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Bioinformatics for the Human Microbiome Project.

PLoS computational biology

Gevers D, Pop M, Schloss PD, Huttenhower C.
PMID: 23209389
PLoS Comput Biol. 2012;8(11):e1002779. doi: 10.1371/journal.pcbi.1002779. Epub 2012 Nov 29.

No abstract available.

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Gevers D, Pop M, Schloss PD, et al. Bioinformatics for the Human Microbiome Project. PLoS Comput Biol. 2012;8(11):e1002779doi: 10.1371/journal.pcbi.1002779.
Gevers, D., Pop, M., Schloss, P. D., & Huttenhower, C. (2012). Bioinformatics for the Human Microbiome Project. PLoS computational biology, 8(11), e1002779. https://doi.org/10.1371/journal.pcbi.1002779
Gevers, Dirk, et al. "Bioinformatics for the Human Microbiome Project." PLoS computational biology vol. 8,11 (2012): e1002779. doi: https://doi.org/10.1371/journal.pcbi.1002779
Gevers D, Pop M, Schloss PD, Huttenhower C. Bioinformatics for the Human Microbiome Project. PLoS Comput Biol. 2012;8(11):e1002779. doi: 10.1371/journal.pcbi.1002779. Epub 2012 Nov 29. PMID: 23209389; PMCID: PMC3510052.
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iLAP: a workflow-driven software for experimental protocol development, data acquisition and analysis.

BMC bioinformatics

Stocker G, Fischer M, Rieder D, Bindea G, Kainz S, Oberstolz M, McNally JG, Trajanoski Z.
PMID: 19941647
BMC Bioinformatics. 2009 Nov 26;10:390. doi: 10.1186/1471-2105-10-390.

BACKGROUND: In recent years, the genome biology community has expended considerable effort to confront the challenges of managing heterogeneous data in a structured and organized way and developed laboratory information management systems (LIMS) for both raw and processed data....

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Stocker G, Fischer M, Rieder D, et al. iLAP: a workflow-driven software for experimental protocol development, data acquisition and analysis. BMC Bioinformatics. 2009;10:390doi: 10.1186/1471-2105-10-390.
Stocker, G., Fischer, M., Rieder, D., Bindea, G., Kainz, S., Oberstolz, M., McNally, J. G., & Trajanoski, Z. (2009). iLAP: a workflow-driven software for experimental protocol development, data acquisition and analysis. BMC bioinformatics, 10390. https://doi.org/10.1186/1471-2105-10-390
Stocker, Gernot, et al. "iLAP: a workflow-driven software for experimental protocol development, data acquisition and analysis." BMC bioinformatics vol. 10 (2009): 390. doi: https://doi.org/10.1186/1471-2105-10-390
Stocker G, Fischer M, Rieder D, Bindea G, Kainz S, Oberstolz M, McNally JG, Trajanoski Z. iLAP: a workflow-driven software for experimental protocol development, data acquisition and analysis. BMC Bioinformatics. 2009 Nov 26;10:390. doi: 10.1186/1471-2105-10-390. PMID: 19941647; PMCID: PMC2789074.
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A method for efficient execution of bioinformatics workflows.

Genome informatics. International Conference on Genome Informatics

Seo J, Kido Y, Seno S, Takenaka Y, Matsuda H.
PMID: 20180269
Genome Inform. 2009 Oct;23(1):139-48.

Efficient execution of data-intensive workflows has been playing an important role in bioinformatics as the amount of data has been rapidly increasing. The execution of such workflows must take into account the volume and pattern of communication. When orchestrating...

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Seo J, Kido Y, Seno S, et al. A method for efficient execution of bioinformatics workflows. Genome Inform. 2009;23(1):139-48
Seo, J., Kido, Y., Seno, S., Takenaka, Y., & Matsuda, H. (2009). A method for efficient execution of bioinformatics workflows. Genome informatics. International Conference on Genome Informatics, 23(1), 139-48.
Seo, Junya, et al. "A method for efficient execution of bioinformatics workflows." Genome informatics. International Conference on Genome Informatics vol. 23,1 (2009): 139-48.
Seo J, Kido Y, Seno S, Takenaka Y, Matsuda H. A method for efficient execution of bioinformatics workflows. Genome Inform. 2009 Oct;23(1):139-48. PMID: 20180269.
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ArrayOU: a web application for microarray data analysis and visualization.

Journal of biomolecular techniques : JBT

Shen K, Wyatt SE, Nadella V.
PMID: 22754383
J Biomol Tech. 2012 Jul;23(2):37-9. doi: 10.7171/jbt.2012-2302-001.

A web-based microarray data analysis tool, ArrayOU (freely available at www.bioinformatics.plantbio.ohiou.edu.), has been developed at the Ohio University Genomics Facility for the research and education community to analyze Agilent microarray data. Agilent's microarray pipeline has gained in popularity as...

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Shen K, Wyatt SE, Nadella V. ArrayOU: a web application for microarray data analysis and visualization. J Biomol Tech. 2012;23(2):37-9doi: 10.7171/jbt.2012-2302-001.
Shen, K., Wyatt, S. E., & Nadella, V. (2012). ArrayOU: a web application for microarray data analysis and visualization. Journal of biomolecular techniques : JBT, 23(2), 37-9. https://doi.org/10.7171/jbt.2012-2302-001
Shen, Kaiyu, et al. "ArrayOU: a web application for microarray data analysis and visualization." Journal of biomolecular techniques : JBT vol. 23,2 (2012): 37-9. doi: https://doi.org/10.7171/jbt.2012-2302-001
Shen K, Wyatt SE, Nadella V. ArrayOU: a web application for microarray data analysis and visualization. J Biomol Tech. 2012 Jul;23(2):37-9. doi: 10.7171/jbt.2012-2302-001. PMID: 22754383; PMCID: PMC3378286.
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Facilitating the use of large-scale biological data and tools in the era of translational bioinformatics.

Briefings in bioinformatics

Kouskoumvekaki I, Shublaq N, Brunak S.
PMID: 23908249
Brief Bioinform. 2014 Nov;15(6):942-52. doi: 10.1093/bib/bbt055. Epub 2013 Aug 01.

As both the amount of generated biological data and the processing compute power increase, computational experimentation is no longer the exclusivity of bioinformaticians, but it is moving across all biomedical domains. For bioinformatics to realize its translational potential, domain...

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Kouskoumvekaki I, Shublaq N, Brunak S. Facilitating the use of large-scale biological data and tools in the era of translational bioinformatics. Brief Bioinform. 2013;15(6):942-52doi: 10.1093/bib/bbt055.
Kouskoumvekaki, I., Shublaq, N., & Brunak, S. (2014). Facilitating the use of large-scale biological data and tools in the era of translational bioinformatics. Briefings in bioinformatics, 15(6), 942-52. https://doi.org/10.1093/bib/bbt055
Kouskoumvekaki, Irene, et al. "Facilitating the use of large-scale biological data and tools in the era of translational bioinformatics." Briefings in bioinformatics vol. 15,6 (2014): 942-52. doi: https://doi.org/10.1093/bib/bbt055
Kouskoumvekaki I, Shublaq N, Brunak S. Facilitating the use of large-scale biological data and tools in the era of translational bioinformatics. Brief Bioinform. 2014 Nov;15(6):942-52. doi: 10.1093/bib/bbt055. Epub 2013 Aug 01. PMID: 23908249.
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HCS road: an enterprise system for integrated HCS data management and analysis.

Journal of biomolecular screening

Jackson D, Lenard M, Zelensky A, Shaikh M, Scharpf JV, Shaginaw R, Nawade M, Agler M, Cloutier NJ, Fennell M, Guo Q, Wardwell-Swanson J, Zhao D, Zhu Y, Miller C, Gill J.
PMID: 20639503
J Biomol Screen. 2010 Aug;15(7):882-91. doi: 10.1177/1087057110374233. Epub 2010 Jul 16.

The effective analysis and interpretation of high-content screening (HCS) data requires joining results to information on experimental treatments and controls, normalizing data, and selecting hits or fitting concentration-response curves. HCS data have unique requirements that are not supported by...

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Jackson D, Lenard M, Zelensky A, et al. HCS road: an enterprise system for integrated HCS data management and analysis. J Biomol Screen. 2010;15(7):882-91doi: 10.1177/1087057110374233.
Jackson, D., Lenard, M., Zelensky, A., Shaikh, M., Scharpf, J. V., Shaginaw, R., Nawade, M., Agler, M., Cloutier, N. J., Fennell, M., Guo, Q., Wardwell-Swanson, J., Zhao, D., Zhu, Y., Miller, C., & Gill, J. (2010). HCS road: an enterprise system for integrated HCS data management and analysis. Journal of biomolecular screening, 15(7), 882-91. https://doi.org/10.1177/1087057110374233
Jackson, Donald, et al. "HCS road: an enterprise system for integrated HCS data management and analysis." Journal of biomolecular screening vol. 15,7 (2010): 882-91. doi: https://doi.org/10.1177/1087057110374233
Jackson D, Lenard M, Zelensky A, Shaikh M, Scharpf JV, Shaginaw R, Nawade M, Agler M, Cloutier NJ, Fennell M, Guo Q, Wardwell-Swanson J, Zhao D, Zhu Y, Miller C, Gill J. HCS road: an enterprise system for integrated HCS data management and analysis. J Biomol Screen. 2010 Aug;15(7):882-91. doi: 10.1177/1087057110374233. Epub 2010 Jul 16. PMID: 20639503.
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TRAM (Transcriptome Mapper): database-driven creation and analysis of transcriptome maps from multiple sources.

BMC genomics

Lenzi L, Facchin F, Piva F, Giulietti M, Pelleri MC, Frabetti F, Vitale L, Casadei R, Canaider S, Bortoluzzi S, Coppe A, Danieli GA, Principato G, Ferrari S, Strippoli P.
PMID: 21333005
BMC Genomics. 2011 Feb 18;12:121. doi: 10.1186/1471-2164-12-121.

BACKGROUND: Several tools have been developed to perform global gene expression profile data analysis, to search for specific chromosomal regions whose features meet defined criteria as well as to study neighbouring gene expression. However, most of these tools are...

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Lenzi L, Facchin F, Piva F, et al. TRAM (Transcriptome Mapper): database-driven creation and analysis of transcriptome maps from multiple sources. BMC Genomics. 2011;12:121doi: 10.1186/1471-2164-12-121.
Lenzi, L., Facchin, F., Piva, F., Giulietti, M., Pelleri, M. C., Frabetti, F., Vitale, L., Casadei, R., Canaider, S., Bortoluzzi, S., Coppe, A., Danieli, G. A., Principato, G., Ferrari, S., & Strippoli, P. (2011). TRAM (Transcriptome Mapper): database-driven creation and analysis of transcriptome maps from multiple sources. BMC genomics, 12121. https://doi.org/10.1186/1471-2164-12-121
Lenzi, Luca, et al. "TRAM (Transcriptome Mapper): database-driven creation and analysis of transcriptome maps from multiple sources." BMC genomics vol. 12 (2011): 121. doi: https://doi.org/10.1186/1471-2164-12-121
Lenzi L, Facchin F, Piva F, Giulietti M, Pelleri MC, Frabetti F, Vitale L, Casadei R, Canaider S, Bortoluzzi S, Coppe A, Danieli GA, Principato G, Ferrari S, Strippoli P. TRAM (Transcriptome Mapper): database-driven creation and analysis of transcriptome maps from multiple sources. BMC Genomics. 2011 Feb 18;12:121. doi: 10.1186/1471-2164-12-121. PMID: 21333005; PMCID: PMC3052188.
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Applying open source data visualization tools to standard based medical data.

Studies in health technology and informatics

Kopanitsa G, Taranik M.
PMID: 24851981
Stud Health Technol Inform. 2014;200:155-7.

Presentation of medical data in personal health records (PHRs) requires flexible platform independent tools to ensure easy access to the information. Different backgrounds of the patients, especially elder people require simple graphical presentation of the data. Data in PHRs...

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Kopanitsa G, Taranik M. Applying open source data visualization tools to standard based medical data. Stud Health Technol Inform. 2014;200:155-7
Kopanitsa, G., & Taranik, M. (2014). Applying open source data visualization tools to standard based medical data. Studies in health technology and informatics, 200155-7.
Kopanitsa, Georgy, and Taranik, Maxim. "Applying open source data visualization tools to standard based medical data." Studies in health technology and informatics vol. 200 (2014): 155-7.
Kopanitsa G, Taranik M. Applying open source data visualization tools to standard based medical data. Stud Health Technol Inform. 2014;200:155-7. PMID: 24851981.
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A simple versatile solution for collecting multidimensional clinical data based on the CakePHP web application framework.

Computer methods and programs in biomedicine

Biermann M.
PMID: 24507951
Comput Methods Programs Biomed. 2014 Apr;114(1):70-9. doi: 10.1016/j.cmpb.2014.01.007. Epub 2014 Jan 17.

Clinical trials aiming for regulatory approval of a therapeutic agent must be conducted according to Good Clinical Practice (GCP). Clinical Data Management Systems (CDMS) are specialized software solutions geared toward GCP-trials. They are however less suited for data management...

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Biermann M. A simple versatile solution for collecting multidimensional clinical data based on the CakePHP web application framework. Comput Methods Programs Biomed. 2014;114(1):70-9doi: 10.1016/j.cmpb.2014.01.007.
Biermann, M. (2014). A simple versatile solution for collecting multidimensional clinical data based on the CakePHP web application framework. Computer methods and programs in biomedicine, 114(1), 70-9. https://doi.org/10.1016/j.cmpb.2014.01.007
Biermann, Martin. "A simple versatile solution for collecting multidimensional clinical data based on the CakePHP web application framework." Computer methods and programs in biomedicine vol. 114,1 (2014): 70-9. doi: https://doi.org/10.1016/j.cmpb.2014.01.007
Biermann M. A simple versatile solution for collecting multidimensional clinical data based on the CakePHP web application framework. Comput Methods Programs Biomed. 2014 Apr;114(1):70-9. doi: 10.1016/j.cmpb.2014.01.007. Epub 2014 Jan 17. PMID: 24507951.
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ResearchTraining.org and AALASLearningLibrary.org: online learning management systems for technicians, researchers, and IACUCs.

Alternatives to laboratory animals : ATLA

Duffee N, Fallon MT.
PMID: 23581132
Altern Lab Anim. 2004 Jun;32:539-43. doi: 10.1177/026119290403201s87.

ResearchTraining.org and the AALASLearningLibrary.org are web-based learning management systems that utilise database architecture in Microsoft SQL Server 2000 and Internet browsers (Microsoft Internet Explorer 6.0, Netscape Navigator 6.0 browsers). Both websites are constructed of active server pages coded with...

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Duffee N, Fallon MT. ResearchTraining.org and AALASLearningLibrary.org: online learning management systems for technicians, researchers, and IACUCs. Altern Lab Anim. 2004;32:539-43doi: 10.1177/026119290403201s87.
Duffee, N., & Fallon, M. T. (2004). ResearchTraining.org and AALASLearningLibrary.org: online learning management systems for technicians, researchers, and IACUCs. Alternatives to laboratory animals : ATLA, 32539-43. https://doi.org/10.1177/026119290403201s87
Duffee, Nicole, and Fallon, Michael T. "ResearchTraining.org and AALASLearningLibrary.org: online learning management systems for technicians, researchers, and IACUCs." Alternatives to laboratory animals : ATLA vol. 32 (2004): 539-43. doi: https://doi.org/10.1177/026119290403201s87
Duffee N, Fallon MT. ResearchTraining.org and AALASLearningLibrary.org: online learning management systems for technicians, researchers, and IACUCs. Altern Lab Anim. 2004 Jun;32:539-43. doi: 10.1177/026119290403201s87. PMID: 23581132.
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Daily management systems in medicine.

Radiographics : a review publication of the Radiological Society of North America, Inc

Donnelly LF.
PMID: 24617697
Radiographics. 2014 Mar-Apr;34(2):549-55. doi: 10.1148/rg.342130035.

"Lean" (continuous improvement) organizations make use of daily management systems (DMS) that are designed so that problems can be quickly identified, front-line staff are empowered to fix the problems that they can, and problems that the front-line staff cannot...

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Donnelly LF. Daily management systems in medicine. Radiographics. 2014;34(2):549-55doi: 10.1148/rg.342130035.
Donnelly, L. F. (2014). Daily management systems in medicine. Radiographics : a review publication of the Radiological Society of North America, Inc, 34(2), 549-55. https://doi.org/10.1148/rg.342130035
Donnelly, Lane F. "Daily management systems in medicine." Radiographics : a review publication of the Radiological Society of North America, Inc vol. 34,2 (2014): 549-55. doi: https://doi.org/10.1148/rg.342130035
Donnelly LF. Daily management systems in medicine. Radiographics. 2014 Mar-Apr;34(2):549-55. doi: 10.1148/rg.342130035. PMID: 24617697.
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An EMR based cancer diary - utilisation and initial usability evaluation of a new cancer data visualization tool.

Studies in health technology and informatics

Ries M, Golcher H, Prokosch HU, Beckmann MW, Bürkle T.
PMID: 22874273
Stud Health Technol Inform. 2012;180:656-60.

We present an EMR based approach to visualize all cancer relevant data in a so-called cancer diary at a single glance. System log and results of a user survey demonstrate increasing use and good usability of the cancer diary...

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Ries M, Golcher H, Prokosch HU, et al. An EMR based cancer diary - utilisation and initial usability evaluation of a new cancer data visualization tool. Stud Health Technol Inform. 2012;180:656-60
Ries, M., Golcher, H., Prokosch, H. U., Beckmann, M. W., & Bürkle, T. (2012). An EMR based cancer diary - utilisation and initial usability evaluation of a new cancer data visualization tool. Studies in health technology and informatics, 180656-60.
Ries, Markus, et al. "An EMR based cancer diary - utilisation and initial usability evaluation of a new cancer data visualization tool." Studies in health technology and informatics vol. 180 (2012): 656-60.
Ries M, Golcher H, Prokosch HU, Beckmann MW, Bürkle T. An EMR based cancer diary - utilisation and initial usability evaluation of a new cancer data visualization tool. Stud Health Technol Inform. 2012;180:656-60. PMID: 22874273.
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Showing 1 to 12 of 22 entries