software design

Summary

Summary: Specifications and instructions applied to the software.

Top Publications

  1. pmc The Bioperl toolkit: Perl modules for the life sciences
    Jason E Stajich
    University Program in Genetics, Duke University, Durham, North Carolina 27710, USA
    Genome Res 12:1611-8. 2002
  2. ncbi The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models
    M Hucka
    Control and Dynamical Systems, MC 107 81, California Institute of Technology, Pasadena, CA 91125, USA
    Bioinformatics 19:524-31. 2003
  3. pmc ArrayExpress--a public repository for microarray gene expression data at the EBI
    Alvis Brazma
    European Bioinformatics Institute, EMBL EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
    Nucleic Acids Res 31:68-71. 2003
  4. pmc MedEx: a medication information extraction system for clinical narratives
    Hua Xu
    Department of Biomedical Informatics, Vanderbilt University, School of Medicine, Nashville, Tennessee 37232, USA
    J Am Med Inform Assoc 17:19-24. 2010
  5. pmc Agile methods in biomedical software development: a multi-site experience report
    David W Kane
    SRA International, 4300 Fair Lakes Court, Fairfax, VA 22033, USA
    BMC Bioinformatics 7:273. 2006
  6. pmc MDL constrained 3-D grayscale skeletonization algorithm for automated extraction of dendrites and spines from fluorescence confocal images
    Xiaosong Yuan
    Jonsson Engineering Center, Center for Subsurface Sensing and Imaging Systems, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
    Neuroinformatics 7:213-32. 2009
  7. ncbi AMIDE: a free software tool for multimodality medical image analysis
    Andreas Markus Loening
    Stanford University, Department of Radiology and the Bio X Program, 318 Campus Drive, East Wing, 1st Floor, Stanford, CA 94305 542, USA
    Mol Imaging 2:131-7. 2003
  8. ncbi Improving the quality of reports of meta-analyses of randomised controlled trials: the QUOROM statement. Quality of Reporting of Meta-analyses
    D Moher
    University of Ottawa, Thomas C Chalmers Centre for Systematic Reviews, Ontario, Canada
    Lancet 354:1896-900. 1999
  9. ncbi Automated water analyser computer supported system (AWACSS) Part I: Project objectives, basic technology, immunoassay development, software design and networking
    Jens Tschmelak
    Institute of Physical and Theoretical Chemistry IPTC, Eberhard Karls University of Tuebingen, Auf der Morgenstelle 8, Tuebingen 72076, Germany
    Biosens Bioelectron 20:1499-508. 2005
  10. pmc PRIMROSE: a computer program for generating and estimating the phylogenetic range of 16S rRNA oligonucleotide probes and primers in conjunction with the RDP-II database
    Kevin E Ashelford
    Cardiff School of Biosciences, Cardiff University, PO Box 915, Cardiff CF10 3TL, UK
    Nucleic Acids Res 30:3481-9. 2002

Detail Information

Publications191 found, 100 shown here

  1. pmc The Bioperl toolkit: Perl modules for the life sciences
    Jason E Stajich
    University Program in Genetics, Duke University, Durham, North Carolina 27710, USA
    Genome Res 12:1611-8. 2002
    ..We conclude with a discussion of how the open-source nature of the project has contributed to the development effort...
  2. ncbi The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models
    M Hucka
    Control and Dynamical Systems, MC 107 81, California Institute of Technology, Pasadena, CA 91125, USA
    Bioinformatics 19:524-31. 2003
    ..Molecular biotechnology now makes it possible to build elaborate systems models, but the systems biology community needs information standards if models are to be shared, evaluated and developed cooperatively...
  3. pmc ArrayExpress--a public repository for microarray gene expression data at the EBI
    Alvis Brazma
    European Bioinformatics Institute, EMBL EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
    Nucleic Acids Res 31:68-71. 2003
    ..With an increasing number of organisations adopting MAGE-ML standard, the volume of submissions to ArrayExpress is increasing rapidly. The database can be accessed at http://www.ebi.ac.uk/arrayexpress...
  4. pmc MedEx: a medication information extraction system for clinical narratives
    Hua Xu
    Department of Biomedical Informatics, Vanderbilt University, School of Medicine, Nashville, Tennessee 37232, USA
    J Am Med Inform Assoc 17:19-24. 2010
    ..5%, 93.9%, and 96.0% respectively. We then applied MedEx unchanged to outpatient clinic visit notes. It performed similarly with F-measures over 90% on a set of 25 clinic visit notes...
  5. pmc Agile methods in biomedical software development: a multi-site experience report
    David W Kane
    SRA International, 4300 Fair Lakes Court, Fairfax, VA 22033, USA
    BMC Bioinformatics 7:273. 2006
    ..We have successfully used agile development approaches to create and maintain biomedical software, including software for bioinformatics. This paper reports on a qualitative study of our experiences using these methods...
  6. pmc MDL constrained 3-D grayscale skeletonization algorithm for automated extraction of dendrites and spines from fluorescence confocal images
    Xiaosong Yuan
    Jonsson Engineering Center, Center for Subsurface Sensing and Imaging Systems, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
    Neuroinformatics 7:213-32. 2009
    ..Spines were detected with false negative rates less than 10% on most datasets (the average is 7.1%), and the average false positive rate was 11.8%. The software is available in open source form...
  7. ncbi AMIDE: a free software tool for multimodality medical image analysis
    Andreas Markus Loening
    Stanford University, Department of Radiology and the Bio X Program, 318 Campus Drive, East Wing, 1st Floor, Stanford, CA 94305 542, USA
    Mol Imaging 2:131-7. 2003
    ..AMIDE runs on UNIX, Macintosh OS X, and Microsoft Windows platforms, and it is freely available with source code under the terms of the GNU General Public License...
  8. ncbi Improving the quality of reports of meta-analyses of randomised controlled trials: the QUOROM statement. Quality of Reporting of Meta-analyses
    D Moher
    University of Ottawa, Thomas C Chalmers Centre for Systematic Reviews, Ontario, Canada
    Lancet 354:1896-900. 1999
    ..The Quality of Reporting of Meta-analyses (QUOROM) conference was convened to address standards for improving the quality of reporting of meta-analyses of clinical randomised controlled trials (RCTs)...
  9. ncbi Automated water analyser computer supported system (AWACSS) Part I: Project objectives, basic technology, immunoassay development, software design and networking
    Jens Tschmelak
    Institute of Physical and Theoretical Chemistry IPTC, Eberhard Karls University of Tuebingen, Auf der Morgenstelle 8, Tuebingen 72076, Germany
    Biosens Bioelectron 20:1499-508. 2005
    ..The second part article reports on the system performance, first real sample measurements, and an international collaborative trial (inter-laboratory tests) to compare the biosensor with conventional anayltical methods...
  10. pmc PRIMROSE: a computer program for generating and estimating the phylogenetic range of 16S rRNA oligonucleotide probes and primers in conjunction with the RDP-II database
    Kevin E Ashelford
    Cardiff School of Biosciences, Cardiff University, PO Box 915, Cardiff CF10 3TL, UK
    Nucleic Acids Res 30:3481-9. 2002
    ..PRIMROSE has an intuitive graphical user interface and runs on the Microsoft Windows 95/NT/2000 operating systems. It is open source and is freely available from the authors...
  11. pmc Osprey: a network visualization system
    Bobby Joe Breitkreutz
    Samuel Lunenfeld Research Institute, Mount Sinai Hospital, University Avenue, Toronto, M5G 1X5, Canada
    Genome Biol 4:R22. 2003
    ..Mouse-over functions allow rapid elaboration and organization of network diagrams in a spoke model format. User-defined large-scale datasets can be readily combined with Osprey for comparison of different methods...
  12. pmc Functional classification of proteins for the prediction of cellular function from a protein-protein interaction network
    Christine Brun
    Laboratoire de Genetique et Physiologie du Developpement, CNRS UMR6545, Parc Scientifique et Technologique de Luminy, Case 907, 13288 Marseille Cedex 9, France
    Genome Biol 5:R6. 2003
    ....
  13. pmc GECKO: a complete large-scale gene expression analysis platform
    Joachim Theilhaber
    Cambridge Genomics Center, Sanofi Aventis, 26 Landsdowne Street, Cambridge, MA 02139, USA
    BMC Bioinformatics 5:195. 2004
    ..Gecko (Gene Expression: Computation and Knowledge Organization) is a complete, high-capacity centralized gene expression analysis system, developed in response to the needs of a distributed user community...
  14. ncbi Complementary methods of system usability evaluation: surveys and observations during software design and development cycles
    Jan Horsky
    Clinical Informatics Research and Development, Partners HealthCare, Boston, USA
    J Biomed Inform 43:782-90. 2010
    ..Appropriate use of these methods consistently during development may significantly improve system usability and contribute to higher adoption rates among clinicians and to improved quality of care...
  15. pmc A multi-layered framework for disseminating knowledge for computer-based decision support
    Aziz A Boxwala
    Division of Biomedical Informatics, Department of Medicine, University of California San Diego, La Jolla, California 92093 0728, USA
    J Am Med Inform Assoc 18:i132-9. 2011
    ..There are several challenges in encoding guideline knowledge in a form that is portable to different clinical sites, including the heterogeneity of clinical decision support (CDS) tools, of patient data representations, and of workflows...
  16. ncbi Probalign: multiple sequence alignment using partition function posterior probabilities
    Usman Roshan
    Department of Computer Science, New Jersey Institute of Technology GITC 4400, University Heights, NJ 07102, USA
    Bioinformatics 22:2715-21. 2006
    ..The partition function methodology is one way of estimating these probabilities. Here, we combine these two ideas for the first time to construct maximal expected accuracy sequence alignments...
  17. pmc OXBench: a benchmark for evaluation of protein multiple sequence alignment accuracy
    G P S Raghava
    School of Life Sciences, University of Dundee, Dow St, Dundee, DD1 5EH, Scotland, UK
    BMC Bioinformatics 4:47. 2003
    ..The benchmark shows the current state-of-the art for alignment accuracy and provides a baseline against which new alignment algorithms may be judged...
  18. pmc The Ensembl analysis pipeline
    Simon C Potter
    The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
    Genome Res 14:934-41. 2004
    ..Here we describe the fundamental software components of the pipeline, and we also highlight some features of the Sanger installation which were necessary to enable the pipeline to scale to whole-genome analysis...
  19. ncbi Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms
    Hongwu Ma
    GBF German Research Center for Biotechnology, Microbial Systems, Mascheroder Weg 1, 38124 Braunschweig, Germany
    Bioinformatics 19:270-7. 2003
    ..These networks are often very large and complex. To properly understand and analyze the global properties of metabolic networks, methods for rationally representing and quantitatively analyzing their structure are needed...
  20. pmc Predicting functional sites with an automated algorithm suitable for heterogeneous datasets
    David La
    Department of Biological Sciences, California State Polytechnic University, Pomona, California 91768, USA
    BMC Bioinformatics 6:116. 2005
    ..However, in our original demonstration of the technique, phylogenetic motif identification is dependent upon a manually determined similarity threshold, prohibiting large-scale application of the technique...
  21. pmc The guideline interchange format: a model for representing guidelines
    L Ohno-Machado
    Decision Systems Group, Brigham and Women s Hospital, Boston, MA 02115, USA
    J Am Med Inform Assoc 5:357-72. 1998
    ..To allow exchange of clinical practice guidelines among institutions and computer-based applications...
  22. pmc Biopipe: a flexible framework for protocol-based bioinformatics analysis
    Shawn Hoon
    Institute of Molecular and Cell Biology, National University of Singapore, Singapore 117609
    Genome Res 13:1904-15. 2003
    ..This will enable researchers to discuss and interpret the data better as the once implicit assumptions are now explicitly defined within the Biopipe framework...
  23. pmc An algorithm and program for finding sequence specific oligonucleotide probes for species identification
    Alexander E Pozhitkov
    University of Cologne, Institute of Genetics, AG Tautz Weyertal 121, D 50931 Cologne, Germany
    BMC Bioinformatics 3:9. 2002
    ..However, it shows also great promise for other small organisms that are taxonomically difficult to tract...
  24. pmc GoMiner: a resource for biological interpretation of genomic and proteomic data
    Barry R Zeeberg
    Genomics and Bioinformatics Group, Laboratory of Molecular Pharmacology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Genome Biol 4:R28. 2003
    ..The first is a tree-like structure analogous to that in the AmiGO browser and the second is a compact, dynamically interactive 'directed acyclic graph'. Genes displayed in GoMiner are linked to major public bioinformatics resources...
  25. ncbi Toward the atomistic simulation of T cell epitopes automated construction of MHC: peptide structures for free energy calculations
    Sarah J Todman
    Department of Crystallography, University of London, Birkbeck College, Malet Street, London WC1E 7HX, United Kingdom
    J Mol Graph Model 26:957-61. 2008
    ..The MHCsim server (http://igrid-ext.cryst.bbk.ac.uk/MHCsim) allows the user to rapidly generate any desired MHC:peptide complex and will facilitate molecular modelling simulation of MHC complexes on an unprecedented scale...
  26. pmc Pegasys: software for executing and integrating analyses of biological sequences
    Sohrab P Shah
    UBC Bioinformatics Centre, University of British Columbia, Vancouver, British Columbia, Canada
    BMC Bioinformatics 5:40. 2004
    ..We present Pegasys--a flexible, modular and customizable software system that facilitates the execution and data integration from heterogeneous biological sequence analysis tools...
  27. ncbi Decision support for teletraining of COPD patients
    B Song
    Bianying Song, Peter L Reichertz Institute for Medical Informatics, University of Braunschweig Institute of Technology and Hannover Medical School, Mühlenpfordtstrasse 23, 38106 Braunschweig, Germany
    Methods Inf Med 49:96-102. 2010
    ..Supervised physical training has been shown to promote rehabilitation of patients affected by chronic obstructive pulmonary disease (COPD). Currently, due to limited resources, not all COPD patients can be trained by an expert supervisor...
  28. pmc B.E.A.R. GeneInfo: a tool for identifying gene-related biomedical publications through user modifiable queries
    Guohui Zhou
    Department of Pathology and Bioinformatics Program, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
    BMC Bioinformatics 5:46. 2004
    ..In these situations having a tool for searching the biomedical literature using the list of identified genes while simultaneously defining additional search terms would be useful...
  29. pmc Why did that happen? Exploring the proliferation of barely usable software in healthcare systems
    C W Johnson
    Department of Computing Science, University of Glasgow, Glasgow G12 8RZ, UK
    Qual Saf Health Care 15:i76-81. 2006
    ....
  30. pmc Clinical decision support capabilities of commercially-available clinical information systems
    Adam Wright
    Partners HealthCare System, 93 Worcester St, Wellesley, MA 02481, USA
    J Am Med Inform Assoc 16:637-44. 2009
    ..Purpose The goal of this project was to describe and quantify the results of a study of decision support capabilities in Certification Commission for Health Information Technology (CCHIT) certified electronic health record systems...
  31. pmc Apollo: a sequence annotation editor
    S E Lewis
    Department of Molecular and Cellular Biology, Life Sciences Addition, University of California, Berkeley, CA 94720 3200, USA
    Genome Biol 3:RESEARCH0082. 2002
    ..FlyBase biologists successfully used Apollo to annotate the Drosophila melanogaster genome and it is increasingly being used as a starting point for the development of customized annotation editing tools for other genome projects...
  32. ncbi Recent developments of the chemistry development kit (CDK) - an open-source java library for chemo- and bioinformatics
    Christoph Steinbeck
    Cologne University Bioinformatics Center CUBIC, Germany
    Curr Pharm Des 12:2111-20. 2006
    ..This article introduces the CDK's new QSAR capabilities and the recently introduced interface to statistical software...
  33. ncbi A simple computer-based measurement and analysis system of pulmonary auscultation sounds
    Hüseyin Polat
    Department of Electronics Computer Education, Faculty of Technical Education, Gazi University, 06500 Teknikokullar, Ankara, Turkey
    J Med Syst 28:665-72. 2004
    ....
  34. ncbi MEA-Tools: an open source toolbox for the analysis of multi-electrode data with MATLAB
    U Egert
    Neurobiology and Biophysics, Institute for Biology III, Albert Ludwigs University Freiburg, Schänzlestr 1, 79104 Freiburg, Germany
    J Neurosci Methods 117:33-42. 2002
    ..g. intracellular amplifiers. Data may be processed as continuous recordings or time windows triggered to some event...
  35. ncbi PROforma: a general technology for clinical decision support systems
    J Fox
    Imperial Cancer Research Fund, London, UK
    Comput Methods Programs Biomed 54:59-67. 1997
    ..This paper provides an overview of the motivation and structure of PROforma, and illustrates its use in the development of clinical applications...
  36. pmc GOTree Machine (GOTM): a web-based platform for interpreting sets of interesting genes using Gene Ontology hierarchies
    Bing Zhang
    Graduate School in Genome Science and Technology, University of Tennessee Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
    BMC Bioinformatics 5:16. 2004
    ..Microarray and other high-throughput technologies are producing large sets of interesting genes that are difficult to analyze directly. Bioinformatics tools are needed to interpret the functional information in the gene sets...
  37. pmc SeeGH--a software tool for visualization of whole genome array comparative genomic hybridization data
    Bryan Chi
    British Columbia Cancer Research Centre, British Columbia Cancer Agency, 601 W, 10th Ave, Vancouver, BC, V5Z 1L3 Canada
    BMC Bioinformatics 5:13. 2004
    ..Since array CGH provides signal ratio for each DNA segment, visualization would require the reassembly of individual data points into chromosome profiles...
  38. ncbi GIMS: an integrated data storage and analysis environment for genomic and functional data
    Michael Cornell
    Department of Computer Science, University of Manchester, Manchester M13 9PL, UK
    Yeast 20:1291-306. 2003
    ..The GIMS database can be accessed remotely using a Java application that can be downloaded from http://img.cs.man.ac.uk/gims...
  39. pmc MARS: microarray analysis, retrieval, and storage system
    Michael Maurer
    Institute for Genomics and Bioinformatics, Christian Doppler Laboratory for Genomics and Bioinformatics, Graz University of Technology, Petersgasse 14, 8010 Graz, Austria
    BMC Bioinformatics 6:101. 2005
    ..The wealth of data generated by this high throughput approach renders adequate database and analysis tools crucial for the pursuit of insights into the transcriptomic behavior of cells...
  40. pmc Systems biology driven software design for the research enterprise
    John Boyle
    Institute for Systems Biology, 1441 N 34th Street, Seattle, WA 98103, USA
    BMC Bioinformatics 9:295. 2008
    ..As scientists work in isolated groups, integration with other groups is rarely a consideration when building the required software tools...
  41. pmc A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure
    Sean R Eddy
    Howard Hughes Medical Institute and Department of Genetics, Washington University School of Medicine, Saint Louis, Missouri 63110 USA
    BMC Bioinformatics 3:18. 2002
    ..The dynamic programming algorithm for aligning a CM to an RNA sequence of length N is O(N3) in memory. This is only practical for small RNAs...
  42. pmc Processing methods for differential analysis of LC/MS profile data
    Mikko Katajamaa
    Turku Centre for Biotechnology, Tykistokatu 6, FIN 20521, Turku, Finland
    BMC Bioinformatics 6:179. 2005
    ..One of the major challenges in this domain remains development of better solutions for processing of LC/MS data...
  43. pmc The caCORE Software Development Kit: streamlining construction of interoperable biomedical information services
    Joshua Phillips
    Science Applications International Corporation, Annapolis, MD, USA
    BMC Med Inform Decis Mak 6:2. 2006
    ..The caCORE Software Development Kit (SDK) was designed to provide developers both within and outside the NCI with the tools needed to construct such interoperable software systems...
  44. ncbi Developing a move-set for protein model refinement
    Marc N Offman
    Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute, Lincoln s Inn Fields Laboratories London, WC2A 3PX, UK
    Bioinformatics 22:1838-45. 2006
    ..The approach presented here carefully blends models created by several different means, in an attempt to combine the good quality regions from each into a final, more refined, model...
  45. ncbi Taverna: a tool for the composition and enactment of bioinformatics workflows
    Tom Oinn
    EMBL European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK
    Bioinformatics 20:3045-54. 2004
    ..A growing number of these resources are being made available with programmatic access in the form of Web services. Bioinformatics scientists will need to orchestrate these Web services in workflows as part of their analyses...
  46. ncbi Globally distributed object identification for biological knowledgebases
    Tim Clark
    Brief Bioinform 5:59-70. 2004
    ..We see the adoption of these methods as important steps toward simpler, more elegant and more reliable integration of the world's biological knowledgebases, and as facilitating stronger global collaboration in biology...
  47. ncbi Swiss-Prot: juggling between evolution and stability
    Amos Bairoch
    Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 rue Michel Servet, 1211 Geneva 4, Switzerland
    Brief Bioinform 5:39-55. 2004
    ....
  48. ncbi An object model and database for functional genomics
    Andrew Jones
    Department of Computing Science, University of Glasgow, Glasgow, UK
    Bioinformatics 20:1583-90. 2004
    ..We believe that all types of functional genomics experiments should be annotated in a consistent manner, and we hope to open up new ways of comparing multiple datasets used in functional genomics...
  49. ncbi The design of Jemboss: a graphical user interface to EMBOSS
    Tim Carver
    MRC UK HGMP Resource Centre, Hinxton, Cambridge CB10 1SB, UK
    Bioinformatics 19:1837-43. 2003
    ..The GUI parses the EMBOSS Ajax Command Definition language for form generation and maximum input flexibility. Jemboss interacts directly with the EMBOSS libraries to allow dynamic generation of application default settings...
  50. pmc MatchMiner: a tool for batch navigation among gene and gene product identifiers
    Kimberly J Bussey
    Genomics and Bioinformatics Group, Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH Building 37, Bethesda, MD 20892 4255, USA
    Genome Biol 4:R27. 2003
    ..The user inputs a list of gene identifiers and then uses the Merge function to find the overlap with a second list of identifiers of either the same or a different type or uses the LookUp function to find corresponding identifiers...
  51. ncbi A systematic approach to modeling, capturing, and disseminating proteomics experimental data
    Chris F Taylor
    School of Biological Sciences, University of Manchester, Oxford Road, Manchester M13 9PL, UK
    Nat Biotechnol 21:247-54. 2003
    ..These make explicit what data might be most usefully captured about proteomics experiments and provide complementary routes toward the implementation of a proteome repository...
  52. ncbi FluxAnalyzer: exploring structure, pathways, and flux distributions in metabolic networks on interactive flux maps
    Steffen Klamt
    Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1, D 39106 Magdeburg, Germany
    Bioinformatics 19:261-9. 2003
    ..The need of a user-friendly platform for stoichiometric modeling of metabolic networks in silico is evident...
  53. ncbi myGrid: personalised bioinformatics on the information grid
    Robert D Stevens
    Department of Computer Science, University of Manchester, Oxford Road, Manchester, UK, M13 9PL
    Bioinformatics 19:i302-4. 2003
    ..Additional services are provided to support the scientific method and best practice found at the bench but often neglected at the workstation, notably provenance management, change notification and personalisation...
  54. pmc Managing attribute--value clinical trials data using the ACT/DB client-server database system
    P M Nadkarni
    Center for Medical Informatics, Yale University School of Medicine, New Haven, CT 06520 8009, USA
    J Am Med Inform Assoc 5:139-51. 1998
    ..It uses a Microsoft Access client running on Windows 95 machines, which communicates with an Oracle server running on a UNIX platform. ACT/DB is being used to manage the data for seven studies in its initial deployment...
  55. pmc Toward high-throughput genotyping: dynamic and automatic software for manipulating large-scale genotype data using fluorescently labeled dinucleotide markers
    J L Li
    Osteoporosis Research Center, Creighton University, Omaha, Nebraska 68131, USA
    Genome Res 11:1304-14. 2001
    ..The modules and programs we developed for the can be extended to other database platforms, such as Microsoft SQL server, if the capability to handle still greater quantities of genotype data simultaneously is desired...
  56. ncbi Software design patterns for information visualization
    Jeffrey Heer
    Computer Science Division, University of California, Berkeley, USA
    IEEE Trans Vis Comput Graph 12:853-60. 2006
    ..By representing design knowledge in a reusable form, these patterns can be used to facilitate software design, implementation, and evaluation, and improve developer education and communication.
  57. pmc PEDRo: a database for storing, searching and disseminating experimental proteomics data
    Kevin Garwood
    Department of Computer Science, University of Manchester, Oxford Road, Manchester M13 9PL, UK
    BMC Genomics 5:68. 2004
    ..However, there is, as yet, no formally accepted standard representation to support the sharing of proteomics data, and little systematic dissemination of comprehensive proteomic data sets...
  58. pmc An integrated computational pipeline and database to support whole-genome sequence annotation
    C J Mungall
    Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
    Genome Biol 3:RESEARCH0081. 2002
    ..The key contributions to overall annotation quality are the marshalling of high-quality sequences for alignments and the design of a system with an adaptable and expandable flexible architecture...
  59. ncbi Software design for analysis of multichannel intracardial and body surface electrocardiograms
    Mark Potse
    Medical Physics Department, Academic Medical Center AMC, University of Amsterdam, PO Box 22700, 1100 DE, Amsterdam, The Netherlands
    Comput Methods Programs Biomed 69:225-36. 2002
    ..The source code is made intelligible using software for structured documentation and is available to the users. The package is currently used by more than ten research groups analysing ECG data worldwide...
  60. ncbi The role of open-source software in innovation and standardization in radiology
    Bradley J Erickson
    Department of Radiology, Radiology Informatics Laboratory, Mayo Clinic, Rochester, MN 55905, USA
    J Am Coll Radiol 2:927-31. 2005
    ..Continued support for OSS is essential for the success of our field...
  61. pmc Computation of elementary modes: a unifying framework and the new binary approach
    Julien Gagneur
    Cellzome AG, Meyerhofstr 1, 69117 Heidelberg, Germany
    BMC Bioinformatics 5:175. 2004
    ..However, computing elementary modes is a hard computational task. In recent years we assisted in a multiplication of algorithms dedicated to it. We require a summarizing point of view and a continued improvement of the current methods...
  62. pmc EON: a component-based approach to automation of protocol-directed therapy
    M A Musen
    Section on Medical Informatics, Stanford University School of Medicine, CA 94305 5479, USA
    J Am Med Inform Assoc 3:367-88. 1996
    ..A test of the reuse of the software components in a different clinical domain demonstrated rapid development of a prototype application to support protocol-based care of patients who have breast cancer...
  63. pmc REDUCE: An online tool for inferring cis-regulatory elements and transcriptional module activities from microarray data
    Crispin Roven
    Department of Biological Sciences, Columbia University, New York, NY, USA
    Nucleic Acids Res 31:3487-90. 2003
    ..bio.columbia.edu/reduce/. This web site provides functionality for the upload and management of microarray data. REDUCE analysis results can be viewed and downloaded, and optionally be shared with other users or made publicly accessible...
  64. ncbi A task framework for the web interface W2H
    Peter Ernst
    DKFZ German Cancer Research Center, Department of Molecular Biophysics, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
    Bioinformatics 19:278-82. 2003
    ..The result of a compound task is given as XML data that is translated according to XSLT data into web pages or plain text to report the result of the task to the user...
  65. pmc AnaBench: a Web/CORBA-based workbench for biomolecular sequence analysis
    Elarbi Badidi
    The Canadian Institute for Advanced Research, Program in Evolutionary Biology, Departement de Biochimie, Universite de Montreal, 2900, Boul, Edouard Montpetit, Montreal, QC H3T 1J4, Canada
    BMC Bioinformatics 4:63. 2003
    ....
  66. pmc HotSwap for bioinformatics: a STRAP tutorial
    Christoph Gille
    Institute for Biochemistry, Charite University Hospital, Humboldt University, Berlin, Germany
    BMC Bioinformatics 7:64. 2006
    ..Repeatedly loading large datasets can significantly slow down the development process. We have incorporated HotSwap functionality into the protein workbench STRAP, allowing developers to create plugins using the Java HotSwap technique...
  67. ncbi Interactive visualization and exploration of relationships between biological objects
    D R Gilbert
    Department of Computing, City University, Northampton Square, London UK EC1V 0HB
    Trends Biotechnol 18:487-94. 2000
    ..Data are visualized without preclustering and can be dynamically explored by the user using 'virtual-reality'. We illustrate this approach with two case studies from protein topology and gene expression...
  68. ncbi FPV: fast protein visualization using Java 3D
    Tolga Can
    Department of Computer Science, University of California at Santa Barbara, Santa Barbara, CA 93117 5110, USA
    Bioinformatics 19:913-22. 2003
    ..This behavior is especially apparent when the number of atoms to be displayed is huge, or when several proteins are to be displayed simultaneously for comparison...
  69. ncbi Expertise in professional software design: a process study
    S Sonnentag
    Department of Psychology, University of Amsterdam, The Netherlands
    J Appl Psychol 83:703-15. 1998
    Forty professional software designers participated in a study in which they worked on a software design task and reported strategies for accomplishing that task...
  70. ncbi Web-based training modules in dermatology
    A Bittorf
    Department of Dermatology, University of Erlangen, Germany
    MD Comput 14:371-6, 381. 1997
    ..The responses to 200 questionnaires completed in a two-month study period are encouraging. The online resources are being used not only for training in dermatology but also for continuing education and reference...
  71. ncbi Enhanced quality and quantity of retrieval of Critically Appraised Topics using the CAT Crawler
    P Dong
    Medical Informatics Group, Bioinformatics Institute, Singapore
    Med Inform Internet Med 29:43-55. 2004
    ..In summary, the application provides physicians with a common interface to retrieve relevant CATs on particular clinical topics from multiple resources, and thus speeds up the decision making process...
  72. pmc Resources for comparing the speed and performance of medical autocoders
    Jules J Berman
    Cancer Diagnosis Program, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
    BMC Med Inform Decis Mak 4:8. 2004
    ....
  73. pmc FOUNTAIN: a JAVA open-source package to assist large sequencing projects
    J M Buerstedde
    Department of Cellular Immunology, Heinrich Pette Institute, Martinistr 52, 20251 Hamburg, Germany
    BMC Bioinformatics 2:6. 2001
    ..The challenges include documentation of clones, templates and sequencing reactions, and the storage, annotation and analysis of the large number of generated sequences...
  74. ncbi An object-oriented programming system for the integration of internet-based bioinformatics resources
    Allan Beveridge
    Max Planck Institute for Molecular Genetics, Berlin, Germany
    Appl Bioinformatics 5:29-39. 2006
    ..The validity of the software has been demonstrated by testing it on several biological databases. We also examine the current limitations of the Internet and discuss the need for the development of universal standards for web-based data...
  75. pmc Construction of a nasopharyngeal carcinoma 2D/MS repository with Open Source XML database--Xindice
    Feng Li
    Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha, China
    BMC Bioinformatics 7:13. 2006
    ..Although there are some cancer proteome databases now, there is still no NPC proteome database...
  76. pmc Workflows in bioinformatics: meta-analysis and prototype implementation of a workflow generator
    Alexander Garcia Castro
    Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
    BMC Bioinformatics 6:87. 2005
    ..Despite the proliferation of GUIs (Graphic User Interfaces) in bioinformatics, only some of them provide workflow capabilities; surprisingly, no meta-analysis of workflow operators and components in bioinformatics has been reported...
  77. pmc MicroGen: a MIAME compliant web system for microarray experiment information and workflow management
    Sarah Burgarella
    Bioengineering Department, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milan, Italy
    BMC Bioinformatics 6:S6. 2005
    ..Furthermore, complete information describing all experimental steps must be orderly collected to allow subsequent correct interpretation of experimental results...
  78. pmc Web services and workflow management for biological resources
    Paolo Romano
    Bioinformatics and Structural Proteomics, National Cancer Research Institute IST, Genova, I 16132, Italy
    BMC Bioinformatics 6:S24. 2005
    ..Information on biological resources and on genomic sequences mutations are two examples of very specialized datasets that are useful for specific research domains...
  79. pmc Statistical Viewer: a tool to upload and integrate linkage and association data as plots displayed within the Ensembl genome browser
    Judith E Stenger
    The Duke Center for Human Genetics, Duke University Medical Center, Durham, North Carolina 27710, USA
    BMC Bioinformatics 6:95. 2005
    ..We have developed a plug-in package for Ensembl called "Statistical Viewer" that facilitates the analysis of genomic features and annotation in the regions of interest defined by linkage analysis...
  80. pmc High performance workflow implementation for protein surface characterization using grid technology
    Ivan Merelli
    Istituto di Tecnologie Biomediche ITB CNR, via F lli Cervi, Segrate, Milan, Italy
    BMC Bioinformatics 6:S19. 2005
    ..The implementation of this workflow is based on the Italian Grid.it project infrastructure, that is a network of several computational resources and storage facilities distributed at different grid sites...
  81. ncbi The role of informatics in the coordinated management of biological resources collections
    Paolo Romano
    Bioinformatics and Structural Proteomics, National Cancer Research Institute, Genoa, Italy
    Appl Bioinformatics 4:175-86. 2005
    ....
  82. pmc FIGENIX: intelligent automation of genomic annotation: expertise integration in a new software platform
    Philippe Gouret
    EA 3781 EGEE Evolution, Genome, Environment, Universite de Provence, Case 36, Pl V Hugo, 13331 Marseille Cedex 03, France
    BMC Bioinformatics 6:198. 2005
    ..Several pipelines already automate some of these complex chaining but still necessitate an important contribution of biologists for supervising and controlling the results at various steps...
  83. pmc YANA - a software tool for analyzing flux modes, gene-expression and enzyme activities
    Roland Schwarz
    Dept of Bioinformatics, Biocenter, University of Wurzburg, Germany
    BMC Bioinformatics 6:135. 2005
    ..Analysis routines for expression levels and the most central, well connected metabolites and their metabolic connections are of particular interest...
  84. pmc Integration of the Gene Ontology into an object-oriented architecture
    Daniel Shegogue
    Department of Biostatistics, Bioinformatics and Epidemiology, Medical University of South Carolina, 135 Cannon Street, Charleston, SC 29425, USA
    BMC Bioinformatics 6:113. 2005
    ....
  85. ncbi Intelligent client for integrating bioinformatics services
    Ismael Navas-Delgado
    Integrated Bioinformatics GNV5 at the University of Málaga, National Institute for Bioinformatics INB, Malaga, Spain
    Bioinformatics 22:106-11. 2006
    ..However, each service demands specific interfaces to accommodate their parameters and it is a complicated task linking the different service inputs and outputs to solve a biological problem...
  86. ncbi Biotool2Web: creating simple Web interfaces for bioinformatics applications
    Mohammad Shahid
    International NRW Graduate School in Bioinformatics and Genome Research, Center of Biotechnology CeBiTec, University of Bielefeld, Bielefeld, Germany
    Appl Bioinformatics 5:63-6. 2006
    ..Biotool2Web uses an XML document containing the parameters to run the tool on the Web, and generates the corresponding HTML and common gateway interface (CGI) files ready to be published on a web server...
  87. ncbi MARVIN: a medical research application framework based on open source software
    Tobias Rudolph
    University of Bern, MEM Research Center, Institute for Surgical Technology and Biomechanics, Stauffacherstrasse 78, 3014 Bern, Switzerland
    Comput Methods Programs Biomed 91:165-74. 2008
    ..Furthermore, it implements an advanced visualization system and interfaces to a wide range of 3D tracking hardware. Since it uses only highly portable libraries, MARVIN applications run on Unix/Linux, Mac OS X and Microsoft Windows...
  88. ncbi Reinforcement learning interfaces for biomedical database systems
    I Rudowsky
    Dept of Comput and Inf Sci, Brooklyn College of the City Univ of New York, NY, USA
    Conf Proc IEEE Eng Med Biol Soc 1:6269-72. 2006
    ..The purpose of this study was to investigate how reinforcement learning algorithms can assist the user in interacting with the database interface application that has been developed to improve the performance of the system...
  89. ncbi Prototyping virtual cancer therapist (VCT): a software engineering approach
    S Liu
    The Henry Samueli School of Engineering, UC Irvine, USA
    Conf Proc IEEE Eng Med Biol Soc 1:5424-7. 2006
    ..The prototype of VCT presented in this paper has not only demonstrated the capability of VCT but also identified problems that need to be addressed in the next cycle of development...
  90. pmc On the way to building an integrated computational environment for the study of developmental patterns and genetic diseases
    Andrei L Turinsky
    Sun Center of Excellence for Visual Genomics, University of Calgary, Faculty of Medicine, Department of Biochemistry and Molecular Biology, Calgary, AB, Canada
    Int J Nanomedicine 1:89-96. 2006
    ....
  91. pmc MAGMA: analysis of two-channel microarrays made easy
    Hubert Rehrauer
    Functional Genomics Center Zurich, UZH ETH Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
    Nucleic Acids Res 35:W86-90. 2007
    ..MAGMA is freely available at www.magma-fgcz.uzh.ch...
  92. pmc iHOP web services
    Jose M Fernandez
    Structural Biology and Biocomputing Program, CNIO and Computer Science and Artificial Intelligence Laboratory, MIT
    Nucleic Acids Res 35:W21-6. 2007
    ..ihop-net.org/UniPub/iHOP/info/logs/). Here we describe a public programmatic API that enables the integration of main iHOP functionalities in bioinformatic programs and workflows...
  93. ncbi Developing a modern web interface for database-driven bioinformatics tools
    Paras Khandheria
    UT Southwestern Medical Center, Dallas, TX 75390 9185, USA
    IEEE Eng Med Biol Mag 26:96-8. 2007
  94. pmc Using co-occurrence network structure to extract synonymous gene and protein names from MEDLINE abstracts
    A M Cohen
    Department of Medical Informatics and Clinical Epidemiology, School of Medicine, Oregon Health and Science University, 3181 S, W, Sam Jackson Park Road, Portland, Oregon 97239 3098, USA
    BMC Bioinformatics 6:103. 2005
    ..The method was applied to the task of automatic gene and protein name synonym extraction...
  95. ncbi The Genome Sequencer FLX System--longer reads, more applications, straight forward bioinformatics and more complete data sets
    Marcus Droege
    Roche Applied Science, Global Marketing, 82372 Penzberg, Germany
    J Biotechnol 136:3-10. 2008
    ....
  96. pmc cPath: open source software for collecting, storing, and querying biological pathways
    Ethan G Cerami
    Computational Biology Center, Memorial Sloan Kettering Cancer Center 1275 York Avenue, Box 460, New York, NY 10021, USA
    BMC Bioinformatics 7:497. 2006
    ..Standard exchange formats for pathway information, such as BioPAX, CellML, SBML and PSI-MI, enable convenient collection of this data for biological research, but mechanisms for common storage and communication are required...
  97. pmc G-InforBIO: integrated system for microbial genomics
    Naoto Tanaka
    Center for Information Biology and DDBJ, National Institute of Genetics 1111 Yata, Mishima, Shizuoka 411 8540, Japan
    BMC Bioinformatics 7:368. 2006
    ..There are few tools for integrated analyses of genomic data, therefore, we developed software that enables users to handle, manipulate, and analyze genome data with a variety of sequence analysis programs...
  98. ncbi Designing for social data analysis
    Martin Wattenberg
    IBM Research, Visual Communication Lab, Cambridge, MA 02142, USA
    IEEE Trans Vis Comput Graph 12:549-57. 2006
    ..We end by discussing the design of an extension of the NameVoyager to a more complex data set, in which the principles of social data analysis played a guiding role...
  99. ncbi GAMOLA: a new local solution for sequence annotation and analyzing draft and finished prokaryotic genomes
    Eric Altermann
    Department of Food Science, Southeast Dairy Foods Research Center, North Carolina State University, Raleigh, North Carolina 27695 7624, USA
    OMICS 7:161-9. 2003
    ..The software is available under the license of North Carolina State University. A website and a downloadable example are accessible under (http://fsweb2.schaub. ncsu.edu/TRKwebsite/index.htm)...
  100. pmc MBEToolbox: a MATLAB toolbox for sequence data analysis in molecular biology and evolution
    James J Cai
    Department of Microbiology, University of Hong Kong, Pokfulam, Hong Kong, China
    BMC Bioinformatics 6:64. 2005
    ..However, few functions are freely available in MATLAB to perform the sequence data analyses specifically required for molecular biology and evolution...
  101. pmc HDBStat!: a platform-independent software suite for statistical analysis of high dimensional biology data
    Prinal Trivedi
    Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
    BMC Bioinformatics 6:86. 2005
    ..HDBStat! provides statisticians and biologists a flexible and easy-to-use interface to analyze complex microarray data using a variety of methods for data preprocessing, quality control analysis and hypothesis testing...

Research Grants73

  1. Relating sleep disordered breathing to daytime function
    INDU A AYAPPA; Fiscal Year: 2010
    ..Validating a measure of sleep disordered breathing that relates to sleepiness will help improve the diagnosis and treatment of obstructive sleep apnea. ..
  2. Clinical management of cochlear implant patients with contralateral hearing aids.
    Mario A Svirsky; Fiscal Year: 2013
    ....
  3. scribIT: a System for Freehand Production, Editing, Communication and Reproductio
    Michael J Rosen; Fiscal Year: 2012
    ..It will also help to understand how visually impaired people create and interpret freehand tactile graphics and how to better use them in teaching and learning practice. ..
  4. ELECTROTACTILE DISPLAY OF COMPUTER GRAPHICS FOR BLIND
    KURT KACZMAREK; Fiscal Year: 2001
    ....
  5. INTERACTIVE VIDEODISC INTERVENTION TO REDUCE CHD
    John Noell; Fiscal Year: 1993
    ..In Phase II we will: (a) complete the Phase I development process for the remaining subpopulations (b) produce a complete stand-alone kiosk, suitable for use in worksites, and (c) evaluate the efficacy of the program...
  6. Preventing Unintended Pregnancy: Male Self-efficacy
    CHRISTY SHERMAN; Fiscal Year: 2003
    ....
  7. INTERACTIVE VIDEODISC SMOKING CESSATION INTERVENTION
    John Noell; Fiscal Year: 1992
    ..Phase II will: (a) complete the Phase I evaluation procedures for the remaining subpopulations, and (b) produce a final smoking cessation program, resulting in a stand-alone kiosk suitable for use in physician's offices...
  8. COMPUTERIZED TOBACCO RISK ASSESSMENT FOR ADOLESCENTS
    Emil Chiauzzi; Fiscal Year: 1999
    ..Phase II will include a three-month follow-up of adolescents exposed to the program. ..
  9. DELIVERY OF THE CGN INFORMATION RESOURCE DATABASE
    Prakash Nadkarni; Fiscal Year: 2006
    ..Informatics assistance will be provided to the individual nodes to assist the task of data exchange, and when necessary, to assist the design of local data collection systems. ..
  10. ROBUST QUERY OF HETEROGENEOUS CLINICAL DATABASES
    Prakash Nadkarni; Fiscal Year: 2002
    ..In particular, research will be performed on utilization of newer database technologies, such as new indexing methods, as well as parallel database implementations. ..
  11. DESIGN AND IMPLEMENTATION OF PHARMACOGENETIC DATABASE
    Prakash Nadkarni; Fiscal Year: 2002
    ..Informatics assistance will be provided to the individual nodes to assist the task of data exchange, and when necessary, to assist the design of local data collection systems. ..
  12. Targeted Aggregation Inhibitors for the Treatment of Amyloid Diseases
    Sean Ekins; Fiscal Year: 2008
    ..unreadable] [unreadable] [unreadable]..
  13. COMPUTER-AIDED DESIGN, SYNTHESIS, AND TESTING OF A NOVEL FAMILY OF TRIAZOLE-BASED
    Sean Ekins; Fiscal Year: 2008
    ..unreadable] [unreadable] [unreadable]..
  14. SOFTWARE ARCHITECTURE FOR GUIDELINE DIRECTED THERAPY
    Mark Musen; Fiscal Year: 2002
    ....
  15. A Computational Testbed for Biosurveillance Methods
    Mark Musen; Fiscal Year: 2007
    ..The computational architecture that we propose will serve[unreadable] as a model for the next generation of such systems.[unreadable]..
  16. Auditory nerve responses to electric pulse trains
    Charles Miller; Fiscal Year: 2009
    ..We expect the results of this work will guide future designs of cochlear-implant speech processors so that modulated stimuli can be better tailored to the encoding capacity of the user's auditory nerve. ..
  17. Diabetes and recombination in the 8.1 MHC haplotype
    Daniel Geraghty; Fiscal Year: 2007
    ..unreadable] [unreadable] [unreadable]..
  18. Enhancing Clinical Effectiveness Research with Natural Language Processing of EMR
    BRIAN L HAZLEHURST; Fiscal Year: 2010
    ..We will demonstrate the utility of this infrastructure by conducting CER studies investigating the effectiveness of interventions in asthma and smoking, across the 6 participating health systems. ..
  19. STRUCTURAL ORGANIZATION AND PROTEOMICS OF TB
    Thomas Terwilliger; Fiscal Year: 2005
    ..The structural and functional information obtained in this project is to be placed in the public domain by timely deposition in publicly available databases. ..
  20. 2006 Diffraction Methods in Structual Biology Conference
    Paul Adams; Fiscal Year: 2006
    ..Junior participation will be encouraged with time for discussion after talks and a session devoted to talks selected from the poster-presentations. [unreadable] [unreadable] [unreadable] [unreadable]..
  21. Workplace Aerosol Sampling at Realistic Low Windspeeds
    James Vincent; Fiscal Year: 2006
    ..The new research will fill these gaps and place occupational aerosol exposure assessment on a still firmer footing. ..
  22. SOFTWARE AND INSTRUMENTATION TO IDENTIFY CANCER GENES
    Harold Garner; Fiscal Year: 2002
    ..This will integrate our system with current major technologies to produce a tool that should be widely available in translational and clinical trials cancer research. ..
  23. DOPAMINE NEUROTRANSMISSION IN EXPERIMENTAL PARKINSONISM
    PAUL GARRIS; Fiscal Year: 2005
    ..Moreover, L-DOPA is associated with adverse side effects after extended use, apparently due to non-physiological dopamine replacement. However, how L-DOPA acts on dopaminergic signaling is not completely established. ..
  24. Patch Clamp Amplifiers on a Chip
    Frederick Sigworth; Fiscal Year: 2007
    ..The characterization of ion channel function, and the development of drugs that modify this function, urgently requires new instrumentation that allows "high throughput" measurements. [unreadable] [unreadable] [unreadable]..
  25. NALTREXONE AND CBT FOR PATIENTS WITH ALCOHOLISM AND PTSD
    Edna Foa; Fiscal Year: 2008
    ..Therefore the findings from this study will be highly credible and should impact significantly on treatment recommendations for this impaired population. ..
  26. Change Detection in Serial MRIs of Patients with Brain Gliomas
    Bradley Erickson; Fiscal Year: 2008
    ..It is our hope that in the future, a measurement method superior to or as an adjunct to human observation will become available, though this study will not attempt to go that far. [unreadable] [unreadable] [unreadable]..
  27. 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. ..
  28. Duplicate Article/Plagiarism Discovery
    Harold Garner; Fiscal Year: 2009
    ..4) Create a secure resource that is available and open to all journals/reviewers, thus enabling them to estimate novelty and probable overlap with previous publications prior to acceptance. ..
  29. HLA-E, F, G interactions & the immunology of pregnancy
    Daniel Geraghty; Fiscal Year: 2008
    ..We also propose to develop materials and reagents useful towards the further understanding of the structure, biochemistry, and function of HLA- E, F, and G. ..
  30. Web-based Family History Screening for Hereditary Breast Cancer Risk
    Louise Acheson; Fiscal Year: 2008
    ..unreadable] [unreadable] [unreadable] [unreadable]..
  31. Computer Adaptive Testing for OA Clinical Trials
    Alan Jette; Fiscal Year: 2006
    ..We expect the gains in precision and efficiency of score estimation to be superior over traditional fixed forms of assessments and transform outcomes monitoring in OA clinical trials research. ..
  32. A Controlled Terminology for Diagnoses and Findings in General Dentistry
    Titus Schleyer; Fiscal Year: 2008
    ..unreadable] [unreadable] [unreadable]..
  33. New Hydropathy-Based computer Tools for Drug Discovery
    GLEN KELLOGG; Fiscal Year: 2009
    ..Specific collaborative arrangements are in place to apply these tools to a range of current drug discovery problems. ..
  34. BioMediator: Biologic Data Integration& Analysis System
    Peter Tarczy Hornoch; Fiscal Year: 2005
    ..abstract_text> ..
  35. PREVENTION INTERVENTIONS IN HISPANIC AND ANGLO CHILDREN
    Christine Kennedy; Fiscal Year: 2003
    ..abstract_text> ..
  36. DENOISING ON MONTE CARLO DOSE DISTRIBUTIONS
    Joseph Deasy; Fiscal Year: 2005
    ..These results would achieve our overall goal of increasing the clinical effectiveness of radiation therapy treatment planning. ..
  37. Three-dimensional structure of a CIC-type CI Channel
    Nikolaus Grigorieff; Fiscal Year: 2005
    ..The location of the labels will be determined using difference Fourier maps. The work will produce the first model of a C1C-type ion channel, key to a more thorough understanding of C1C channel function. ..
  38. Personal Profile-Prostate:An Internet Decision Support
    Donna Berry; Fiscal Year: 2004
    ..After the programming is complete and the innovative web-based intervention is created, we will pilot test the program in 20 men with localized prostate cancer. ..
  39. New Technologies for Patch-Clamp Recording
    Frederick Sigworth; Fiscal Year: 2002
    ..The proposed simplification of the patch-clamp technique will have far-reaching benefits in the search for ion channel and transporter genes and in the discovery of new pharmacological agents. ..
  40. NURSING SUPPORT OF DECISIONS BY MEN WITH PROSTATE CANCER
    Donna Berry; Fiscal Year: 2002
    ..A prototype decision support aid will be developed and a pilot test conducted to guide men through the personal issues, expectations, and preferences to be considered in treatment decision-making after a diagnosis of prostate cancer. ..
  41. Visual Preference and Receptive Vocabulary in Infancy
    Margaret Friend; Fiscal Year: 2003
    ..2. The assessment of the convergent validity of parental report and visual preference measures of comprehension. 3. The longitudinal assessment of the predictive validity of the measures. ..
  42. Polymorphism & Transplantation Biology of Novel MHC loci
    Daniel Geraghty; Fiscal Year: 2004
    ..abstract_text> ..
  43. The Role of Microsatellite Instability in Cancer
    Harold Garner; Fiscal Year: 2005
    ..We will also (Aim 3) investigate the effects of these mutations identified in Aim 2 on splicing by correlating them with the results of a quantitative global survey of splicing isoforms. ..
  44. REAL TIME IMAGING OF MENTAL ACTIVITY
    Mark Cohen; Fiscal Year: 2001
    ..The focus of the continued development will be on extending the basic capabilities and in packaging the data analysis tools and disseminating them to other researchers and institutions. ..
  45. CREATING GUIDELINES THAT ADAPT TO LOCAL CONTEXTS
    Aziz Boxwala; Fiscal Year: 2003
    ..We will compare the acceptance of recommendations contained in guidelines that have been adapted to acceptance of recommendations contained in guidelines that have not been adapted. ..
  46. RELATIONSHIP BETWEEN BIO. AND PSYCH. CORRELATES OF PTSD
    Edna Foa; Fiscal Year: 2005
    ..The resolution of these questions has important implications for understanding the pathophysiology of PTSD, and may provide insight into the mechanisms associated with successful psychological treatment for this disorder. ..
  47. PATIENT SPECIFIC MODELS IN LUNG CANCER SCREENING WITH CT
    Matthew Brown; Fiscal Year: 2004
    ..4] To compare radiologist accuracy and interpretation times of HR-hCT scans, both with and without assistance from the automated detection system, against pre-existing nodule detection methods. ..
  48. TRAINING PROGRAM IN MOLECULAR NEUROPHYSIOLOGY
    Frederick Sigworth; Fiscal Year: 2003
    ..The program offers an environment for intellectual breadth and collaboration, as well as training in the professional and ethical conduct of research. ..
  49. IS NON-ADHERENCE A REVEALED PREFERENCE
    Leslie Lenert; Fiscal Year: 2003
    ..We will also use an expert panel to assess the clinical match between patients' regimens and their preferences. ..
  50. COMPUTATIONAL ANALYSIS OF HUMAN 'AT-RISK' DNA MOTIFS
    JUDITH STENGER; Fiscal Year: 2003
    ..3) To set up an interactive on-line database and program server so that the scientific community can use the information and apply it to drive experimental research. ..
  51. DISTRIBUTED CORTICAL CODES FOR VISUAL MOTION
    David Bradley; Fiscal Year: 2004
    ..These will be the first studies to directly explore the link between distributed MT activity and the perception of visual motion. ..
  52. PROBABILISTIC MODELS OF PROTEIN AND RNA STRUCTURE
    Sean Eddy; Fiscal Year: 2006
    ..A final aim proposes a method for identifying the mRNA targets of regulatory RNAs (such as the newly discovered micro RNAs) by comparative genome analysis. ..
  53. FACTORS AFFECTING USE OF MEDICATION TO TREAT ALCOHOLISM
    TAMI MARK; Fiscal Year: 2001
    ..We propose to collect this information through experts panels and a national survey of physicians specialized in treating substance abuse. ..
  54. New Technologies for Patch-Clamp Recording
    Frederick Sigworth; Fiscal Year: 2005
    ..The proposed simplification of the patch-clamp technique will have far-reaching benefits in the search for ion channel and transporter genes and in the discovery of new pharmacological agents. ..
  55. Mediated Integration of Neuroscience Resources
    Luis Marenco; Fiscal Year: 2008
    ..abstract_text> ..
  56. PARASPINAL MUSCLE DENERVATION AND SYMPTOMS IN LUMBAR SS
    Andrew Haig; Fiscal Year: 2005
    ..Subjects will repeat the test battery (MRI, EMG, and clinical evaluation) approximately 18 months later. Appropriate statistics will test each of the four hypotheses. ..
  57. Maintenance of blocks-based tools for functional genomic
    Steven Henikoff; Fiscal Year: 2006
    ..These various components will be packaged to facilitate updates and local implementations. [unreadable] [unreadable]..
  58. ONS Research Agenda Conference
    Donna Berry; Fiscal Year: 2007
    ..The ONS Research Agenda will be evaluated after each conference from 2003-2007. [unreadable] [unreadable]..
  59. COMPUTER EDUCATION FOR BREAST CANCER GENETIC TESTING
    Michael Green; Fiscal Year: 2001
    ..abstract_text> ..
  60. Diffraction Methods in Structural Biology 2008 Gordon Research Conference
    Paul Adams; Fiscal Year: 2008
    ..There is a growing recognition that the use of such complementary techniques highly benefits the study of the increasingly complex assemblies of biological molecules now under investigation. [unreadable] [unreadable] [unreadable]..
  61. Data Mining Based Noninvasive Intracranial Pressure Assessment
    Xiao Hu; Fiscal Year: 2008
    ..unreadable] [unreadable] [unreadable]..
  62. Usability Testing of a CDSS for Tobacco Use Treatment
    THEODORE MARCY; Fiscal Year: 2005
    ..The effectiveness of the developed through this process would be assessed in a subsequent research proposal using a randomized controlled trial design. ..
  63. Physician Adherence to Tobacco Use Treatment Guidelines
    THEODORE MARCY; Fiscal Year: 2005
    ..The candidate's work will be under the sponsorship of Dr. Brian Flynn of the Office of Health Promotion Research at the University of Vermont. ..
  64. Innovative Methods for Function and Disability Assessment
    Alan Jette; Fiscal Year: 2007
    ..The public health research and clinical communities would be the likely markets [unreadable] interested in the CAT technology that would be developed and evaluated in this STTR. [unreadable] [unreadable] [unreadable] [unreadable]..
  65. Biophysical studies of a Sulfolobus icosahedral virus
    Reza Khayat; Fiscal Year: 2007
    ..Detailed characterization of Archaea viruses may also expand our knowledge of viral evolution. ..
  66. Interoperation of Genome Databases and Tools
    Kei Hoi Cheung; Fiscal Year: 2005
    ..We will extend our approach to other types of genomic data such as microarray data, which both laboratories and others will soon be generating in large quantities. ..
  67. Evaluating optimal methods for UV-risk assessment
    Joel Hillhouse; Fiscal Year: 2007
    ..This improvement in the measurement of skin cancer related behaviors should improve prevention efforts and lead to the prevention of future skin cancer. [unreadable] [unreadable] [unreadable]..
  68. A Data Fusion Method for Bedside Monitoring of Lumped Cerebral Arterial Radii
    Xiao Hu; Fiscal Year: 2008
    ..abstract_text> ..
  69. Automated (AI) Analysis of Sleep Disordered Breathing
    Indu Ayappa; Fiscal Year: 2004
    ..Successful completion of the training and research program will allow Dr. Ayappa to contribute independently to research in the field of sleep physiology. ..
  70. PARAMEDIC FIELD INITIATION OF MAGNESIUM NEUROPROTECTIVE
    Jeffrey Saver; Fiscal Year: 2003
    ..abstract_text> ..
  71. Reducing Breast Cancer Recurrence Risk in Black Women
    Melinda Stolley; Fiscal Year: 2007
    ..Aims include a 7% reduction in weight, a reduction in dietary fat intake, an increase in fruit and vegetable consumption, an increase in physical activity, and improved quality of life. ..
  72. Simulation Tool to Rapidly Design, Optimize, and Prototype Microfluidic Devices
    ADITYA BEDEKAR; Fiscal Year: 2006
    ..Interfaces to other microfabrication processes will be developed. [unreadable] [unreadable] [unreadable]..
  73. Bioimage Suite: A structural, functional and metabolic image analysis platform
    Xenophon Papademetris; Fiscal Year: 2009
    ..g. diabetes, cardiovascular disease, autism, epilepsy), planning therapy (e.g. neurosurgery) and evaluating other proposed treatment procedures (e.g. new drugs) ..