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Analysis of Trivium Using Compressed Right Hand Side Equations
(Springer Berlin Heidelberg, 2012)We study a new representation of nonlinear multivariate equations for algebraic cryptanalysis. Using a combination of multiple right hand side equations and binary decision diagrams, our new representation allows a ... 
Binding Leverage as a Molecular Basis for Allosteric Regulation
(Public Library of Science, 20110915)Allosteric regulation involves conformational transitions or fluctuations between a few closely related states, caused by the binding of effector molecules. We introduce a quantity called binding leverage that measures ... 
Blind search for posttranslational modifications and amino acid substitutions using peptide mass fingerprints from two proteases
(BioMed Central, 20081219)Background: Mass spectrometric analysis of peptides is an essential part of protein identification and characterization, the latter meaning the identification of modifications and amino acid substitutions. There are two ... 
CCZequivalence of bent vectorial functions and related constructions
(Springer, 20110106)We observe that the CCZequivalence of bent vectorial functions over F2nFn2 (n even) reduces to their EAequivalence. Then we show that in spite of this fact, CCZequivalence can be used for constructing bent functions ... 
Characteristics of 454 pyrosequencing data—enabling realistic simulation with flowsim
(Oxford University Press, 2010)Motivation: The commercial launch of 454 pyrosequencing in 2005was a milestone in genome sequencing in terms of performance and cost. Throughout the three available releases, average read lengths have increased to ∼500 ... 
Coherent Conformational Degrees of Freedom as a Structural Basis for Allosteric Communication
(Public Library of Science, 20111208)Conformational changes in allosteric regulation can to a large extent be described as motion along one or a few coherent degrees of freedom. The states involved are inherent to the protein, in the sense that they are ... 
Comparison of Discrete and Continuous Models for the Pooling Problem
(Dagstuhl Publishing, 2011)The pooling problem is an important global optimization problem which is encountered in many industrial settings. It is traditionally modeled as a bilinear, nonconvex optimization problem, and solved by branchandbound ... 
Conserved BK ChannelProtein Interactions Reveal Signals Relevant to Cell Death and Survival
(Public Library of Science, 20111209)The largeconductance Ca2+activated K+ (BK) channel and its bsubunit underlie tuning in nonmammalian sensory or hair cells, whereas in mammals its function is less clear. To gain insights into species differences and ... 
Curve Density Estimates
(Blackwell Publishing Ltd., 20110628)In this work, we present a technique based on kernel density estimation for rendering smooth curves. With this approach, we produce uncluttered and expressive pictures, revealing frequency information about one, or, ... 
CurveCentric Volume Reformation for Comparative Visualization
(IEEE, 20091011)We present two visualization techniques for curvecentric volume reformation with the aim to create compelling comparative visualizations. A curvecentric volume reformation deforms a volume, with regards to a curve in ... 
Differential Fault Analysis of Trivium
(Springer Berlin Heidelberg, 2008)Trivium is a hardwareoriented stream cipher designed in 2005 by de Canni`ere and Preneel for the European project eStream, and it has successfully passed the first and the second phase of this project. Its design has ... 
Directed graph representation of halfrate additive codes over GF(4)
(Springer, 2010)We show that (n, 2n) additive codes over GF(4) can be represented as directed graphs. This generalizes earlier results on selfdual additive codes over GF(4), which correspond to undirected graphs. Graph representation ... 
Energyscale Aware Feature Extraction for Flow Visualization
(Blackwell Publishing Ltd., 2011)In the visualization of flow simulation data, feature detectors often tend to result in overly rich response, making some sort of filtering or simplification necessary to convey meaningful images. In this paper we present ... 
Filtering duplicate reads from 454 pyrosequencing data
(Oxford University Press, 2013)Motivation: Throughout the recent years, 454 pyrosequencing has emerged as an efficient alternative to traditional Sanger sequencing and is widely used in both de novo wholegenome sequencing and metagenomics. Especially ... 
Filtering of FTLE for Visualizing Spatial Separation in Unsteady 3D Flow
(Springer, 2012)In many cases, feature detection for flow visualization is structured in two phases: first candidate identification, and then filtering. With this paper, we propose to use the directional information contained in the ... 
Floating Fault Analysis of Trivium
(Springer Berlin Heidelberg, 2008)One of the eSTREAM final portfolio ciphers is the hardwareoriented stream cipher Trivium. It is based on 3 nonlinear feedback shift registers with a linear output function. Although Trivium has attached a lot of interest, ... 
Generating a synthetic diffusion tensor dataset
(IEEE, 2005)During the last years, many techniques for denoising, segmentation and fibertracking have been applied to diffusion tensor MR image data (DTI) from human and animal brains. However, evaluating such methods may be difficult ... 
A geometrybased generic predictor for catalytic and allosteric sites
(Oxford University Press, 2011)An important aspect of understanding protein allostery, and of artificial effector design, is the characterization and prediction of substrate and effectorbinding sites. To find binding sites in allosteric enzymes, many ... 
The Inclusion Problem for Regular Expressions
(Springer, 2010)This paper presents a new polynomialtime algorithm for the inclusion problem for certain pairs of regular expressions. The algorithm is not based on construction of finite automata, and can therefore be faster than the ... 
Lower bounds on the size of spheres of permutations under the Chebychev distance
(Springer, 2010)Lower bounds on the number of permutations p of {1, 2, . . . , n} satisfying pi − i ≤ d for all i are given