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EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats
(Peer reviewed; Journal article, 2013)Motivation: Advancing the search, publication and integration of bioinformatics tools and resources demands consistent machineunderstandable descriptions. A comprehensive ontology allowing such descriptions is therefore ... 
Editing to Eulerian Graphs
(Conference object, 2014)We investigate the problem of modifying a graph into a connected graph in which the degree of each vertex satisfies a prescribed parity constraint. Let ea, ed and vd denote the operations edge addition, edge deletion and ... 
Efficient CRISPRCas9mediated generation of knockin human pluripotent stem cells lacking undesired mutations at the targeted locus
(Peer reviewed; Journal article, 201505)The CRISPRCas9 system has the potential to revolutionize genome editing in human pluripotent stem cells (hPSCs), but its advantages and pitfalls are still poorly understood. We systematically tested the ability of CRISPRCas9 ... 
Efficient hash maps to G2 on BLS curves
(Journal article; Peer reviewed, 2020)When a pairing e:G1×G2→GT, on an elliptic curve E defined over a finite field Fq, is exploited for an identitybased protocol, there is often the need to hash binary strings into G1 and G2. Traditionally, if E admits a ... 
Efficient implementation of LowMC in HElib
(Master thesis, 20180619)LowMC is a symmetric block cipher designed for fully homomorphic encryption. This thesis focuses on Martin Albrecht’s implementation of the cipher in the FHE library HElib, and how his implementation can be improved when ... 
Efficiently Locating Schema Incompatibilities in an eXtensible Markup Language
(Master thesis, 2003) 
Efforts towards accessible and reliable bioinformatics
(Doctoral thesis, 20151119)The aim of the presented work was contributing to making scientific computing more accessible, reliable, and thus more efficient for researchers, primarily computational biologists and molecular biologists. Many approaches ... 
Elastic Grid Resources using Cloud Technologies
(Master thesis, 20140602)A Large Ion Collider Experiment (ALICE) is one of four experiments at the Large Hadron Collider (LHC) at CERN. The detectors in the ALICE experiment produce data at a rate of 4 GB/s after being filtered and compressed ... 
The EMBRACE web service collection
(Peer reviewed; Journal article, 20100510)The EMBRACE (European Model for Bioinformatics Research and Community Education) web service collection is the culmination of a 5year project that set out to investigate issues involved in developing and deploying web ... 
Employing Deep Learning for Fish Recognition
(Master thesis, 20180821)Underwater imagery processing is in high demand, but the unrestricted environment makes it difficult to develop methods for analyzing it. Not only is obtaining a dataset for a single species difficult, but there are reported ... 
Energyscale Aware Feature Extraction for Flow Visualization
(Peer reviewed; Journal article, 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 ... 
Enhancing Content Management in DPG
(Master thesis, 20131120)This thesis analyzes the usability aspects of PCE and implements a new Single Page Application that attempts to solve this issues 
An Ensemble Feature Selection Framework Integrating Stability
(Chapter; Conference object; Peer reviewed, 2019)Ensemble feature selection has drawn more and more attention in recent years. There are mainly two strategies for ensemble feature selection, namely data perturbation and function perturbation. Data perturbation performs ... 
Enumerating minimal connected dominating sets in graphs of bounded chordality
(Conference object; Peer reviewed; Journal article, 2015)Listing, generating or enumerating objects of specified type is one of the principal tasks in algorithmics. In graph algorithms one often enumerates vertex subsets satisfying a certain property. We study the enumeration ... 
Error Detection and Correction for Symmetric and Asymmetric Channels
(Doctoral thesis, 20070827)When a message is sent over a channel errors can occur due to noise during the transmission. So it is very important to know the error correction and detection capability of the code, which is used to encode the message. ... 
ETHtight algorithms for long path and cycle on unit disk graphs
(Journal article; Peer reviewed, 2020)We present an algorithm for the extensively studied Long Path and Long Cycle problems on unit disk graphs that runs in time 2O(√k)(n + m). Under the Exponential Time Hypothesis, Long Path and Long Cycle on unit disk graphs ... 
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 ... 
Exact algorithms for MAX2SAT and MAX3SAT via multidimensional matrix multiplication
(Master thesis, 20150601)In this thesis it is showed how an \(O(n^{4\epsilon})\) algorithm for the cube multiplication problem (that is defined in the thesis) would imply a faster than naive \(O^{*}(2^{n(1\frac{\epsilon}{4})})\) algorithm for ... 
Exact algorithms for treewidth and minimum fillin
(Journal article, 2006) 
Exact and approximate digraph bandwidth
(Journal article; Peer reviewed, 2019)In this paper, we introduce a directed variant of the classical Bandwidth problem and study it from the viewpoint of moderately exponential time algorithms, both exactly and approximately. Motivated by the definitions of ...