Abstract is missing.
- STEROID: in silico heuristic target combination identification for disease-related signaling networksHuey-Eng Chua, Sourav S. Bhowmick, Lisa Tucker-Kellogg, Charles Forbes Dewey Jr.. 4-11 [doi]
- ERNE-BS5: aligning BS-treated sequences by multiple hits on a 5-letters alphabetNicola Prezza, Cristian Del Fabbro, Francesco Vezzi, Emanuale De Paoli, Alberto Policriti. 12-19 [doi]
- NetPipe: a network-based pipeline for discovery of genes and protein complexes regulating meiotic recombination hotspotsMin Wu, Chee Keong Kwoh, Jie Zheng, Xiaoli Li. 20-27 [doi]
- Improved multiple sequence alignments using coupled pattern miningK. S. M. Tozammel Hossain, Debprakash Patnaik, Srivatsan Laxman, Prateek Jain 0002, Chris Bailey-Kellogg, Naren Ramakrishnan. 28-35 [doi]
- ArtSurf: a method for deformable partial matching of protein small-molecule binding sitesJeffrey R. Van Voorst, Yiying Tong, Leslie A. Kuhn. 36-43 [doi]
- A multi-directional rapidly exploring random graph (mRRG) for protein foldingShuvra Kanti Nath, Shawna L. Thomas, Chinwe Ekenna, Nancy M. Amato. 44-51 [doi]
- Supervised logistic principal component analysis for pathway based genome-wide association studiesMeng Lu, Jianhua Z. Huang, Xiaoning Qian. 52-59 [doi]
- Multi-target protein-chemical interaction prediction using task-regularized and boosted multi-task learningJintao Zhang, Gerald H. Lushington, Jun Huan. 60-67 [doi]
- Reverse engineering molecular hypergraphsAhsanur Rahman, Christopher L. Poirel, David Badger, T. M. Murali. 68-75 [doi]
- Functional site prediction by exploiting correlations between labels of interacting residuesSaradindu Kar, Deepak Vijayakeerthi, Ashish V. Tendulkar, Balaraman Ravindran. 76-83 [doi]
- Non-overlapping clone pooling for high-throughput sequencingReginaldo Kuroshu. 84-89 [doi]
- Coalescent-based method for learning parameters of admixture events from large-scale genetic variation dataMing-Chi Tsai, Guy E. Blelloch, Russell Schwartz, R. Ravi. 90-97 [doi]
- OCR-based image features for biomedical image and article classification: identifying documents relevant to cis-regulatory elementsHagit Shatkay, Ramya Narayanaswamy, Santosh S. Nagaral, Na Harrington, M. V. Rohith, Gowri Somanath, Ryan Tarpine, Kyle Schutter, Tim Johnstone, Dorothea Blostein, Sorin Istrail, Chandra Kambhamettu. 98-104 [doi]
- Inferring ancestry in admixed populations using microarray probe intensitiesChen-Ping Fu, Catherine E. Welsh, Fernando Pardo-Manuel de Villena, Leonard McMillan. 105-112 [doi]
- Anaphora resolution in biomedical literature: a hybrid approachJennifer D'Souza, Vincent Ng. 113-122 [doi]
- Functional module identification by block modeling using simulated annealing with path relinkingYijie Wang, Xiaoning Qian. 123-130 [doi]
- Biased decoy sampling to aid the selection of near-native protein conformationsKevin Molloy, Amarda Shehu. 131-138 [doi]
- Protein blocks versus hydrogen bonds based alphabets for protein structure classificationDino Franklin. 139-146 [doi]
- Discovering geometric patterns in genomic dataWenxuan Gao, Lijia Ma, Christopher Brown, Matthew Slattery, Philip S. Yu, Robert L. Grossman, Kevin P. White. 147-154 [doi]
- Exploring objective functions and cross-terms in the optimization of an energy function for protein designYao-ming Huang, Christopher Bystroff. 155-162 [doi]
- Efficient SNP-sensitive alignment and database-assisted SNP calling for low coverage samplesRuibang Luo, Chang Yu, Chi-Man Liu, Tak Wah Lam, Thomas K. F. Wong, Siu-Ming Yiu, Ruiqiang Li, Hing-Fung Ting. 163-169 [doi]
- Automatic segmentation and quantification of filamentous structures in electron tomographyLeandro A. Loss, George Bebis, Hang Chang, Manfred Auer, Purbasha Sarkar, Bahram Parvin. 170-177 [doi]
- PseudoDomain: identification of processed pseudogenes based on protein domain classificationYuan Zhang, Yanni Sun. 178-185 [doi]
- Complexity reduction of stochastic master equation simulation based on Kronecker product analysisMehmet Umut Caglar, Ranadip Pal. 186-193 [doi]
- Algorithms for detecting complementary SNPs within a region of interest that are associated with diseasesSinan Erten, Marzieh Ayati, Yu Liu, Mark R. Chance, Mehmet Koyutürk. 194-201 [doi]
- Protein function prediction using weak-label learningGuo-Xian Yu, Guoji Zhang, Huzefa Rangwala, Carlotta Domeniconi, Zhiwen Yu. 202-209 [doi]
- Detecting ECG abnormalities via transductive transfer learningKang Li, Nan Du, Aidong Zhang. 210-217 [doi]
- Biological interpretation of morphological patterns in histopathological whole-slide imagesSonal Kothari, Adeboye O. Osunkoya, John H. Phan, May D. Wang. 218-225 [doi]
- Predicting expression-related features of chromosomal domain organization with network-structured analysis of gene expression and chromosomal locationVinodh N. Rajapakse, Wojciech Czaja, Yves Pommier, William C. Reinhold, Sudhir Varma. 226-233 [doi]
- Multivariate hypergeometric similarity measureChanchala Kaddi, R. Mitchell Parry, May D. Wang. 234-241 [doi]
- A volumetric method for representing and comparing regions of electrostatic focusing in molecular structureBrian Y. Chen, Debdas Paul. 242-249 [doi]
- Evolutionary analysis of functional modules in dynamic PPI networksNan Du, Yuan Zhang, Kang Li, Jing Gao, Supriya D. Mahajan, Bindukumar B. Nair, Stanley A. Schwartz, Aidong Zhang. 250-257 [doi]
- thaliana: deducing the relationship between primordia growth, gene expression and cell behaviorsOben M. Tataw, G. Venugopala Reddy, A. K. Roy-Chowdhurry. 258-265 [doi]
- Parallel syntenic alignment on GPUsJunjie Li, Sanjay Ranka, Sartaj Sahni. 266-273 [doi]
- Finding informative genes for prostate cancer: a general framework of integrating heterogeneous sourcesLiang Ge, Jing Gao, Nan Du, Aidong Zhang. 274-281 [doi]
- A new algorithm for finding enriched regions in ChIP-Seq dataIman Rezaeian, Luis Rueda. 282-288 [doi]
- Hybrid pattern matching for complex ontology term recognitionJung-jae Kim, Anh Tuan Luu. 289-296 [doi]
- Integration of genomic and epigenomic features to predict meiotic recombination hotspots in human and mouseMin Wu, Chee Keong Kwoh, Teresa M. Przytycka, Jing Li, Jie Zheng. 297-304 [doi]
- Efficient implementation of the hybrid method for stochastic simulation of biochemical systemsShuo Wang, Yang Cao. 305-312 [doi]
- A collective ranking method for genome-wide association studiesJie Liu, Elizabeth S. Burnside, Humberto Vidaillet, David Page. 313-320 [doi]
- Parallel verlet neighbor list algorithm for GPU-optimized MD simulationsTyson J. Lipscomb, Anqi Zou, Samuel S. Cho. 321-328 [doi]
- DACIDR: deterministic annealed clustering with interpolative dimension reduction using a large collection of 16S rRNA sequencesYang Ruan, Saliya Ekanayake, Mina Rho, Haixu Tang, Seung-Hee Bae, Judy Qiu, Geoffrey Fox. 329-336 [doi]
- Signed network propagation for detecting differential gene expressions and DNA copy number variationsWei Zhang 0032, Nicholas Johnson, Baolin Wu, Rui Kuang. 337-344 [doi]
- Memory-based local search for simplified protein structure predictionSwakkhar Shatabda, Muhammad Abdul Hakim Newton, Duc Nghia Pham, Abdul Sattar. 345-352 [doi]
- Remote homology detection on alpha-structural proteins using simulated evolutionMengfei Cao, Lenore J. Cowen. 353-360 [doi]
- 3D bone microarchitecture modeling and fracture risk predictionHui Li, Cathy Buyea, Xiaoyi Li, Murali Ramanathan, Lawrence Bone, Aidong Zhang. 361-368 [doi]
- An integer programming approach to novel transcript reconstruction from paired-end RNA-Seq readsSerghei Mangul, Adrian Caciula, Sahar Al Seesi, Dumitru Brinza, Abdul Rouf Banday, Rahul Kanadia. 369-376 [doi]
- Scalable genome scaffolding using integer linear programmingJames Lindsay, Hamed Salooti, Alexander Zelikovsky, Ion I. Mandoiu. 377-383 [doi]
- Alignment seeding strategies using contiguous pyrimidine purine matchesMinmei Hou, Louxin Zhang, Robert S. Harris. 384-391 [doi]
- An integrated optimization framework for inferring two generation kinships and parental genotypes from microsatellite samplesDaehan Won, Chun-An Chou, Wanpracha Art Chaovalitwongse, Tanya Y. Berger-Wolf, Bhaskar DasGupta, Ashfaq A. Khokhar, Marco Maggioni, Saad I. Sheikh, Mary V. Ashley, Jason Palagi. 392-399 [doi]
- Semantic querying over knowledge in biomedical text corpora annotated with multiple ontologiesWatson Wei Khong Chua, Jung-jae Kim. 400-407 [doi]
- Towards biophysical validation of constraint modeling for rigidity analysis of proteinsFilip Jagodzinski, Ileana Streinu. 408-413 [doi]
- A fast computation of pairwise sequence alignment scores between a protein and a set of single-locus variants of another proteinYongwook Choi. 414-417 [doi]
- Network-based classification of recurrent endometrial cancers using high-throughput DNA methylation dataJianhua Ruan, Md. Jamiul Jahid, Fei Gu, Chengwei Lei, Yi-Wen Huang, Ya-Ting Hsu, David G. Mutch, Chun-Liang Chen, Nameer B. Kirma, Tim Hui-Ming Huang. 418-425 [doi]
- Predicting protective bacterial antigens using random forest classifiersYasser El-Manzalawy, Drena Dobbs, Vasant Honavar. 426-433 [doi]
- ADANET: inferring gene regulatory networks using ensemble classifiersJanusz Slawek, Tomasz Arodz. 434-441 [doi]
- On enumerating the DNA sequencesM. Oguzhan Külekci. 442-449 [doi]
- Microarray vs. RNA-Seq: a comparison for active subnetwork discoveryAyat Hatem, Kamer Kaya, Ümit V. Çatalyürek. 450-457 [doi]
- Simulation and analysis of antibody aggregation on cell surfaces using motion planning and graph analysisKasra Manavi, Bridget S. Wilson, Lydia Tapia. 458-465 [doi]
- Inferring novel associations between SNP sets and gene sets in eQTL study using sparse graphical modelWei Cheng, Xiang Zhang, Yubao Wu, Xiaolin Yin, Jing Li, David Heckerman, Wei Wang. 466-473 [doi]
- QSEA for fuzzy subgraph querying of KEGG pathwaysThair Judeh, Tin Chi Nguyen, Dongxiao Zhu. 474-481 [doi]
- Rational design of orthogonal libraries of protein coding genesDaniel Ryan, Dimitris Papamichail. 482-489 [doi]
- Building the initial chain of the proteins through de novo modeling of the cryo-electron microscopy volume data at the medium resolutionsKamal Al-Nasr, Lin Chen, Dong-Si, Desh Ranjan, Mohammad Zubair, Jing He. 490-497 [doi]
- A pattern mining based integrative framework for biomarker discoverySanjoy Dey, Kelvin O. Lim, Gowtham Atluri, Angus W. MacDonald III, Michael Steinbach, Vipin Kumar. 498-505 [doi]
- A novel approach for mining representative spatial motifs of proteinsWajdi Dhifli, Rabie Saidi, Engelbert Mephu Nguifo. 506-508 [doi]
- Systems biology approach to identify markers of differentiation in bladder cancerJens-Peter Volkmer, Debashis Sahoo, Robert K. Chin. 509 [doi]
- 454 and SOLiD™ complementary used to filter and build the draft genome of highly abundant cyanobacteria in biological desert crustYoram Shotland. 510-512 [doi]
- An in-depth analysis of the molecular dynamics and structural aspects of IKB proteinsShaherin Basith, Sangdun Choi. 513-514 [doi]
- mHMM (multivariate hidden Markov model) application in studying BRD4 and JMJD6 function cooperatively on promoter-proximal polymerase-II (Pol II) pausing releaseQi Ma, Wen Liu, Michael G. Rosenfeld. 515 [doi]
- Phylogenetic and functional divergence analysis of vertebrate IRAK family membersVijayakumar Gosu, Sangdun Choi. 516-517 [doi]
- Multi-level structural domain-domain interactions for prediction of obligate and non-obligate protein-protein interactionsMichael Hall, Mina Maleki, Luis Rueda. 518-520 [doi]
- Identification of protein stability patches that pinpoint key structural or functional sitesDe Laet Marie, Dehouck Yves, Gilis Dimitri, Rooman Marianne. 521-523 [doi]
- Searching for the relics of primitive codonsSatoshi Mizuta, Taro Mori. 524-526 [doi]
- Efficient SDH computation in molecular simulations dataYi-Cheng Tu, Shaoping Chen, Sagar Pandit, Anand Kumar 0002, Vladimir Grupcev. 527-529 [doi]
- A computational metabolic model of the NG108-15 cell for high content drug screening with electrophysiological readoutAditya Reddy Kolli, Frank Sommerhage, Peter Molnar, Jonathan E. Hood, Jerry J. Jenkins, Faraz Hussain, Arup K. Ghosh, Sumit Kumar Jha, James J. Hickman. 530-532 [doi]
- A novel mathematical basis for predicting somatic single nucleotide variants from next-generation sequencingEric Bareke, Jean-François Spinella, Ramon Vidal, Jasmine Healy, Daniel Sinnett, Miklós Csürös. 533-535 [doi]
- Nuclear localization signal prediction based on sequential pattern miningJhih-rong Lin, Jianjun Hu. 536-538 [doi]
- Pattern analysis: a web-based tool for analyzing response patterns in low-replication, many-treatment gene expression dataNam S. Vo, Vinhthuy Phan. 539-541 [doi]
- ngALL database: a flexible framework for the management and integration of childhood leukemia next generation sequencing dataPascal St-Onge, Robert Hamon, Virginie Saillour, Jasmine Healy, Patrick Beaulieu, Daniel Sinnett. 542-544 [doi]
- Secondary structure predictions for long RNA sequences based on inversion excursions: preliminary resultsDaniel T. Yehdego, Boyu Zhang, Michela Taufer, Vikram Kumar Reddy Kodimala, Rahulsimham Vegesna, Sameera Viswakula, Kyle L. Johnson, Ming-Ying Leung. 545-547 [doi]
- Rapid efficient macromolecular substructure searching in a cloudJeffrey R. Van Voorst, Barry C. Finzel. 548-550 [doi]
- in-situ hybridization (M-FISH) image using regularized multinomial logistic regressionJingyao Li, Hongbao Cao, Yu-Ping Wang. 551-554 [doi]
- Copy number variation estimation from multiple next-generation sequencing samplesJunbo Duan, Ji-Gang Zhang, Hongbao Cao, Hong-Wen Deng, Yu-Ping Wang. 555-557 [doi]
- Entropy-based evaluation function for the investigation of genetic code adaptabilityLariza Laura de Oliveira, Renato Tinós. 558-560 [doi]
- Shortest paths ranking methodology to identify alterations in PPI networks of complex diseasesSérgio Nery Simões, David Correa Martins Jr., Helena Brentani, Ronaldo Fumio Hashimoto. 561-563 [doi]
- Prediction of candidate genes for neuropsychiatric disorders using feature-based enrichmentBinqing Xie, Gady Agam, Dinanath Sulakhe, Natalia Maltsev, Bhadrachalam Chitturi, T. Conrad Gilliam. 564-566 [doi]
- A graph-based cluster ensemble method to detect protein functional modules from multiple information sourcesYuan Zhang, Liang Ge, Nan Du, Guoqiang Fan, Kebin Jia, Aidong Zhang. 567-569 [doi]
- Nicotiana tabacum LMarcelo Filipe Breda de Moraes, Nilson Nicolau Junior, Silvana Giuliatti. 570-572 [doi]
- A continuum hard-sphere model of protein adsorptionCraig A. Finch, James J. Hickman. 573-575 [doi]
- Genecentric: a package to uncover graph-theoretic structure in high-throughput epistasis dataAndrew Gallant, Mark D. M. Leiserson, Maxim Kachalov, Lenore J. Cowen, Benjamin J. Hescott. 576-578 [doi]
- Predicting possible directed-graph patterns of gene expressions in studies involving multiple treatmentsNam S. Vo, Vinhthuy Phan, Thomas R. Sutter. 579-581 [doi]
- A brief comparison of DSP and HMM methods for gene findingSajid Marhon, Stefan C. Kremer. 582-584 [doi]
- Computational tool for large-scale GPIomic analysisClemente Aguilar-Bonavides, Ming-Ying Leung, Ernesto S. Nakayasu, Felipe G. Lopes, Igor C. Almeida. 585-587 [doi]
- A machine-learning approach to retrieving diabetic retinopathy imagesParag S. Chandakkar, Ragav Venkatesan, Baoxin Li, Helen K. Li. 588-589 [doi]
- An evolutionary search framework to efficiently sample local minima in the protein conformational spaceBrian S. Olson, Amarda Shehu. 590 [doi]
- Empirical metabolite identification via GA feature selection and Bayes classificationPaul Anderson, Michael Peterson. 591-593 [doi]
- A next generation sequence processing and analysis platform with integrated cloud-storage and high performance computing resourcesJeremy C. Morgan, Robert W. Chapman, Paul E. Anderson. 594 [doi]
- gLIMS: Google cloud-based laboratory information management system for NMR metabolomicsEdward Pharr, Aspen Olmsted, Paul E. Anderson. 595-597 [doi]
- A comparative study of codon adaptation in ssDNA and dsDNA phagesShivapriya Chithambaram, Ramanandan Prabhakaran, Xuhua Xia. 598-600 [doi]
- RNA-DV: an interactive tool for editing and visualizing RNA secondary structuresHerbert H. Tsang, Denny C. Dai. 601-603 [doi]
- Robust differential co-expression discovery: an insight into pharmacodynamics of tyrosine kinase inhibitorXi Gao, Tomasz Arodz. 604-606 [doi]
- Towards sequence-based DNA flexibility analysisEmily Flynn, Filip Jagodzinski, Ileana Streinu. 607-609 [doi]
- Simulation and study of large-scale bacteria-materials interactions via BioScape enabled by GPUsJie Li, Vishakha Sharma, Narayan Ganesan, Adriana B. Compagnoni. 610-612 [doi]
- How to select microscopy image similarity metrics?Peter Bajcsy, Joe Chalfoun, Mary Brady. 613-615 [doi]
- Approximate subspace pattern mining for mapping copy-number variationsNicholas Johnson, Gang Fang, Rui Kuang. 616 [doi]
- Microbial source tracking by molecular fingerprintingJan Lorenz Soliman, Alex Dekhtyar, Jennifer Vanderkellen, Aldrin Montana, Michael Black, Emily Neal, Kevin Webb, Chris Kitts, Anya Goodman. 617-619 [doi]
- Random-walk: a stagnation recovery technique for simplified protein structure predictionMahmood A. Rashid, Swakkhar Shatabda, M. A. Hakim Newton, Tamjidul Hoque, Duc Nghia Pham, Abdul Sattar. 620-622 [doi]
- Serum antibody repertoire profiling using virtual antigen screenXinyue Liu, Luke J. Tallon, Lisa Sadzewicz, Elena N. Klyushnenkova, Yurij Ionov. 623-624 [doi]
- miHA-match: computational detection of tissue-specific minor histocompatibility antigensMagdalena Feldhahn, Karin Schilbach, Pierre Dönnes, Hans-Georg Rammensee, Benjamin Schubert, Oliver Kohlbacher. 625-626 [doi]
- Decoding dendritic cell function through module and network analysisGaurav Pandey, Ariella Cohain, Jennifer Miller, Miriam Merad. 627-628 [doi]
- Using quantitative dose-response data to benchmark B-cell epitope prediction for antipeptide antibodiesSalvador Eugenio C. Caoili. 629-636 [doi]
- Immunoinformatic analysis of Chinese hamster ovary (CHO) protein contaminants in therapeutic protein formulationsAndres H. Gutierrez, Leonard Moise, Frances Terry, Kristen Dasilva, Chris Bailey-Kellogg, William Martin, Anne S. De Groot. 637-642 [doi]
- Genome scale inference of transcriptional regulatory networks using mutual information on complex interactionsVijender Chaitankar, Preetam Ghosh, Mohamed O. Elasri, Kurt A. Gust, Edward J. Perkins. 643-648 [doi]
- Unraveling multiple miRNA-mRNA associations through a graph-based approachPietro Hiram Guzzi, Pierangelo Veltri, Mario Cannataro. 649-654 [doi]
- A collective NMF method for detecting protein functional module from multiple data sourcesYuan Zhang, Nan Du, Liang Ge, Kebin Jia, Aidong Zhang. 655-660 [doi]
- An iterative MapReduce approach to frequent subgraph mining in biological datasetsSteven Hill, Bismita Srichandan, Rajshekhar Sunderraman. 661-666 [doi]
- High performance phosphorylation site assignment algorithm for mass spectrometry data using multicore systemsFahad Saeed, Jason D. Hoffert, Trairak Pisitkun, Mark A. Knepper. 667-672 [doi]
- Parallelization of the spectral deconvolution stage of the proteomic discovery processNeelam N. Deshpande, John A. Springer. 673-676 [doi]
- A system for acquiring and management of ECG signals by using mobile devices: a support for first intervention in heart attacksPietro Cinaglia, Giuseppe Tradigo, Pierangelo Veltri. 677-682 [doi]
- Feature extraction in protein sequences classification: a new stability measureRabie Saidi, Sabeur Aridhi, Engelbert Mephu Nguifo, Mondher Maddouri. 683-689 [doi]
- Robustness measure for an adeno-associated viral shell self-assembly is accurately predicted by configuration space atlasing using EASALRuijin Wu, Aysegul Ozkan, Antonette Bennett, Mavis Agbandje-Mckenna, Meera Sitharam. 690-695 [doi]
- A Monte Carlo approach to measure the robustness of Boolean networksVitor H. P. Louzada, Fabrício Martins Lopes, Ronaldo Fumio Hashimoto. 696-699 [doi]