Table of Contents

• Extracting phylogenetic signals from multi-labeled gene trees and its significance for species tree constructionRyan Cobb, Rasha Elhesha, J. Gordon Burleigh, Tamer Kahveci. 3-12 [doi]
• Automated ranking of stem cell colonies by translating biological rules to computational modelsAdele Peskin, Steve Lund, Ya-Shian Li-Baboud, Michael Halter, Anne L. Plant, Peter Bajcsy. 13-22 [doi]
• Docking features for predicting binding loss due to protein mutationNorman Goodacre, Nathan Edwards, Mark Danielsen, Peter Uetz, Cathy Wu. 23-32 [doi]
• Resolving healthcare forum posts via similar thread retrievalJason H. D. Cho, Parikshit Sondhi, ChengXiang Zhai, Bruce R. Schatz. 33-42 [doi]
• A novel classification method for predicting acute hypotensive episodes in critical careSakyajit Bhattacharya, Vaibhav Rajan, Vijay Huddar. 43-52 [doi]
• Towards a natural walking monitor for pulmonary patients using simple smart phonesJoshua Juen, Qian Cheng, Bruce R. Schatz. 53-62 [doi]
• Fast dendrogram-based OTU clustering using sequence embeddingThuy-Diem Nguyen, Bertil Schmidt, Chee Keong Kwoh. 63-72 [doi]
• Analysing the distribution of synaptic vesicles using a spatial point process modelMahdieh Khanmohammadi, Rasmus Waagepetersen, Nicoletta Nava, Jens Rondel Nyengaard, Jon Sporring. 73-78 [doi]
• Scaled sparse high-dimensional tests for localizing sequence variantsShaolong Cao, Huaizhen Qin, Jian Li, Hong-Wen Deng, Yu-Ping Wang. 79-87 [doi]
• Automating risk of bias assessment for clinical trialsIain James Marshall, Joël Kuiper, Byron C. Wallace. 88-95 [doi]
• Leveraging hierarchy in medical codes for predictive modelingAnima Singh, Girish Nadkarni, John V. Guttag, Erwin P. Bottinger. 96-103 [doi]
• Amb-EM: a SNP-based prediction of HLA alleles using ambiguous HLA dataVanja Paunic, Michael Steinbach, Abeer Madbouly, Vipin Kumar. 104-113 [doi]
• Unconstrained gene tree diameters for deep coalescencePawel Górecki, Jaroslaw Paszek, Oliver Eulenstein. 114-121 [doi]
• Integrated miRNA and mRNA analysis of time series microarray dataJulian Dymacek, Nancy Lan Guo. 122-127 [doi]
• CNVnet: combining sparse learning and biological networks to capture joint effect of copy number variantsZhiyong Wang, Jinbo Xu, Xinghua Shi. 128-137 [doi]
• SimConcept: a hybrid approach for simplifying composite named entities in biomedicineChih-Hsuan Wei, Robert Leaman, Zhiyong Lu. 138-146 [doi]
• InstantGenotype: a non-parametric model for genotype inference using microarray probe intensitiesChia-Yu Kao, Chen-Ping Fu, Leonard McMillan. 147-154 [doi]
• Graph-theoretic analysis of epileptic seizures on scalp EEG recordingsNimit Dhulekar, Basak Oztan, Bülent Yener, Haluk O. Bingol, Gulcin Irim, Berrin Aktekin, Canan Aykut-Bingöl. 155-163 [doi]
• Improving identification of key players in aging via network de-noisingBoyoung Yoo, Huili Chen, Fazle Elahi Faisal, Tijana Milenkovic. 164-173 [doi]
• FStitch: a fast and simple algorithm for detecting nascent RNA transcriptsJoseph Azofeifa, Mary A. Allen, Manuel E. Lladser, Robin D. Dowell. 174-183 [doi]
• A Hadoop-Galaxy adapter for user-friendly and scalable data-intensive bioinformatics in GalaxyLuca Pireddu, Simone Leo, Nicola Soranzo, Gianluigi Zanetti. 184-191 [doi]
• Joint inference for end-to-end coreference resolution for clinical notesPrateek Jindal, Dan Roth, Carl A. Gunter. 192-201 [doi]
• IPED2: inheritance path based pedigree reconstruction algorithm for complicated pedigreesDan He, Zhanyong Wang, Laxmi Parida, Eleazar Eskin. 202-210 [doi]
• icuARM-II: improving the reliability of personalized risk prediction in pediatric intensive care unitsChihwen Cheng, Nikhil Chanani, Kevin Maher, May D. Wang. 211-219 [doi]
• Understanding user intents in online health forumsThomas Zhang, Jason H. D. Cho, ChengXiang Zhai. 220-229 [doi]
• Learning parameter sets for alignment advisingDan F. DeBlasio, John D. Kececioglu. 230-239 [doi]
• Prioritization of genomic locus pairs for testing epistasisMarzieh Ayati, Mehmet Koyutürk. 240-248 [doi]
• Pathway analysis with signaling hypergraphsAnna M. Ritz, T. M. Murali. 249-258 [doi]
• Couplet supertree by equivalence partitioning of taxa set and DAG formationSourya Bhattacharyya, Jayanta Mukhopadhyay. 259-268 [doi]
• A multiscale hybrid evolutionary algorithm to obtain sample-based representations of multi-basin protein energy landscapesRudy Clausen, Amarda Shehu. 269-278 [doi]
• Knowledge-based search and multi-objective filters: proposed structural models of GPCR dimerizationIrina Hashmi, Daniel Veltri, Nadine Kabbani, Amarda Shehu. 279-288 [doi]
• AccuRMSD: a machine learning approach to predicting structure similarity of docked protein complexesBahar Akbal-Delibas, Marc Pomplun, Nurit Haspel. 289-296 [doi]
• Utilizing twilight zone sequence similarities to increase the accuracy of protein 3D structure comparisonAleksandar Poleksic, Paul Gray. 297-303 [doi]
• Mining massive SNP data for identifying associated SNPs and uncovering gene relationshipsAmy Webb, Aaron Albin, Zhan Ye, Majid Rastegar-Mojarad, Kun Huang, Jeffrey D. Parvin, Wolfgang Sadee, Lang Li, Simon Lin, Yang Xiang. 304-313 [doi]
• Spectral feature selection and its application in high dimensional gene expression studiesZixing Wang, Peng Qiu, Wenlong Xu, Yin Liu. 314-320 [doi]
• SideEffectPTM: an unsupervised topic model to mine adverse drug reactions from health forumsSheng Wang, Yanen Li, Duncan Ferguson, ChengXiang Zhai. 321-330 [doi]
• Using mobile phones to simulate pulse oximeters: gait analysis predicts oxygen saturationQian Cheng, Joshua Juen, Bruce R. Schatz. 331-340 [doi]
• A method for reducing the severity of epidemics by allocating vaccines according to centralityKrzysztof Drewniak, Joseph Helsing, Armin R. Mikler. 341-350 [doi]
• Data mining to aid beam angle selection for intensity-modulated radiation therapyStuart Price, Bruce L. Golden, Edward A. Wasil, Hao Howard Zhang. 351-359 [doi]
• Approximation algorithms for sorting by signed short reversalsGustavo Rodrigues Galvão, Zanoni Dias. 360-369 [doi]
• Conditional random fields for morphological analysis of wireless ECG signalsAnnamalai Natarajan, Edward Gaiser, Gustavo Angarita, Robert Malison, Deepak Ganesan, Benjamin M. Marlin. 370-379 [doi]
• Modeling climate-dependent population dynamics of mosquitoes to guide public health policiesAditya Vaidya, Angel Bravo-Salgado, Armin R. Mikler. 380-389 [doi]
• Large highly connected clusters in protein-protein interaction networksSuzanne Renick Gallagher, Debra S. Goldberg. 390-399 [doi]
• An improved algorithm for the sorting by reversals and transpositions problemUlisses Dias, Andre Rodrigues Oliveira, Zanoni Dias. 400-409 [doi]
• Dynamic coordinate registration method for image-guided surgeryXi Wen, Hong Wang, Weiming Zhai. 410-415 [doi]
• A comparison of combined p-value methods for gene differential expression using RNA-seq dataAbdallah M. Eteleeb, Hunter N. B. Moseley, Eric C. Rouchka. 417-425 [doi]
• One feature doesn't fit all: characterizing topological features of targets in signaling networksHuey-Eng Chua, Sourav S. Bhowmick, Lisa Tucker-Kellogg. 426-435 [doi]
• Data-driven prediction of cancer cell fates with a nonlinear model of signaling pathwaysFan Zhang, Chee Keong Kwoh, Min Wu, Jie Zheng. 436-444 [doi]
• A flexible volumetric comparison of protein cavities can reveal patterns in ligand binding specificityZiyi Guo, Trevor Kuhlengel, Steven Stinson, Seth Blumenthal, Brian Y. Chen, Soutir Bandyopadhyay. 445-454 [doi]
• MotionTalk: personalized home rehabilitation system for assisting patients with impaired mobilityJanani Venugopalan, Chihwen Cheng, May D. Wang. 455-463 [doi]
• Constructing burrows-wheeler transforms of large string collections via mergingJames Holt, Leonard McMillan. 464-471 [doi]
• Quantitative trait loci mapping with microarray marker intensitiesChen-Ping Fu, Fernando Pardo-Manuel de Villena, Leonard McMillan. 472-478 [doi]
• Are we there yet?: feasibility of continuous stress assessment via wireless physiological sensorsMd. Mahbubur Rahman, Rummana Bari, Amin Ahsan Ali, Moushumi Sharmin, Andrew Raij, Karen Hovsepian, Syed Monowar Hossain, Emre Ertin, Ashley Kennedy, David H. Epstein, Kenzie Preston, Michelle Jobes, J. Gayle Beck, Satish Kedia, Kenneth D. Ward, Mustafa al'Absi, Santosh Kumar. 479-488 [doi]
• Focus: a new multilayer graph model for short read analysis and extraction of biologically relevant featuresJulia Warnke, Hesham H. Ali. 489-498 [doi]
• Haplotype-centered mapping for improved alignments and genetic association studiesPaul M. Bodily, Mark J. Clement, Quinn Snell, M. Stanley Fujimoto, Perry G. Ridge. 499-505 [doi]
• Strand: fast sequence comparison using mapreduce and locality sensitive hashingJake Drew, Michael Hahsler. 506-513 [doi]
• omniClassifier: a desktop grid computing system for big data prediction modelingJohn H. Phan, Sonal Kothari, May D. Wang. 514-523 [doi]
• Discovering dysregulated phenotype-related gene patternsRami Alroobi, Saeed Salem. 524-532 [doi]
• Deep autoencoder neural networks for gene ontology annotation predictionsDavide Chicco, Peter J. Sadowski, Pierre Baldi. 533-540 [doi]
• A noise-aware method for building radiation hybrid mapsRaed I. Seetan, Anne M. Denton, Omar Al Azzam, Ajay Kumar, Muhammad Javed Iqbal, Shahryar F. Kianian. 541-550 [doi]
• Challenges in adapting text mining for full text articles to assist pathway curationK. E. Ravikumar, Kavishwar B. Wagholikar, Hongfang Liu. 551-558 [doi]
• Community detection-based features for sequence classificationKarthik Tangirala, Doina Caragea. 559-568 [doi]
• PseudoLasso: leveraging read alignment in homologous regions to correct pseudogene expression estimates via RNASeqChelsea J.-T. Ju, Zhuangtian Zhao, Wei Wang. 569-578 [doi]
• Dynamic networks reveal key players in agingFazle Elahi Faisal, Tijana Milenkovic. 579 [doi]
• Global network alignment in the context of agingFazle Elahi Faisal, Han Zhao, Tijana Milenkovic. 580 [doi]
• A powerful and robust co-expression network analysis algorithmJuli Petereit, Karen Schlauch. 581 [doi]
• DTC genetic testing and consumer comprehensionScott McGrath, Dhundy Kiran Bastola. 582-583 [doi]
• The epitope landscape of CRC liver metastases analyzed by whole-exome sequencing and in silico epitope predictionZeynep Kosaloglu, Inka Zoernig, Niels Halama, Eliana Ruggiero, Benedikt Brors, Dirk Jaeger. 584 [doi]
• vibrio cholerae AphB: a LysR-type transcriptional regulatorRahul S. Mandal, Atri Ta, Santasabuj Das. 585 [doi]
• Apoptosis centric Bayesian network perturbation analysis of signaling pathways in colorectal cancer for synergistic drug targets discoveryPranav Srinivas. 586 [doi]
• Disease named entity recognition and normalization with DNormRobert Leaman, Zhiyong Lu. 587 [doi]
• Identification of protein coding regions in RNA transcriptsShiyuyun Tang, Alexandre Lomsadze, Mark Borodovsky. 588 [doi]
• The UniFrac significance test generates different outputs given semantically equivalent inputsJeffrey R. Long, Qingxiang Yan, Brett Trost, Anthony J. Kusalik. 589 [doi]
• Text mining tools for assisting literature curationChih-Hsuan Wei, Hung-Yu Kao, Zhiyong Lu. 590-591 [doi]
• An analysis of conformational changes upon RNA-protein bindingKannan Sankar, Rasna R. Walia, Carla M. Mann, Robert L. Jernigan, Vasant G. Honavar, Drena Dobbs. 592-593 [doi]
• Dose and time relationship through probabilistic graphical models of gene expression time course toxicogenomics dataRoberto A. Cárdenas-Ovando, Héctor A. Rueda-Zárate, Julieta Noguez-Monroy, Claudia Rangel-Escareño. 594-595 [doi]
• Validation and implementation of whole-exome sequencing bioinformatics processes for clinical applicationsRimma Shakhbatyan, Himanshu Sharma, Ellen Tsai, Mark J. Bowser, Birgit Funke, Matthew S. Lebo. 596-597 [doi]
• Antidote application: an educational system for treatment of common toxin overdoseJon Long, Yingyuan Zhang, Lubomir T. Chitkushev, Vladimir Brusic, Guanglan Zhang. 598-599 [doi]
• High-performance recursive dynamic programming for bioinformatics using MM-like flexible kernelsJesmin Jahan Tithi, Pramod Ganapathi, Aakrati Talati, Rezaul Alam Chowdhury. 600-601 [doi]
• CLARK, accurate and efficient classification of DNA sequencesRachid Ounit, Timothy J. Close, Steve Wanamaker, Stefano Lonardi. 602 [doi]
• Comparing and optimizing transcriptome assembly pipeline for diploid wheatNatasha Pavlovikj, Kevin Begcy, Sairam Behera, Malachy Campbell, Harkamal Walia, Jitender S. Deogun. 603-604 [doi]
• A structured approach to ensemble learning for Alzheimer's disease predictionMatthew Seeley, Mark J. Clement, Christophe G. Giraud-Carrier, Quinn Snell, Paul Bodily, Stanley Fujimoto. 605-606 [doi]
• An author topic analysis on NCI DCP/DCCPS PIsDingcheng Li, Janet Okamoto, Hongfang Liu, Scott Leischow. 607-608 [doi]
• De novo assembly of ultra-deep sequencing dataHamid Mirebrahim, Timothy J. Close, Stefano Lonardi. 609 [doi]
• Identifying causal variants at loci with multiple signals of associationFarhad Hormozdiari, Emrah Kostem, Eun Yong Kang, Bogdan Pasaniuc, Eleazar Eskin. 610-611 [doi]
• A web-based tool to analyze semantic similarity networksMarianna Milano, Pietro Hiram Guzzi, Pierangelo Veltri, Mario Cannataro. 612-613 [doi]
• Graph methods for protein-nucleotide interactionsChanghui Yan, Wen Cheng. 614 [doi]
• Individual haplotyping prediction agreementsSepideh Mazrouee, Wei Wang. 615-616 [doi]
• Detecting privacy-sensitive events in medical textPrateek Jindal, Carl A. Gunter, Dan Roth. 617-620 [doi]
• A fast and lightweight filter-based algorithm for circular pattern matchingMd. Aashikur Rahman Azim, Costas S. Iliopoulos, Mohammad Sohel Rahman, M. Samiruzzaman. 621-622 [doi]
• NINJA: boolean modelling and formal verification of tiered-rate chemical reaction networks (extended abstract)Aadithya V. Karthik, David Soloveichik, Sayak Ray, Baruch Sterin, Alan Mishchenko, Robert K. Brayton, Jaijeet Roychowdhury. 623-624 [doi]
• Computational analysis of the stability of SCF ligases employing domain informationMina Maleki, Luis Rueda, Mohammad Haj Dezfulian, William Crosby. 625-626 [doi]
• An automated pipeline for discovering gene expression patterns associated with increased cancer survival timeJeffrey A. Thompson, Christine Duarte, Peter Marks, Clare Bates Congdon. 627-628 [doi]
• A novel semi-supervised learning approach to analyzing metagenomic readsYuliang Geng, Xuewen Chen, Dongxiao Zhu. 629-630 [doi]
• GraphSpace: sharing and collaborating through networks on the webCraig Estep, Jaeil Yi, Anna M. Ritz, T. M. Murali. 631-632 [doi]
• Genome dynamics in coevolved genomes: database management system for tracing mutationsSahith Sai Nareddy, Erik Westover, Kristina Hillesland, WooYoung Kim. 633-634 [doi]
• Care coordination metrics of patients sharing among physicians: a social network analytic approachAhmed Abdelzaher, Preetam Ghosh, Ahmad F. Al Musawi, David S. Jackson, John A. Palesis, Jonathan P. DeShazo. 635-636 [doi]
• Inferring ancestry in mouse genomes using a hidden Markov modelDaniel Malmer, Phillip Richmond, Aaron Odell, Richard Radcliffe, Robin Dowell. 637-638 [doi]
• A collaborative filtering approach to assess individual condition risk based on patients' social network dataXiang Ji, Soon Ae Chun, James Geller. 639-640 [doi]
• DDI2PPI: an integrated web server for protein-protein interaction and residue contact matrix predictionsTianchuan Du, Alvaro J. González, Qinghua Wang, Hongzhan Huang, Li Liao, Cathy H. Wu. 641-642 [doi]
• A workflow for the computational identification of candidate regulatory elements in noncoding DNAJeffrey A. Thompson, Craig R. Lessard, Samuel McFarland, Robert L. Morris, Clare Bates Congdon. 643-644 [doi]
• Multi-channel synapse validation on confocal images of mammalian neuronsVenkata Pasupuleti, Jie Zhou. 645-646 [doi]
• Using 2-node hypergraph clustering coefficients to analyze disease-gene networksSuzanne Renick Gallagher, Micah Dombrower, Debra S. Goldberg. 647-648 [doi]
• Predicting protein contact maps by bagging decision treesChuqiao Ren, Brian R. King. 649-650 [doi]
• On clinical decision supportArman Cohan, Luca Soldaini, Andrew Yates, Nazli Goharian, Ophir Frieder. 651-652 [doi]
• Big data challenges for estimating genome assembler qualityAbhishek Biswas, David Gauthier, Desh Ranjan, Mohammad Zubair. 653-660 [doi]
• RNA-seq gene and transcript expression analysis using the BioExtract server and iPlant collaborativeEtienne Z. Gnimpieba, Abalo Chango, Carol M. Lushbough. 661-669 [doi]
• AlignMR: mass spectrometry peak alignment using Hadoop MapReduceUrmi Bhayani, John Springer. 670-672 [doi]
• Feature subset selection for inferring relative importance of taxonomyGregory Ditzler, Gail L. Rosen. 673-679 [doi]
• Promises and challenges in analysis of biological big dataJason McDermott. 680 [doi]
• Simultaneous identification of robust synergistic subnetwork markers for effective cancer prognosisNavadon Khunlertgit, Byung-Jun Yoon. 681 [doi]
• Optimal cancer prognosis under network uncertaintyMohammadmahdi R. Yousefi, Lori A. Dalton. 682-683 [doi]
• A novel context-sensitive random walk model for estimating node correspondence between two biological networksHyundoo Jeong, Byung-Jun Yoon. 684 [doi]
• Fusarium verticillioidesMansuck Kim, Huan Zhang, Charles Woloshuk, Won Bo Shim, Byung-Jun Yoon. 685 [doi]
• Network-regularized bi-clique finding for tumor stratificationAmin Ahmadi-Adl, Xiaoning Qian. 686-687 [doi]
• Biological network clustering by robust NMFYijie Wang, Xiaoning Qian. 688-689 [doi]
• Orientations of beta-strand traces and near maximum twistDong-Si, Jing He. 690-694 [doi]
• A computational model for data acquisition in SAXSHui Dong, Gregory S. Chirikjian. 695-702 [doi]
• Variational Bayesian clustering on protein cavity conformations for detecting influential amino acidsZiyi Guo, Brian Y. Chen. 703-710 [doi]
• Construction of protein backbone pieces using segment-based FBCCD and Cryo-EM skeletonKamal Al-Nasr, Jing He. 711-716 [doi]
• Improving decoy databases for protein folding algorithmsAaron Lindsey, Hsin-Yi Cindy Yeh, Chih-Peng Wu, Shawna L. Thomas, Nancy M. Amato. 717-724 [doi]
• An integrative framework for structure-based prediction of biological effects mediated by antipeptide antibodiesSalvador Eugenio C. Caoili. 725-732 [doi]
• Development and validation of a broad scheme for prediction of HLA class II restricted T cell epitopesSinu Paul, John Sidney, Bjoern Peters, Alessandro Sette. 733-738 [doi]
• The interplay of sequence conservation and T cell immune recognitionAnne Bresciani, Jason Greenbaum, Cecilia S. Lindestam Arlehamn, Alessandro Sette, Morten Nielsen, Bjoern Peters. 739-743 [doi]
• Relapsing-remitting multiple scleroris and the role of vitamin D: an agent based modelFrancesco Pappalardo, Marzio Pennisi, Abdul Mateen Rajput, Ferdinando Chiacchio, Santo Motta. 744-748 [doi]
• Towards the characterization of normal peripheral immune cells with data from ImmPortSandra Andorf, Jennifer B. Bollyky, Patrick Dunn, Jeffrey A. Wiser, Sanchita Bhattacharya, Atul J. Butte. 749-750 [doi]
• RImmPort: enabling ready-for-analysis immunology research dataRavi D. Shankar, Sandra Andorf, Sanchita Bhattacharya, Jeffrey A. Wiser, Atul J. Butte. 751 [doi]
• Incremental network querying in biological networksMd Mahmudul Hasan, Tamer Kahveci. 752-759 [doi]
• On the impact of data integration and edge enrichment in mining significant signals from biological networksSean West, Hesham H. Ali. 760-767 [doi]
• An R-based tool for miRNA data analysis and correlation with clinical ontologiesFrancesca Cristiano, Pierangelo Veltri. 768-773 [doi]
• Evidence of post translational modification bias extracted from the tRNA and corresponding amino acid interplay across a set of diverse organismsOliver Bonham-Carter, Ishwor Thapa, Dhundy Bastola. 774-781 [doi]
• Heuristic parallelizable algorithm for similarity based biosystems comparisonMathialakan Thavappiragasam, Carol M. Lushbough, Etienne Z. Gnimpieba. 782-789 [doi]
• Automatic biosystems comparison using semantic and name similarityMathialakan Thavappiragasam, Carol M. Lushbough, Etienne Z. Gnimpieba. 790-796 [doi]
• Pheno2GRN: a workflow for phenotype to gene network study and reverse engineering comparisonNick Weinandt, Laura M. Jackson, Etienne Z. Gnimpieba, Carol Lushbough. 797-804 [doi]
• A taxonomy for bioinformatics tools: exploiting semantics, parallelism, and services for analyzing omics dataMario Cannataro, Pietro Hiram Guzzi. 805-812 [doi]
• A system for ubiquitous distributed acquisition of voice alteration samples through a mobile applicationPietro Cinaglia, Manuela Macrí, Barbara Calabrese, Patrizia Vizza, Giuseppe Tradigo, Pierangelo Veltri. 813-818 [doi]
• A schema-matching tool for Alzheimer's disease data integrationPeehoo Dewan, Naveen Ashish, Arthur W. Toga. 819-820 [doi]
• The DOE systems biology knowledgebase (KBase): progress towards a system for collaborative and reproducible inference and modeling of biological functionRobert W. Cottingham. 821 [doi]