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1.  BMC Biotechnology reviewer acknowledgement 2014 
BMC Biotechnology  2015;15(1):8.
Contributing reviewers
The editors of BMC Biotechnology would like to thank all our reviewers who have contributed to the journal in Volume 14 (2014).
doi:10.1186/s12896-015-0119-y
PMCID: PMC4332893
2.  ISA-TAB-Nano: A Specification for Sharing Nanomaterial Research Data in Spreadsheet-based Format 
BMC Biotechnology  2013;13:2.
Background and motivation
The high-throughput genomics communities have been successfully using standardized spreadsheet-based formats to capture and share data within labs and among public repositories. The nanomedicine community has yet to adopt similar standards to share the diverse and multi-dimensional types of data (including metadata) pertaining to the description and characterization of nanomaterials. Owing to the lack of standardization in representing and sharing nanomaterial data, most of the data currently shared via publications and data resources are incomplete, poorly-integrated, and not suitable for meaningful interpretation and re-use of the data. Specifically, in its current state, data cannot be effectively utilized for the development of predictive models that will inform the rational design of nanomaterials.
Results
We have developed a specification called ISA-TAB-Nano, which comprises four spreadsheet-based file formats for representing and integrating various types of nanomaterial data. Three file formats (Investigation, Study, and Assay files) have been adapted from the established ISA-TAB specification; while the Material file format was developed de novo to more readily describe the complexity of nanomaterials and associated small molecules. In this paper, we have discussed the main features of each file format and how to use them for sharing nanomaterial descriptions and assay metadata.
Conclusion
The ISA-TAB-Nano file formats provide a general and flexible framework to record and integrate nanomaterial descriptions, assay data (metadata and endpoint measurements) and protocol information. Like ISA-TAB, ISA-TAB-Nano supports the use of ontology terms to promote standardized descriptions and to facilitate search and integration of the data. The ISA-TAB-Nano specification has been submitted as an ASTM work item to obtain community feedback and to provide a nanotechnology data-sharing standard for public development and adoption.
doi:10.1186/1472-6750-13-2
PMCID: PMC3598649  PMID: 23311978
3.  Comments on the paper "A statistical assessment of differences and equivalences between genetically modified and reference plant varieties" by van der Voet et al. 2011 
BMC Biotechnology  2012;12:13.
van der Voet et al. (2011) describe statistical methodology that the European Food Safety Authority expects an applicant to adopt when making a GM crop regulatory submission. Key to their proposed methodology is the inclusion of reference varieties in the experimental design to provide a measure of natural variation amongst commercially grown crops. While taking proper account of natural variation amongst commercial varieties in the safety assessment of GM plants makes good sense, the methodology described by the authors is shown here to be fundamentally flawed and consequently cannot be considered fit for purpose in its current form.
doi:10.1186/1472-6750-12-13
PMCID: PMC3489575  PMID: 22533372
4.  Effects of research tool patents on biotechnology innovation in a developing country: A case study of South Korea 
BMC Biotechnology  2009;9:25.
Background
Concerns have recently been raised about the negative effects of patents on innovation. In this study, the effects of patents on innovations in the Korean biotech SMEs (small and medium-sized entrepreneurs) were examined using survey data and statistical analysis.
Results
The survey results of this study provided some evidence that restricted access problems have occurred even though their frequency was not high. Statistical analysis revealed that difficulties in accessing patented research tools were not negatively correlated with the level of innovation performance and attitudes toward the patent system.
Conclusion
On the basis of the results of this investigation in combination with those of previous studies, we concluded that although restricted access problems have occurred, this has not yet deterred innovation in Korea. However, potential problems do exist, and the effects of restricted access should be constantly scrutinized.
doi:10.1186/1472-6750-9-25
PMCID: PMC2682799  PMID: 19321013
5.  Effective inhibition of lytic development of bacteriophages λ, P1 and T4 by starvation of their host, Escherichia coli 
BMC Biotechnology  2007;7:13.
Background
Bacteriophage infections of bacterial cultures cause serious problems in genetic engineering and biotechnology. They are dangerous not only because of direct effects on the currently infected cultures, i.e. their devastation, but also due to a high probability of spreading the phage progeny throughout a whole laboratory or plant, which causes a real danger for further cultivations. Therefore, a simple method for quick inhibition of phage development after detection of bacterial culture infection should be very useful.
Results
Here, we demonstrate that depletion of a carbon source from the culture medium, which provokes starvation of bacterial cells, results in rapid inhibition of lytic development of three Escherichia coli phages, λ, P1 and T4. Since the effect was similar for three different phages, it seems that it may be a general phenomenon. Moreover, similar effects were observed in flask cultures and in chemostats.
Conclusion
Bacteriophage lytic development can be inhibited efficiently by carbon source limitation in bacterial cultures. Thus, if bacteriophage contamination is detected, starvation procedures may be recommended to alleviate deleterious effects of phage infection on the culture. We believe that this strategy, in combination with the use of automated and sensitive bacteriophage biosensors, may be employed in the fermentation laboratory practice to control phage outbreaks in bioprocesses more effectively.
doi:10.1186/1472-6750-7-13
PMCID: PMC1820593  PMID: 17324284

Results 1-5 (5)