• Blind search for post-translational modifications and amino acid substitutions using peptide mass fingerprints from two proteases 

      Barsnes, Harald; Mikalsen, Svein-Ole; Eidhammer, Ingvar (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 ...
    • Block-Diagonal and LT Codes for Distributed Computing with Straggling Servers 

      Severinson, Albin; Graell i Amat, Alexandre; Rosnes, Eirik (Peer reviewed; Journal article, 2019-03)
      We propose two coded schemes for the distributed computing problem of multiplying a matrix by a set of vectors. The first scheme is based on partitioning the matrix into submatrices and applying maximum distance separable ...
    • Caligus rogercresseyi acetylcholinesterase types and variants: a potential marker for organophosphate resistance 

      Agusti-Ridaura, Celia; Dondrup, Michael; Horsberg, Tor Einar; Leong, Jong S; Koop, Ben F; Bravo, Sandra; Mendoza, Julio; Kaur, Kiranpreet (Peer reviewed; Journal article, 2018-10-30)
      Background Control of the sea louse Caligus rogercresseyi in the Chilean salmonid industry is reliant on chemical treatments. Azamethiphos was introduced in 2013, although other organophosphates were previously used. In ...
    • CCZ-equivalence of bent vectorial functions and related constructions 

      Budaghyan, Lilya; Carlet, Claude (Peer reviewed; Journal article, 2011-01-06)
      We observe that the CCZ-equivalence of bent vectorial functions over F2nFn2 (n even) reduces to their EA-equivalence. Then we show that in spite of this fact, CCZ-equivalence can be used for constructing bent functions ...
    • Characteristics of 454 pyrosequencing data—enabling realistic simulation with flowsim 

      Balzer, Susanne Mignon; Malde, Ketil; Lanzén, Anders; Sharma, Animesh; Jonassen, Inge (Peer reviewed; Journal article, 2010)
      Motivation: The commercial launch of 454 pyrosequencing in 2005was a milestone in genome sequencing in terms of performance and cost. Throughout the three available releases, average read lengths have increased to ∼500 ...
    • Characteristics of Pyrosequencing Data – Analysis, Methods, and Tools 

      Balzer, Susanne Mignon (Doctoral thesis; Peer reviewed, 2013-06-17)
      The introduction of this thesis provides background knowledge on the 454 sequencing technology and a detailed review of the most relevant sequencing artifacts. Chapter 1 puts the 454 sequencing technology into a historical ...
    • CHOPCHOP v3: expanding the CRISPR web toolbox beyond genome editing 

      Labun, Kornel; Montague, Tessa G.; Krause, Maximilian; Torres Cleuren, Yamila Nicole; Tjeldnes, Håkon; Valen, Eivind (Peer reviewed; Journal article, 2019-07-02)
      The CRISPR–Cas system is a powerful genome editing tool that functions in a diverse array of organisms and cell types. The technology was initially developed to induce targeted mutations in DNA, but CRISPR–Cas has now been ...
    • Chromatin accessibility established by Pou5f3, Sox19b and Nanog primes genes for activity during zebrafish genome activation 

      Pálfy, Máté; Schulze, Gunnar; Valen, Eivind; Vastenhouw, Nadine L. (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 ...
    • Chromatin and epigenetic features of long-range gene regulation 

      Harmston, Nathan; Lenhard, Boris (Peer reviewed; Journal article, 2013-06-13)
      The precise regulation of gene transcription during metazoan development is controlled by a complex system of interactions between transcription factors, histone modifications and modifying enzymes and chromatin conformation. ...
    • Classifying and Measuring Student Problems and Misconceptions 

      Rosbach, Alexander Hoem; Bagge, Anya Helene (Norsk informatikkonferanse, Chapter; Peer reviewed, 2013)
      In this paper we report on an attempt to classify student problems and mistakes, and measuring the frequency of particular problems in a firstsemester programming course. We also propose a scheme for annotating student ...
    • Clustering to Given Connectivities 

      Golovach, Petr; Thilikos, Dimitrios M. (Peer reviewed; Journal article, 2019)
      We define a general variant of the graph clustering problem where the criterion of density for the clusters is (high) connectivity. In Clustering to Given Connectivities, we are given an n-vertex graph G, an integer k, and ...
    • Coherent Conformational Degrees of Freedom as a Structural Basis for Allosteric Communication 

      Mitternacht, Simon; Berezovsky, Igor N. (Peer reviewed; Journal article, 2011-12-08)
      Conformational changes in allosteric regulation can to a large extent be described as motion along one or a few coherent degrees of freedom. The states involved are inherent to the protein, in the sense that they are visited ...
    • Combining Aspect-Oriented and Strategic Programming 

      Kalleberg, Karl Trygve; Visser, Eelco (Peer reviewed; Journal article, 2006-01)
      Properties such as logging, persistence, debugging, tracing, distribution, performance monitoring and exception handling occur in most programming paradigms and are normally very difficult or even impossible to modularizewith ...
    • Community curation of bioinformatics software and data resources 

      Ison, Jon; Ménager, Hervé; Brancotte, Bryan; Jaaniso, Erik; Salumets, Ahto; Raček, Tomáš; Lamprecht, Anna-Lena; Palmblad, Magnus; Kalaš, Matúš; Chmura, Piotr; Hancock, John M; Schwämmle, Veit; Ienasescu, Hans-Ioan (Peer reviewed; Journal article, 2019)
      The corpus of bioinformatics resources is huge and expanding rapidly, presenting life scientists with a growing challenge in selecting tools that fit the desired purpose. To address this, the European Infrastructure for ...
    • Community Detection on the GPU 

      Naim, Md.; Manne, Fredrik; Halappanavar, Mahantesh; Tumeo, Antonino (Conference object; Peer reviewed, 2017)
      We present and evaluate a new GPU algorithm based on the Louvain method for community detection. Our algorithm is the first for this problem that parallelizes the access to individual edges. In this way we can fine tune ...
    • Community-driven development for computational biology at Sprints, Hackathons and Codefests 

      Möller, Steffen; Afgan, Enis; Banck, Michael; Bonnal, Raoul J. P.; Booth, Timothy; Chilton, John; Cock, Peter J. A.; Gumbel, Markus; Harris, Nomi; Holland, Richard; Kalaš, Matúš; Kaján, László; Kibukawa, Eri; Powel, David R.; Prins, Pjotr; Quinn, Jacqueline; Sallou, Olivier; Strozzi, Francesco; Seemann, Torsten; Sloggett, Clare; Soiland-Reyes, Stian; Spooner, William; Steinbiss, Sascha; Tille, Andreas; Travis, Anthony J.; Guimera, Roman V.; Katayama, Toshiaki; Chapman, Brad A. (Peer reviewed; Journal article, 2014-11-27)
      Background: Computational biology comprises a wide range of technologies and approaches. Multiple technologies can be combined to create more powerful workflows if the individuals contributing the data or providing tools ...
    • A Comparative Analysis of Feature Selection Methods for Biomarker Discovery in Study of Toxicant-Treated Atlantic Cod (Gadus Morhua) Liver 

      Zhang, Xiaokang; Jonassen, Inge (Chapter; Conference object; Peer reviewed, 2019)
      Univariate and multivariate feature selection methods can be used for biomarker discovery in analysis of toxicant exposure. Among the univariate methods, differential expression analysis (DEA) is often applied for its ...
    • Comparative Visualization of Protein Secondary Structures 

      Kocincova, Lucia; Jaresova, Miroslava; Byska, Jan; Parulek, Julius; Hauser, Helwig; Kozlikova, Barbora (Peer reviewed; Journal article, 2017-02-15)
      Background: Protein function is determined by many factors, namely by its constitution, spatial arrangement, and dynamic behavior. Studying these factors helps the biochemists and biologists to better understand the protein ...
    • Comparison of Discrete and Continuous Models for the Pooling Problem 

      Alfaki, Mohammed; Haugland, Dag (Chapter; Peer reviewed, 2011)
      The pooling problem is an important global optimization problem which is encountered in many industrial settings. It is traditionally modeled as a bilinear, nonconvex optimization problem, and solved by branch-and-bound ...
    • A complexity dichotomy for critical values of the b-chromatic number of graphs 

      Jaffke, Lars; Lima, Paloma T. (Peer reviewed; Journal article, 2019-08-20)
      A b-coloring of a graph G is a proper coloring of its vertices such that each color class contains a vertex that has at least one neighbor in all the other color classes. The b-Coloring problem asks whether a graph G has ...