Search results for "Quantitative Biology::Genomics"
showing 9 items of 39 documents
Additional file 2: of Where is the limit of prostate cancer biomarker research? Systematic investigation of potential prognostic and diagnostic bioma…
2019
Table S1 Pairwise comparison of the gene expression of normal and tumor tissue using negative binomial generalized log-linear model and correction for false discovery rate (FDR). (TXT 2100 kb)
Nonequilibrium thermodynamics of the RNA-RNA interaction underlying a genetic transposition program
2021
Thermodynamic descriptions are powerful tools to formally study complex gene expression programs evolved in living cells on the basis of macromolecular interactions. While transcriptional regulations are often modeled in the equilibrium, other interactions that occur in the cell follow a more complex pattern. Here, we adopt a nonequilibrium thermodynamic scheme to explain the RNA-RNA interaction underlying IS10 transposition. We determine the energy landscape associated with such an interaction at the base-pair resolution, and we present an original scaling law for expression prediction that depends on different free energies characterizing that landscape. Then, we show that massive experim…
Embedding Evolution in Epidemic-Style Forwarding
2007
International audience; In this work, we introduce a framework to let forwarding schemes evolve in order to adapt to changing and a priori unknown environments. The framework is inspired by genetic algorithms: at each node a genotype describes the forwarding scheme used, a selection process fosters the diffusion of the fittest genotypes in the system and new genotypes are created by combining existing ones or applying random changes. A case study implementation is presented and its performance evaluated via numerical simulations.
Additional file 4 of Development and validation of prediction model to estimate 10-year risk of all-cause mortality using modern statistical learning…
2021
Additional file 4. Distributions of the variables at baseline before and after multiple imputations.
Conjugate and cut loci in averaged orbital transfer
2006
The objective of this Note is to describe the conjugate and cut loci associated with the averaged energy minimization problem in coplanar orbit transfer.
Expanding genetic graphs' potential to analyse ecological connectivity: assessment of graphs construction methods
2019
International audience; Dispersal movements are often constrained in human-shaped landscapes, thereby threatening species survival. Landscape genetics approaches are commonly used to analyse ecological connectivity because genetic data well reflect dispersal capacities. When species occupy discrete habitat patches, graph-theoretic methods are a particularly relevant approach to study dispersal-driven gene flow. The links of a genetic graph can be weighted using different genetic distances between populations (nodes). Similarly, graph pruning (link set selection) can rely on different criteria. However, despite growing interest in genetic graphs, the influence of these parameters remains mos…
Sorting of Enhanced Reference Raman Spectra of a Single Amino Acid Molecule
2014
In this contribution, we report the identification of the principal reference Raman spectra of a single cystein molecule. To that purpose, we design an active Surface Enhanced Raman Spectroscopy (SERS) template based on surfactant-less Chebyshev nanoparticles operating in a microfluidic platform. A principal component analysis is obtained from fluctuating spectra to sort the reference spectra of cystein. The assignment of Raman bands brings new insight into the conformation of an amino acid adsorbed onto gold nanoparticle.
Cyclobutane Pyrimidine Photodimerization of DNA/RNA Nucleobases in the Triplet State
2010
The photoinduced formation of cyclobutane pyrimidine dimers in the triplet excited state of the DNA/RNA pyrimidine nucleobases pairs has been studied at the CASPT2 level of theory. A stepwise mechanism through the triplet state of the homodimer is proposed for the pairs of nucleobases cytosine, thymine, and uracil involving a singlet−triplet crossing intermediary structure of biradical character representing the most favorable triplet state conformation of the nucleobases as found in the DNA environment. The efficiency of the mechanism will be modulated by two factors: the effectiveness of the triplet−triplet energy transfer process from a donor photosensitizer molecule, which relates to th…
Analysing gene flow in heterogeneous landscapes: why and how to use genetic graphs?
2019
International audience; In heterogeneous landscapes, when species occupy discrete habitat patches, ecological connectivity is influenced by populations’ topology. Graph-theoretic methods constitute a relevant tool to reveal this topology and better analyse gene flow. Despite growing interest in genetic graphs, a better understanding of when and how to use them is lacking.To fill this gap, we simulated gene flow between 50 populations in different landscape configurations and constructed genetic graphs using various genetic distances and pruning (link selection) methods. We then compared metrics derived from these graphs to analogous metrics describing the topology and connectivity of the di…