198 research outputs found
Noise-induced oscillatory shuttling of NF-{\kappa}B in a two compartment IKK-NF-{\kappa}B-I{\kappa}B-A20 signaling model
NF-{\kappa}B is a pleiotropic protein whose nucleo-cytoplasmic trafficking is
tightly regulated by multiple negative feedback loops embedded in the
NF-{\kappa}B signaling network and contributes to diverse gene expression
profiles important in immune cell differentiation, cell apoptosis, and innate
immunity. The intracellular signaling processes and their control mechanisms,
however, are susceptible to both extrinsic and intrinsic noise. In this
article, we present numerical evidence for a universal dynamic behavior of
NF-{\kappa}B, namely oscillatory nucleo-cytoplasmic shuttling, due to the
fundamentally stochastic nature of the NF-{\kappa}B signaling network. We
simulated the effect of extrinsic noise with a deterministic ODE model, using a
statistical ensemble approach, generating many copies of the signaling network
with different kinetic rates sampled from a biologically feasible parameter
space. We modeled the effect of intrinsic noise by simulating the same networks
stochastically using the Gillespie algorithm. The results demonstrate that
extrinsic noise diversifies the shuttling patterns of NF-{\kappa}B response,
whereas intrinsic noise induces oscillatory behavior in many of the otherwise
non-oscillatory patterns. We identify two key model parameters which
significantly affect the NF-{\kappa}B dynamic response and deduce a
two-dimensional phase-diagram of the NF-{\kappa}B response as a function of
these parameters. We conclude that if single-cell experiments are performed, a
rich variety of NF-{\kappa}B response will be observed, even if
population-level experiments, which average response over large numbers of
cells, do not evidence oscillatory behavior.Comment: 49 pages, 12 figure
Random forests with random projections of the output space for high dimensional multi-label classification
We adapt the idea of random projections applied to the output space, so as to
enhance tree-based ensemble methods in the context of multi-label
classification. We show how learning time complexity can be reduced without
affecting computational complexity and accuracy of predictions. We also show
that random output space projections may be used in order to reach different
bias-variance tradeoffs, over a broad panel of benchmark problems, and that
this may lead to improved accuracy while reducing significantly the
computational burden of the learning stage
Sensitivity analysis of a computational model of the IKK-NF-{\kappa}B-I{\kappa}B{\alpha}-A20 signal transduction network
The NF-{\kappa}B signaling network plays an important role in many different
compartments of the immune system during immune activation. Using a
computational model of the NF-{\kappa}B signaling network involving two
negative regulators, I{\kappa}B{\alpha} and A20, we performed sensitivity
analyses with three different sampling methods and present a ranking of the
kinetic rate variables by the strength of their influence on the NF-{\kappa}B
signaling response. We also present a classification of temporal response
profiles of nuclear NF-{\kappa}B concentration into six clusters, which can be
regrouped to three biologically relevant clusters. Lastly, based upon the
ranking, we constructed a reduced network of the
IKK-NF-{\kappa}B-I{\kappa}B{\alpha}-A20 signal transduction.Comment: 32 pages, 8 figure
A constructive approach for discovering new drug leads: Using a kernel methodology for the inverse-QSAR problem
<p>Abstract</p> <p>Background</p> <p>The inverse-QSAR problem seeks to find a new molecular descriptor from which one can recover the structure of a molecule that possess a desired activity or property. Surprisingly, there are very few papers providing solutions to this problem. It is a difficult problem because the molecular descriptors involved with the inverse-QSAR algorithm must adequately address the forward QSAR problem for a given biological activity if the subsequent recovery phase is to be meaningful. In addition, one should be able to construct a feasible molecule from such a descriptor. The difficulty of recovering the molecule from its descriptor is the major limitation of most inverse-QSAR methods.</p> <p>Results</p> <p>In this paper, we describe the reversibility of our previously reported descriptor, the vector space model molecular descriptor (VSMMD) based on a vector space model that is suitable for kernel studies in QSAR modeling. Our inverse-QSAR approach can be described using five steps: (1) generate the VSMMD for the compounds in the training set; (2) map the VSMMD in the input space to the kernel feature space using an appropriate kernel function; (3) design or generate a new point in the kernel feature space using a kernel feature space algorithm; (4) map the feature space point back to the input space of descriptors using a pre-image approximation algorithm; (5) build the molecular structure template using our VSMMD molecule recovery algorithm.</p> <p>Conclusion</p> <p>The empirical results reported in this paper show that our strategy of using kernel methodology for an inverse-Quantitative Structure-Activity Relationship is sufficiently powerful to find a meaningful solution for practical problems.</p
Novel techniques for automorphism group computation
Graph automorphism (GA) is a classical problem, in which the objective is to compute the automorphism group of an input graph.
In this work we propose four novel techniques to speed up algorithms that solve the GA problem by exploring a search tree. They increase the performance of the algorithm by allowing to reduce the depth of the search tree, and by effectively pruning it.
We formally prove that a GA algorithm that uses these techniques correctly computes the automorphism group of the input graph. We also describe how the techniques have been incorporated into the GA algorithm conauto, as conauto-2.03, with at most an additive polynomial increase in its asymptotic time complexity.
We have experimentally evaluated the impact of each of the above techniques with several graph families. We have observed that each of the techniques by itself significantly reduces the number of processed nodes of the search tree in some subset of graphs, which justifies the use of each of them. Then, when they are applied together, their effect is combined, leading to reductions in the number of processed nodes in most graphs. This is also reflected in a reduction of the running time, which is substantial in some graph families
Visual Network Analysis of Dynamic Metabolic Pathways
Abstract. We extend our previous work on the exploration of static metabolic
networks to evolving, and therefore dynamic, pathways. We apply our visualization software to data from a simulation of early metabolism. Thereby, we show
that our technique allows us to test and argue for or against different scenarios for
the evolution of metabolic pathways. This supports a profound and efficient analysis of the structure and properties of the generated metabolic networks and its
underlying components, while giving the user a vivid impression of the dynamics
of the system. The analysis process is inspired by Ben Shneiderman’s mantra of
information visualization. For the overview, user-defined diagrams give insight
into topological changes of the graph as well as changes in the attribute set associated with the participating enzymes, substances and reactions. This way, “interesting features” in time as well as in space can be recognized. A linked view
implementation enables the navigation into more detailed layers of perspective
for in-depth analysis of individual network configuration
Learning a peptide-protein binding affinity predictor with kernel ridge regression
We propose a specialized string kernel for small bio-molecules, peptides and
pseudo-sequences of binding interfaces. The kernel incorporates
physico-chemical properties of amino acids and elegantly generalize eight
kernels, such as the Oligo, the Weighted Degree, the Blended Spectrum, and the
Radial Basis Function. We provide a low complexity dynamic programming
algorithm for the exact computation of the kernel and a linear time algorithm
for it's approximation. Combined with kernel ridge regression and SupCK, a
novel binding pocket kernel, the proposed kernel yields biologically relevant
and good prediction accuracy on the PepX database. For the first time, a
machine learning predictor is capable of accurately predicting the binding
affinity of any peptide to any protein. The method was also applied to both
single-target and pan-specific Major Histocompatibility Complex class II
benchmark datasets and three Quantitative Structure Affinity Model benchmark
datasets.
On all benchmarks, our method significantly (p-value < 0.057) outperforms the
current state-of-the-art methods at predicting peptide-protein binding
affinities. The proposed approach is flexible and can be applied to predict any
quantitative biological activity. The method should be of value to a large
segment of the research community with the potential to accelerate
peptide-based drug and vaccine development.Comment: 22 pages, 4 figures, 5 table
EC-BLAST: a tool to automatically search and compare enzyme reactions.
We present EC-BLAST (http://www.ebi.ac.uk/thornton-srv/software/rbl/), an algorithm and Web tool for quantitative similarity searches between enzyme reactions at three levels: bond change, reaction center and reaction structure similarity. It uses bond changes and reaction patterns for all known biochemical reactions derived from atom-atom mapping across each reaction. EC-BLAST has the potential to improve enzyme classification, identify previously uncharacterized or new biochemical transformations, improve the assignment of enzyme function to sequences, and assist in enzyme engineering
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