automated pattern recognition

Summary

Summary: In INFORMATION RETRIEVAL, machine-sensing or identification of visible patterns (shapes, forms, and configurations). (Harrod's Librarians' Glossary, 7th ed)

Top Publications

  1. ncbi Minimum redundancy feature selection from microarray gene expression data
    Chris Ding
    Computational Research Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, CA 94720, USA
    J Bioinform Comput Biol 3:185-205. 2005
  2. ncbi A review of feature selection techniques in bioinformatics
    Yvan Saeys
    Department of Plant Systems Biology, VIB, B 9052 Ghent, Belgium
    Bioinformatics 23:2507-17. 2007
  3. ncbi ROCR: visualizing classifier performance in R
    Tobias Sing
    Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrucken, Germany
    Bioinformatics 21:3940-1. 2005
  4. ncbi I/NI-calls for the exclusion of non-informative genes: a highly effective filtering tool for microarray data
    Willem Talloen
    Johnson and Johnson Pharmaceutical Research and Development, Division of Janssen Pharmaceutica N V, Beerse, Belgium
    Bioinformatics 23:2897-902. 2007
  5. ncbi Automated segmentation, classification, and tracking of cancer cell nuclei in time-lapse microscopy
    Xiaowei Chen
    HCNR Center for Bioinformatics, Harvard Medical School, Boston, MA 02115, USA
    IEEE Trans Biomed Eng 53:762-6. 2006
  6. ncbi Computational cluster validation in post-genomic data analysis
    Julia Handl
    School of Chemistry, University of Manchester, Faraday Building, Sackville Street, PO Box 88, Manchester M60 1QD, UK
    Bioinformatics 21:3201-12. 2005
  7. ncbi Training a support vector machine in the primal
    Olivier Chapelle
    Max Planck Institute for Biological Cybernetics, 72076 Tuebingen, Germany
    Neural Comput 19:1155-78. 2007
  8. ncbi Automated protein function prediction--the genomic challenge
    Iddo Friedberg
    Burnham Institute for Medical Research, Program in Bioinformatics and Systems Biology, La Jolla, CA 92037, USA
    Brief Bioinform 7:225-42. 2006
  9. pmc STEM: a tool for the analysis of short time series gene expression data
    Jason Ernst
    Center for Automated and Learning and Discovery, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
    BMC Bioinformatics 7:191. 2006
  10. pmc Gene selection and classification of microarray data using random forest
    Ramon Diaz-Uriarte
    Bioinformatics Unit, Biotechnology Programme, Spanish National Cancer Centre CNIO, Melchor Fernandez Almagro 3, Madrid, 28029, Spain
    BMC Bioinformatics 7:3. 2006

Detail Information

Publications276 found, 100 shown here

  1. ncbi Minimum redundancy feature selection from microarray gene expression data
    Chris Ding
    Computational Research Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, CA 94720, USA
    J Bioinform Comput Biol 3:185-205. 2005
    ..SUPPLIMENTARY: The top 60 MRMR genes for each of the datasets are listed in http://crd.lbl.gov/~cding/MRMR/. More information related to MRMR methods can be found at http://www.hpeng.net/...
  2. ncbi A review of feature selection techniques in bioinformatics
    Yvan Saeys
    Department of Plant Systems Biology, VIB, B 9052 Ghent, Belgium
    Bioinformatics 23:2507-17. 2007
    ....
  3. ncbi ROCR: visualizing classifier performance in R
    Tobias Sing
    Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrucken, Germany
    Bioinformatics 21:3940-1. 2005
    ..Being equipped with only three commands and reasonable default values for optional parameters, ROCR combines flexibility with ease of usage...
  4. ncbi I/NI-calls for the exclusion of non-informative genes: a highly effective filtering tool for microarray data
    Willem Talloen
    Johnson and Johnson Pharmaceutical Research and Development, Division of Janssen Pharmaceutica N V, Beerse, Belgium
    Bioinformatics 23:2897-902. 2007
    ..A Bayesian factor analysis with specifically chosen prior settings, which models this probe level information, is providing an objective feature filtering technique, named informative/non-informative calls (I/NI calls)...
  5. ncbi Automated segmentation, classification, and tracking of cancer cell nuclei in time-lapse microscopy
    Xiaowei Chen
    HCNR Center for Bioinformatics, Harvard Medical School, Boston, MA 02115, USA
    IEEE Trans Biomed Eng 53:762-6. 2006
    ..Experimental results show that the proposed method is efficient and effective in cell tracking and phase identification...
  6. ncbi Computational cluster validation in post-genomic data analysis
    Julia Handl
    School of Chemistry, University of Manchester, Faraday Building, Sackville Street, PO Box 88, Manchester M60 1QD, UK
    Bioinformatics 21:3201-12. 2005
    ..Suitable computational cluster validation techniques are available in the general data-mining literature, but have been given only a fraction of the same attention in bioinformatics...
  7. ncbi Training a support vector machine in the primal
    Olivier Chapelle
    Max Planck Institute for Biological Cybernetics, 72076 Tuebingen, Germany
    Neural Comput 19:1155-78. 2007
    ..On the contrary, from the primal point of view, new families of algorithms for large-scale SVM training can be investigated...
  8. ncbi Automated protein function prediction--the genomic challenge
    Iddo Friedberg
    Burnham Institute for Medical Research, Program in Bioinformatics and Systems Biology, La Jolla, CA 92037, USA
    Brief Bioinform 7:225-42. 2006
    ..This article briefly outlines the history of automated protein function prediction and surveys the latest innovations in all three topics...
  9. pmc STEM: a tool for the analysis of short time series gene expression data
    Jason Ernst
    Center for Automated and Learning and Discovery, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
    BMC Bioinformatics 7:191. 2006
    ..Previously short time series gene expression data has been mainly analyzed using more general gene expression analysis tools not designed for the unique challenges and opportunities inherent in short time series gene expression data...
  10. pmc Gene selection and classification of microarray data using random forest
    Ramon Diaz-Uriarte
    Bioinformatics Unit, Biotechnology Programme, Spanish National Cancer Centre CNIO, Melchor Fernandez Almagro 3, Madrid, 28029, Spain
    BMC Bioinformatics 7:3. 2006
    ..Thus, it is important to understand the performance of random forest with microarray data and its possible use for gene selection...
  11. ncbi An algorithm for constraint-based structural template matching: application to 3D templates with statistical analysis
    Jonathan A Barker
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Bioinformatics 19:1644-9. 2003
    ..In the context of template matching, there is an urgent need for normalization of scores so that results from templates with differing sensitivity may be compared directly...
  12. ncbi Textural analysis of contrast-enhanced MR images of the breast
    Peter Gibbs
    Academic Department of Radiology, University of Hull, Hull, United Kingdom
    Magn Reson Med 50:92-8. 2003
    ..On combining features obtained using textural analysis with lesion size, time to maximum enhancement, and patient age, a diagnostic accuracy of A(z) = 0.92 +/- 0.05 was demonstrated...
  13. pmc A strategy for identifying locomotion modes using surface electromyography
    He Huang
    Department of Electrical, Computer, and Biomedical Engineering, University of Rhode Island, Kingston, RI 02881, USA
    IEEE Trans Biomed Eng 56:65-73. 2009
    ..1%, and 5.2% +/- 3.7%, respectively. Comparable results were also observed in our pilot study on the subjects with TF amputations. The outcome of this investigation could promote the future design of neural-controlled artificial legs...
  14. ncbi Image analysis algorithms for cell contour recognition in budding yeast
    Mats Kvarnström
    Fraunhofer Chalmers Research Centre, Chalmers Science Park, SE 412 88 Göteborg, Sweden
    Opt Express 16:12943-57. 2008
    ..The cell contours can be used to effectively quantify cell morphology parameters as well as protein abundance and subcellular localization from overlaid fluorescence data...
  15. ncbi Texture analysis of medical images
    G Castellano
    Neuroimage Laboratory, Faculty of Medical Sciences, State University of Campinas, Brazil
    Clin Radiol 59:1061-9. 2004
    ..In this article we clarify the principles of texture analysis and give examples of its applications, reviewing studies of the technique...
  16. ncbi Venn Mapping: clustering of heterologous microarray data based on the number of co-occurring differentially expressed genes
    Marcel Smid
    Department of Pathology, Josephine Nefkens Institute, Erasmus MC, P O Box 1738, 3000 DR Rotterdam, The Netherlands
    Bioinformatics 19:2065-71. 2003
    ..As the clustering algorithm searches for similarities between experiments, it will most likely first separate the data sets, masking relationships that exist between samples from different databases...
  17. pmc Clustering cancer gene expression data: a comparative study
    Marcilio C P De Souto
    Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
    BMC Bioinformatics 9:497. 2008
    ..There have been no studies thus far performing a large-scale evaluation of different clustering methods in this context...
  18. ncbi A wavelet-based continuous classification scheme for multifunction myoelectric control
    K Englehart
    Department of Electrical and Computer Engineering and the Institute of Biomedical Engineering, University of New Brunswick, Fredericton, Canada
    IEEE Trans Biomed Eng 48:302-11. 2001
    ..Although in its preliminary stages of development, this scheme promises a more natural and efficient means of myoelectric control than one based on discrete, transient bursts of activity...
  19. ncbi A study on several machine-learning methods for classification of malignant and benign clustered microcalcifications
    Liyang Wei
    Department of Biomedical Engineering, Illinois Institute of Technology, Chicago, IL 60616, USA
    IEEE Trans Med Imaging 24:371-80. 2005
    ..e., SVM, KFD, and RVM) yielded the best performance (Az = 0.85, SVM), significantly outperforming a well-established, clinically-proven CADx approach that is based on neural network (Az = 0.80)...
  20. ncbi Slow feature analysis: unsupervised learning of invariances
    Laurenz Wiskott
    Computational Neurobiology Laboratory, Salk Institute for Biological Studies, San Diego, CA 92168, USA
    Neural Comput 14:715-70. 2002
    ..The generated representation is suitable for object recognition. Performance degrades if the network is trained to learn multiple invariances simultaneously...
  21. ncbi Towards adaptive classification for BCI
    Pradeep Shenoy
    Computer Science Department, University of Washington, Box 352350, Seattle, WA 98195, USA
    J Neural Eng 3:R13-23. 2006
    ..An encouraging result of our study is that surprisingly simple adaptive methods in combination with an offline feature selection scheme can significantly increase BCI performance...
  22. pmc Ensemble non-negative matrix factorization methods for clustering protein-protein interactions
    Derek Greene
    School of Computer Science and Informatics, University College Dublin, Dublin, Ireland
    Bioinformatics 24:1722-8. 2008
    ..Here we propose a new algorithm for aggregating a diverse collection of matrix factorizations to produce a more informative clustering, which takes the form of a 'soft' hierarchy of clusters...
  23. ncbi Normalized cuts in 3-D for spinal MRI segmentation
    Julio Carballido-Gamio
    Joint Graduate Group in Bioengineering, University of California, San Francisco, 94143 1290, USA
    IEEE Trans Med Imaging 23:36-44. 2004
    ..Results of the segmentation as well as limitations and challenges in this area are presented...
  24. pmc Comparison of public peak detection algorithms for MALDI mass spectrometry data analysis
    Chao Yang
    Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, PR China
    BMC Bioinformatics 10:4. 2009
    ..The main objective of this paper is to provide such a survey and to compare the performance of single spectrum based peak detection methods...
  25. ncbi Anatomically constrained region deformation for the automated segmentation of the hippocampus and the amygdala: Method and validation on controls and patients with Alzheimer's disease
    Marie Chupin
    Department of Clinical and Experimental Epilepsy, Institute of Neurology, UCL, UK
    Neuroimage 34:996-1019. 2007
    ..The proposed approach provides a new framework for further developments in quantitative analyses of the pathological hippocampus and amygdala in MRI scans...
  26. ncbi Sparse multinomial logistic regression: fast algorithms and generalization bounds
    Balaji Krishnapuram
    Computer Aided Diagnosis and Therapy Group, Siemens Medical Solutions USA, Inc, 51 Valley Stream Pkwy, Malvern, PA 19355, USA
    IEEE Trans Pattern Anal Mach Intell 27:957-68. 2005
    ..Third, we show how nontrivial generalization bounds can be derived for our classifier in the binary case. Experimental results on standard benchmark data sets attest to the accuracy, sparsity, and efficiency of the proposed methods...
  27. ncbi Wavelets in bioinformatics and computational biology: state of art and perspectives
    Pietro Lio
    Department of Zoology, University of Cambridge, UK
    Bioinformatics 19:2-9. 2003
    ..Wavelets are more efficient and faster than Fourier methods in capturing the essence of data. Nowadays there is a growing interest in using wavelets in the analysis of biological sequences and molecular biology-related signals...
  28. ncbi Open source clustering software
    M J L de Hoon
    Human Genome Center, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo, 108 8639 Japan
    Bioinformatics 20:1453-4. 2004
    ..In addition, we generated a Python and a Perl interface to the C Clustering Library, thereby combining the flexibility of a scripting language with the speed of C...
  29. ncbi Prediction of protein structural class for the twilight zone sequences
    Lukasz Kurgan
    Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Alberta, Canada
    Biochem Biophys Res Commun 357:453-60. 2007
    ....
  30. ncbi A comprehensive evaluation of multicategory classification methods for microarray gene expression cancer diagnosis
    Alexander Statnikov
    Department of Biomedical Informatics, Vanderbilt University Nashville, TN, USA
    Bioinformatics 21:631-43. 2005
    ....
  31. pmc A comprehensive comparison of random forests and support vector machines for microarray-based cancer classification
    Alexander Statnikov
    Department of Biomedical Informatics, Vanderbilt University, Nashville, TN, USA
    BMC Bioinformatics 9:319. 2008
    ..Recent work, however, suggests that random forest classifiers may outperform support vector machines in this domain...
  32. ncbi Segmentation of clustered nuclei with shape markers and marking function
    Jierong Cheng
    School of Computer Engineering, Nanyang Technological University, Singapore 638798, Singapore
    IEEE Trans Biomed Eng 56:741-8. 2009
    ..On mouse neuronal and Drosophila cellular images, we achieved 6%-7% improvement of segmentation accuracies over earlier methods...
  33. ncbi A neural-network-based method for predicting protein stability changes upon single point mutations
    Emidio Capriotti
    Laboratory of Biocomputing, CIRB Department of Biology, University of Bologna, Bologna, Italy
    Bioinformatics 20:i63-8. 2004
    ..This allows the application of machine learning techniques to predicting free energy stability changes upon mutation starting from the protein sequence...
  34. ncbi MedScan, a natural language processing engine for MEDLINE abstracts
    Svetlana Novichkova
    Ariadne Genomics, Inc, 9100 Great Seneca HWY, Rockville, MD 20850, USA
    Bioinformatics 19:1699-706. 2003
    ..Most proposals to date make rather simplistic assumptions about the syntactic aspect of natural language. There is an urgent need for a system that has broad coverage and performs well in real-text applications...
  35. ncbi Pyrobayes: an improved base caller for SNP discovery in pyrosequences
    Aaron R Quinlan
    Department of Biology, Boston College, 140 Commonwealth Avenue, Chestnut Hill, Massachusetts 02467, USA
    Nat Methods 5:179-81. 2008
    ..Pyrobayes permits accurate single-nucleotide polymorphism (SNP) calling in resequencing applications, even in shallow read coverage, primarily because it produces more confident base calls than the native base calling program...
  36. pmc Targeted muscle reinnervation for real-time myoelectric control of multifunction artificial arms
    Todd A Kuiken
    Neural Engineering Center for Artificial Limbs, Rehabilitation Institute of Chicago, 345 E Superior St, Room 1309, Chicago, IL 60611, USA
    JAMA 301:619-28. 2009
    ..After reinnervation, these target muscles produce electromyogram (EMG) signals on the surface of the skin that can be measured and used to control prosthetic arms...
  37. ncbi Robust object recognition with cortex-like mechanisms
    Thomas Serre
    Massachusetts Institute of Technology, Center for Biological and Computational Learning, McGovern Institute for Brain Research and Brain and Cognitive Sciences Department, MA 02139, USA
    IEEE Trans Pattern Anal Mach Intell 29:411-26. 2007
    ..In addition to its relevance for computer vision, the success of this approach suggests a plausibility proof for a class of feedforward models of object recognition in cortex...
  38. ncbi A systematic comparison and evaluation of biclustering methods for gene expression data
    Amela Prelic
    Computer Engineering and Networks Laboratory, ETH Zurich, 8092 Zurich, Switzerland
    Bioinformatics 22:1122-9. 2006
    ....
  39. pmc NERBio: using selected word conjunctions, term normalization, and global patterns to improve biomedical named entity recognition
    Richard Tzong Han Tsai
    Institute of Information Science, Academia Sinica, Nankang, Taipei 115, Taiwan, Republic of China
    BMC Bioinformatics 7:S11. 2006
    ..We use global patterns generated by the Smith-Waterman local alignment algorithm to identify such structures and modify the results of our ML-based tagger. This is called pattern-based post-processing...
  40. ncbi Three-dimensional reconstruction and quantification of cervical carcinoma invasion fronts from histological serial sections
    Ulf Dietrich Braumann
    Interdisciplinary Center for Bioinformatics, University Leipzig, Leipzig, Germany
    IEEE Trans Med Imaging 24:1286-307. 2005
    ..By this, we achieved the most detailed 3-D reconstruction of the invasion of solid tumors so far. Once reconstructed, the invasion front of the segmented tumor is quantified using discrete compactness...
  41. ncbi Optimal word sizes for dissimilarity measures and estimation of the degree of dissimilarity between DNA sequences
    Tiee Jian Wu
    Department of Statistics, National Cheng Kung University, Tainan, Taiwan
    Bioinformatics 21:4125-32. 2005
    ..These simulated data can be used to estimate the degree of dissimilarity beta between any pair of DNA sequences...
  42. pmc Subcellular location prediction of proteins using support vector machines with alignment of block sequences utilizing amino acid composition
    Takeyuki Tamura
    Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611 0011, Japan
    BMC Bioinformatics 8:466. 2007
    ..Since existing predictors are based on various heuristics, it is important to develop a simple method with high prediction accuracies...
  43. ncbi A reliable method for cell phenotype image classification
    Loris Nanni
    Department of Electronic, Informatics and Systems DEIS, Universita di Bologna, Via Venezia 52, 47023 Cesena, Italy
    Artif Intell Med 43:87-97. 2008
    ..Image-based approaches have proven to be of great utility in the automated cell phenotype classification, it is very important to develop a method that efficiently quantifies, distinguishes and classifies sub-cellular images...
  44. ncbi Asymmetric bagging and random subspace for support vector machines-based relevance feedback in image retrieval
    Dacheng Tao
    School of Computer Science and Information Systems, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
    IEEE Trans Pattern Anal Mach Intell 28:1088-99. 2006
    ..Finally, by integrating AB-SVM and RS-SVM, an asymmetric bagging and random subspace SVM (ABRS-SVM) is built to solve these three problems and further improve the relevance feedback performance...
  45. ncbi Classification and knowledge discovery in protein databases
    Predrag Radivojac
    Center for Information Science and Technology, Temple University, USA
    J Biomed Inform 37:224-39. 2004
    ..In our experiments, training classifiers specialized to the class distributions of each cluster resulted in a further decrease in classification error...
  46. ncbi BaCelLo: a balanced subcellular localization predictor
    Andrea Pierleoni
    Biocomputing Group, Dept of Biology University of Bologna, Via Irnerio 42, 40126 Bologna, Italy
    Bioinformatics 22:e408-16. 2006
    ..Computational procedures are then needed for annotating the subcellular location of proteins in large scale genomic projects...
  47. ncbi Automatic detection of voice impairments by means of short-term cepstral parameters and neural network based detectors
    J I Godino-Llorente
    Universidad Politecnica de Madrid, Escuela Universitaria de Ingeniería Técnica de Telecomunicación, Dpt of Ingeniería de Circuitos y Sistemas, Ctra Valencia km 7, 28031, Madrid
    IEEE Trans Biomed Eng 51:380-4. 2004
    ..Within this context, the Learning Vector quantization methodology demonstrated to be more reliable than the multilayer perceptron architecture yielding 96% frame accuracy under similar working conditions...
  48. pmc Quantitative analysis of lesion morphology and texture features for diagnostic prediction in breast MRI
    Ke Nie
    Tu and Yuen Center for Functional Onco Imaging, University of California, CFOI, 164 Irvine Hall, Irvine, CA 92697, USA
    Acad Radiol 15:1513-25. 2008
    ....
  49. ncbi Efficient and robust feature extraction by maximum margin criterion
    Haifeng Li
    Department of Computer Science and Engineering, University of California, Riverside, CA 92521, USA
    IEEE Trans Neural Netw 17:157-65. 2006
    ..The kernelized (nonlinear) counterpart of this linear feature extractor is also established in the paper. Our extensive experiments demonstrate that the new feature extractors are effective, stable, and efficient...
  50. pmc Biclustering of gene expression data by Non-smooth Non-negative Matrix Factorization
    Pedro Carmona-Saez
    Biocomputing Unit, National Center of Biotechnology, Campus Universidad Autonoma de Madrid, 28049 Spain
    BMC Bioinformatics 7:78. 2006
    ..These patterns may provide clues about the main biological processes associated to different physiological states...
  51. ncbi A naive Bayes model to predict coupling between seven transmembrane domain receptors and G-proteins
    Jack Cao
    Department of Molecular Sciences, AstraZeneca R and D Montreal, 7171 Frederick Banting Street, St Laurent, Quebec H4S 1Z9, Canada
    Bioinformatics 19:234-40. 2003
    ..The sampling of an intracellular domain sequence was achieved by identifying the cluster containing the homologue with the highest sequence similarity...
  52. ncbi Multiple spaced seeds for homology search
    Lucian Ilie
    Department of Computer Science, University of Western Ontario, N6A 5B7, London, Ontario, Canada
    Bioinformatics 23:2969-77. 2007
    ..The multiple spaced seed of PatternHunterII, with 16 weight 11 seeds, was computed in 12 days. It takes us 17 s to find a better one. Our approach changes the way of looking at multiple spaced seeds...
  53. ncbi Comparison of linear, nonlinear, and feature selection methods for EEG signal classification
    Deon Garrett
    Department of Computer Science, Colorado State University, Fort Collins 80523, USA
    IEEE Trans Neural Syst Rehabil Eng 11:141-4. 2003
    ..An approach to feature selection based on genetic algorithms is also presented with preliminary results of application to EEG during finger movement...
  54. ncbi OCTOPUS: improving topology prediction by two-track ANN-based preference scores and an extended topological grammar
    Håkan Viklund
    Department of Biochemistry and Biophysics Center for Biomembrane Research Stockholm Bioinformatics Center, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE 10691 Stockholm, Sweden
    Bioinformatics 24:1662-8. 2008
    ..Because structural knowledge of transmembrane proteins is difficult to attain experimentally, improved methods for prediction of structural features of these proteins are important...
  55. ncbi Pattern identification and classification in gene expression data using an autoassociative neural network model
    Silvio Bicciato
    Department of Chemical Process Engineering, University of Padova, Via Marzolo, 9, 35131, Padova, Italy
    Biotechnol Bioeng 81:594-606. 2003
    ..At the same time, the neural network outputs provide assignment to multiple classes, such as different pathological conditions or tissue samples, for previously unseen instances...
  56. ncbi Terminology-driven mining of biomedical literature
    Goran Nenadic
    Computer Science, University of Salford, Salford M5 4WT, UK
    Bioinformatics 19:938-43. 2003
    ..Although the knowledge is organized around sets of domain-specific terms, few literature mining systems incorporate deep and dynamic terminology processing...
  57. pmc Scoring diverse cellular morphologies in image-based screens with iterative feedback and machine learning
    Thouis R Jones
    The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
    Proc Natl Acad Sci U S A 106:1826-31. 2009
    ..By using this approach, we successfully scored images in RNA interference screens in 2 organisms for the prevalence of 15 diverse cellular morphologies, some of which were previously intractable...
  58. ncbi A fuzzy clustering neural network architecture for multifunction upper-limb prosthesis
    Bekir Karlik
    Department of Computer Engineering, College of Information Technology, University of Bahrain, Kingdom of Bahrain
    IEEE Trans Biomed Eng 50:1255-61. 2003
    ..The results suggest that FCNN can generalize better than other NN algorithms and help the user learn better and faster. This method has the potential of being very efficient in real-time applications...
  59. ncbi Predicting protein subnuclear location with optimized evidence-theoretic K-nearest classifier and pseudo amino acid composition
    Hong Bin Shen
    Institute of Image Processing and Pattern Recognition, Shanghai Jiaotong University, Shanghai 200030, China
    Biochem Biophys Res Commun 337:752-6. 2005
    ..The OET-KNN classifier will be available at www.pami.sjtu.edu.cn/people/hbshen...
  60. ncbi Gene networks inference using dynamic Bayesian networks
    Bruno Edouard Perrin
    Laboratoire d Informatique de Paris 6, CNRS UMR 7606, Paris, France
    Bioinformatics 19:ii138-48. 2003
    ..Good prediction abilities on unlearned data are observed. These first results are very promising: they show the power of the learning algorithm and the ability of the model to capture gene interactions...
  61. pmc Local graph alignment and motif search in biological networks
    Johannes Berg
    Institut fur Theoretische Physik, Universitat zu Koln, Zülpicherstrasse 77, 50937 Cologne, Germany
    Proc Natl Acad Sci U S A 101:14689-94. 2004
    ..The algorithm is applied to the gene regulation network of Escherichia coli...
  62. pmc A kinetic-based sigmoidal model for the polymerase chain reaction and its application to high-capacity absolute quantitative real-time PCR
    Robert G Rutledge
    Natural Resources Canada, Canadian Forest Service, 1055 du PEPS, Quebec, Quebec G1V 4C7, Canada
    BMC Biotechnol 8:47. 2008
    ....
  63. ncbi Texture analysis of optical coherence tomography images: feasibility for tissue classification
    Kirk W Gossage
    University of Arizona, Biomedical Engineering Program, Tucson, Arizona 85721 0104, USA
    J Biomed Opt 8:570-5. 2003
    ..0 and 88.6%, respectively). This study shows that texture analysis of OCT images may be capable of differentiating tissue types without reliance on visible structures...
  64. pmc Comparative analysis of five protein-protein interaction corpora
    Sampo Pyysalo
    Turku Centre for Computer Science TUCS, Department of IT, University of Turku, Joukahaisenkatu 3 5, 20520 Turku, Finland
    BMC Bioinformatics 9:S6. 2008
    ..However, there is no general consensus regarding PPI annotation and consequently resources are largely incompatible and methods are difficult to evaluate...
  65. ncbi Computational methods for analysis of human breast tumor tissue in optical coherence tomography images
    Adam M Zysk
    Department of Electrical and Computer Engineering, University of Illinois at Urbana Champaign, Beckman Institute for Advanced Science and Technology, 405 N Mathews Ave, Urbana, Illinois 61801, USA
    J Biomed Opt 11:054015. 2006
    ..Derived from preliminary OCT data, these methods are aimed at the development of automated diagnostic tools that will aid in the translation of this technology into the clinical environment...
  66. pmc Independent histogram pursuit for segmentation of skin lesions
    David Delgado Gómez
    Computational Imaging Lab, Department of Information and Communication Technologies, Universitat Pompeu Fabra, Barcelona, Spain
    IEEE Trans Biomed Eng 55:157-61. 2008
    ..The boundary detection precision using k-means segmentation was close to 97%. The proposed algorithm can be easily combined with the majority of classification algorithms...
  67. pmc Quantitative prediction of mouse class I MHC peptide binding affinity using support vector machine regression (SVR) models
    Wen Liu
    Department of Neuroscience, University of Minnesota, Minneapolis, MN 55455, USA
    BMC Bioinformatics 7:182. 2006
    ....
  68. pmc Protein structure similarity from Principle Component Correlation analysis
    Xiaobo Zhou
    Center for Neurodegeneration and Repair, Center for Bioinformatics, Harvard Medical School, Boston, MA 02215, USA
    BMC Bioinformatics 7:40. 2006
    ..We propose new algorithms for extracting geometrical invariants of proteins that can be effectively used to identify homologous protein structures or topologies in order to quantify both close and remote structural similarities...
  69. ncbi Prediction of linear B-cell epitopes using amino acid pair antigenicity scale
    J Chen
    Institute of Image Processing and Pattern Recognition, Shanghai Jiaotong University, Shanghai, China
    Amino Acids 33:423-8. 2007
    ..It is anticipated that with the continuous increase of the known epitope data, the power of the AAP antigenicity scale approach will be further enhanced...
  70. ncbi Sequence alignment kernel for recognition of promoter regions
    Leo Gordon
    Department of Computer Science, Royal Holloway, University of London, Egham, Surrey TW20 0EX, UK
    Bioinformatics 19:1964-71. 2003
    ..The results show that our method performs well and achieves 16.5% average error rate on positive & coding negative data and 18.6% average error rate on positive & non-coding negative data...
  71. pmc The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists
    Da Wei Huang
    Laboratory of Immunopathogenesis and Bioinformatics, Clinical Services Program, SAIC Frederick, Inc, National Cancer Institute at Frederick, Frederick, MD 21702, USA
    Genome Biol 8:R183. 2007
    ..It is a powerful method to group functionally related genes and terms into a manageable number of biological modules for efficient interpretation of gene lists in a network context...
  72. pmc Adaptive pattern recognition of myoelectric signals: exploration of conceptual framework and practical algorithms
    Jonathon W Sensinger
    Neural Engineering Center for Artificial Limbs, Rehabilitation Institute of Chicago, Chicago, IL 60611, USA
    IEEE Trans Neural Syst Rehabil Eng 17:270-8. 2009
    ..Supervised adaptation should be considered for incorporation into any clinically viable pattern recognition controller, and unsupervised adaptation should receive renewed interest in order to provide transparent adaptation...
  73. ncbi Automatic clustering of orthologs and inparalogs shared by multiple proteomes
    Andrey Alexeyenko
    Center for Genomics and Bioinformatics, Karolinska Institutet, S 17177 Stockholm, Sweden
    Bioinformatics 22:e9-15. 2006
    ..Identification of orthologous groups shared by multiple proteomes therefore becomes a clustering problem in which an optimal compromise between conflicting evidences needs to be found...
  74. ncbi A fully on-line adaptive BCI
    C Vidaurre
    Department of Electrical Engineering and Electronics, State University of Navarra, Pamplona, Spain
    IEEE Trans Biomed Eng 53:1214-9. 2006
    ..The success of the feedback was studied analyzing the error rate and mutual information of each session and this analysis showed a clear improvement of the subject's control of the BCI from session to session...
  75. ncbi Efficient discovery of conserved patterns using a pattern graph
    I Jonassen
    Department of Informatics, University of Bergen, Norway
    Comput Appl Biosci 13:509-22. 1997
    ..In many cases, this version of Pratt was very efficient, but in other cases it was too time consuming to be applied. Hence, a more efficient algorithm was needed...
  76. ncbi A novel method of protein secondary structure prediction with high segment overlap measure: support vector machine approach
    S Hua
    Institute of Bioinformatics, State key Laboratory of Biemembrane and Membrane Biotechnology, Department of Biological Sciences and Biotechnology, Tsinghua University, Beijing 100084, China
    J Mol Biol 308:397-407. 2001
    ..The SVM method is conveniently applied to many other pattern classification tasks in biology...
  77. ncbi A genetic similarity algorithm for searching the Gene Ontology terms and annotating anonymous protein sequences
    Razib M Othman
    Department of Software Engineering, Faculty of Computer Science and Information Systems, Universiti Teknologi Malaysia, 81310 UTM Skudai, Malaysia
    J Biomed Inform 41:65-81. 2008
    ..The computational results and comparison with other related tools are presented to show the effectiveness of the proposed algorithm and tools...
  78. ncbi Graph-based consensus clustering for class discovery from gene expression data
    Zhiwen Yu
    Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong
    Bioinformatics 23:2888-96. 2007
    ..By consensus clustering, one can discover the underlying classes of the samples in gene expression data...
  79. pmc An evaluation of GO annotation retrieval for BioCreAtIvE and GOA
    Evelyn B Camon
    European Molecular Biology Laboratory, European Bionformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
    BMC Bioinformatics 6:S17. 2005
    ..Finally, we provide the results of the first inter-annotator agreement study for manual GO curation, as well as an assessment of our current electronic GO annotation strategies...
  80. ncbi EDGE: extraction and analysis of differential gene expression
    Jeffrey T Leek
    Department of Biostatistics, University of Washington, Seattle 98195, USA
    Bioinformatics 22:507-8. 2006
    ..EDGE can perform both standard and time course differential expression analysis. The functions are based on newly developed statistical theory and methods. This document introduces the EDGE software package...
  81. ncbi Optimal number of features as a function of sample size for various classification rules
    Jianping Hua
    Department of Electrical Engineering, Texas A and M University, College Station, TX 77843, USA
    Bioinformatics 21:1509-15. 2005
    ..For fixed sample size and feature-label distribution, the issue is to find an optimal number of features...
  82. ncbi Motif-based protein ranking by network propagation
    Rui Kuang
    Department of Computer Science, Columbia University New York, NY 10027, USA
    Bioinformatics 21:3711-8. 2005
    ..The most widely-used pairwise sequence comparison algorithms for homology detection, such as BLAST and PSI-BLAST, often fail to detect less conserved remotely-related targets...
  83. pmc Critical evaluation of methods used to determine amplification efficiency refutes the exponential character of real-time PCR
    Robert G Rutledge
    Natural Resources Canada, Canadian Forest Service, 1055 du PEPS, Quebec, Quebec G1V 4C7, Canada
    BMC Mol Biol 9:96. 2008
    ..Called "linear regression of efficiency" or LRE, this kinetic-based approach redefines amplification efficiency as the maximal efficiency (Emax) generated at the onset of thermocycling...
  84. ncbi Characterization of breast cancer types by texture analysis of magnetic resonance images
    Kirsi Holli
    Medical Imaging Centre, Tampere University Hospital, Post Box 2000, 33521 Tampere, Finland
    Acad Radiol 17:135-41. 2010
    ....
  85. ncbi Gene prediction with a hidden Markov model and a new intron submodel
    Mario Stanke
    Institut fur Mikrobiologie und Genetik, Abteilung Bioinformatik, Universitat Gottingen, Gottingen, Germany
    Bioinformatics 19:ii215-25. 2003
    ..Gene finding programs have achieved relatively high accuracy on short genomic sequences but do not perform well on longer sequences with an unknown number of genes in them. Here existing programs tend to predict many false exons...
  86. ncbi Knowledge discovery by automated identification and ranking of implicit relationships
    Jonathan D Wren
    Advanced Center for Genome Technology, Department of Botany and Microbiology, The University of Oklahoma, 620 Parrington Oval Rm 106, Norman, OK 73019, USA
    Bioinformatics 20:389-98. 2004
    ....
  87. ncbi RONN: the bio-basis function neural network technique applied to the detection of natively disordered regions in proteins
    Zheng Rong Yang
    School of Engineering and Computer Science, Exeter University, Exeter EX4 4QF, UK
    Bioinformatics 21:3369-76. 2005
    ..The study and detection of such disordered regions is important both for understanding protein function and for facilitating structural analysis since disordered regions may affect solubility and/or crystallizability...
  88. pmc Nonnegative matrix factorization: an analytical and interpretive tool in computational biology
    Karthik Devarajan
    Division of Population Science, Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA
    PLoS Comput Biol 4:e1000029. 2008
    ..In this paper, we review this method as a data analytical and interpretive tool in computational biology with an emphasis on these applications...
  89. ncbi Pathway analysis using random forests classification and regression
    Herbert Pang
    Division of Biostatistics, Department of Epidemiology and Public Health, Yale University School of Medicine New Haven, CT 06520, USA
    Bioinformatics 22:2028-36. 2006
    ..Pathway-based analysis in microarray studies may lead to more informative and relevant knowledge for biological researchers...
  90. ncbi Classification of single-trial electroencephalogram during finger movement
    Yong Li
    Department of Biomedical Engineering, Tsinghua University, Beijing 100084, China
    IEEE Trans Biomed Eng 51:1019-25. 2004
    ..This technique can be employed in an EEG-based brain-computer interface due to its high recognition rate, insensitivity to noise, and simplicity in computation...
  91. ncbi Prostate cancer multi-feature analysis using trans-rectal ultrasound images
    S S Mohamed
    Electrical and Computer Engineering Department, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
    Phys Med Biol 50:N175-85. 2005
    ..The accuracy classification results range from 87.5% to 93.75%, where the performance of the SVM and that of the DT are significantly better than the performance of the CNN...
  92. ncbi Multidimensional support vector machines for visualization of gene expression data
    D Komura
    Research Center for Advanced Science and Technology, University of Tokyo Tokyo 153 8904, Japan
    Bioinformatics 21:439-44. 2005
    ..However, in the case of binary classification of gene expression data, PCA does not utilize class information when choosing axes. Thus clearly separable data in the original space may not be so in the reduced space used in PCA...
  93. ncbi A comparative study of feature selection and multiclass classification methods for tissue classification based on gene expression
    Tao Li
    Computer Science Department, University of Rochester, Rochester, NY 14627 0226, USA
    Bioinformatics 20:2429-37. 2004
    ..While increasing the number of samples is a plausible solution to the problem of accuracy degradation, it is important to develop algorithms that are able to analyze effectively multiple-class expression data for these special datasets...
  94. ncbi A robust, real-time control scheme for multifunction myoelectric control
    Kevin Englehart
    Department of Biomedical Engineering, University of New Brunswick, 25 Dineen Drive, Fredericton, NB E3B5A3, Canada
    IEEE Trans Biomed Eng 50:848-54. 2003
    ..Finally, minimal storage capacity is required, which is an important factor in embedded control systems...
  95. ncbi Is cross-validation valid for small-sample microarray classification?
    Ulisses M Braga-Neto
    Section of Clinical Cancer Genetics, University of Texas MD Anderson Cancer Center, Houston, TX, USA
    Bioinformatics 20:374-80. 2004
    ..Bootstrap methods provide improved performance relative to variance, but at a high computational cost and often with increased bias (albeit, much less than with resubstitution)...
  96. ncbi Computer-aided tumor detection in endoscopic video using color wavelet features
    Stavros A Karkanis
    Realtime Systems and Image Analysis Group, Department of Informatics and Telecommunications, University of Athens, Greece
    IEEE Trans Inf Technol Biomed 7:141-52. 2003
    ..The performance in the detection of abnormal colonic regions corresponding to adenomatous polyps has been estimated high, reaching 97% specificity and 90% sensitivity...
  97. ncbi Feature selection for the classification of movements from single movement-related potentials
    Elad Yom-Tov
    Technion Israel Institute of Technology, Haifa 32000, Israel
    IEEE Trans Neural Syst Rehabil Eng 10:170-7. 2002
    ..With the addition of a simple coding scheme, this method can be applied to multiple limb classification and a 63% classification accuracy rate can be reached when attempting to distinguish between three limbs...
  98. pmc High throughput profile-profile based fold recognition for the entire human proteome
    Liam J McGuffin
    The Biocentre, University of Reading, Whiteknights, PO Box 221, Reading RG6 6AS, UK
    BMC Bioinformatics 7:288. 2006
    ..We use the most recent profile-profile version of our mGenTHREADER software in order to annotate the latest version of the Human proteome against the latest sequence and structure databases in as short a time as possible...
  99. pmc SLiMFinder: a probabilistic method for identifying over-represented, convergently evolved, short linear motifs in proteins
    Richard J Edwards
    University College Dublin Complex and Adaptive Systems Laboratory, University College Dublin, Dublin, Ireland
    PLoS ONE 2:e967. 2007
    ..Incorporating ambiguous amino acid positions and/or variable-length wildcard spacers between defined residues further complicates the matter...
  100. ncbi Prediction of integral membrane protein type by collocated hydrophobic amino acid pairs
    Ke Chen
    Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Alberta, Canada
    J Comput Chem 30:163-72. 2009
    ..This conclusion is supported by a recent study on potential of mean force for membrane protein folding and a study of scales for membrane propensity of amino acids...
  101. ncbi Prediction of human protein function according to Gene Ontology categories
    L J Jensen
    Center for Biological Sequence Analysis, BioCentrum DTU, Building 208, The Technical University of Denmark, DK 2800 Lyngby, Denmark
    Bioinformatics 19:635-42. 2003
    ..As a large fraction of these are functionally uncharacterized, it is of interest to develop methods for predicting their molecular function from sequence...

Research Grants63

  1. Emergency Neurophysiological Assessment Bedside Logic Engine
    Don M Tucker; Fiscal Year: 2010
    ..Reliable automated pattern recognition is required, yet in the past this has often failed to separate real neurological disorder from ..
  2. Predict Near Future Bed Exit for Effective Intervention to Avoid Nighttime Falls
    THOMAS HENRY WHALEN; Fiscal Year: 2012
    ..Therefore, with a rapidly aging population, ever-increasing healthcare costs, and limited healthcare resources, there is significant and critical relevance to reducing the number of falls, and fall-related injuries among the elderly. ..
  3. EVASION OF ANTIGEN PRESENTATION BY VACUOLAR PATHOGENS
    Craig R Roy; Fiscal Year: 2013
    ..Thus, this project is focused on identifying molecular mechanisms that mediate host protection by investigating the role of immune surveillance pathways in generating a response against the intracellular pathogen Legionella pneumophila. ..
  4. SBIR PHASE II- TOPIC 234- AUTOMATED PATTERN RECOGNITION IN SATELLITE IMAGERY
    PIERRE E GOOVAERTS; Fiscal Year: 2009
    ..abstract_text> ..
  5. A Virtual Reality Environment for Genomic Data Visualization
    Fatima Merchant; Fiscal Year: 2007
    ..The primary healthcare benefits that will accrue from this development will result from the accelerated development of diagnostics and treatments for diseases. [unreadable] [unreadable] [unreadable]..
  6. NEUROTOXICITY OF CNS PROPHYLACTIC THERAPIES IN ALL
    PHYLLIS MULLENIX; Fiscal Year: 1993
    ..Consequently, this animal model can provide important information on how CNS prophylactic therapies can be manipulated to reduce neurotoxicity...
  7. NEW TECHNIQUES FOR MAP/SEQUENCE PATTERN RECOGNITION
    TERENCE THOMPSON; Fiscal Year: 1993
    ..growth of genomic data and the inherent complexity and variability of its biological significance, automated pattern recognition is critical for efficiently identifying structural and functional relationships in the genomic ..
  8. Vector Quantization for Image Pattern Recognition
    DIRK SOENKSEN; Fiscal Year: 2003
    ..Virtual slides set the stage for automating microscopic inspection using automated pattern recognition. This research aims to adapt and optimize Aperio's existing and novel algorithms for vector ..
  9. Three-dimensional Molecular Pattern Recognition
    Niels Volkmann; Fiscal Year: 2006
    ..For each step, computer-generated model systems will also be used as a tool for development and evaluation. Documentation, tutorials and an easy to-use interface will be developed. ..
  10. Clinical decision-making using a data-driven display
    James Harrison; Fiscal Year: 2005
    ..abstract_text> ..
  11. Continued Development and Maintenance of a Computational Morphometry Toolkit
    Torsten Rohlfing; Fiscal Year: 2010
    ..This project will enhance a proven soft- ware system for imaging-based morphometric studies and make it freely avail- able to the scientific community. ..
  12. 3D Massive Training ANN for CAD for Colon Cancer in CT Colonography
    Kenji Suzuki; Fiscal Year: 2010
    ....
  13. Multimodality CAD system with image references for breast mass characterization
    Berkman Sahiner; Fiscal Year: 2007
    ..Any reduction in this number without a decrease in breast cancer detection sensitivity will decrease health care costs, as well as contribute to the well-being of the patient by reducing anxiety and morbidity. ..
  14. Enhancement and Dissemination of ART: An Automatic Registration Toolbox
    Babak Ardekani; Fiscal Year: 2007
    ..unreadable] [unreadable] [unreadable] [unreadable]..
  15. Three-Class ROC Analysis for Task-Based Medical Image Quality Assessment
    Xin He; Fiscal Year: 2008
    ..unreadable] [unreadable] [unreadable]..
  16. Iron Status: A Pathway Analysis in Multiple Ethnicities
    Christine McLaren; Fiscal Year: 2009
    ..Potential study results could be used to identify individuals at risk for iron deficiency and to develop innovative prevention and treatment strategies. ..
  17. Information theoretic assays of exploration in aged mice
    Stephen Bonasera; Fiscal Year: 2007
    ..unreadable] [unreadable] [unreadable]..
  18. Serotonergic Regulation of Behavioral Disinhibition
    Stephen Bonasera; Fiscal Year: 2007
    ..abstract_text> ..
  19. Subcortical Hyperintensities in Sleep Apnea Syndrome
    Mark Aloia; Fiscal Year: 2007
    ..We expect to analyze data on approximately 1,120 participants based on our preliminary studies with this data set. [unreadable] [unreadable]..
  20. CD4+ T cell subset function in antitumor immune response
    Piotr Kraj; Fiscal Year: 2009
    ..We will also investigate what is the origin of T cells with effector and regulatory function-in tumor tissue and try to identify precursors of these cells in the T cell population of healthy mice. ..
  21. Mycobacterium tuberculosis-reactive thymocytes
    MARIELLE GOLD; Fiscal Year: 2007
    ..unreadable] [unreadable] [unreadable]..
  22. Statistical Methods for the Analysis of Functional Genomic Data
    Debashis Ghosh; Fiscal Year: 2008
    ..unreadable] 5. Dissemination of these results in user-friendly statistical software. ..
  23. Subharmonic Microbubble Signals for Pressure Estimation
    Flemming Forsberg; Fiscal Year: 2008
    ..This will allow potentially life-threatening diseases, such as increased pressure in the liver, to be diagnosed early. [unreadable] [unreadable] [unreadable]..
  24. ROBUST PORTABLE SOFTWARE FOR LOCATION PROTEOMICS
    Robert Murphy; Fiscal Year: 2006
    ..unreadable] [unreadable]..
  25. Low-cost, portable, computer assisted imaging for diabe*
    Michael Abramoff; Fiscal Year: 2008
    ..Our overall aim is to validate and optimize a low-cost, high quality, patient friendly imaging system for the early diagnosis of diabetic retinopathy. ..
  26. Contrast-Enhanced Ultrasound Detection of Angiogenesis
    Flemming Forsberg; Fiscal Year: 2004
    ..If successful, this project will permit non-invasive ultrasound evaluations of anti-angiogenic tumor therapies in animals as well as humans. ..
  27. Data Communication with Implantable Micro Devices
    Mingui Sun; Fiscal Year: 2002
    ..We will implant this device within the brain of laboratory dogs and evaluate its performance. ..
  28. Head mounted display apparatus for visual field test
    DARIUSZ WROBLEWSKI; Fiscal Year: 2004
    ..Incorporation of gaze tracking device increases test reliability and accuracy. The goal of Phase I work is to design and construct a prototype of head-mounted visual field apparatus. ..
  29. Cortical Reconstruction and Analysis Software
    Dzung Pham; Fiscal Year: 2009
    ..Source code to all developed software will be made publicly available. ..
  30. Mapping spatial working memory and attention in cortex
    Donald Hagler; Fiscal Year: 2004
    ..This project is an investigation into the neurobiological basis for memory of and attention to spatial location. ..
  31. Separating Intensity Change from Atrophy in Serial MRI
    Colin Studholme; Fiscal Year: 2004
    ..These applications are aimed at helping distinguish vascular disease from other dementias and at a better understanding of the biological mechanisms underlying the chronic effects of alcohol and recovery on the brain. ..
  32. Evolutionary Computation for Gene Expression Analysis
    GARY FOGEL; Fiscal Year: 2003
    ..The commercial potential for such a system is significant especially with regard to cell classification of any kind from molecular data. ..
  33. Four-Color Microscope For Single-Molecule Sequencing
    GREGORY BASHFORD; Fiscal Year: 2002
    ..Fields-of-use include research, diagnostics and personalized medicine. Public health applications include rapid sequencing (without cloning) of "designer germs" carrying engineered genomes that could cause novel symptoms. ..
  34. Archiving the Charleston Heart Study
    Paul Nietert; Fiscal Year: 2002
    ..abstract_text> ..
  35. Analytic Methods for Functional Neuroimaging Data
    F Dubois Bowman; Fiscal Year: 2010
    ..The focus here on fMRI and PET data related to schizophrenia, depression, and cocaine-dependence illustrates the potential applicability and relevance of the proposed methods across a range of mental health disorders. ..
  36. Effects of Drug Use and Cessation on Monkey Brain
    Itamar Ronen; Fiscal Year: 2003
    ..2. Cessation of drug use will result in a normalization of brain measures. This will address the important issue of whether or not there is significant brain recovery following cessation of drug use. ..
  37. CD-HIT: A Fast Program to Cluster and Compare Large Sets of Biological Sequences
    Weizhong Li; Fiscal Year: 2010
    ..Continued development of CD-HIT will better serve researchers who are facing more challenges in sequence analysis by the explosive growth of public sequence databases. ..
  38. SPATIALLY ORIENTED DATABASE FOR DIGITAL BRAIN IMAGES
    Edward H Herskovits; Fiscal Year: 2010
    ..We expect that, as we implement more components of this software suite, neuroscientists will find it much easier to perform complex multivariate analyses of their data relating structure and function of the human brain. ..
  39. Regional Lung Mechanics by 3D Image Registration
    Joseph M Reinhardt; Fiscal Year: 2010
    ..This information is now critical to the development and evaluation of new pulmonary disease therapies. ..
  40. Real-Time Monitoring of Laser Ablation with OCT
    BRIAN GOLDBERG; Fiscal Year: 2008
    ..Although our approach is applicable to a spectrum of diseases, we will specifically focus on the treatment of Barrett's esophagus. [unreadable] [unreadable] [unreadable]..
  41. Decision Support Systems for MAG3 Renography
    Andrew Taylor; Fiscal Year: 2005
    ..abstract_text> ..
  42. Computer Aided Diagnosis of Lung Cancer
    Heang Ping Chan; Fiscal Year: 2006
    ..When fully developed and clinically implemented, a CAD system for lung nodules will increase the efficacy of lung cancer screening with helical CT, improve early detection, and improve the chance of survival of patients. ..
  43. Expression Analysis of Prostate Cancer
    Phillip Febbo; Fiscal Year: 2006
    ....
  44. Statistical Methods for Neuroimaging Data
    F Bowman; Fiscal Year: 2006
    ..Computer software for these research developments will be made accessible to neuroimaging scientists. ..
  45. Novel Machine Learning Methods for Analysis of MALDI-TOF Mass Spectrometry Data
    Habtom Ressom; Fiscal Year: 2008
    ..Furthermore, the peptides represented by the selected candidate biomarkers will be identified. Finally, the performance of the algorithm will be compared with existing methods. [unreadable] [unreadable] [unreadable]..
  46. Nonparametric Inference for Neuroimaging Data
    Timothy Johnson; Fiscal Year: 2008
    ..abstract_text> ..
  47. DETECTION AND LOCALIZATION IN MAMMOGRAPHY
    Bin Zheng; Fiscal Year: 2002
    ..It will also investigate augmented CAD cues that code information about correlations between the two ipsilateral projections. ..
  48. Interactive CAD for Mammography
    Bin Zheng; Fiscal Year: 2007
    ..unreadable] [unreadable]..
  49. PERCEPTUAL MODEL FOR WORKSTATION DISPLAY OPTIMIZATION
    Dev Chakraborty; Fiscal Year: 2002
    ..Also to be generated are iso-contour plots of the effects of common workstation variables on image quality in both tasks. This will allow digital mammography workstations to be more intelligently used. ..
  50. Phase resetting using DC stimulation for seizure blockage
    Ivan Osorio; Fiscal Year: 2007
    ..3B. The significant advances made in the control of fatal arrhythmias are in part attributable to the use by cardiologists of phase resetting as an investigative and therapeutic tool. [unreadable] [unreadable] [unreadable]..
  51. Digital Mammography: Advanced Computer-Aided Breast Can*
    Heang Ping Chan; Fiscal Year: 2007
    ..abstract_text> ..
  52. BCI2000: SOFTWARE FOR BRAIN-COMPUTER INTERFACE RESEARCH
    Gerwin Schalk; Fiscal Year: 2009
    ..This project will greatly facilitate this development by improving and maintaining general-purpose BCI software and continuing to provide it to BCI research groups throughout the world. ..
  53. DEVELOPMENT OF TC-99M RENAL TUBULAR AGENTS
    Andrew Taylor; Fiscal Year: 2008
    ..abstract_text> ..
  54. DTI and MRS Correlates of Aging in Monkeys
    Itamar Ronen; Fiscal Year: 2008
    ..Our specific aims are: (1) Collection of preliminary data on the effects of aging on the monkey brain; (2) Validation of the MRI/MRS findings with post-mortem data on the same brains. [unreadable] [unreadable] [unreadable]..
  55. Exploration of Stereo Display for Lung Cancer Screening
    Xiao Hui Wang; Fiscal Year: 2005
    ..We expect to demonstrate that the use of a stereo display for lung cancer screening will result in improved accuracy and efficiency, and this could greatly increase the efficacy of this screening process. ..
  56. Probabilistic Modeling of Information from Images and Text in Online Journals
    Robert Murphy; Fiscal Year: 2008
    ..unreadable] [unreadable] [unreadable]..
  57. Automated Literature Mining for Validation of High-Throughput Function Prediction
    KARIN MARIA VERSPOOR; Fiscal Year: 2010
    ..It is time to truly integrate the biological literature into the protein function prediction problem. By doing so, we will enable a critical advance in high-throughput protein function prediction ..
  58. Computer Surgical Simulation for Craniofacial Surgery
    James Xia; Fiscal Year: 2008
    ..In the United States each year, a significant number of patients undergo reconstructive surgery for these types of defects and deformities. [unreadable] [unreadable] [unreadable]..
  59. PERCEPTUAL MODEL FOR WORKSTATION DISPLAY OPTIMIZATION
    Dev Chakraborty; Fiscal Year: 2003
    ..Also to be generated are iso-contour plots of the effects of common workstation variables on image quality in both tasks. This will allow digital mammography workstations to be more intelligently used. ..
  60. OBJECT RECOGNITION & NAVIGATION--NORMAL & LOW VISION
    GORDON LEGGE; Fiscal Year: 2003
    ..field loss, on the formation and use of cognitive maps. Their hypothesis is that cognitive maps, although difficult to learn with visual impairment, will be esp. beneficial to people with low vision. ..
  61. Detection of chewing and swallowing to estimate eating patterns and energy intake
    Edward Sazonov; Fiscal Year: 2006
    ..Modern methods of computational intelligence such as artificial neural networks and fuzzy logic will be used along with statistical methods to achieve the highest 'accuracy of pattern recognition. ..
  62. Statistical and Computational Methods for Systematically Mining the SNP and Gene
    Zhenqiu Liu; Fiscal Year: 2008
    ..We hope our researches have the impact of encouraging more people to contribute to this challenging problem. [unreadable] [unreadable] [unreadable]..