Abstract is missing.
- Analysis of molecular networksMark Gerstein. 1 [doi]
- Personalized medicine - challenges and opportunities for informatics researchVipin Kumar. 3-4 [doi]
- Next generation sequencing data analysisJing Li, Kun Huang. 5 [doi]
- Intelligent pattern recognition and applicationsPatrick Wang. 6 [doi]
- Relationship preserving feature selection for unlabelled clinical trials time-seriesFatih Altiparmak, Michael Gibas, Hakan Ferhatosmanoglu. 7-16 [doi]
- Comparison of virus interactions with human signal transduction pathwaysIrtisha Singh, Oznur Tastan, Judith Klein-Seetharaman. 17-24 [doi]
- Relational operators for prioritizing candidate biomarkers in high-throughput differential expression dataGetiria Onsongo, Hongwei Xie, Timothy J. Griffin, John V. Carlis. 25-34 [doi]
- Effect of sequences on the shape of protein energy landscapesYue Li, Gary S. Tyson, Jinfeng Zhang. 35-42 [doi]
- Genome-wide compatible SNP intervals and their propertiesJeremy W. Wang, Kyle J. Moore, Qi Zhang, Fernando Pardo-Manuel de Villena, Wei Wang 0010, Leonard McMillan. 43-52 [doi]
- Alignment-based versus variation-based transformation methods for clustering microarray time-series dataYifeng Li, Numanul Subhani, Alioune Ngom, Luis Rueda. 53-61 [doi]
- Protein structure alignment using elastic shape analysisWei Liu, Anuj Srivastava, Jinfeng Zhang. 62-70 [doi]
- Computational modeling of the effects of oxidative stress on the IGF-1 signaling pathway in human articular chondrocytesPamela F. Marcott, Jacquelyn S. Fetrow, Richard F. Loeser, Edward E. Allen. 71-78 [doi]
- An annotated ::::k::::-deep prefix tree for (1-::::k::::)-mer based sequence comparisonsAdrienne Breland, Karen Schlauch, Monica N. Nicolescu, Frederick C. Harris Jr.. 79-85 [doi]
- A parameter estimation approach for non-linear systems biology models using spline approximationChoujun Zhan, Lam Fat Yeung. 86-91 [doi]
- RepFrag: a graph based method for finding repeats and transposons from fragmented genomesNirmalya Bandyopadhyay, A. Mark Settles, Tamer Kahveci. 92-101 [doi]
- Functional similarities of reaction sets in metabolic pathwaysFerhat Ay, Tamer Kahveci. 102-111 [doi]
- On the border length minimization problem (BLMP) on a square arrayVamsi Kundeti, Sanguthevar Rajasekaran, Hieu Dinh. 112-119 [doi]
- Random forest-based prediction of protein sumoylation sites from sequence featuresShaolei Teng, Hong Luo, Liangjiang Wang. 120-126 [doi]
- SplittingHeirs: inferring haplotypes by optimizing resultant dense graphsSharlee Climer, Alan R. Templeton, Weixiong Zhang. 127-136 [doi]
- Analyzing metabolite measurements for automated prediction of underlying biological mechanismsAli Cakmak, Arun Dsouza, Richard W. Hanson, Z. Meral Özsoyoglu. 137-146 [doi]
- Exact ILP solutions for phylogenetic minimum flip problemsMarkus Chimani, Sven Rahmann, Sebastian Böcker. 147-153 [doi]
- REAL: an efficient REad ALigner for next generation sequencing readsKimon Frousios, Costas S. Iliopoulos, Laurent Mouchard, Solon P. Pissis, German Tischler. 154-159 [doi]
- ReFHap: a reliable and fast algorithm for single individual haplotypingJorge Duitama, Thomas Huebsch, Gayle McEwen, Eun-Kyung Suk, Margret R. Hoehe. 160-169 [doi]
- MetaCluster: unsupervised binning of environmental genomic fragments and taxonomic annotationBin Yang, Yu Peng, Henry C. M. Leung, Siu-Ming Yiu, Junjie Qin, Ruiqiang Li, Francis Y. L. Chin. 170-179 [doi]
- Enzymatic target identification with dynamic statesBin Song, Sanjay Ranka, Tamer Kahveci. 180-187 [doi]
- Identifying gene functions using functional expression profiles obtained by voxelationLi An, Desmond J. Smith, Hongbo Xie, Vasileios Megalooikonomou, Zoran Obradovic. 188-197 [doi]
- Inferring species trees from gene duplication episodesJ. Gordon Burleigh, Mukul S. Bansal, Oliver Eulenstein, Todd J. Vision. 198-203 [doi]
- Automatic selection of near-native protein-ligand conformations using a hierarchical clustering and volunteer computingTrilce Estrada, Roger Armen, Michela Taufer. 204-213 [doi]
- A Bayesian decision fusion approach for microRNA target predictionDong Yue, Hui Liu, Mingzhu Lu, Philip Chen, Yidong Chen, Yufei Huang. 214-221 [doi]
- Ring optimization of edit metric codes in DNADaniel A. Ashlock, Sheridan K. Houghten. 222-229 [doi]
- Homology prediction refinement and reconstruction of gene content and order of ancestral bacterial genomesKuan Yang, João C. Setubal. 230-236 [doi]
- Parallel stochastic simulations of budding yeast cell cycle: load balancing strategies and theoretical analysisTae-Hyuk Ahn, Adrian Sandu. 237-246 [doi]
- Markov clustering of protein interaction networks with improved balance and scalabilityVenu Satuluri, Srinivasan Parthasarathy, Duygu Ucar. 247-256 [doi]
- Semi-supervised sequence classification using abstraction augmented Markov modelsCornelia Caragea, Adrian Silvescu, Doina Caragea, Vasant Honavar. 257-264 [doi]
- Comparative analysis of biclustering algorithmsDoruk Bozdag, Ashwin S. Kumar, Ümit V. Çatalyürek. 265-274 [doi]
- Differential biclustering for gene expression analysisOmar Odibat, Chandan K. Reddy, Craig N. Giroux. 275-284 [doi]
- Guiding belief propagation using domain knowledge for protein-structure determinationAmeet Soni, Craig A. Bingman, Jude W. Shavlik. 285-294 [doi]
- Promoter prediction based on a multiple instance learning schemeXuefeng Zhou, Jianhua Ruan, Weixiong Zhang. 295-301 [doi]
- The solution space of genome sequence alignment and LIS graph decompositionFangrui Ma, Jitender S. Deogun. 302-311 [doi]
- Derived distribution points heuristic for fast pairwise statistical significance estimationAnkit Agrawal, Alok N. Choudhary, Xiaoqiu Huang. 312-321 [doi]
- Unsupervised mapping of sentences to biomedical concepts based on integrated information retrieval model and clusteringMi-Young Kim, Qing Dou, Osmar R. Zaïane, Randy Goebel. 322-329 [doi]
- Gene set analysis using principal componentsIsa Kemal Pakatci, Wei Wang 0010, Leonard McMillan. 330-333 [doi]
- An improved 1.375-approximation algorithm for the transposition distance problemUlisses Dias, Zanoni Dias. 334-337 [doi]
- Spectrally resolved bioluminescence tomography with Huber-Markov random-field regularizationJinchao Feng, Kebin Jia. 338-341 [doi]
- A novel network model for molecular prognosisYing-Wooi Wan, Swetha Bose, James Denvir, Nancy Lan Guo. 342-345 [doi]
- A graph and hierarchical clustering based approach for population structure inferenceJun Wang, Maozu Guo. 346-349 [doi]
- Modeling the competitive effects of nucleosomes on transcription factors bindingQian Xiang, Xianhua Dai. 350-353 [doi]
- Feature selection for semi-supervised multi-label learning with application to gene function analysisGuo-Zheng Li, Mingyu You, Lei Ge, Jack Y. Yang, Mary Qu Yang. 354-357 [doi]
- Enhanced flux balance analysis to model metabolic networksNishanth Ulhas Nair, Navin Goyal, Nagasuma R. Chandra. 358-361 [doi]
- lgl-type and wild-type neuronsJinane Mounsef, Lina J. Karam, Patricia Estes, Daniela Zamescu. 362-365 [doi]
- Discovering overlapping modules and bridge proteins in proteomic networksEmad Ramadan, Christopher Osgood, Alex Pothen. 366-369 [doi]
- Semantic classification and dependency parsing enabled automated bio-molecular event extraction from textSyed Toufeeq Ahmed, Radhika Nair, Chintan Patel, Sheela P. Kanwar, Jörg Hakenberg, Hasan Davulcu. 370-373 [doi]
- Examining effects of variability on systems biology modeling algorithmsRachel A. Black, David J. John, Jacquelyn S. Fetrow, James L. Norris. 374-377 [doi]
- SNP specific extraction and analysis using shrunken dissimilarity measureYang Liu, Michael K. Ng, Jin Zhou. 378-381 [doi]
- An effective filtering gene selection method for microarray data via shuffling and statistical analysisZejin Jason Ding, Yan-Qing Zhang. 382-385 [doi]
- DNA sequence feature selection for intrinsic nucleosome positioning signals using AdaBoostYu Zhang, Xiuwen Liu, Justin A. Fincher, Jonathan H. Dennis. 386-389 [doi]
- An integrated approach to predictive genomic analyticsJason E. McDermott, Bob Baddeley, Susan L. Stevens, Antonio Sanfilippo, Rick Riensche, Mary P. Stenzel-Poore, Ronald C. Taylor, Russ Jensen. 390-393 [doi]
- Comparison of discrete- and continuous-state stochastic methods to model neuronal signal transductionTiina Manninen, Daniel X. Keller. 394-397 [doi]
- An intelligent data-centric approach toward identification of conserved motifs in protein sequencesKathryn Dempsey, Benjamin Currall, Richard Hallworth, Hesham H. Ali. 398-401 [doi]
- Parallel computation and interactive visualization of time-varying solvent excluded surfacesMichael Krone, Carsten Dachsbacher, Thomas Ertl. 402-405 [doi]
- Using Fourier phase analysis on genomic sequences to identify retrovirusesWendy Ashlock, Suprakash Datta. 406-409 [doi]
- Effects of cDNA microarray time-series data size on gene regulatory network inference accuracyVijender Chaitankar, Preetam Ghosh, Chaoyang Zhang, Ping Gong, Edward J. Perkins. 410-413 [doi]
- Compositional modelling of signalling pathways in timed concurrent constraint programmingDavide Chiarugi, Moreno Falaschi, Carlos Olarte, Catuscia Palamidessi. 414-417 [doi]
- Accelerating HMMER on GPUs by implementing hybrid data and task parallelismNarayan Ganesan, Roger D. Chamberlain, Jeremy Buhler, Michela Taufer. 418-421 [doi]
- Evaluation of different complexity measures for signal detection in genome sequencesMehdi Kargar, Aijun An. 422-425 [doi]
- Genomics information retrieval using a Bayesian model for learning and re-rankingQinmin Vivian Hu, Jimmy Xiangji Huang. 426-429 [doi]
- In silico identification of microRNAs from expressed sequence tags of three earthworm speciesPing Gong, Fuliang Xie, Baohong Zhang, Edward J. Perkins. 430-434 [doi]
- Systematic data integration platform for functional glycomicsMahesh Visvanathan, Sasidhar R. Siddam, In-Hee Lee, Gerald H. Lushington, George R. Bousfield. 435-438 [doi]
- Coupling between heparan sulfate proteoglycans and FGF-2 receptors is key to FGF-2 capture under flow: a computational studyChangjiang Zhang, Kimberly Forsten-Williams, Bing Zhao, Michael Fannon, Jun Zhang 0001. 439-441 [doi]
- Shortest path edit distance for detecting duplicate biological entitiesAlex Rudniy, Min Song, James Geller. 442-444 [doi]
- Docking arachidonic acid to 8R-lipoxygenase using internal coordinate mechanicsTianchuan Du, Shuju Bai, Ebrahim Khosravi. 445-447 [doi]
- EGGSlicer: predicting biologically meaningful gene sets from gene clusters using gene ontology informationHeejoon Chae, Kwangmin Choi, Sun Kim, Haleh Ashki. 448-450 [doi]
- Estimating the dynamics of protofibril elongation involved in Aβ42 peptide aggregation in Alzheimer s diseasePreetam Ghosh, Amit Kumar, Bhaswati Datta, Vijayaraghavan Rangachari. 451-453 [doi]
- Efficient query evaluation for DAG-shaped hierarchiesEn Cheng, Ali Cakmak, Z. Meral Özsoyoglu. 454-456 [doi]
- Use of ternary similarities in graph based clustering for protein structural family classificationGuillaume Santini, Henry Soldano, Joël Pothier. 457-459 [doi]
- Visualization of biological shape transformation by 3D model morphingMei Xiao, Jung Soh, Morgan L. Taschuk, Andrei L. Turinsky, Trish E. Parsons, Benedikt Hallgrímsson, Christoph W. Sensen. 460-462 [doi]
- Breast cancer plasma protein biomarker discovery by coupling LC-MS/MS proteomics and systems biologyFan Zhang, Mu Wang, Jake Y. Chen. 463-465 [doi]
- Performance evaluation of the time-delayed dynamic Bayesian network approach to inferring gene regulatory networks from time series microarray dataHaoni Li, Peng Li, Chaoyang Zhang, Nan Wang, Ping Gong, Edward J. Perkins. 466-468 [doi]
- A computational exploration of gene regulation by nucleosome positionJustin A. Fincher, Gary Tyson, Jonathan H. Dennis. 469-471 [doi]
- Ontology for MicroRNA Target prediction in human cancerJingshan Huang, Ming Tan, Dejing Dou, Lei He, Christopher Townsend, Patrick J. Hayes. 472-474 [doi]
- Pulmonary artery smooth muscle responses to KCl under normoxic and hypoxic conditions studied by means of a spatial network modelMarko Gosak, Marko Marhl, Christelle Guibert, Marie Billaud, Etienne Roux. 475-477 [doi]
- Applying graph theoretic approaches to microbial metagenomes: ecological perspectives on functionWolfgang Hankeln, Pier Luigi Buttigieg, Ivaylo Kostadinov, Renzo Kottmann, Pelin Yilmaz, Melissa Beth Duhaime, Frank Oliver Glöckner. 478-480 [doi]
- Hunting for truly relevant articles in bioinformatics literature: a preliminary studyCen Li, Suk Jai Seo, Ralph Butler. 481-483 [doi]
- Faster coevolution detection of proteins using maximum similar cliquesAlex Rodionov, Alexandr Bezginov, Jonathan Rose, Elisabeth R. M. Tillier. 484-486 [doi]
- ::::In silico:::: predicted essential genes required for zebrafish (::::Danio rerio::::) steroid hormone productionDavid Hala, Duane B. Huggett, Dalma Martinovic. 487-489 [doi]
- F-statistics algorithm for gene clustering evaluationMohamad Qayoom, Qi Zhang, Christopher Taylor. 490-492 [doi]
- A novel cancer classifier based on differentially expressed gene networkJaegyoon Ahn, Youngmi Yoon, Sanghyun Park. 493-495 [doi]
- Process calculi for systems biologyCaroline Baroukh, Anthony Rowe, Yike Guo. 496-497 [doi]
- Alzheimer s disease target selection: a data integration approachBradley W. Poland, Panayiotis Zagouras, Snehal Naik, Eric Fauman, Karl Richter, Robert M. Peitzsch. 498 [doi]
- Data mining of mRNA-Seq and small RNA-Seq data to find microRNA targetsHyunsoo Kim, Ramana V. Davuluri. 499-501 [doi]
- Dysfunctional gene/protein networks in hepatitis C virus-induced hepatocellular cirrhosis and carcinomaTao Huang, Guohui Ding, Yixue Li, Lei Liu, Eugene Tan, Hongyue Dai, Qi Liu, Zhidong Tu, Lu Xie. 502-507 [doi]
- A multi-tier data mining workflow to analyze the age related shift from diglycosylated- to tetra-glycosylated-FSH secretion by the anterior pituitaryMahesh Visvanathan, Shanker Rao, Vijay Anand, Gerald H. Lushington, Michael Netzer, Christian Baumgartner, George R. Bousfield. 508-514 [doi]
- Learning biological networks via bootstrapping with optimized go-based gene similarityRonald C. Taylor, Bob Baddeley, Antonio Sanfilippo, Rick Riensche, Marc Verhagen, Jason E. McDermott, Russ Jensen. 515-519 [doi]
- Constructing a compound mode-of-action network for personalized drug effectiveness predictionChifeng Ma, Hung-I Harry Chen, Yufei Huang, Yidong Chen. 520-528 [doi]
- Regulatory network nodes of ::::check point factors:::: in DNA repair pathwaysLaura Elnitski, Jens Lichtenberg, Lonnie R. Welch. 529-536 [doi]
- Using support vector machine for improving protein-protein interaction prediction utilizing domain interactionsMudita Singhal, Anuj R. Shah, Joshua N. Adkins, Roslyn Brown. 537-545 [doi]
- Predicting prognostic markers for glioma using gene co-expression network analysisPraneeth Uppalapati, Yang Xiang, Kun Huang. 546-551 [doi]
- De novo proteomics of neuronal ischemic toleranceAn Zhou, Larry David, Roger Simon. 552-555 [doi]
- A hyper-graph approach for analyzing transcriptional networks in breast cancerEmad Ramadan, Sudhir Perincheri, David Tuck. 556-562 [doi]
- A graph-based approach for computational model of bone microstructureTaehyong Kim, Murali Ramanathan, Aidong Zhang. 563-568 [doi]
- A software tool for network topology analysis under a metabolic engineering perspectiveJosé P. Pinto, Isabel Rocha, Miguel Rocha. 569-578 [doi]
- Crosstalk measures for analyzing biological networks in breast cancerEmad Ramadan, Sudhir Perincheri, David Tuck. 579-586 [doi]
- Topological analysis of structural roles of proteins in interactome networksYoung-Rae Cho. 587-593 [doi]
- Fast graph approaches to measure influenza transmission across geographically distributed host typesAdrienne Breland, Karen Schlauch, Mehmet Hadi Gunes, Frederick C. Harris Jr.. 594-601 [doi]
- B-cell epitope prediction for peptide-based vaccine design: towards a paradigm of biological outcomesSalvador Eugenio C. Caoili. 602-610 [doi]
- Immunoinformatic-driven ::::H. pylori:::: vaccine designMatthew Ardito, Songhua Zhang, William Martin, Steven F. Moss, Anne S. De Groot, Leonard Moise. 611-615 [doi]
- Immunoinformatic approach to a multi-pathogen genome-derived epitope-driven vaccineMatthew Ardito, Leonard Moise, William Martin, Anne S. De Groot. 616-620 [doi]
- Immunoglobulin functional motions and their effects on the complementarity determining regionsMichael T. Zimmermann, Aris Skliros, Saras Saraswathi, Andrzej Kloczkowski, Robert L. Jernigan. 621-626 [doi]
- How do amino acid mismatches affect the outcome of hematopoietic cell transplants?: a structural perspectiveChen Yanover, Mari Malkki, Ted Gooley, Effie W. Petersdorf, Philip Bradley. 627-633 [doi]
- An automatic computational pipeline to display MHC binding motifsPeng Wang, Björn Peters, John Sidney, Alessandro Sette. 634-641 [doi]
- A novel representation of HLA allele specificity and prediction algorithm for HLA class I bindingDavid K. Crockett, Perry G. Ridge. 642-643 [doi]
- Feature selection for characterizing HLA class I peptide motif anchorsPerry G. Ridge, David K. Crockett. 644-645 [doi]
- Application of systems biology for understanding of disease and selection of molecular targets for therapyAndreas Heinzel, Johannes Söllner, Suszan Szathmary. 647 [doi]
- Highly conserved and associated HIV-1 CTL and T-Helper epitopes in global HIV-1 population: potential candidates for multi-epitope HIV-1 vaccineSinu Paul, Helen Piontkivska. 648 [doi]
- Universal immune system simulator framework (UISS)Francesco Pappalardo, Marzio Pennisi, Santo Motta. 649-650 [doi]
- Structural landscape of immunoglobulin lambda light chainsAnna Chailyan, Davide Cirillo, Paolo Marcatili, Anna Tramontano. 651-652 [doi]
- Immunological implications of a structural analysis of two different porcine IL1β proteins expressed in macrophages and embryosAtaur R. Katebi, Pawel Gniewek, Michael Zimmermann, Saras Saraswathi, Zhenming Gong, Christopher K. Tuggle, Andrzej Kloczkowski, Robert L. Jernigan. 653-655 [doi]
- Effective neutralization and neutralization epitope masking signatures for four anti-V3 mAbsAlpna Agarwal, Susan Zolla-Pazner, James Swetnam, Timothy Cardozo. 656 [doi]
- Immunological response in normal healthy twins across ageSanchita Bhattacharya, Shai Shen-Orr, Holden Maecker, Laura Lazzeroni, Gary E. Swan, J. David Clark, Martin S. Angst, Atul J. Butte, Mark M. Davis. 657 [doi]
- PopCover: a method for selecting of peptides with optimal population and pathogen coverageClaus Lundegaard, M. Buggert, A. C. Karlsson, Ole Lund, Carina Perez, Morten Nielsen. 658-659 [doi]
- A framework for developing epitope prediction toolsYasser El-Manzalawy, Vasant Honavar. 660-662 [doi]
- Rheumatoid Arthritis molecular heterogeneitySarah K. Kummerfeld, Jason A. Hackney, Michael J. Townsend, Hilary F. Clark. 663 [doi]
- Using RDF for managing protein-protein interaction dataMario Cannataro, Pietro Hiram Guzzi, Pierangelo Veltri. 664-670 [doi]
- Experimental comparison of biclustering algorithms for PPI networksVera Tomaino, Pietro Hiram Guzzi, Mario Cannataro, Pierangelo Veltri. 671-676 [doi]
- A combinatorics based solution for input generation in the context of classification frameworks aimed to learning interacting protein classMaria Persico. 684-689 [doi]