Department of Informatics
Recent Submissions
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Evolution and developmental system drift in the endoderm gene regulatory network of Caenorhabditis and other nematodes
(Journal article; Peer reviewed, 2020)Developmental gene regulatory networks (GRNs) underpin metazoan embryogenesis and have undergone substantial modification to generate the tremendous variety of animal forms present on Earth today. The nematode Caenorhabditis ... -
RASflow: an RNA-Seq analysis workflow with Snakemake
(Journal article; Peer reviewed, 2020)Background With the cost of DNA sequencing decreasing, increasing amounts of RNA-Seq data are being generated giving novel insight into gene expression and regulation. Prior to analysis of gene expression, the RNA-Seq ... -
Typical Sequences Revisited – Computing Width Parameters of Graphs
(Journal article; Peer reviewed, 2020)In this work, we give a structural lemma on merges of typical sequences, a notion that was introduced in 1991 [Lagergren and Arnborg, Bodlaender and Kloks, both ICALP 1991] to obtain constructive linear time parameterized ... -
Algorithmic Complexity of Clustering and Low-Rank Approximation Problems
(Doctoral thesis, 2021-03-29)The two most popular unsupervised learning problems are k-Clustering and Low-Rank Approximation. Consider a set of n datapoints, in the k-Clustering problem, the objective is to partition these points into k clusters and ... -
ReCodLiver0.9: Overcoming Challenges in Genome-Scale Metabolic Reconstruction of a Non-model Species
(Journal article; Peer reviewed, 2020-11)The availability of genome sequences, annotations, and knowledge of the biochemistry underlying metabolic transformations has led to the generation of metabolic network reconstructions for a wide range of organisms in ... -
Profiling of Small Ribosomal Subunits Reveals Modes and Regulation of Translation Initiation
(Journal article; Peer reviewed, 2020)Translation initiation is often attributed as the rate-determining step of eukaryotic protein synthesis and key to gene expression control. Despite this centrality, the series of steps involved in this process is poorly ... -
Learning Description Logic Ontologies: Five Approaches. Where Do They Stand?
(Journal article; Peer reviewed, 2020)The quest for acquiring a formal representation of the knowledge of a domain of interest has attracted researchers with various backgrounds into a diverse field called ontology learning. We highlight classical machine ... -
Chromatin accessibility established by Pou5f3, Sox19b and Nanog primes genes for activity during zebrafish genome activation
(Journal article; Peer reviewed, 2020-01)In many organisms, early embryonic development is driven by maternally provided factors until the controlled onset of transcription during zygotic genome activation. The regulation of chromatin accessibility and its ... -
Subgraph Complementation
(Journal article; Peer reviewed, 2020-02)A subgraph complement of the graph G is a graph obtained from G by complementing all the edges in one of its induced subgraphs. We study the following algorithmic question: for a given graph G and graph class G, is there ... -
Fast and accurate CNN-based brushing in scatterplots
(Journal article; Peer reviewed, 2018)Brushing plays a central role in most modern visual analytics solutions and effective and efficient techniques for data selection are key to establishing a successful human‐computer dialogue. With this paper, we address ... -
Quantitative Externalization of Visual Data Analysis Results Using Local Regression Models
(Journal article; Peer reviewed, 2017)Both interactive visualization and computational analysis methods are useful for data studies and an integration of both approaches is promising to successfully combine the benefits of both methodologies. In interactive ... -
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 ... -
Personalized Sketch-Based Brushing in Scatterplots
(Journal article; Peer reviewed, 2019)Brushing is at the heart of most modern visual analytics solutions and effective and efficient brushing is crucial for successful interactive data exploration and analysis. As the user plays a central role in brushing, ... -
Complexity of the Steiner Network Problem with Respect to the Number of Terminals
(Journal article; Peer reviewed, 2019)In the Directed Steiner Network problem we are given an arc-weighted digraph G, a set of terminals T subseteq V(G) with |T|=q, and an (unweighted) directed request graph R with V(R)=T. Our task is to output a subgraph H ... -
On KDE-based brushing in scatterplots and how it compares to CNN-based brushing
(Chapter, 2019)In this paper, we investigate to which degree the human should be involved into the model design and how good the empirical model can be with more careful design. To find out, we extended our previously published Mahalanobis ... -
Parameterized complexity classification of deletion to list matrix-partition for low-order matrices
(Journal article; Peer reviewed, 2019)Given a symmetric l x l matrix M=(m_{i,j}) with entries in {0,1,*}, a graph G and a function L : V(G) - > 2^{[l]} (where [l] = {1,2,...,l}), a list M-partition of G with respect to L is a partition of V(G) into l parts, ... -
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 ... -
Packing cycles faster than Erdos-Posa
(Journal article; Peer reviewed, 2019)The Cycle Packing problem asks whether a given undirected graph $G=(V,E)$ contains $k$ vertex-disjoint cycles. Since the publication of the classic Erdös--Pósa theorem in 1965, this problem received significant attention ... -
Rank vertex cover as a natural problem for algebraic compression
(Journal article; Peer reviewed, 2019)The question of the existence of a polynomial kernelization of the Vertex Cover Above LP problem was a long-standing, notorious open problem in parameterized complexity. Some years ago, the breakthrough work by Kratsch and ... -
Packing arc-disjoint cycles in tournaments
(Journal article; Peer reviewed, 2019)A tournament is a directed graph in which there is a single arc between every pair of distinct vertices. Given a tournament T on n vertices, we explore the classical and parameterized complexity of the problems of determining ...
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