Table of Contents

• Fuse: towards multi-level functional summarization of protein interaction networksBoon-Siew Seah, Sourav S. Bhowmick, Charles Forbes Dewey Jr., Hanry Yu. 2-11 [doi]
• Biological assessment of grid and spot detection in cDNA microarray imagesIman Rezaeian, Luis Rueda. 12-19 [doi]
• Parallel simulation of multiple proteins through a bioreactor coupled with biochemical reactionsChangjiang Zhang, Kimberly Forsten-Williams, Michael Fannon, Wensheng Shen, Jun Zhang 0001. 20-28 [doi]
• Win percentage: a novel measure for assessing the suitability of machine classifiers for biological problemsR. Mitchell Parry, John H. Phan, May D. Wang. 29-38 [doi]
• Using inversion signatures to generate draft genome sequence scaffoldsZanoni Dias, Ulisses Dias, João C. Setubal. 39-48 [doi]
• Neural system modeling and simulation using hybrid functional Petri netYin Tang, Fei Wang. 49-58 [doi]
• Sensitive detection of pathway perturbations in cancers: extended abstractCorban G. Rivera, Brett M. Tyler, T. M. Murali. 59-68 [doi]
• Mathematical network model for bone mineral density (BMD) and bone quality assessmentTaehyong Kim, Murali Ramanathan, Lawrence Bone, Aidong Zhang. 69-75 [doi]
• 15N-NOESYRichard Jang, Xin Gao, Ming Li. 76-86 [doi]
• Detecting fuzzy amino acid tandem repeats in protein sequencesMarco Pellegrini, M. Elena Renda, Alessio Vecchio. 87-95 [doi]
• Scalable multiple global network alignment for biological dataYu-Keng Shih, Srinivasan Parthasarathy. 96-105 [doi]
• Improved machine learning models for predicting selective compoundsXia Ning, Michael Walters, George Karypis. 106-115 [doi]
• de novo metagenome assembly from short sequence readsToshiaki Namiki, Tsuyoshi Hachiya, Hideaki Tanaka, Yasubumi Sakakibara. 116-124 [doi]
• Tetrahedral image-to-mesh conversion for biomedical applicationsAndrey N. Chernikov, Nikos Chrisochoides. 125-134 [doi]
• Multi-view prediction of protein functionArtem Sokolov, Asa Ben-Hur. 135-142 [doi]
• Algorithms for optimizing cross-overs in DNA shufflingLu He, Alan M. Friedman, Chris Bailey-Kellogg. 143-152 [doi]
• Classification of breast cancer grades through quantitative characterization of ductal structure morphology in three-dimensional culturesBasak Oztan, Lindsey M. Polizzotti, Cemal Çagatay Bilgin, Kira M. Henderson, George E. Plopper, Bülent Yener. 153-161 [doi]
• A fast method for large-scale multichromosomal breakpoint median problemsMaryam Haghighi, Sylvia Boyd. 162-171 [doi]
• Inference of tumor phylogenies from genomic assays on heterogeneous samplesAyshwarya Subramanian, Stanley Shackney, Russell Schwartz. 172-181 [doi]
• Identifying pair-wise gene functional similarity by multiplex gene expression maps and supervised learningLi An, Haibin Ling, Zoran Obradovic, Desmond J. Smith, Vasileios Megalooikonomou. 182-190 [doi]
• A two-way multi-dimensional mixture model for clustering metagenomic sequencesShruthi Prabhakara, Raj Acharya. 191-200 [doi]
• Mycobacterium tuberculosis complex sublineagesMinoo Aminian, Amina Shabbeer, Kane Hadley, Cagri Ozcaglar, Scott Vandenberg, Kristin P. Bennett. 201-208 [doi]
• NcRNA homology search using Hamming distance seedsOsama Aljawad, Yanni Sun, Alex Liu, Jikai Lei. 209-217 [doi]
• An integrative approach to infer regulation programs in a transcription regulatory module networkJianlong Qi, Tom Michoel, Gregory Butler. 218-225 [doi]
• Similarity boosting for label noise tolerance in protein-chemical interaction predictionAaron Smalter Hall, Jun Huan, Gerald H. Lushington. 226-234 [doi]
• Using compact encodings for path-based computations on pedigree graphsLei Yang, En Cheng, Z. Meral Özsoyoglu. 235-244 [doi]
• Predicting folding pathways between RNA conformational structures guided by RNA stacksYuan Li, Shaojie Zhang. 245-253 [doi]
• Knowledge-guided differential dependency network learning for detecting structural changes in biological networksYe Tian, Bai Zhang, Ie-Ming Shih, Yue Joseph Wang. 254-263 [doi]
• Probabilistic ensembles for improved inference in protein-structure determinationAmeet Soni, Jude W. Shavlik. 264-273 [doi]
• A novel framework for large scale metabolic network alignments by compressionMichael Dang, Ferhat Ay, Tamer Kahveci. 274-283 [doi]
• Pani: a novel algorithm for fast discovery of putative target nodes in signaling networksHuey-Eng Chua, Qing Zhao, Sourav S. Bhowmick, Charles Forbes Dewey Jr., Lisa Tucker-Kellogg, Hanry Yu. 284-288 [doi]
• An efficient algorithm for matching protein binding sites for protein function predictionLeif Ellingson, Jinfeng Zhang. 289-293 [doi]
• Improving protein flexibility predictions by combining statistical sampling with a mean-field virtual Pebble GameLuis C. González, Dennis R. Livesay, Donald J. Jacobs. 294-298 [doi]
• A tripartite clustering analysis on microRNA, gene and disease modelChengcheng Shen, Ying Liu. 299-303 [doi]
• Modeling of multi domain contribution to protein interactionWoo-Hyuk Jang, Suk Hoon Jung, Bo-ra Hyun, Dong-Soo Han. 304-308 [doi]
• Sequence-based prediction of HIV-1 coreceptor usage: utility of n-grams for representing gp120 V3 loopsMajid Masso. 309-314 [doi]
• Formatt: correcting protein multiple structural alignments by sequence peekingShilpa Nadimpalli, Noah M. Daniels, Lenore Cowen. 315-319 [doi]
• A fuzzy entropy based approach for development of gene prediction networks (GPNs): detecting altered dependency in carcinogenic stateAnupam Ghosh, Rajat K. De. 320-324 [doi]
• Generation of synthetic data in evaluating interactions for association studiesYixuan Chen, Jing Li. 325-329 [doi]
• DynMap: mapping short reads to multiple related genomesTomás Flouri, Costas S. Iliopoulos, Solon P. Pissis. 330-334 [doi]
• Dynamic visualization and comparative analysis of multiple collinear genomic dataJeremy W. Wang, Fernando Pardo-Manuel de Villena, Leonard McMillan. 335-339 [doi]
• Classification and feature selection for craniosynostosisShulin Yang, Linda G. Shapiro, Michael L. Cunningham, Matthew L. Speltz, Su-In Lee. 340-344 [doi]
• A scalable approach for inferring transcriptional regulation in the yeast cell cycleAkther Shermin, Hasan Jamil, Mehmet A. Orgun. 345-349 [doi]
• Ranking differential genes in co-expression networksOmar Odibat, Chandan K. Reddy. 350-354 [doi]
• A graph model and an exact algorithm for finding transcription factor modulesSongjian Lu, Xinghua Lu. 355-359 [doi]
• An ACO based functional module detection algorithm for protein interaction networksLei Shi, Aidong Zhang. 360-365 [doi]
• A novel K-mer mixture logistic regression for methylation susceptibility modeling of CpG dinucleotides in human gene promotersYoungik Yang. 366-370 [doi]
• Mixture of logistic models and an ensemble approach for protein-protein interaction extractionLindsey Bell, Jinfeng Zhang, Xufeng Niu. 371-375 [doi]
• A Bayesian integration model for improved gene functional inference from heterogeneous data sourcesNoor Alaydie, Chandan K. Reddy, Farshad Fotouhi. 376-380 [doi]
• Kernel methods for Calmodulin binding and binding site predictionMichael Hamilton, A. S. N. Reddy, Asa Ben-Hur. 381-386 [doi]
• Computational interpretation of metabolomics measurements: steady-state metabolic network dynamics analysisAli Cakmak, Xinjian Qi, A. Ercument Cicek, Gultekin Özsoyoglu. 387-392 [doi]
• Changes in gene expression near evolutionary breakpointsAdriana Muñoz, David Sankoff. 393-398 [doi]
• Counting cells in 3D confocal images based on discriminative modelsJie Zhou, Hanchuan Peng. 399-403 [doi]
• ISO: numeric representation of nucleic acid formM. Leigh Fanning, Joanne Macdonald, Darko Stefanovic. 404-408 [doi]
• Resolving observation conflicts in steady state metabolic network dynamics analysisA. Ercument Cicek, Gultekin Özsoyoglu. 409-414 [doi]
• Detection of novel tandem duplication with next-generation sequencingXuan Liu, Shing-Wan Choi, Thomas K. F. Wong, Tak Wah Lam, Siu-Ming Yiu. 415-419 [doi]
• Mapping short sequencing reads to distant relativesVinicio Reynoso, Catherine Putonti. 420-424 [doi]
• Erlang-delayed stochastic chemical kinetic formalism for efficient analysis of biological systems with non-elementary reaction effectsHiroyuki Kuwahara, Chris J. Myers. 425-429 [doi]
• Inferring conflict-sensitive phosphorylation dynamicsQiong Cheng, Mitsunori Ogihara, Vineet Gupta. 430-434 [doi]
• Topology aware coloring of gene regulatory networksGünhan Gülsoy, Bhavik Gandhi, Tamer Kahveci. 435-440 [doi]
• Ranking docked models of protein-protein complexes using predicted partner-specific protein-protein interfaces: a preliminary studyLi C. Xue, Rafael A. Jordan, Yasser El-Manzalawy, Drena Dobbs, Vasant Honavar. 441-445 [doi]
• Association between response to brief trastuzumab exposure in cell lines and early stage HER2+ breast tumorsEmmett Sprecher, Sudipa Sarkar, Steven H. Kleinstein, Murli Narayan, Eric P. Winer, David Tuck, Kimberly Lezon-Geyda, Ian Krop, Lyndsay Harris. 446-450 [doi]
• TreeLign: simultaneous stepwise alignment and phylogenetic positioning, with its application to automatic phylogenetic assignment of 16S rRNAsYuan Li, Aaron L. Halpern, Shaojie Zhang. 451-456 [doi]
• Geometric visualization of TF binding sites in contextChih Lee, Chun-Hsi Huang. 457-461 [doi]
• Human gene/protein synonym dictionary from WikiLinksKavishwar Wagholikar, Manabu Torii, Hongfang Liu. 462-464 [doi]
• Experimentation of an automatic resolution method for protein abbreviations in full-text papersPaolo Atzeni, Fabio Polticelli, Daniele Toti. 465-467 [doi]
• Phylogenetic and mutational analysis of 2008, 2009 & 2010 neuraminidase of H1N1 influenza AChee Keong Kwoh, Lakshmi Chandrasekaran. 468-470 [doi]
• Learning to compute the plane of symmetry for human facesJia Wu, Raymond Tse, Carrie Heike, Linda G. Shapiro. 471-474 [doi]
• Extension of Animal QTLdb: QTL meta-analysis on the flyZhi-Liang Hu, Xiao-Lin Wu, James M. Reecy. 475-477 [doi]
• A machine learning based approach to improve sidechain optimizationSabareesh Subramaniam, Sriraam Natarajan, Alessandro Senes. 478-480 [doi]
• An effective approach for mining frequent patterns in multiple biological sequencesLing Chen, Wei Liu. 481-483 [doi]
• Algorithms for pseudoknot classificationThomas K. F. Wong, Hui-Ting Yu, Bay-Yuan Hsu, Tak Wah Lam, Wing-Kai Hon, Siu-Ming Yiu. 484-486 [doi]
• Volume matching with application in medical treatment planningYam Ki Cheung, Ovidiu Daescu, Lech Papiez. 487-489 [doi]
• Approximate string-matching with a single gap for sequence alignmentTomás Flouri, Kunsoo Park, Kimon Frousios, Solon P. Pissis, Costas S. Iliopoulos, German Tischler. 490-492 [doi]
• Protein subcellular localization prediction with associative classification and multi-class SVMYifeng Liu, Zhaochen Guo, Xiaodi Ke, Osmar R. Zaïane. 493-495 [doi]
• Gaussian logic and its applications in bioinformaticsOndrej Kuzelka, Andrea Szabóová, Filip Zelezný. 496-498 [doi]
• Heterodimeric protein complex identificationOsamu Maruyama. 499-501 [doi]
• Constraint graphs as security filters for privacy assurance in medical transactionsGeorge Mathew, Zoran Obradovic. 502-504 [doi]
• Partial enumeration of solutions traces for the problem of sorting by signed reversalsChristian Baudet, Zanoni Dias. 505-507 [doi]
• A whole genome simulator of prokaryote genome evolutionKuan Yang, João Carlos Setubal. 508-510 [doi]
• Graph-based approach for gene markers and applications in next-generation sequencing data analysisDaniel Johnson, Kun Wang, Carole L. Cramer, Xiuzhen Huang. 511-513 [doi]
• Evaluating the quality of conformation sampling methods using experimental residual dipolar coupling dataTu-Liang Lin, Santhosh Kumar Vammi, Guang Song. 514-518 [doi]
• CCR5/CXCR4 discriminating sites in the HIV-1 gp120 coreAlpna Agarwal, Eron Oronsaye, Arthur Nadas, Susan Zolla-Pazner, Timothy Cardozo. 519-521 [doi]
• Feature selection method using WF-LASSO for gene expression data analysisHo-Sun Shon, Kyung-Sook Yang, Che Woo Yoo, Keun Ho Ryu. 522-524 [doi]
• A molecular systems analysis of HOX PPI networks in hematopoiesis and leukemogenesisMaragaille R. Capiroso, Marla A. Endriga, Valerie Diane V. Valeriano, Custer C. Deocaris. 525-527 [doi]
• Modeling malaria: stretch-delay effect of temperature in the sporogonic cycle and disease dynamicsAngel Bravo-Salgado, Jessica Beckham, Armin R. Mikler. 528-530 [doi]
• Gene Co-Adaboost: a semi-supervised approach for classifying gene expression dataNan Du, Kang Li, Supriya D. Mahajan, Stanley A. Schwartz, Bindukumar B. Nair, Chiu Bin Hsiao, Aidong Zhang. 531-535 [doi]
• Emulation of biological networks in reconfigurable hardwareNatasa Miskov-Zivanov, Andrew Bresticker, Deepa Krishnaswamy, Sreesan Venkatakrishnan, Diana Marculescu, James R. Faeder. 536-540 [doi]
• SecureMed-ID: memorable and private identifiers for off-site access to medical recordsTodd H. Stokes, Richard A. Moffitt, May D. Wang. 541-543 [doi]
• Automated peak alignment for nucleic acid capillary electrophoresis data by dynamic programmingFethullah Karabiber, Kevin Weeks, Oleg V. Favorov. 544-546 [doi]
• Automatic detection of vaccine adverse reactions by incorporating historical medical conditionsZhonghua Jiang, George Karypis. 547-549 [doi]
• Extracting targets and attributes of medical findings from radiology reports in a mixture of languagesHeung-Seon Oh, Jong-Beom Kim, Sung-Hyon Myaeng. 550-552 [doi]
• Arabidopsis thalianaVishal Bahirwani, Doina Caragea. 553-555 [doi]
• Improving protein-RNA interface prediction by combining sequence homology based method with a naive Bayes classifier: preliminary resultsLi C. Xue, Rasna R. Walia, Yasser El-Manzalawy, Drena Dobbs, Vasant Honavar. 556-558 [doi]
• Clustering for bioinformatics via matrix optimizationSuely Oliveira, David E. Stewart. 559-563 [doi]
• Cancer stem cell based adjuvant for oncoantingen-driven vaccinationFrancesca Cordero, Stefania Lanzardo, Maddalena Arigoni, Chiara Fornari, Laura Conti, Gianfranco Balbo, Federica Cavallo, Daniele Manini, Raffaele Calogero. 564-568 [doi]
• Affinity limits in B-cell epitope prediction for immunity mediated by antipeptide antibodiesSalvador Eugenio C. Caoili. 569-578 [doi]
• Generation of novel Chagas vaccines: evolving studies/work in progressChristopher S. Eickhoff, Matthew Ardito, Eric Gustafson, William Martin, Daniel F. Hoft. 579-583 [doi]
• T-cell epitope prediction based on self-toleranceNora C. Toussaint, Magdalena Feldhahn, Matthias Ziehm, Stefan Stevanovic, Oliver Kohlbacher. 584-588 [doi]
• Immunoinformatic discovery of potential cross-reactive T cell epitopes in the measles genomeLeonard Moise, Matthew Ardito, William Martin, Eric Gustafson, Alan Rothman, Anne S. De Groot. 589-593 [doi]
• Using HLA binding prediction algorithms for epitope mapping in HIV vaccine clinical trialsDan He, Pratima Kunwar, Eleazar Eskin, Helen Horton, Peter Gilbert, Tomer Hertz. 594-601 [doi]
• mafa: a system for prediction of peptide binding to several MHC class I molecules in cynomolgus macaquesGuanglan Zhang, Melisa L. Budde, Jennifer J. Lhost, David H. O'Connor, William H. Hildebrand, Vladimir Brusic. 602-606 [doi]
• Determining positional bias of MHC class I restricted T-cell epitopes in viral antigensYohan Kim, Jonathan W. Yewdell, Bjoern Peters. 607-611 [doi]
• Designing an ontology to support the creation of diagnostic decision support systemAlejandro Rodríguez González, Enrique Jiménez-Domingo, Ángel García-Crespo, Giner Alor-Hernández, Juan Miguel Gómez Berbís, Rubén Posada-Gómez. 612-616 [doi]
• Using ontologies for supporting genomic sequence annotation projectsMaría Del Carmen Legaz-García, José Antonio Miñarro-Giménez, Marisa Madrid, Santiago Torres Martínez, Jesualdo Tomás Fernández-Breis. 617-625 [doi]
• Application of the spreading activation technique for recommending concepts of well-known ontologies in medical systemsJose María Álvarez Rodríguez, Luis Polo, Weena Jimenez, Pablo Abella, José Emilio Labra Gayo. 626-635 [doi]
• Towards an OWL-based framework for extracting information from clinical textsNate Blaylock, William de Beaumont, James F. Allen, Hyuckchul Jung. 636-640 [doi]
• Differentiating party and date hubs in protein interaction networks using semantic similarity measuresEdward Casey Kenley, Lyles Kirk, Young-Rae Cho. 641-645 [doi]
• CLARM: an integrative approach for functional modules discoverySaeed Salem, Loqmane Seridi, Rami Alroobi, James E. Brewer, Shadi Banitaan, Ibrahim Aljarah. 646-650 [doi]
• Brain tumor pathway identification by integrating transcriptome and interactome dataKim Jong Kwang. 651-655 [doi]
• Experimental evaluation of OntoPIN: an ontology-annotated PPI databasePietro Hiram Guzzi, Pierangelo Veltri, Mario Cannataro. 656-660 [doi]