IID 2021: towards context-specific protein interaction analyses by increased coverage, enhanced annotation and enrichment analysis
M Kotlyar, C Pastrello, Z Ahmed, J Chee… - Nucleic acids …, 2022 - academic.oup.com
Improved bioassays have significantly increased the rate of identifying new protein-protein
interactions (PPIs), and the number of detected human PPIs has greatly exceeded early …
interactions (PPIs), and the number of detected human PPIs has greatly exceeded early …
Functional annotation of hypothetical proteins from the Exiguobacterium antarcticum strain B7 reveals proteins involved in adaptation to extreme environments …
WLO da Costa, CLA Araújo, LM Dias, LCS Pereira… - PloS one, 2018 - journals.plos.org
Exiguobacterium antarcticum strain B7 is a psychrophilic Gram-positive bacterium that
possesses enzymes that can be used for several biotechnological applications. However …
possesses enzymes that can be used for several biotechnological applications. However …
PrimAlign: PageRank-inspired Markovian alignment for large biological networks
Motivation Cross-species analysis of large-scale protein–protein interaction (PPI) networks
has played a significant role in understanding the principles deriving evolution of cellular …
has played a significant role in understanding the principles deriving evolution of cellular …
In silico functional annotation of hypothetical proteins from the Bacillus paralicheniformis strain Bac84 reveals proteins with biotechnological potentials and …
MA Rahman, UH Heme, MAK Parvez - Plos one, 2022 - journals.plos.org
Members of the Bacillus genus are industrial cell factories due to their capacity to secrete
significant quantities of biomolecules with industrial applications. The Bacillus …
significant quantities of biomolecules with industrial applications. The Bacillus …
Volta: adVanced mOLecular neTwork analysis
Motivation Network analysis is a powerful approach to investigate biological systems. It is
often applied to study gene co-expression patterns derived from transcriptomics …
often applied to study gene co-expression patterns derived from transcriptomics …
Screening strategies for biosurfactant discovery
The isolation and screening of bacteria and fungi for the production of surface-active
compounds has been the basis for the majority of the biosurfactants discovered to date …
compounds has been the basis for the majority of the biosurfactants discovered to date …
Data-driven network alignment
S Gu, T Milenković - PloS one, 2020 - journals.plos.org
In this study, we deal with the problem of biological network alignment (NA), which aims to
find a node mapping between species' molecular networks that uncovers similar network …
find a node mapping between species' molecular networks that uncovers similar network …
Multiscale Graph Comparison via the Embedded Laplacian Discrepancy
Laplacian eigenvectors capture natural community structures on graphs and are widely
used in spectral clustering and manifold learning. The use of Laplacian eigenvectors as …
used in spectral clustering and manifold learning. The use of Laplacian eigenvectors as …
MONACO: accurate biological network alignment through optimal neighborhood matching between focal nodes
Motivation Alignment of protein–protein interaction networks can be used for the
unsupervised prediction of functional modules, such as protein complexes and signaling …
unsupervised prediction of functional modules, such as protein complexes and signaling …
TOPAS: network-based structural alignment of RNA sequences
Motivation For many RNA families, the secondary structure is known to be better conserved
among the member RNAs compared to the primary sequence. For this reason, it is important …
among the member RNAs compared to the primary sequence. For this reason, it is important …