Browsing Department of Informatics by Document Types "Peer reviewed"
Now showing items 1-20 of 244
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Accurate analysis of genuine CRISPR editing events with ampliCan
(Peer reviewed; Journal article, 2019)We present ampliCan, an analysis tool for genome editing that unites highly precise quantification and visualization of genuine genome editing events. ampliCan features nuclease-optimized alignments, filtering of experimental ... -
Additive Schwarz preconditioner for the finite volume element discretization of symmetric elliptic problems
(Peer reviewed; Journal article, 2015-09-25)A symmetric and a nonsymmetric variant of the additive Schwarz preconditioner are proposed for the solution of a class of finite volume element discretization of the symmetric elliptic problem in two dimensions, with large ... -
Analysis of Trivium Using Compressed Right Hand Side Equations
(Chapter; Peer reviewed, 2012)We study a new representation of non-linear multivariate equations for algebraic cryptanalysis. Using a combination of multiple right hand side equations and binary decision diagrams, our new representation allows a very ... -
An Approach to Flexible Multilevel Modelling
(Peer reviewed; Journal article, 2018-07-12)Multilevel modelling approaches tackle issues related to lack of flexibility and mixed levels of abstraction by providing features like deep modelling and linguistic extension. However, the lack of a clear consensus on ... -
Approximating Acyclicity Parameters of Sparse Hypergraphs
(Conference object; Peer reviewed; Journal article, 2009)The notions of hypertree width and generalized hypertree width were introduced by Gottlob, Leone, and Scarcello (PODS'99, PODS'01) in order to extend the concept of hypergraph acyclicity. These notions were further generalized ... -
Approximating cube roots of integers, after Heron’s Metrica III.20
(Peer reviewed; Journal article, 2013) -
Approximation algorithms in combinatorial scientific computing
(Journal article; Peer reviewed, 2019)We survey recent work on approximation algorithms for computing degreeconstrained subgraphs in graphs and their applications in combinatorial scientific computing. The problems we consider include maximization versions of ... -
Associations Between Natural Physiological and Supraphysiological Estradiol Levels and Stress Perception
(Peer reviewed; Journal article, 2019-06-11)Stress is a risk factor for impaired general, mental, and reproductive health. The role of physiological and supraphysiological estradiol concentrations in stress perception and stress processing is less well understood. ... -
The Atlantic salmon genome provides insights into rediploidization
(Peer reviewed; Journal article, 2016-05)The whole-genome duplication 80 million years ago of the common ancestor of salmonids (salmonid-specific fourth vertebrate whole-genome duplication, Ss4R) provides unique opportunities to learn about the evolutionary fate ... -
Automatic interpretation of otoliths using deep learning
(Peer reviewed; Journal article, 2018-12-17)The age structure of a fish population has important implications for recruitment processes and population fluctuations, and is a key input to fisheries-assessment models. The current method of determining age structure ... -
Axiom-Based Transformations: Optimisation and Testing
(Peer reviewed; Journal article, 2009-10-10)Programmers typically have knowledge about properties of their programs that aren't explicitly expressed in the code properties that may be very useful for, e.g., compiler optimisation and automated testing. Although ... -
Axis patterning by BMPs: cnidarian network reveals evolutionary constraints
(Peer reviewed; Journal article, 2015-03)BMP signaling plays a crucial role in the establishment of the dorso-ventral body axis in bilaterally symmetric animals. However, the topologies of the bone morphogenetic protein (BMP) signaling networks vary drastically ... -
B-chromatic number: Beyond NP-hardness
(Conference object; Peer reviewed; Journal article, 2015)The b-chromatic number of a graph G, chi_b(G), is the largest integer k such that G has a k-vertex coloring with the property that each color class has a vertex which is adjacent to at least one vertex in each of the other ... -
Balanced judicious bipartition is fixed-parameter tractable
(Journal article; Peer reviewed, 2019)The family of judicious partitioning problems, introduced by Bollobás and Scott to the field of extremal combinatorics, has been extensively studied from a structural point of view for over two decades. This rich realm of ... -
Binding Leverage as a Molecular Basis for Allosteric Regulation
(Peer reviewed; Journal article, 2011-09-15)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 the ... -
The bio.tools registry of software tools and data resources for the life sciences
(Peer reviewed; Journal article, 2019-08-12)Bioinformaticians and biologists rely increasingly upon workflows for the flexible utilization of the many life science tools that are needed to optimally convert data into knowledge. We outline a pan-European enterprise ... -
BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains
(Peer reviewed; Journal article, 2014-02-05)Abstract The application of semantic technologies to the integration of biological data and the interoperability of bioinformatics analysis and visualization tools has been the common theme of a series of annual BioHackathons ... -
BioXSD: the common data-exchange format for everyday bioinformatics web services
(Peer reviewed; Journal article, 2010)Motivation: The world-wide community of life scientists has access to a large number of public bioinformatics databases and tools, which are developed and deployed using diverse technologies and designs. More and more of ... -
Bisection of Bounded Treewidth Graphs by Convolutions
(Journal article; Peer reviewed, 2019)In the Bisection problem, we are given as input an edge-weighted graph G. The task is to find a partition of V(G) into two parts A and B such that ||A| - |B|| <= 1 and the sum of the weights of the edges with one endpoint ... -
Blind search for post-translational modifications and amino acid substitutions using peptide mass fingerprints from two proteases
(Peer reviewed; Journal article, 2008-12-19)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 ...