Related papers: Some inverse problems in biophysics
In this study, we explore how the combination of synthetic biology, neuroscience modeling, and neuromorphic electronic systems offers a new approach to creating an artificial system that mimics the natural sense of smell. We argue that a…
Four chapters of the synthesis represent four major areas of my research interests: 1) data analysis in molecular biology, 2) mathematical modeling of biological networks, 3) genome evolution, and 4) cancer systems biology. The first…
This thesis is designed to be a self-contained exposition of the neurobiological and mathematical aspects of sensory perception, memory, and learning with a bias towards olfaction. The final chapters introduce a new approach to modeling…
The concepts and methods of Systems Biology are being extended to neuropharmacology, to test and design drugs against neurological and psychiatric disorders. Computational modeling by integrating compartmental neural modeling technique and…
These are notes for a set of 7 two-hour lectures given at the 2010 Summer School on Quantitative Evolutionary and Comparative Genomics at OIST, Okinawa, Japan. The emphasis is on understanding how biological systems process information. We…
Advances in neural sensing technology are making it possible to observe the olfactory process in great detail. In this paper, we conceptualize smell from a Data Science and AI perspective, that relates the properties of odorants to how they…
The dynamics of biological systems, from proteins to cells to organisms, is complex and stochastic. To decipher their physical laws, we need to bridge between experimental observations and theoretical modeling. Thanks to progress in…
Despite recent molecular technique improvements, biological knowledge remains incomplete. Reasoning on living systems hence implies to integrate heterogeneous and partial informations. Although current investigations successfully focus on…
Combination therapies are often needed for effective clinical outcomes in the management of complex diseases, but presently they are generally based on empirical clinical experience. Here we suggest a novel application of search algorithms,…
Exploiting the information provided by the molecular noise of a biological process has proven to be valuable in extracting knowledge about the underlying kinetic parameters and sources of variability from single cell measurements. However,…
Biology has taken strong steps towards becoming a computer science aiming at reprogramming nature after the realisation that nature herself has reprogrammed organisms by harnessing the power of natural selection and the digital prescriptive…
Recent experimental advances in neuroscience have opened new vistas into the immense complexity of neuronal networks. This proliferation of data challenges us on two parallel fronts. First, how can we form adequate theoretical frameworks…
Multi-agent systems have emerged as a powerful paradigm for automating scientific discovery. To differentiate agent behavior in the multi-agent system, current frameworks typically assign generic role-based personas such as ''reviewer'' or…
We study the build up of complexity on the example of 1 kg matter in different forms. We start on the simplest example of ideal gases, and then continue with more complex chemical, biological, life and social and technical structures. We…
Network inference approaches are now widely used in biological applications to probe regulatory relationships between molecular components such as genes or proteins. Many methods have been proposed for this setting, but the connections and…
The analysis of live-cell single-molecule imaging experiments can reveal valuable information about the heterogeneity of transport processes and interactions between cell components. These characteristics are seen as motion changes in the…
The Chapter starts with introductory information about quantitative linguistics notions, like rank--frequency dependence, Zipf's law, frequency spectra, etc. Similarities in distributions of words in texts with level occupation in quantum…
Studies of insect olfactory processing indicate that odors are represented by rich spatio-temporal patterns of neural activity. These patterns are very difficult to predict a priori, yet they are stimulus specific and reliable upon repeated…
In systems biology, it is common to measure biochemical entities at different levels of the same biological system. One of the central problems for the data fusion of such data sets is the heterogeneity of the data. This thesis discusses…
Genomes may be analyzed from an information viewpoint as very long strings, containing functional elements of variable length, which have been assembled by evolution. In this work an innovative information theory based algorithm is…