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ObjectiveBipartite graphs are widely used to model relationships between pairs of heterogeneous data types. Maximal bicliques are foundational structures in such graphs, and their enumeration is an important task in systems biology, epidemiology and many other problem domains. Thus, there is a need for an efficient, general purpose, publicly available tool to enumerate maximal bicliques in bipartite graphs. The statistical programming language R is a logical choice for such a tool, but until now no R package has existed for this purpose. Our objective is to provide such a package, so that the research community can more easily perform this computationally demanding task.ResultsBiclique is an R package that takes as input a bipartite graph and produces a listing of all maximal bicliques in this graph. Input and output formats are straightforward, with examples provided both in this paper and in the package documentation. Biclique employs a state-of-the-art algorithm previously developed for basic research in functional genomics. This package, along with its source code and reference manual, are freely available from the CRAN public repository at https://cran.r-project.org/web/packages/biclique/index.html.

Fermentation of pulses as a clean processing technique has been reported to have a favorable impact on the functional and nutritional quality of the starting materials. Compared to commonly fermented pulses such as peas and chickpeas, limited information is available on the effect of fermentation on lentils, especially when using a high protein isolate (>80% protein) as compared to seeds or flours. Therefore, in the present work, lentil protein isolate was used as a feedstock for submerged fermentation with Aspergillus niger, Aspergillus oryzae, or Lactobacillus plantarum. After 48 h, the samples showed increased protein content with enhanced solubility and oil‐holding capacity. Controlled fermentation, as opposed to spontaneous fermentation, maintained the high foaming capacity; however, all fermented samples had lower foam and emulsion stabilizing properties and reduced water‐holding capacity compared to the control. The fermented proteins were also less digestible, possibly due to an increase in phenolics and saponins. New volatile compounds were identified in fermented samples that show promise for improved sensory attributes. Significant differences were observed in specific quality attributes depending on the microbial strain used. Further research is required to better understand the fermentative metabolism of microbial communities when provided high‐protein lentil ingredients as growth substrates. Practical Application: Fermented lentil protein isolate has promising flavor profiles that may improve its sensory properties for food application. [ABSTRACT FROM AUTHOR]

Background and Objectives: There has been a significant increase in the use of fermentation for protein modification by the food industry. This research aimed to investigate the use of solid‐state fermentation (SSF) by Aspergillus oryzae NRRL 5590 on pea and navy bean protein isolates (PPI and NBPI, respectively) to enhance their physicochemical and functional properties. Findings: The impact of fermentation was more profound on PPI than NBPI with a higher degree of hydrolysis achieved for the former (9.3% vs. 4.4%). Fermented PPI had significantly increased protein content, surface charge and hydrophobicity, solubility, and foaming properties, but decreased emulsion stability. For NBPI, modifications were only observed for surface hydrophobicity and water hydration capacity (WHC), which both increased after fermentation. Overall, navy bean proteins were less susceptible to protein hydrolysis than pea proteins upon fermentation, possibly due to the phaseolin protein in navy bean. Conclusions: In summary, fermentation may be used to enhance the solubility and foaming properties of PPI and WHC of NBPI for their use as ingredients in applications where such higher functionalities are favorable. Significance and Novelty: The results provide insights into pulse protein modification by bioprocessing, specifically fermentation, and opportunities for potential value‐added applications for pea and navy bean proteins. [ABSTRACT FROM AUTHOR]

Background and Objectives: Fermentation has been increasingly used as a "clean" processing technique to modify proteins. The goal of this research was to assess the use of solid‐state fermentation (SSF) by Aspergillus oryzae on pea (pea protein isolate [PPI]) and navy bean protein isolates (NBPI) for different time periods (0–48 or 0−72 h, respectively) and its impact on their nutrition and volatile profile. Findings: The SSF process resulted in higher total phenolic content and lower protein digestibility, and consequently, the protein quality was reduced for both pulses. The quantity of the volatile compounds initially present in the samples did not change substantially after SSF; however, many new compounds were identified in fermented PPI, which have been reported to have pleasant sensory properties. Conclusions: The protein quality of PPI or NBPI was not improved by A. oryzae SSF; however, the results suggest the potential for using SSF to positively modify the volatile profile of PPI. Significance and Novelty: The findings of this research strengthened our knowledge base of fermented pulse ingredients with the use of protein isolates and navy beans, narrowing the somewhat limited gap for fermentation application to high protein substrates. [ABSTRACT FROM AUTHOR]