Abstract:
:Recent advances in miniaturization and automation of technologies have enabled cell-based assay high-throughput screening, bringing along new challenges in data analysis. Automation, standardization, reproducibility have become requirements for qualitative research. The Bioconductor community has worked in that direction proposing several R packages to handle high-throughput data including flow cytometry (FCM) experiment. Altogether, these packages cover the main steps of a FCM analysis workflow, that is, data management, quality assessment, normalization, outlier detection, automated gating, cluster labeling, and feature extraction. Additionally, the open-source philosophy of R and Bioconductor, which offers room for new development, continuously drives research and improvement of theses analysis methods, especially in the field of clustering and data mining. This review presents the principal FCM packages currently available in R and Bioconductor, their advantages and their limits.
journal_name
Curr Opin Biotechnoljournal_title
Current opinion in biotechnologyauthors
Le Meur Ndoi
10.1016/j.copbio.2012.09.003subject
Has Abstractpub_date
2013-02-01 00:00:00pages
105-11issue
1eissn
0958-1669issn
1879-0429pii
S0958-1669(12)00130-9journal_volume
24pub_type
杂志文章,评审abstract::Academic microfluidics has decisively shifted in recent years from the research on phenomenology and proof-of-concept fluidic functionalities to the developments oriented at applications with biology, medicine and biotechnology in prime focus. Significant efforts are made to demonstrate that microfluidics can be used ...
journal_title:Current opinion in biotechnology
pub_type: 杂志文章,评审
doi:10.1016/j.copbio.2018.08.004
更新日期:2019-02-01 00:00:00
abstract::Signal transduction is the process of converting one kind of signal or stimulus into another, with the goal of processing external or internal signals into diverse functions. In recent years, progress has been made in identifying signaling pathways, investigating cross-talk and feedbacks in signaling modules, analyzin...
journal_title:Current opinion in biotechnology
pub_type: 杂志文章,评审
doi:10.1016/j.copbio.2011.10.004
更新日期:2012-06-01 00:00:00
abstract::The use of ultrafast laser pulses in surgery has allowed for unprecedented precision with minimal collateral damage to surrounding tissues. For these reasons, ultrafast laser nanosurgery, as an injury model, has gained tremendous momentum in experimental biology ranging from in vitro manipulations of subcellular struc...
journal_title:Current opinion in biotechnology
pub_type: 杂志文章,评审
doi:10.1016/j.copbio.2009.01.008
更新日期:2009-02-01 00:00:00
abstract::The biosynthesis of the solvents 1-butanol and acetone is restricted to species of the genus Clostridium, a diverse group of Gram-positive, endospore forming anaerobes comprising toxin-producing strains as well as terrestrial non-pathogenic species of biotechnological impact. Among solventogenic clostridia, Clostridiu...
journal_title:Current opinion in biotechnology
pub_type: 杂志文章,评审
doi:10.1016/j.copbio.2011.01.011
更新日期:2011-10-01 00:00:00
abstract::Microbes have long been adapted for the biosynthetic production of useful compounds. There is increasing demand for the rapid and cheap microbial production of diverse molecules in an industrial setting. Microbes can now be designed and engineered for a particular biosynthetic purpose, thanks to recent developments in...
journal_title:Current opinion in biotechnology
pub_type: 杂志文章,评审
doi:10.1016/j.copbio.2014.02.014
更新日期:2014-10-01 00:00:00
abstract::A mechanistic understanding of gene regulatory network dynamics requires quantitative single-cell data of multiple network components in response to well-defined perturbations. Recent advances in the development of fluorescent biomarkers for proteins, detection of RNA and interactions, microfluidic technology, and hig...
journal_title:Current opinion in biotechnology
pub_type: 杂志文章,评审
doi:10.1016/j.copbio.2011.11.006
更新日期:2012-02-01 00:00:00
abstract::Within Escherichia coli and other species, a clear codon bias exists among the 61 amino acid codons found within the population of mRNA molecules, and the level of cognate tRNA appears directly proportional to the frequency of codon usage. Given this situation, one would predict translational problems with an abundant...
journal_title:Current opinion in biotechnology
pub_type: 杂志文章,评审
doi:10.1016/0958-1669(95)80082-4
更新日期:1995-10-01 00:00:00
abstract::Silk combines biological properties, such as non-toxicity and biodegradability, with physico-chemical ones, for example, mechanical strength. Base on molecular engineering, nowadays also new non-silk functions can be implemented in silk materials. Driven by rational design and ingenuity, innovative recombinant silk pr...
journal_title:Current opinion in biotechnology
pub_type: 杂志文章,评审
doi:10.1016/j.copbio.2019.05.005
更新日期:2019-12-01 00:00:00
abstract::The continuing expansion of protein and genome sequence databases is an opportunity to identify novel enzymes with biotechnological applications. Whether applied to enzymology, chemical biology, systems biology, and microbiology, database mining must be 'user-friendly' so that experimentalists can devise focused strat...
journal_title:Current opinion in biotechnology
pub_type: 杂志文章,评审
doi:10.1016/j.copbio.2020.12.004
更新日期:2021-01-05 00:00:00
abstract::Considerable progress has been made in understanding the relationship between local amino acid sequence and local protein structure. Recent highlights include numerous studies of the structures adopted by short peptides, new approaches to correlating sequence patterns with structure patterns, and folding simulations u...
journal_title:Current opinion in biotechnology
pub_type: 杂志文章,评审
doi:10.1016/s0958-1669(96)80117-0
更新日期:1996-08-01 00:00:00
abstract::The past decade has witnessed rapid advance in microbial production of 'drop-in' biofuels from renewable resources. Various biosynthetic pathways have been constructed to produce biofuels with diverse structures, and multiple metabolic engineering strategies have been developed to increase biofuel titers, yields, prod...
journal_title:Current opinion in biotechnology
pub_type: 杂志文章,评审
doi:10.1016/j.copbio.2017.10.010
更新日期:2018-10-01 00:00:00
abstract::Advances in metabolic engineering have given rise to the biological production of novel fuels and chemicals, but yields are often low without significant optimization. One generalizable solution is to create a specialized organelle for the sequestration of engineered metabolic pathways. Bacterial microcompartments are...
journal_title:Current opinion in biotechnology
pub_type: 杂志文章,评审
doi:10.1016/j.copbio.2012.11.012
更新日期:2013-08-01 00:00:00
abstract::During 1993, significant advances have been achieved in applications of DNA analysis to forensic science, disease assessment, and animal/plant identification. These advances include the development of simple and high sample-throughput techniques for highly informative personal identification, rapid screening for patho...
journal_title:Current opinion in biotechnology
pub_type: 杂志文章,评审
doi:10.1016/s0958-1669(05)80066-7
更新日期:1994-02-01 00:00:00
abstract::The increasing demand for a steady, healthy food supply requires an efficient control of the major pests and plant diseases. Current management practices are based largely on the application of synthetic pesticides. The excessive use of agrochemicals has caused serious environmental and health problems. Therefore, the...
journal_title:Current opinion in biotechnology
pub_type: 杂志文章,评审
doi:10.1016/j.copbio.2010.12.003
更新日期:2011-04-01 00:00:00
abstract::The most significant feature of the current transgenic models of Alzheimer's disease continues to be the amyloid phenotype. In the past year, mice have been more extensively characterized in terms of the effect of amyloid accumulation on downstream events, such as neurodegeneration and behavioral changes, but the resu...
journal_title:Current opinion in biotechnology
pub_type: 杂志文章,评审
doi:10.1016/s0958-1669(98)80132-8
更新日期:1998-12-01 00:00:00
abstract::Herbicides are economically important, but the non-point pollution that they cause may disrupt the surrounding environment. Phytoremediation of herbicides has been well studied using conventional plants. Transgenic plants produced for metabolizing herbicides and long-persisting pollutants can be used for phytoremediat...
journal_title:Current opinion in biotechnology
pub_type: 杂志文章,评审
doi:10.1016/j.copbio.2009.01.010
更新日期:2009-04-01 00:00:00
abstract::Stabilization of enzymes without diminishing and diluting their activity is crucial for their use as industrial catalysts. One practically proven approach involves crystallization of the enzyme (size 1-200 microm) followed by subsequent crosslinking. In many cases, the resulting crosslinked enzyme crystals exhibit inc...
journal_title:Current opinion in biotechnology
pub_type: 杂志文章,评审
doi:10.1016/S0958-1669(99)80060-3
更新日期:1999-08-01 00:00:00
abstract::In spite of many efforts and achievements to optimize the prokaryotic expression systems, there are still general and specific problems in obtaining sufficient yields of the functionally active gene products. The main problems concern the formation of inclusion bodies, incorrect folding, toxicity for the producer cell...
journal_title:Current opinion in biotechnology
pub_type: 杂志文章,评审
doi:10.1016/s0958-1669(98)80037-2
更新日期:1998-10-01 00:00:00
abstract::Driven by the demand to enhance the economic balance of chemical processes, the transformation of a racemate into a single stereoisomer (the deracemization process) is one of the most important areas of research. The recent development of the combined use of enzyme and metal catalysis has led to efficient deracemizati...
journal_title:Current opinion in biotechnology
pub_type: 杂志文章,评审
doi:10.1016/s0958-1669(03)00097-1
更新日期:2003-08-01 00:00:00
abstract::The conservation and sustainable use of freshwater resources is of global importance. Microorganisms are not only the most abundant organisms in natural freshwater systems, but are also key players in ecological processes controlling water quality. Detailed knowledge of the diversity and function of microorganisms dwe...
journal_title:Current opinion in biotechnology
pub_type: 杂志文章,评审
doi:10.1016/j.copbio.2006.05.006
更新日期:2006-06-01 00:00:00
abstract::The concept of whole genome amplification is something that has arisen in the past few years as the polymerase chain reaction (PCR) has been adapted to replicate regions of genomes that are of biological interest. The applications are many--forensic science, embryonic disease diagnosis, bioterrorism genome detection, ...
journal_title:Current opinion in biotechnology
pub_type: 杂志文章,评审
doi:10.1016/s0958-1669(02)00286-0
更新日期:2002-02-01 00:00:00
abstract::The human gut microbiome is composed of an enormous number of microorganisms, generally regarded as commensal bacteria. Without this inherent microbial community, we would be unable to digest plant polysaccharides and would have trouble extracting lipids from our diet. Resident gut bacteria are an important contributo...
journal_title:Current opinion in biotechnology
pub_type: 杂志文章,评审
doi:10.1016/j.copbio.2014.10.007
更新日期:2015-04-01 00:00:00
abstract::Soft rot pathogens cause significant losses worldwide in fruit and vegetable production during the growing season and after harvest. These pathogens engage in molecular interactions with their plant hosts via acyl-homoserine lactone (AHL) quorum sensing, pectin metabolites, phenolic acids, and auxin. The AHL-based int...
journal_title:Current opinion in biotechnology
pub_type: 杂志文章,评审
doi:10.1016/j.copbio.2009.01.005
更新日期:2009-04-01 00:00:00
abstract::Recent advances in research on natural products (of both low and high molecular weight) of plant origin and their commercial potential as medicines are discussed. Substances with immunomodulating, antiviral, antimicrobial, antiparasite, antitumor, anti-inflammatory, hypoglycemic, tranquillizer and antifeedant activiti...
journal_title:Current opinion in biotechnology
pub_type: 杂志文章,评审
doi:10.1016/0958-1669(91)90011-s
更新日期:1991-04-01 00:00:00
abstract::Generating novel functionality from well characterised synthetic parts and modules lies at the heart of synthetic biology. Ideally, circuitry is rationally designed in silico with quantitatively predictive models to predetermined design specifications. Synthetic circuits are intrinsically stochastic, often dynamically...
journal_title:Current opinion in biotechnology
pub_type: 杂志文章,评审
doi:10.1016/j.copbio.2020.02.002
更新日期:2020-06-01 00:00:00
abstract::Lactococcus lactis is the primary model organism for lactic acid bacteria (LAB) and is widely used in the production of fermented dairy products. In recent years there has been increasing interest in strains isolated from non-dairy environments, as these exhibit a high metabolic diversity and have unique flavour-formi...
journal_title:Current opinion in biotechnology
pub_type: 杂志文章,评审
doi:10.1016/j.copbio.2006.02.007
更新日期:2006-04-01 00:00:00
abstract::During the past decade, the increasing knowledge of flavonoid biosynthesis and the important function of flavonoid compounds in plants and in human and animal nutrition have made the biosynthetic pathways to flavonoids and isoflavonoids excellent targets for metabolic engineering. Recent strategies have included intro...
journal_title:Current opinion in biotechnology
pub_type: 杂志文章,评审
doi:10.1016/s0958-1669(00)00192-0
更新日期:2001-04-01 00:00:00
abstract::Bacteriophage endolysins (peptidoglycan hydrolases) have emerged as a new class of antimicrobial agents useful for controlling bacterial infection or other unwanted contaminations in various fields, particularly in the light of the worldwide increasing frequency of drug-resistant pathogens. This review summarizes and ...
journal_title:Current opinion in biotechnology
pub_type: 杂志文章,评审
doi:10.1016/j.copbio.2015.10.005
更新日期:2016-02-01 00:00:00
abstract::Enormous fuel consumption and growing environmental concerns have been spurring development of renewable biofuels. Among various biofuels, fatty acid-derived biohydrocarbons are ideal alternatives to non-renewable fossil fuels due to their closest properties to petroleum-based fuels. In the past decade, novel hydrocar...
journal_title:Current opinion in biotechnology
pub_type: 杂志文章,评审
doi:10.1016/j.copbio.2019.07.005
更新日期:2020-04-01 00:00:00
abstract::Bioindustry is expanding to an increasing variety of food, chemical and pharmaceutical products, each requiring rapid development of a dedicated cell factory and bioprocess. Microfluidic tools are, together with tools from synthetic biology and metabolic modeling, being employed in cell factory and bioprocess developm...
journal_title:Current opinion in biotechnology
pub_type: 杂志文章,评审
doi:10.1016/j.copbio.2018.08.011
更新日期:2019-02-01 00:00:00