Summary: Computer-assisted analysis and processing of problems in a particular area.
- Hokamp K, Shields D, Wolfe K, Caffrey D. Wrapping up BLAST and other applications for use on Unix clusters. Bioinformatics. 2003;19:441-2 pubmed..The packages were developed in Perl on a 20-node Linux cluster and are provided together with a configuration script and documentation. They can be freely downloaded from http://wolfe.gen.tcd.ie/wrapper. ..
- Kleinjung J, Douglas N, Heringa J. Parallelized multiple alignment. Bioinformatics. 2002;18:1270-1 pubmed..nimr.mrc.ac.uk/~jkleinj/tools/mpicode. The 'message passing interface' package (MPICH) is available from http:/www.unix.mcs.anl.gov/mpi/mpich. firstname.lastname@example.org Praline is accessible at http://mathbio.nimr.mrc.ac.uk/praline. ..
- Grant J, Dunbrack R, Manion F, Ochs M. BeoBLAST: distributed BLAST and PSI-BLAST on a Beowulf cluster. Bioinformatics. 2002;18:765-6 pubmed..The underlying system can also handle automated querying for high throughput work. Source code is available under the GNU public license at http://bioinformatics.fccc.edu/ ..
- Mathog D. Parallel BLAST on split databases. Bioinformatics. 2003;19:1865-6 pubmed..Each query is run on all nodes in parallel and the resultant BLAST output files from all nodes merged to yield the final output. Source code is available from ftp://saf.bio.caltech.edu/ ..
- Alessandri A, Cervellera C, Sanguineti M. Design of asymptotic estimators: an approach based on neural networks and nonlinear programming. IEEE Trans Neural Netw. 2007;18:86-96 pubmed..Numerical results are reported and comparisons with those obtained by the extended Kalman filter are made. ..
- Windeatt T. Accuracy/diversity and ensemble MLP classifier design. IEEE Trans Neural Netw. 2006;17:1194-211 pubmed..For the output-coding technique, a random code matrix is shown to give better performance than one-per-class code, even when the base classifier is well-tuned. ..
- Xu Q, Zhou Z, Peng J, Zhu J. [Design of a miniaturized blood temperature-varying system based on computer distributed control]. Sheng Wu Yi Xue Gong Cheng Xue Za Zhi. 2007;24:969-72 pubmed..Simulation results illustrate that this system provides precise temperature control with good performance in various operation conditions. ..
- Prinz A. Computational exploration of neuron and neural network models in neurobiology. Methods Mol Biol. 2007;401:167-79 pubmed publisher..This chapter describes the construction and analysis of databases of neuron or neuronal network models and describes some of the advantages and downsides of such exploration methods. ..
- Carpi F, De Rossi D. Electroactive polymer-based devices for e-textiles in biomedicine. IEEE Trans Inf Technol Biomed. 2005;9:295-318 pubmed
- Southern J, Plank G, Vigmond E, Whiteley J. Solving the coupled system improves computational efficiency of the bidomain equations. IEEE Trans Biomed Eng. 2009;56:2404-12 pubmed publisher..However, in tests on two 3-D rabbit ventricle benchmarks, it is shown that the coupled method is up to 80% faster than the conventional uncoupled method-and that parallel performance is better for the larger coupled problem. ..
- Shegogue D, Zheng W. Integration of the Gene Ontology into an object-oriented architecture. BMC Bioinformatics. 2005;6:113 pubmed
- Koelstra S, Pantic M, Patras I. A dynamic texture-based approach to recognition of facial actions and their temporal models. IEEE Trans Pattern Anal Mach Intell. 2010;32:1940-54 pubmed publisher..The generalization performance of the FFD method has been tested using the Cohn-Kanade database. Finally, we also explored the performance on spontaneous expressions in the Sensitive Artificial Listener data set. ..
- Russell D, Otu H, Sayood K. Grammar-based distance in progressive multiple sequence alignment. BMC Bioinformatics. 2008;9:306 pubmed publisher..The results are especially striking for large datasets. We introduce a computationally efficient progressive alignment algorithm using a grammar based sequence distance particularly useful in aligning large datasets. ..
- Du X, Callister S, Manes N, Adkins J, Alexandridis R, Zeng X, et al. A computational strategy to analyze label-free temporal bottom-up proteomics data. J Proteome Res. 2008;7:2595-604 pubmed publisher..This paper describes a strategy that addresses these issues and demonstrates its values for analyzing temporal bottom-up proteomics data using data from a Rhodobacter sphaeroides 2.4.1 time-course study. ..
- Saadi K, Talbot N, Cawley G. Optimally regularised kernel Fisher discriminant classification. Neural Netw. 2007;20:832-41 pubmed..Results obtained on real-world and synthetic benchmark datasets indicate that the proposed method is competitive with model selection based on k-fold cross-validation in terms of generalisation, whilst being considerably faster. ..
- Duncan P, Nguyen T, Hui E. Pneumatic oscillator circuits for timing and control of integrated microfluidics. Proc Natl Acad Sci U S A. 2013;110:18104-9 pubmed publisher..On-chip clocks and pumps both constitute critical building blocks on the path toward achieving autonomous laboratory-on-a-chip devices. ..
- Nandedkar A, Biswas P. A fuzzy min-max neural network classifier with compensatory neuron architecture. IEEE Trans Neural Netw. 2007;18:42-54 pubmed..e., maximum hyperbox size. The paper demonstrates the performance of FMCN by comparing it with fuzzy min-max neural network (FMNN) classifier and general fuzzy min-max neural network (GFMN) classifier, using several examples. ..
- Padhi R, Unnikrishnan N, Wang X, Balakrishnan S. A single network adaptive critic (SNAC) architecture for optimal control synthesis for a class of nonlinear systems. Neural Netw. 2006;19:1648-60 pubmed..One of these problems is a real-life Micro-Electro-Mechanical-system (MEMS) problem, which demonstrates that the SNAC technique is applicable to complex engineering systems. ..
- Zeng Z, Wang J. Multiperiodicity of discrete-time delayed neural networks evoked by periodic external inputs. IEEE Trans Neural Netw. 2006;17:1141-51 pubmed..These conditions improve and extend the existing stability results in the literature. Simulations results are also discussed in three illustrative examples. ..
- Velayutham C, Kumar S. Asymmetric subsethood-product fuzzy neural inference system (ASuPFuNIS). IEEE Trans Neural Netw. 2005;16:160-74 pubmed
- Cickovski T, Huang C, Chaturvedi R, Glimm T, Hentschel H, Alber M, et al. A framework for three-dimensional simulation of morphogenesis. IEEE/ACM Trans Comput Biol Bioinform. 2005;2:273-88 pubmed..Binaries and source code are available, along with documentation and input files for sample simulations, at http:// compucell.sourceforge.net. ..
- Ng C, Xiao Y, Putnam W, Lum B, Tropsha A. Quantitative structure-pharmacokinetic parameters relationships (QSPKR) analysis of antimicrobial agents in humans using simulated annealing k-nearest-neighbor and partial least-square analysis methods. J Pharm Sci. 2004;93:2535-44 pubmed
- Huang G, Saratchandran P, Sundararajan N. A generalized growing and pruning RBF (GGAP-RBF) neural network for function approximation. IEEE Trans Neural Netw. 2005;16:57-67 pubmed
- Li B, Lingsma H, Steyerberg E, Lesaffre E. Logistic random effects regression models: a comparison of statistical packages for binary and ordinal outcomes. BMC Med Res Methodol. 2011;11:77 pubmed publisher..The starting value for the variance parameter may be also critical for the convergence of the Markov chain. ..
- Beume N. S-Metric calculation by considering dominated hypervolume as Klee's measure problem. Evol Comput. 2009;17:477-92 pubmed publisher..The performance of the new algorithm is studied in comparison to another state of the art algorithm on a set of academic test functions. ..
- Chang W, Guo M, Ho M. Fast parallel molecular algorithms for DNA-based computation: factoring integers. IEEE Trans Nanobioscience. 2005;4:149-63 pubmed..Furthermore, this work indicates that the cryptosystems using public-key are perhaps insecure and also presents clear evidence of the ability of molecular computing to perform complicated mathematical operations. ..
- Shedlock D, Haghighat A. Neutron analysis of spent fuel storage installation using parallel computing and advance discrete ordinates and Monte Carlo techniques. Radiat Prot Dosimetry. 2005;116:662-6 pubmed..Moreover, this calculation was performed on a relatively inexpensive PC-cluster. Possible inadequacies of the CASK cross section library still need to be evaluated. ..
- Villmann T, Schleif F, Kostrzewa M, Walch A, Hammer B. Classification of mass-spectrometric data in clinical proteomics using learning vector quantization methods. Brief Bioinform. 2008;9:129-43 pubmed publisher..We demonstrate the power of both methods for two exemplary examples: the classification of bacteria (listeria types) and neoplastic and non-neoplastic cell populations in breast cancer tissue sections. ..
- Teh C, Lim C. Monitoring the formation of kernel-based topographic maps in a hybrid SOM-kMER model. IEEE Trans Neural Netw. 2006;17:1336-41 pubmed..The empirical results demonstrate that the proposed approach is able to accelerate the formation of a topographic map and, at the same time, to simplify the monitoring procedure. ..
- Chen S, Chen H, Chan H. A real-time QRS detection method based on moving-averaging incorporating with wavelet denoising. Comput Methods Programs Biomed. 2006;82:187-95 pubmed..5% of the detection rate for the standard database, and also, it could function reliably even under the condition of poor signal quality in the measured ECG data. ..
- Konagaya A. Trends in life science grid: from computing grid to knowledge grid. BMC Bioinformatics. 2006;7 Suppl 5:S10 pubmed
- Kaiser M. Brain architecture: a design for natural computation. Philos Trans A Math Phys Eng Sci. 2007;365:3033-45 pubmed..Finally, we discuss mechanisms of self-organization for such architectures. After all, the organization of the brain might again inspire computer architecture. ..
- Cagnoni S, Bergenti F, Mordonini M, Adorni G. Evolving binary classifiers through parallel computation of multiple fitness cases. IEEE Trans Syst Man Cybern B Cybern. 2005;35:548-55 pubmed..The approach was tested on a digit recognition problem and compared with a reference classifier. ..
- Johnson C. Top scientific visualization research problems. IEEE Comput Graph Appl. 2004;24:13-7 pubmed
- Macdonald J, Li Y, Sutovic M, Lederman H, Pendri K, Lu W, et al. Medium scale integration of molecular logic gates in an automaton. Nano Lett. 2006;6:2598-603 pubmed..In silicon terminology, MAYA-II represents the first "medium-scale integrated molecular circuit", integrating 128 deoxyribozyme-based logic gates, 32 input DNA molecules, and 8 two-channel fluorescent outputs across 8 wells. ..
- Hurt A. Digital technology in the orthodontic laboratory. Am J Orthod Dentofacial Orthop. 2012;141:245-7 pubmed publisher..The purposes of this article are to briefly describe these technologies and to explain how they are used in the orthodontic laboratory. ..
- Nam S, Kim Y, Park Y, Baek S, Hayashi K, Kim K, et al. Three-dimensional dental model constructed from an average dental form. Am J Orthod Dentofacial Orthop. 2012;141:213-8 pubmed publisher..The average dental model constructed in this study might serve as a guide for treatment planning in orthodontic and prosthodontic dentistry. ..
- Hong X, Chen S, Harris C. A kernel-based two-class classifier for imbalanced data sets. IEEE Trans Neural Netw. 2007;18:28-41 pubmed..Numerical examples are used to demonstrate the efficacy of the algorithm. ..
- Vlasblom J, Wu S, Pu S, Superina M, Liu G, Orsi C, et al. GenePro: a Cytoscape plug-in for advanced visualization and analysis of interaction networks. Bioinformatics. 2006;22:2178-9 pubmed..The GenePro plugin is available at the website http://genepro.ccb.sickkids.ca. ..
- Nguyen N, Nguyen H, Su S. Optimal path-following control of a smart powered wheelchair. Conf Proc IEEE Eng Med Biol Soc. 2008;2008:5025-8 pubmed publisher..After the calibration, the accuracy is improved significantly. Two real-time experimental results obtained from square tracking and door passing tasks confirm the performance of proposed approach. ..
- Giritharan B, Yuan X, Liu J, Buckles B, Oh J, Tang S. Bleeding detection from capsule endoscopy videos. Conf Proc IEEE Eng Med Biol Soc. 2008;2008:4780-3 pubmed publisher..Our preliminary results demonstrated superior performance in sensitivity and comparative subjectivity with slight improvement. ..
- Hill J, Hambley M, Forster T, Mewissen M, Sloan T, Scharinger F, et al. SPRINT: a new parallel framework for R. BMC Bioinformatics. 2008;9:558 pubmed publisher..It is easy to use and with further development will become more useful as more functions are added to the framework. ..
- Chen C, Zhou X, Tian Y, Zou X, Cai P. Predicting protein structural class with pseudo-amino acid composition and support vector machine fusion network. Anal Biochem. 2006;357:116-21 pubmed..A significant enhancement in success rates was observed, indicating that the current approach may serve as a powerful complementary tool to other existing methods in this area. ..
- Hewett P, Mensch B, Ribeiro M, Jones H, Lippman S, Montgomery M, et al. Using sexually transmitted infection biomarkers to validate reporting of sexual behavior within a randomized, experimental evaluation of interviewing methods. Am J Epidemiol. 2008;168:202-11 pubmed publisher..Results strongly suggest that computerized interviewing provides more accurate and reliable behavioral data. The analyses also confirm the benefits of using data on prevalent STIs for externally validating behavioral reporting. ..
- Collins M, Buehren T, Bece A, Voetz S. Corneal optics after reading, microscopy and computer work. Acta Ophthalmol Scand. 2006;84:216-24 pubmed..015). Reading, microscopy and computer work have different effects on corneal aberrations. The results are in agreement with the hypothesis that lid-induced corneal aberrations may play a role in myopia development. ..
- Zhou D, Kloepper K, Winter K, Rienstra C. Band-selective 13C homonuclear 3D spectroscopy for solid proteins at high field with rotor-synchronized soft pulses. J Biomol NMR. 2006;34:245-57 pubmed..Soft pulses with a small bandwidth-duration product are best for exciting the approximately 70 ppm bandwidth required for aliphatic-only dimensions. ..
- Xu P, Chang C, Paplinski A. Self-organizing topological tree for online vector quantization and data clustering. IEEE Trans Syst Man Cybern B Cybern. 2005;35:515-26 pubmed
- Rhodes N, Clark D, Willett P. Similarity searching in databases of flexible 3D structures using autocorrelation vectors derived from smoothed bounded distance matrices. J Chem Inf Model. 2006;46:615-9 pubmed
- Becker G. Bioinformatics, computational biology, and the National Centers for Biomedical Computing. J Am Coll Radiol. 2005;2:398-400 pubmed