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The male germ cell gene regulator CTCFL is functionally different from CTCF and binds CTCFlike consensus sites in a nucleosome compositiondependent manner
(Peer reviewed; Journal article, 20120618)Background: CTCF is a highly conserved and essential zinc finger protein expressed in virtually all cell types. In conjunction with cohesin, it organizes chromatin into loops, thereby regulating gene expression and epigenetic ... 
Managing spatial selections with contextual snapshots
(Peer reviewed; Journal article, 201412)Spatial selections are a ubiquitous concept in visualization. By localizing particular features, they can be analysed and compared in different views. However, the semantics of such selections often depend on specific ... 
MassAnalyzer, a program to help find labeled peptides and compare them to their unlabeled counterparts in a SILAC experiment
(Master thesis, 20081127)Mass spectrometry(MS) have become an increasingly popular analysis method for high throughput experiments on proteins in biology. SILAC(stable isotope labeling by amino acids in cell culture) is a method within MS that ... 
MassSorter: a tool for administrating and analyzing data from mass spectrometry experiments on proteins with known amino acid sequences
(Peer reviewed; Journal article, 20060126)Background: Proteomics is the study of the proteome, and is critical to the understanding of cellular processes. Two central and related tasks of proteomics are protein identification and protein characterization. Many ... 
Mathematical modelling of nitric oxide/cyclic GMP/cyclic AMP signalling in platelets
(Peer reviewed; Journal article, 20180219)Platelet activation contributes to normal haemostasis but also to pathologic conditions like stroke and cardiac infarction. Signalling by cGMP and cAMP inhibit platelet activation and are therefore attractive targets for ... 
A matrixfree method for regularisation with unrestricted variables
(Master thesis, 2008)In this thesis a method for the partially norm constrained least squares problem is presented. The method relies on a largescale trustregion solver and has a low storage requirement. A combination of image misalignment ... 
Maximum matching width: New characterizations and a fast algorithm for dominating set
(Conference object; Peer reviewed; Journal article, 2015)We give alternative definitions for maximum matching width, e.g., a graph G has mmw(G) <= k if and only if it is a subgraph of a chordal graph H and for every maximal clique X of H there exists A,B,C \subseteq X with A ... 
Maximum number of edges in graph classes under degree and matching constraints
(Master thesis, 20150512)In extremal graph theory, we ask how large or small a property of a graph can be, when the graph has to satisfy certain constraints. In this thesis, we ask how many edges a graph can have with restrictions on its degree ... 
Maximum number of objects in graph classes.
(Master thesis, 20150531)The focus of this thesis is the study and implementation of two exact exponential time algorihms. These algorihms finds and lists the number of minimal dominating sets and the number of minimal subset feedback vertex sets ... 
MedUse: A Visual Analysis Tool for Medication Use Data in the ABCD Study
(Peer reviewed; Journal article, 2019)The RxNorm vocabulary is a yearlypublished biomedical resource providing normalized names for medications. It is used to capture medication use in the Adolescent Brain Cognitive Development (ABCD) study, an active and ... 
Memento: Localized time‐warping for spatio‐temporal selection
(Peer reviewed; Journal article, 2020)Interaction techniques for temporal data are often focused on affecting the spatial aspects of the data, for instance through the use of transfer functions, camera navigation or clipping planes. However, the temporal aspect ... 
The mersenne low hamming combination search problem can be reduced to an ILP problem
(Lecture Notes in Computer Science, Chapter; Peer reviewed; Journal article, 2019)In 2017, Aggarwal, Joux, Prakash, and Santha proposed an innovative NTRUlike publickey cryptosystem that was believed to be quantum resistant, based on Mersenne prime numbers q=2N−1 . After a successful attack designed ... 
Methods for analysing 2D electrophoretic gel images
(Master thesis, 2002) 
MimWidth II. The Feedback Vertex Set Problem
(Peer reviewed; Journal article, 2020)We give a first polynomialtime algorithm for (WEIGHTED) FEEDBACK VERTEX SET on graphs of bounded maximum induced matching width (mimwidth). Explicitly, given a branch decomposition of mimwidth w, we give an nO(w)time ... 
MimWidth III. Graph powers and generalized distance domination problems
(Peer reviewed; Journal article, 2019)We generalize the family of (σ,ρ) problems and locally checkable vertex partition problems to their distance versions, which naturally captures wellknown problems such as Distancer Dominating Set and Distancer Independent ... 
Minimizing Fillin Size and Elimination Tree Height in Parallel Cholesky Factorization
(Master thesis, 1992) 
Minimum Fillin of Sparse Graphs: Kernelization and Approximation
(Conference object; Peer reviewed; Journal article, 2011)The Minimum Fillin problem is to decide if a graph can be triangulated by adding at most k edges. The problem has important applications in numerical algebra, in particular in sparse matrix computations. We develop ... 
A minimum requiring angle trisection
(Peer reviewed; Journal article, 2009) 
Model Checking Healthcare Workflows Using Alloy
(Conference object; Peer reviewed, 2014)Workflows are used to organize business processes, and workflow management tools are used to guide users in which order these processes should be performed. These tools increase organizational efficiency and enable users ... 
Model Checking with the SweepLine Method
(Master thesis, 20170621)Explicitstate model checking is a formal software verification technique that differs from peer review and unit testing, in that model checking does an exhaustive state space search. With model checking one takes a system ...