni Sun. 508 [doi]
• Predictive model of the treatment effect for patients with major depressive disorderIgor Akushevich, Julia Kravchenko, Kenneth Gersing, Ketan K. Mane. 518 [doi]
• Towards Independent Particle Reconstruction from Cryogenic Transmission Electron MicroscopyW. Lewis Collier, Jean-Yves Hervé, Lenore Martin. 525 [doi]
• ChainKnot: a comparative H-type pseudoknot prediction tool using multiple ab initio folding toolsJikai Lei, Prapaporn Techa-angkoon, Yanni Sun, Rujira Achawanantakun. 535 [doi]
• A Framework for Identifying Affinity Classes of Inorganic Materials Binding Peptide SequencesNan Du, Marc R. Knecht, Paras N. Prasad, Mark T. Swihart, Tiffany Walsh, Aidong Zhang. 545 [doi]
• Clustering Coefficients in Protein Interaction HypernetworksSuzanne Renick Gallagher, Debra S. Goldberg. 552 [doi]
• A Privacy Preserving Markov Model for Sequence ClassificationSuxin Guo, Sheng Zhong, Aidong Zhang. 561 [doi]
• Classification of Alzheimer Diagnosis from ADNI Plasma Biomarker DataJue Mo, Sana Siddiqui, Stuart Maudsley, Huey Cheung, Bronwen Martin, Calvin A. Johnson. 569 [doi]
• The Forward Stem Matrix: An Efficient Data Structure for Finding Hairpins in RNA Secondary StructuresRichard Beal, Donald A. Adjeroh, Ahmed Abbasi. 575 [doi]
• Fine-Scale Recombination Mapping of High-Throughput Sequence DataCatherine E. Welsh, Chen-Ping Fu, Fernando Pardo-Manuel de Villena, Leonard McMillan. 585 [doi]
• Transforming Genomes Using MOD Files with ApplicationsShunping Huang, Chia-Yu Kao, Leonard McMillan, Wei Wang 0010. 595 [doi]
• Read Annotation Pipeline for High-Throughput Sequencing DataJames Holt, Shunping Huang, Leonard McMillan, Wei Wang. 605 [doi]
• Simulating Anti-adhesive and Antibacterial Bifunctional Polymers for Surface Coating using BioScapeVishakha Sharma, Adriana B. Compagnoni, Matthew Libera, Agnieszka K. Muszanska, Henk J. Busscher, Henny C. van der Mei. 613 [doi]
• Systematic Assessment of RNA-Seq Quantification Tools Using Simulated Sequence DataRaghu Chandramohan, Po-Yen Wu, John H. Phan, May D. Wang. 623 [doi]
• GPU-Optimized Hybrid Neighbor/Cell List Algorithm for Coarse-Grained MD Simulations of Protein and RNA Folding and AssemblyAndrew J. Proctor, Cody A. Stevens, Samuel S. Cho. 633 [doi]
• Gene Set Cultural Algorithm: A Cultural Algorithm Approach to Reconstruct Networks from Gene SetsThair Judeh, Thaer Jayyousi, Lipi R. Acharya, Robert G. Reynolds, Dongxiao Zhu. 641 [doi]
• Predicting protein transport mechanism and immune response using spatial protein motifs and epitopes: a case study of Chlamydophila MOMPF. O. Atanu, E. Oveido-Orta, K. A. Watson. 649 [doi]
• In silico analysis of autoimmune diseases and genetic relationships to vaccination against infectious diseasesPeter B. McGarvey, Baris E. Suzek, Shruti Rao, Subha Madhavan, James N. Baraniuk, Samir Lababidi, Andrea Sutherland, Richard Forshee. 650 [doi]
• Modularity and community detection in Semantic Similarity Networks trough Spectral Based Transformation and Markov ClusteringPietro Hiram Guzzi, Simone Truglia, Marianna Milano, Pierangelo Veltri, Mario Cannataro. 652 [doi]
• Age-Specific Signatures of Glioblastoma at the Genomic, Genetic, and Epigenetic levelsSerdar Bozdag, Aiguo Li, Gregory Riddick, Yuri Kotliarov, Mehmet Baysan, Fabio M. Iwamoto, Margaret C. Cam, Svetlana Kotliarova, Howard A. Fine. 654 [doi]
• SNP2Structure: A public database for mapping and modeling nsSNPs on human protein structuresDifei Wang, Kevin Rosso, Shruti Rao, Lei Song, Varun Singh, Shailendra Singh, Michael Harris, Subha Madhavan. 655 [doi]
• An integrated pharmacogenomic analysis of doxorubicin response using genotype information on DMET genesKrithika Bhuvaneshwar, Michael Harris, Thanemozhi Natarajan, Laura Sheahan, Difei Wang, Subha Madhavan, Mahlet G. Tadesse, John Deeken. 657 [doi]
• Classifying Proteins by Amino Acid Variations of Sequence PatternsEn-Shiun Annie Lee. 659 [doi]
• Using Global Network Alignment In The Context Of AgingTijana Milenkovic, Han Zhao, Fazle Elahi Faisal. 661 [doi]
• Dynamic networks reveal key players in agingFazle Elahi Faisal, Tijana Milenkovic. 662 [doi]
• Computational methods for alternative splicing detection using RNA-seqRuolin Liu, Julie A. Dickerson. 663 [doi]
• Computer Assisted Surgery-Planning for Microwave AblationXi Wen, Hong Wang, Weiming Zhai. 664 [doi]
• Improvement of Protein-Protein Interaction Prediction by Integrating Template-Based and Template-Free Protein DockingMasahito Ohue, Yuri Matsuzaki, Takehiro Shimoda, Takashi Ishida, Yutaka Akiyama. 666 [doi]
• The MEGADOCK project: Ultra-high-speed protein-protein interaction prediction tools on supercomputing environmentsTakehiro Shimoda, Masahito Ohue, Yuri Matsuzaki, Takayuki Fujiwara, Nobuyuki Uchikoga, Takashi Ishida, Yutaka Akiyama. 667 [doi]
• Semi-automated Constraint-based Metabolic Model GenerationJesse R. Walsh, Julie A. Dickerson. 668 [doi]
• Incorporating Gene Annotations as Node Metadata to Improve Network Centrality Measures for Better Node RankingDivya Mistry, Julie A. Dickerson. 669 [doi]
• Protein-protein Docking Using Information from Native Interaction InterfacesIrina Hashmi, Amarda Shehu. 670 [doi]
• Determining miRNA-disease associations using bipartite graph modellingJoseph Nalluri, Bhanu K. Kamapantula, Preetam Ghosh, Debmalya Barh, Neha Jain, Lucky Juneja, Neha Barve. 672 [doi]
• Statistical Methods for Ambiguous Sequence MappingsTamer Aldwairi, Bindu Nanduri, Mahalingam Ramkumar, Dilip Gautam, Michael Johnson, Andy D. Perkins. 674 [doi]
• ngPhylo: N-Gram Modeled Proteins with Substitution Matrices for Phylogenetic AnalysisBrigitte Hofmeister, Brian R. King. 676 [doi]
• Automated protein structure refinement using i3Drefine software and its assessment in CASP10Debswapna Bhattacharya, Jianlin Cheng. 678 [doi]
• A PCA-guided Search Algorithm to Probe the Conformational Space of the Ras ProteinRudy Clausen, Amarda Shehu. 679 [doi]
• A Novel Algorithm for Feature Detection and Hiding from Ultrasound ImagesHaris Godil, Sonya Davey, Raj Shekhar. 681 [doi]
• Bacterial pan-genomes: data representation and analysisLeonid Zaslavsky, Boris Fedorov, Tatiana A. Tatusova. 683 [doi]
• Using Machine Learning to Predict the Health of HIV-Infected PatientsCharles L. Cole, Brian R. King. 684 [doi]
• RNA-Seq analyses to reveal the human transcriptome landscapeNan Deng, Dongxiao Zhu. 686 [doi]
• Initial Results In Using de Novo Motif Inference to Detect Cis-Regulatory ModulesJeffrey A. Thompson, Clare Bates Congdon. 687 [doi]
• Comparative network analysis of gene co-expression networks reveals the conserved and species-specific functions of cell-wall related genes between Arabidopsis and PoplarDaifeng Wang, Eric Pan, Gang Fang, Sunita Kumari, Fei He, Doreen Ware, Sergei Maslov, Mark Gerstein. 689 [doi]
• Reachability analysis in large probabilistic biological networksAndrei Todor, Haitham Gabr, Alin Dobra, Tamer Kahveci. 691 [doi]
• Scheduling of virtual screening application on multi-user pilot-agent platform on grid/cloud to optimize the stretchBui The Quang, Nguyen Hong Quang, Emmanuel Medernach, Vincent Breton. 692 [doi]
• Exploring Local Features and the Bag-of-Visual-Words Approach for Bioimage ClassificationAfzal Godil, Zhouhui Lian, Asim Wagan. 694 [doi]
• Quality of Care and Electronic Health Record SystemsArshia Khan, John Grillo. 696 [doi]
• Prediction of Biological Protein-protein Interaction Types Using Short-Linear MotifsManish Pandit, Luis Rueda, Alioune Ngom. 698 [doi]
• Conditional Random Field for Candidate Gene PrioritizationBinqing Xie, Gady Agam, Natalia Maltsev, T. Conrad Gilliam. 700 [doi]
• Quantum Sequence Analysis: A New Alignment-free Technique For Analyzing Sequences in Feature SpaceMosaab Daoud. 702 [doi]
• Predicting Breast Cancer Patient Survival Using Machine LearningDavid Solti, Haijun Zhai. 704 [doi]
• ngsShoRT: A Software for Pre-processing Illumina Short Read Sequences for De Novo Genome AssemblyChuming Chen, Sari S. Khaleel, Hongzhan Huang, Cathy H. Wu. 706 [doi]
• Role of Quality in Electronic Health Record SystemsArshia Khan, John Grillo. 708 [doi]
• Sparse and Stable Reconstruction of Genetic Regulatory Networks Using Time Series Gene Expression DataRoozbeh Manshaei, Matthew Kyan. 710 [doi]
• Listing Sorting Sequences of Reversals and TranslocationsAmritanjali, G. Sahoo. 712 [doi]
• Modularity and community detection in Semantic Similarity Networks trough Spectral Based Transformation and Markov ClusteringPietro Hiram Guzzi, Marco Mina, Concettina Guerra, Mario Cannataro. 714 [doi]
• decisivatoR: an R infrastructure package that addresses the problem of phylogenetic decisivenessIlya Y. Zhbannikov, Joseph W. Brown, James A. Foster. 716 [doi]
• Estimating the Number of Manually Segmented Cellular Objects Required to Evaluate the Performance of a Segmentation AlgorithmAdele P. Peskin, Joe Chalfoun, Karen Kafadar, John T. Elliott. 718 [doi]
• Abstraction of Kinetic Models For Biochemical NetworksCalvin Hopkins, Soha Hassoun. 720 [doi]
• Co-occurrence Clusters of Aligned Pattern ClustersSanderz Fung. 721 [doi]
• Three-Dimensional Spot Detection in Ratiometric Fluorescence Imaging For Measurement of Subcellular OrganellesWilliam W. Lau, Calvin A. Johnson, Sara Lioi, Joseph A. Mindell. 722 [doi]
• Evaluating theoretical models of protein interaction network evolution without seed graphsTodd A. Gibson, Debra S. Goldberg. 724 [doi]
• The Atomizer: Extracting Implicit Molecular Structure from Reaction Network ModelsJosé Juan Tapia, James R. Faeder. 726 [doi]
• Studies of biological networks with statistical model checking: application to immune system cellsNatasa Miskov-Zivanov, Paolo Zuliani, Edmund M. Clarke, James R. Faeder. 728 [doi]
• An Algorithm for Constructing Hypothetical Evolutionary Trees Using Common Mutation Similarity MatricesPeter Z. Revesz. 730 [doi]
• Predicting Protein Families using Protein Shape ContextJun Tan, Donald Adjeroh. 733 [doi]
• Fast and Accurate Structure-Based Prediction of Resistance to the HIV-1 Integrase Inhibitor RaltegravirMajid Masso. 735 [doi]
• Improving the Prediction of Kinase Binding Affinity Using Homology ModelsJeffrey Chyan, Mark Moll, Lydia E. Kavraki. 741 [doi]
• A Constrained K-shortest Path Algorithm to Rank the Topologies of the Protein Secondary Structure Elements Detected in CryoEM Volume MapsKamal Al-Nasr, Lin Chen, Desh Ranjan, Mohammad Zubair, Dong-Si, Jing He. 749 [doi]
• Exploring the Structure Space of Wildtype Ras Guided by Experimental DataRudy Clausen, Amarda Shehu. 756 [doi]
• Beta-sheet Detection and Representation from Medium Resolution Cryo-EM Density MapsDong-Si, Jing He. 764 [doi]
• Informatics-driven Protein-protein DockingIrina Hashmi, Amarda Shehu. 771 [doi]
• An Evolutionary Conservation & Rigidity Analysis Machine Learning Approach for Detecting Critical Protein ResiduesFilip Jagodzinski, Bahar Akbal-Delibas, Nurit Haspel. 779 [doi]
• Multi-Resolution Rigidity-Based Sampling of Protein Conformational PathsDong Luo, Nurit Haspel. 786 [doi]
• A Combined Molecular Dynamics, Rigidity Analysis Approach for Studying Protein ComplexesBrian Orndorff, Filip Jagodzinski. 793 [doi]
• Relating mammalian replication program to large-scale chromatin foldingBenjamin Audit, Antoine Baker, R. E. Boulos, H. Julienne, Alain Arneodo, C. L. Chen, Yves D'Aubenton-Carafa, Claude Thermes, Arach Goldar, Guillaume Guilbaud, Aurélien Rappailles, Olivier Hyrien. 799 [doi]
• Chromatin structure fully determines replication timing program in human cellsSven Bilke, Yevgeniy Gindin, Paul S. Meltzer. 811 [doi]
• Unsupervised pattern discovery in human chromatin structure through genomic segmentationMichael M. Hoffman, Orion J. Buske, Jie Wang, Zhiping Weng, Jeff A. Bilmes, William Stafford Noble. 813 [doi]
• iAtheroSim: atherosclerosis process simulator on smart devicesFrancesco Pappalardo, Marzio Pennisi, Ferdinando Chiacchio, Salvatore Musumeci, Santo Motta. 815 [doi]
• Characterizing Amino Acid Variations of Scavenger Receptors by Class Information GainEn-Shiun Annie Lee, Fiona J. Whelan, Dawn M. E. Bowdish, Andrew K. C. Wong. 818 [doi]
• Biomarkers in Immunology: from Concepts to ApplicationsPing Zhang 0008, Lou Chitkushev, Vladimir Brusic, Guanglan Zhang. 826 [doi]
• Landscape of neutralizing assessment of monoclonal antibodies against dengue virusJing Sun, Guanglan Zhang, Lars Rønn Olsen, Ellis L. Reinherz, Vladimir Brusic. 836 [doi]
• HPVdb: a Data Mining System for Knowledge Discovery in Human Papillomavirus with Applications in T cell Immunology and VaccinologyGuanglan Zhang, Angelika Riemer, Derin B. Keskin, Lou Chitkushev, Ellis L. Reinherz, Vladimir Brusic. 843 [doi]
• DNA Vaccine Design for Chikungunya Virus Based On the Conserved Epitopes Derived from Structural ProteinParvez Singh Slathia. 849 [doi]
• Defining Functional Redundancy of Epitope Data as Potential Antigenic Cross-ReactivitySalvador Eugenio C. Caoili. 851 [doi]
• Identifying Pathway Proteins in Networks using ConvergenceKathryn Dempsey, Hesham H. Ali. 853 [doi]
• A Neural-network Algorithm for All k Shortest Paths ProblemKun Zhao, Abdoul Sylla. 861 [doi]
• Revealing Protein Structures by Co-Occurrence Clustering of Aligned Pattern ClustersSanderz Fung, En-Shiun Annie Lee, Andrew K. C. Wong. 869 [doi]
• Comparative analysis of network algorithms to address modularity with gene expression temporal dataSuhaib Mohammed. 876 [doi]
• MEGADOCK-GPU: Acceleration of Protein-Protein Docking Calculation on GPUsTakehiro Shimoda, Takashi Ishida, Shuji Suzuki, Masahito Ohue, Yutaka Akiyama. 883 [doi]
• pXAlign: A parallel implementation of XAlignAditi A. Magikar, John A. Springer. 890 [doi]
• GaitTrack: Health Monitoring of Body Motion from Spatio-Temporal Parameters of Simple Smart PhonesQian Cheng, Joshua Juen, Yanen Li, Valentin Prieto-Centurion, Jerry A. Krishnan, Bruce R. Schatz. 897 [doi]
• Aggregating Personal Health Messages for Scalable Comparative Effectiveness ResearchJason H. D. Cho, Vera Q. Z. Liao, Yunliang Jiang, Bruce R. Schatz. 907 [doi]
• Locating Discharge Medications in Natural Language SummariesSimon Diemert, Morgan Price, Jens H. Weber. 917 [doi]
• Evidence of a Pathway of Reduction in Bacteria: Reduced Quantities of Restriction Sites Impact tRNA Activity in a Trial SetOliver Bonham-Carter, Lotfollah Najjar, Dhundy Bastola. 926 [doi]
• Mobility Patterns of Doctors Using Electronic Health Records on iPadsAllan C. Lin, Meng-Hsiu Chang, Mike Y. Chen, Travis Yu, Lih-Ching Chou, Dian-Je Tsai, Jackey Wang. 933 [doi]
• Modeling Incidental Findings in Radiology RecordsEamon Johnson, W. Christopher Baughman, Gultekin Özsoyoglu. 940 [doi]
• Enforcing Minimum Necessary Access in Healthcare Through Integrated Audit and Access ControlPaul Martin, Aviel D. Rubin, Rafae Bhatti. 946 [doi]