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Predicting Fixation Tendencies of the H3N2 Influenza Virus by Free Energy Calculation
Fixation Tendencies of the H3N2 Influenza Virus Free Energy Calculation Biomolecules
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2012/5/2
Influenza virus evolves to escape from immune system antibodies that bind to it. We used free energy calculations with Einstein crystals as reference states to calculate the difference of antibody bin...
Modeling coupled transcription, translation and degradation and miRNA-based regulation of this process
Modeling coupled transcription miRNA-based regulation of this process Molecular Networks
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2012/5/2
The translation-transcription process with the description of the most basic "elementary" processes consists in: 1) production of mRNA molecules, 2) initiation of these molecules by circularization wi...
Synthetic spatially graded Rac activation drives directed cell polarization and locomotion
Synthetic spatially graded Rac directed cell polarization and locomotion Molecular Networks
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2012/5/2
Migrating cells possess intracellular gradients of Rho GTPases, but it is unknown whether these shallow gradients themselves can induce motility. Here we describe a new method to present cells with in...
Jerarca: Efficient Analysis of Complex Networks Using Hierarchical Clustering
Jerarca Efficient Analysis of Complex Networks Hierarchical Clustering Molecular Networks
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2012/5/2
How to extract useful information from complex biological networks is a major goal in many fields, especially in genomics and proteomics. We have shown in several works that iterative hierarchical clu...
Nonspecific Protein-DNA Binding Is Widespread in the Yeast Genome
Nonspecific protein-DNA binding Free energy of nonspecific protein-DNA binding Biomolecules
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2012/5/2
Recent genome-wide measurements of binding preferences of ~200 transcription regulators in the vicinity of transcription start sites in yeast, have provided a unique insight into the cis- regulatory c...
Switching between oscillations and homeostasis in competing negative and positive feedback motifs
negative feedback positive feedback oscillation noise circadian rhythm
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2012/5/2
We analyze a class of network motifs in which a short, two-node positive feed- back motif is inserted in a three-node negative feedback loop. We demonstrate that such networks can undergo a bifurcatio...
Asymptotic distribution of motifs in a stochastic context-free grammar model of RNA folding
Asymptotic distribution of motifs stochastic context-free grammar model of RNA folding Biomolecules
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2012/5/2
We analyze the distribution of RNA secondary structures given by the Knudsen-Hein stochastic context-free grammar used in the prediction program Pfold. We prove that the distribution of base pairs, he...
Stochastic resonance in a self-repressing gene with transcriptional memory
Stochastic resonance self-repressing gene transcriptional memory Molecular Networks
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2012/4/28
Biochemical reaction networks are subjected to large fluctuations due to small molecule numbers, yet underlie reliable biological functions. Most theoretical approaches describe them as purely determi...
Protein sequence and structure: Is one more fundamental than the other?
Protein sequence and structure Biomolecules Soft Condensed Matter
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2012/4/28
We argue that protein native state structures reside in a novel "phase" of matter which confers on proteins their many amazing characteristics. This phase arises from the common features of all globul...
Soluble oligomerization provides a beneficial fitness effect on destabilizing mutations
Soluble oligomerization beneficial fitness effect destabilizing mutations Biomolecules
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2012/4/28
Mutations create the genetic diversity on which selective pressures can act, yet also create structural instability in proteins. How, then, is it possible for organisms to ameliorate mutation-induced ...
Autonomous motility of active filaments with nonlocal Stokesian hydrodynamics
Autonomous motility of active filaments nonlocal Stokesian hydrodynamics Biomolecules
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2012/5/3
We simulate the non-local Stokesian hydrodynamics of an elastic filament with a permanent distribution of stresslets along its contour. A bending instability of an initially straight filament induces ...
Multi-plectoneme phase of double-stranded DNA under torsion
Multi-plectoneme phase double-stranded DNA torsion Biomolecules
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2012/4/28
We use the worm-like chain model to study supercoiling of DNA under tension and torque. The model reproduces experimental data for a much broader range of forces, salt concentrations and contour lengt...
Continuous time Boolean modeling for biological signaling: application of Gillespie algorithm
Continuous time Boolean modeling biological signaling application of Gillespie algorithm Molecular Networks
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2012/4/28
This article presents an algorithm that allows modeling of biological networks in a qualitative framework with continuous time. Mathematical modeling is used as a systems biology tool to answer biolog...
McGenus: A Monte Carlo algorithm to predict RNA secondary structures with pseudoknots
McGenus Monte Carlo algorithm RNA secondary structures pseudoknots
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2012/4/28
We present McGenus, an algorithm to predict RNA secondary structures with pseudoknots. The method is based on a classification of RNA structures according to their topological genus. McGenus can treat...
Dynamic phenotypes as criteria for model discrimination: fold-change detection in R. sphaeroides
Dynamic phenotypes criteria model discrimination fold-change detection R. sphaeroides Molecular Networks
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2012/4/28
The chemotaxis pathway of the bacterium Rhodobacter sphaeroides has many similarities to the well-studied pathway in Escherichia coli. It exhibits robust adaptation and has several homologues of the l...