computing methodologies


Summary: Computer-assisted analysis and processing of problems in a particular area.

Top Publications

  1. Li K. ClustalW-MPI: ClustalW analysis using distributed and parallel computing. Bioinformatics. 2003;19:1585-6 pubmed
    ..The software uses a message-passing library called MPI (Message Passing Interface) and runs on distributed workstation clusters as well as on traditional parallel computers. ..
  2. Stamatakis A, Ludwig T, Meier H. RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics. 2005;21:456-63 pubmed
    ..Availability RAxML-III including all alignments and final trees mentioned in this paper is freely available as open source code at http://wwwbode.cs.tum/~stamatak ..
  3. Fernandez J. High performance computing in structural determination by electron cryomicroscopy. J Struct Biol. 2008;164:1-6 pubmed publisher
    ..Moreover, the HPC capabilities available in the most common cryoEM packages are surveyed, as an evidence of the importance of HPC in addressing the future challenges. ..
  4. Bohannon J. Distributed computing. Grassroots supercomputing. Science. 2005;308:810 pubmed
  5. Tang F, Chua C, Ho L, Lim Y, Issac P, Krishnan A. Wildfire: distributed, Grid-enabled workflow construction and execution. BMC Bioinformatics. 2005;6:69 pubmed
    ..Wildfire simplifies the tasks of constructing and executing bioinformatics workflows. ..
  6. Field D, Tiwari B, Booth T, Houten S, Swan D, Bertrand N, et al. Open software for biologists: from famine to feast. Nat Biotechnol. 2006;24:801-3 pubmed
    ..Developing and deploying specialized computing systems for specific research communities is achievable, cost effective and has wide-ranging benefits. ..
  7. Keane T, Naughton T. DSEARCH: sensitive database searching using distributed computing. Bioinformatics. 2005;21:1705-6 pubmed
    ..The software is publicly available under the GNU general public licence from Full documentation and a user manual is available from ..
  8. Schmidt H, Strimmer K, Vingron M, von Haeseler A. TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics. 2002;18:502-4 pubmed
    ..To run the parallel version of PUZZLE, a Message Passing Interface (MPI) library has to be installed on the system. Free MPI implementations are available on the Web (cf. ..
  9. Wang G, Dunbrack R. PISCES: a protein sequence culling server. Bioinformatics. 2003;19:1589-91 pubmed
    ..PDB sequences are updated weekly. PISCES can also cull non-PDB sequences provided by the user as a list of GenBank identifiers, a FASTA format file, or BLAST/PSI-BLAST output. ..

More Information


  1. 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 ..
  2. Kleinjung J, Douglas N, Heringa J. Parallelized multiple alignment. Bioinformatics. 2002;18:1270-1 pubmed The 'message passing interface' package (MPICH) is available from http:/ Praline is accessible at ..
  3. 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 ..
  4. 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 ..
  5. 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. ..
  6. 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. ..
  7. 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. ..
  8. 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. ..
  9. Carpi F, De Rossi D. Electroactive polymer-based devices for e-textiles in biomedicine. IEEE Trans Inf Technol Biomed. 2005;9:295-318 pubmed
  10. 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. ..
  11. Shegogue D, Zheng W. Integration of the Gene Ontology into an object-oriented architecture. BMC Bioinformatics. 2005;6:113 pubmed
  12. Wen C, Long X, Mu Y. Adaptive controller for dynamic power and performance management in the virtualized computing systems. PLoS ONE. 2013;8:e57551 pubmed publisher
  13. 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. ..
  14. 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. ..
  15. 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. ..
  16. Mandl K, Kohane I. Escaping the EHR trap--the future of health IT. N Engl J Med. 2012;366:2240-2 pubmed publisher
  17. 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. ..
  18. 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. ..
  19. 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. ..
  20. 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. ..
  21. McCoy A, Schneider T. Advances in experimental phasing. Acta Crystallogr D Struct Biol. 2016;72:291-2 pubmed publisher
  22. 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. ..
  23. Velayutham C, Kumar S. Asymmetric subsethood-product fuzzy neural inference system (ASuPFuNIS). IEEE Trans Neural Netw. 2005;16:160-74 pubmed
  24. 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:// ..
  25. 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
  26. 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
  27. 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. ..
  28. 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. ..
  29. 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. ..
  30. 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. ..
  31. 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. ..
  32. 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. ..
  33. 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. ..
  34. Konagaya A. Trends in life science grid: from computing grid to knowledge grid. BMC Bioinformatics. 2006;7 Suppl 5:S10 pubmed
  35. 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. ..
  36. 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. ..
  37. Johnson C. Top scientific visualization research problems. IEEE Comput Graph Appl. 2004;24:13-7 pubmed
  38. 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. ..
  39. 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. ..
  40. 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. ..
  41. 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. ..
  42. 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 ..
  43. 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. ..
  44. 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. ..
  45. 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. ..
  46. 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. ..
  47. 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. ..
  48. 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. ..
  49. 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. ..
  50. Vogt M, Bajorath J. Predicting the performance of fingerprint similarity searching. Methods Mol Biol. 2011;672:159-73 pubmed publisher
  51. 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
  52. 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
  53. Becker G. Bioinformatics, computational biology, and the National Centers for Biomedical Computing. J Am Coll Radiol. 2005;2:398-400 pubmed