Undergraduate training programs
Brazas MD, Schwartz R.
GSID: 8NQYRHW4ozsJ
N Mulder, R Schwartz, MD Brazas… - PLoS computational …, 2018 - journals.plos.org
… face a special challenge compared with more traditional degree programs, in that the lack of clear standards for training at the undergraduate level means that there is little one can …
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Mulder, N., Schwartz, R., Brazas, M. D., Brooksbank, C., Gaeta, B., Morgan, S. L., ... & Welch, L. (2018). The development and application of bioinformatics core competencies to improve bioinformatics training and education. PLoS computational biology, 14(2), e1005772.
Mulder, Nicola, et al. "The development and application of bioinformatics core competencies to improve bioinformatics training and education." PLoS computational biology 14.2 (2018): e1005772.
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discipline specific-education (e.g., chemistry education, biology education, economics education)
[No authors listed]
GSID: 8pEeDvp1QmIJ
World Health Organization - 2005 - apps.who.int
Outstanding advances have been made in the past few decades in the life sciences and in biotechnology, including genetic engineering, genomics, proteomics and bioinformatics …
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World Health Organization. (2005). Life science research: opportunities and risks for public health: mapping the issues (No. WHO/CDS/CSR/LYO/2005.20). World Health Organization.
World Health Organization. Life science research: opportunities and risks for public health: mapping the issues. No. WHO/CDS/CSR/LYO/2005.20. World Health Organization, 2005.
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EPSCoR Research Infrastructure Improvement Program: Bridging EPSCoR Communities AND Program Evaluation
Hsu WH.
GSID: ffUDK1YEfScJ
WH Hsu - Manhattan (KS): Department of Computing and …, 2001 - kdd.cs.ksu.edu
2 Background Because we will build on the existing XML implementation of the MAGE (Microarray Gene Expression)[83] data standard developed by the Microarray Gene Expression Database (MGED) group [84], we provide a short summary of MAGE, its ancestors, and...
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Hsu, W. H. (2001). Activities of the KSU Bioinformatics and Medical Informatics (BMI) Working Group, 2001-2002. Manhattan (KS): Department of Computing and Information Science, Kansas State University.
Hsu, William H. "Activities of the KSU Bioinformatics and Medical Informatics (BMI) Working Group, 2001-2002." Manhattan (KS): Department of Computing and Information Science, Kansas State University (2001).
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EPSCoR Research Infrastructure Improvement Program AND Program Evaluation
Arighi CN, King BL, Polson SW, Wang Q.
GSID: wcLXvSCVsRkJ
Q Wang, CN Arighi, BL King, SW Polson, J Vincent… - Database, 2012 - academic.oup.com
Recent advances in high-throughput DNA sequencing technologies have equipped biologists with a powerful new set of tools for advancing research goals. The resulting flood of sequence data has made it critically important to train the next generation of scientists...
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Wang, Q., Arighi, C. N., King, B. L., Polson, S. W., Vincent, J., Chen, C., ... & North East Bioinformatics Collaborative Curation Team. (2012). Community annotation and bioinformatics workforce development in concert—Little Skate Genome Annotation Workshops and Jamborees. Database, 2012.
Wang, Qinghua, et al. "Community annotation and bioinformatics workforce development in concert—Little Skate Genome Annotation Workshops and Jamborees." Database 2012 (2012).
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pipeline programs
Winn MD.
GSID: 5qw-tdlvosIJ
RM Keegan, MD Winn - Acta Crystallographica Section D: Biological …, 2008 - iucr.org
… to the core molecular-replacement programs. For routine molecular-replacement problems, the pipeline automates what a crystallographer might … Bioinformatics, 15, 87-88.] ), but the conclusions of such tests do not necessarily transfer to our particular usage of these programs....
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Keegan, R. M., & Winn, M. D. (2008). MrBUMP: an automated pipeline for molecular replacement. Acta Crystallographica Section D: Biological Crystallography, 64(1), 119-124.
Keegan, Ronan M., and Martyn D. Winn. "MrBUMP: an automated pipeline for molecular replacement." Acta Crystallographica Section D: Biological Crystallography 64.1 (2008): 119-124.
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pipeline programs
Griffiths SM, Fox G, Donaldson IJ.
GSID: IQOURKTVWNEJ
SM Griffiths, G Fox, PJ Briggs, IJ Donaldson… - Conservation Genetics …, 2016 - Springer
… We developed a bioinformatics pipeline for microsatellite development from Illumina paired-end … The pipeline utilises existing programs along with our own novel program and wrappers to: … The complete pipeline is freely available for use via a pre-configured...
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Griffiths, S. M., Fox, G., Briggs, P. J., Donaldson, I. J., Hood, S., Richardson, P., ... & Preziosi, R. F. (2016). A Galaxy-based bioinformatics pipeline for optimised, streamlined microsatellite development from Illumina next-generation sequencing data. Conservation Genetics Resources, 8(4), 481-486.
Griffiths, Sarah M., et al. "A Galaxy-based bioinformatics pipeline for optimised, streamlined microsatellite development from Illumina next-generation sequencing data." Conservation Genetics Resources 8.4 (2016): 481-486.
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science instructors
[No authors listed]
GSID: _DT-VzZ_V8cJ
A McGrath, K Champ, CA Shang… - PLoS computational …, 2019 - journals.plos.org
… has led to a shift in the practise of life science research itself. Applied bioinformatics skills are now … occupies a core part of undergraduate life science degree courses. Yet productive life … Bioinformatics itself is a rapidly...
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McGrath, A., Champ, K., Shang, C. A., van Dam, E., Brooksbank, C., & Morgan, S. L. (2019). From trainees to trainers to instructors: Sustainably building a national capacity in bioinformatics training. PLoS computational biology, 15(6), e1006923.
McGrath, Annette, et al. "From trainees to trainers to instructors: Sustainably building a national capacity in bioinformatics training." PLoS computational biology 15.6 (2019): e1006923.
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science curriculum
Ben-Dor S.
GSID: uproqzAcIY8J
Y Machluf, H Gelbart, S Ben-Dor… - Briefings in …, 2017 - academic.oup.com
… curriculum design, classroom enactment, teacher education and research. For example, we recommend teaching bioinformatics in an integrative and comprehensive manner, through an inquiry process, and linking it to the wider science curriculum… the wider science curriculum. …
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Machluf, Y., Gelbart, H., Ben-Dor, S., & Yarden, A. (2017). Making authentic science accessible—the benefits and challenges of integrating bioinformatics into a high-school science curriculum. Briefings in bioinformatics, 18(1), 145-159.
Machluf, Yossy, et al. "Making authentic science accessible—the benefits and challenges of integrating bioinformatics into a high-school science curriculum." Briefings in bioinformatics 18.1 (2017): 145-159.
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case studies
Chang V, De D, Wills G.
GSID: GQP8jUxZHjAJ
V Chang, D De Roure, G Wills… - Journal of Computing …, 2011 - hrcak.srce.hr
… We illustrate its use with two case studies. The first case study concerns a National Health Service (NHS) Trust UK Infrastructure and confirms … The second case study shows 3D Visualisation being used to confirm incremental improvements to...
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Chang, V., De Roure, D., Wills, G., John Walters, R., & Barry, T. (2011). Organisational sustainability modelling for return on investment (ROI): Case studies presented by a national health service (NHS) trust UK. Journal of Computing and Information Technology, 19(3), 177-192.
Chang, Victor, et al. "Organisational sustainability modelling for return on investment (ROI): Case studies presented by a national health service (NHS) trust UK." Journal of Computing and Information Technology 19.3 (2011): 177-192.
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k-12
Edwards JS, Palsson BO.
GSID: SYOhVtZZY7wJ
JS Edwards, BO Palsson - BMC bioinformatics, 2000 - bmcbioinformatics.biomedcentral …
Genome sequencing and bioinformatics are producing detailed lists of the molecular components contained in many prokaryotic organisms. From this 'parts catalogue' of a microbial cell, in silico representations of integrated metabolic functions can be constructed and analyzed …
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Edwards, J. S., & Palsson, B. O. (2000). Metabolic flux balance analysis and the in silico analysis of Escherichia coli K-12 gene deletions. BMC bioinformatics, 1(1), 1-10.
Edwards, Jeremy S., and Bernhard O. Palsson. "Metabolic flux balance analysis and the in silico analysis of Escherichia coli K-12 gene deletions." BMC bioinformatics 1.1 (2000): 1-10.
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Undergraduate training programs
Arthur JW.
GSID: h2F5Dxriar0J
S Cattley, JW Arthur - Briefings in bioinformatics, 2007 - academic.oup.com
… installation and maintenance of all these programs makes BioManager a convenient resource for undergraduate teaching and other training programs in bioinformatics. Furthermore, …
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Cattley, S., & Arthur, J. W. (2007). BioManager: the use of a bioinformatics web application as a teaching tool in undergraduate bioinformatics training. Briefings in bioinformatics, 8(6), 457-465.
Cattley, Sonia, and Jonathan W. Arthur. "BioManager: the use of a bioinformatics web application as a teaching tool in undergraduate bioinformatics training." Briefings in bioinformatics 8.6 (2007): 457-465.
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Computer and Information Science and Engineering Minority-Serving Institutions Research Expansion Program AND Program Evaluation
Kulikowski CA, Maojo V.
GSID: Iq71e_pkADoJ
V Maojo, CA Kulikowski - … of the American Medical Informatics …, 2003 - academic.oup.com
In this report, the authors compare and contrast medical informatics (MI) and bioinformatics (BI) and provide a viewpoint on their complementarities and potential for collaboration in various subfields. The authors compare MI and BI along several dimensions, including:(1) historical...
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Maojo, V., & Kulikowski, C. A. (2003). Bioinformatics and medical informatics: collaborations on the road to genomic medicine?. Journal of the American Medical Informatics Association, 10(6), 515-522.
Maojo, Victor, and Casimir A. Kulikowski. "Bioinformatics and medical informatics: collaborations on the road to genomic medicine?." Journal of the American Medical Informatics Association 10.6 (2003): 515-522.
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