Recent Submissions

• ThermoRawFileParser: Modular, Scalable, and Cross-Platform RAW File Conversion ﻿

(Journal article; Peer reviewed, 2020)
The field of computational proteomics is approaching the big data age, driven both by a continuous growth in the number of samples analyzed per experiment as well as by the growing amount of data obtained in each analytical ...
• Path contraction faster than $2^n$ ﻿

(Journal article; Peer reviewed, 2020)
A graph $G$ is contractible to a graph $H$ if there is a set $X \subseteq E(G)$, such that $G/X$ is isomorphic to $H$. Here, $G/X$ is the graph obtained from $G$ by contracting all the edges in $X$. For a family of graphs ...
• Accuracy and efficiency of germline variant calling pipelines for human genome data ﻿

(Journal article; Peer reviewed, 2020)
Advances in next-generation sequencing technology have enabled whole genome sequencing (WGS) to be widely used for identification of causal variants in a spectrum of genetic-related disorders, and provided new insight into ...
• Dynamics-function relationship in the catalytic domains of N-terminal acetyltransferases ﻿

(Journal article; Peer reviewed, 2020)
N-terminal acetyltransferases (NATs) belong to the superfamily of acetyltransferases. They are enzymes catalysing the transfer of an acetyl group from acetyl coenzyme A to the N-terminus of polypeptide chains. N-terminal ...
• Model-Driven Automatic Question Generation for a Gamified Clinical Guideline Training System ﻿

(Journal article; Peer reviewed, 2020)
Clinical practice guidelines (CPGs) are a cornerstone of modern medical practice since they summarize the vast medical literature and provide care recommendations based on the current best evidence. However, there are ...
• IsoTrotter: Visually Guided Empirical Modelling of Atmospheric Convection ﻿

(Journal article; Peer reviewed, 2020)
Empirical models, fitted to data from observations, are often used in natural sciences to describe physical behaviour and support discoveries. However, with more complex models, the regression of parameters quickly becomes ...
• Partitioning a graph into degenerate subgraphs ﻿

(Journal article; Peer reviewed, 2020-01)
Let G = (V, E) be a connected graph with maximum degree k ≥ 3 distinct from Kk+1. Given integers s ≥ 2 and p1, . . . , ps ≥ 0, G is said to be (p1, . . . , ps)-partitionable if there exists a partition of V into sets ...
• Relative Persistent Homology ﻿

(Journal article; Peer reviewed, 2020)
The alpha complex efficiently computes persistent homology of a point cloud X in Euclidean space when the dimension d is low. Given a subset A of X, relative persistent homology can be computed as the persistent homology ...
• On shared use of renewable stocks ﻿

(Journal article; Peer reviewed, 2020)
Considered here is multi-party exploitation of common property, renewable resources. The parties play various dynamic games differing in degree of cooperation and commitment. Comparisons of steady states clarify issues on ...
• 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 ...