Related papers: Redundancies in Large-scale Protein Interaction Ne…
Numerous experiments demonstrate a high level of promiscuity and structural disorder in organismal proteomes. Here we ask the question what makes a protein promiscuous, i.e., prone to non-specific interactions, and structurally disordered.…
Inferring the structural properties of a protein from its amino acid sequence is a challenging yet important problem in biology. Structures are not known for the vast majority of protein sequences, but structure is critical for…
Understanding why some cellular components are conserved across species, while others evolve rapidly is a key question of modern biology. Here we demonstrate that in S. cerevisiae proteins organized in cohesive patterns of interactions are…
A critical task in systems biology is the identification of genes that interact to control cellular processes by transcriptional activation of a set of target genes. Many methods have been developed to use statistical correlations in…
Mutualistic interactions, which are beneficial for both interacting species, are recurrently present in ecosystems. Observations of natural systems showed that, if we draw mutualistic relationships as binary links between species, the…
Our work is motivated by and illustrated with application of association networks in computational biology, specifically in the context of gene/protein regulatory networks. Association networks represent systems of interacting elements,…
Network theorists have developed methods to characterize the complex interactions in natural phenomena. The structure of the network of interactions between proteins is important in the field of proteomics, and has been subject to intensive…
Central to the functioning of a living cell is its ability to control the readout or expression of information encoded in the genome. In many cases, a single transcription factor protein activates or represses the expression of many genes.…
We predict analytically that diagonal correlations of amino acid positions within protein sequences statistically enhance protein propensity for nonspecific binding. We use the term 'promiscuity' to describe such nonspecific binding.…
A major part of membrane function is conducted by proteins, both integral and peripheral. Peripheral membrane proteins temporarily adhere to biological membranes, either to the lipid bilayer or to integral membrane proteins with…
Living systems rely on coordinated molecular interactions, especially those related to gene expression and protein activity. The Unfolded Protein Response is a crucial mechanism in eukaryotic cells, activated when unfolded proteins exceed a…
The characterization of drug-protein interactions is crucial in the high-throughput screening for drug discovery. The deep learning-based approaches have attracted attention because they can predict drug-protein interactions without…
Fluctuations in the measured mRNA levels of unperturbed cells under fixed conditions have often been viewed as an impediment to the extraction of information from expression profiles. Here, we argue that such expression fluctuations should…
We generalize a sampling algorithm for lattice animals (connected clusters on a regular lattice) to a Monte Carlo algorithm for `graph animals', i.e. connected subgraphs in arbitrary networks. As with the algorithm in [N. Kashtan et al.,…
Biological networks have so many possible states that exhaustive sampling is impossible. Successful analysis thus depends on simplifying hypotheses, but experiments on many systems hint that complicated, higher order interactions among…
Popular online enrichment analysis tools from the field of molecular systems biology provide users with the ability to submit their experimental results as gene sets for individual analysis. Such queries are kept private, and have never…
The majority of mammalian genomic transcripts do not directly code for proteins and it is currently believed that most of these are not under evolutionary constraint. However given the abundance non-coding RNA (ncRNA) and its strong…
The native conformation of structured proteins is stabilized by a complex network of interactions. We analyzed the elementary patterns that constitute such network and ranked them according to their importance in shaping protein sequence…
Statistical analysis of evolutionary-related protein sequences provides insights about their structure, function, and history. We show that Restricted Boltzmann Machines (RBM), designed to learn complex high-dimensional data and their…
Protein-protein interactions (PPIs) are crucial in regulating numerous cellular functions, including signal transduction, transportation, and immune defense. As the accuracy of multi-chain protein complex structure prediction improves, the…