High-throughput
omics data often contain systematic biases introduced during various
steps of sample processing and data generation. As the source of these
biases is usually unknown, it is difficult to select an optimal normalization
method for a given data set. To facilitate this process, we introduce
the open-source tool “Normalyzer”. It normalizes the
data with 12 different normalization methods and generates a report
with several quantitative and qualitative plots for comparative evaluation
of different methods. The usefulness of Normalyzer is demonstrated
with three different case studies from quantitative proteomics and
transcriptomics. The results from these case studies show that the
choice of normalization method strongly influences the outcome of
downstream quantitative comparisons. Normalyzer is an R package and
can be used locally or through the online implementation at .
Food wastage and its accumulation are becoming a critical problem around the globe due to continuous increase of the world population. The exponential growth in food waste is imposing serious threats to our society like environmental pollution, health risk, and scarcity of dumping land. There is an urgent need to take appropriate measures to reduce food waste burden by adopting standard management practices. Currently, various kinds of approaches are investigated in waste food processing and management for societal benefits and applications. Anaerobic digestion approach has appeared as one of the most ecofriendly and promising solutions for food wastes management, energy, and nutrient production, which can contribute to world's ever-increasing energy requirements. Here, we have briefly described and explored the different aspects of anaerobic biodegrading approaches for food waste, effects of cosubstrates, effect of environmental factors, contribution of microbial population, and available computational resources for food waste management researches.
Plant mutagenesis is rapidly coming of age in the aftermath of recent developments in high-resolution molecular and biochemical techniques. By combining the high variation of mutagenised populations with novel screening methods, traits that are almost impossible to identify by conventional breeding are now being developed and characterised at the molecular level. This paper provides a comprehensive overview of the various techniques and workflows available to researchers today in the field of molecular breeding, and how these tools complement the ones already used in traditional breeding. Both genetic (Targeting Induced Local Lesions in Genomes; TILLING) and phenotypic screens are evaluated. Finally, different ways of bridging the gap between genotype and phenotype are discussed.
Technical biases
are introduced in omics data sets during data
generation and interfere with the ability to study biological mechanisms.
Several normalization approaches have been proposed to minimize the
effects of such biases, but fluctuations in the electrospray current
during liquid chromatography–mass spectrometry gradients cause
local and sample-specific bias not considered by most approaches.
Here we introduce a software named NormalyzerDE that includes a generic
retention time (RT)-segmented approach compatible with a wide range
of global normalization approaches to reduce the effects of time-resolved
bias. The software offers straightforward access to multiple normalization
methods, allows for data set evaluation and normalization quality
assessment as well as subsequent or independent differential expression
analysis using the empirical Bayes Limma approach. When evaluated
on two spike-in data sets the RT-segmented approaches outperformed
conventional approaches by detecting more peptides (8–36%)
without loss of precision. Furthermore, differential expression analysis
using the Limma approach consistently increased recall (2–35%)
compared to analysis of variance. The combination of RT-normalization
and Limma was in one case able to distinguish 108% (2597 vs 1249)
more spike-in peptides compared to traditional approaches. NormalyzerDE
provides widely usable tools for performing normalization and evaluating
the outcome and makes calculation of subsequent differential expression
statistics straightforward. The program is available as a web server
at .
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