Related papers: In silico evidence of the relationship between miR…
RNAs play crucial and versatile roles in biological processes. Computational prediction approaches can help to understand RNA structures and their stabilizing factors, thus providing information on their functions, and facilitating the…
My analysis uses methods developed for data mining microarray experiments, adapted for ageing research. Methods bridge knowledge of statistical mechanics with data mining methods developed in statistical mathematics. Analyses can reveal how…
Regulatory interactions between genes show a large amount of cross-species variability, even when the underlying functions are conserved: There are many ways to achieve the same function. Here we investigate the ability of regulatory…
Synthetic reverberating activity patterns are experimentally generated by stimulation of a subset of neurons embedded in a spontaneously active network of cortical cells in-vitro. The neurons are artificially connected by means of…
Phase-separated biomolecular condensates containing proteins and RNAs can assemble into higher-order structures by forming thermodynamically stable interfaces between immiscible phases. Using a minimal model of a protein/RNA interaction…
Intermittent control has a long history in the physiological literature and there is strong experimental evidence that some human control systems are intermittent. Intermittent control has also appeared in various forms in the engineering…
Understanding the complexity of biological neural networks like the human brain is one of the scientific challenges of our century. The organization of the brain can be described at different levels, ranging from small neural networks to…
RNA secondary structure prediction and classification are two important problems in the field of RNA biology. Here, we propose a new permutation based approach to create logical non-disjoint clusters of different secondary structures of a…
Whether, when, and how causal interactions between neurons can be meaningfully studied from observations of neural activity alone are vital questions in neural data analysis. Here we aim to better outline the concept of functional…
The predictive properties of a retina are studied by measuring the mutual information (MI) between its stimulation and the corresponding firing rates while it is being probed by a train of short pulses with stochastic intervals. Features of…
We investigate various versions of multi-dimensional systems involving many species, modeling aggregation phenomena through nonlocal interaction terms. We establish a rigorous connection between kinetic and macroscopic descriptions by…
Navigation of microorganisms is controlled by internal processes ultimately sensitive to mechanical or chemical signaling encountered along the path. In many natural environments, such as porous soils or physiological ducts, motile species…
Networks represent relationships between entities in many complex systems, spanning from online social interactions to biological cell development and brain connectivity. In many cases, relationships between entities are unambiguously…
The set of regulatory interactions between genes, mediated by transcription factors, forms a species' transcriptional regulatory network (TRN). By comparing this network with measured gene expression data one can identify functional…
Multielectrode arrays allow recording of the activity of many single neurons, from which correlations can be calculated. The functional roles of correlations can be revealed by the measures of the information conveyed by neuronal activity;…
The living-together of distinct organisms in a single termite nest along with the termite builder colony, is emblematic in its ecological and evolutionary significance. On top of preserving biodiversity, these interspecific and…
In recent studies, non-coding protein RNAs have been identified as microRNA that can be used as biomarkers for early diagnosis and treatment of cancer, that decrease mortality in cancer. A microRNA may target hundreds or thousands of genes…
This paper is about creating digital musical instruments where a predictive neural network model is integrated into the interactive system. Rather than predicting symbolic music (e.g., MIDI notes), we suggest that predicting future control…
The intrinsic stochasticity of gene expression is usually mitigated in higher eukaryotes by post-transcriptional regulation channels that stabilise the output layer, most notably protein levels. The discovery of small non-coding RNAs…
A non-linear Penner type interaction is introduced and studied in the random matrix model of homo-RNA. The asymptotics in length of the partition function is discussed for small and large $N$ (size of matrix). The interaction doubles the…