• 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 ...
    • 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 ...
    • FreeContact: fast and free software for protein contact prediction from residue co-evolution 

      Kaján, László; Hopf, Thomas A.; Kalaš, Matúš; Marks, Debora S.; Rost, Burkhard (Peer reviewed; Journal article, 2014-03-26)
      Background: 20 years of improved technology and growing sequences now renders residue-residue contact constraints in large protein families through correlated mutations accurate enough to drive de novo predictions of protein ...
    • Highlights from the Eighth International Society for Computational Biology (ISCB) Student Council Symposium 2012 

      Goncearenco, Alexander; Grynberg, Priscila; Botvinnik, Olga B.; Macintyre, Geoff; Abeel, Thomas (Peer reviewed; Journal article, 2012-12-14)
      Abstract The report summarizes the scientific content of the annual symposium organized by the Student Council of the International Society for Computational Biology (ISCB) held in conjunction with the Intelligent Systems ...
    • Identifying elemental genomic track types and representing them uniformly 

      Gundersen, Sveinung; Kalaš, Matúš; Abul, Osman; Frigessi, Arnoldo; Hovig, Eivind; Sandve, Geir Kjetil (Peer reviewed; Journal article, 2011-12-30)
      Background: With the recent advances and availability of various high-throughput sequencing technologies, data on many molecular aspects, such as gene regulation, chromatin dynamics, and the three-dimensional organization ...
    • Interactive Exploration of Ligand Transportation through Protein Tunnels 

      Furmanova, Katarina; Jaresova, Miroslava; Byska, Jan; Jurcik, Adam; Parulek, Julius; Hauser, Helwig; Kozlikova, Barbora (Peer reviewed; Journal article, 2017-02-15)
      Background: Protein structures and their interaction with ligands have been in the focus of biochemistry and structural biology research for decades. The transportation of ligand into the protein active site is often complex ...
    • Interactively illustrating polymerization using three-level model fusion 

      Kolesar, Ivan; Parulek, Julius; Viola, Ivan; Bruckner, Stefan; Stavrum, Anne-Kristin; Hauser, Helwig (Peer reviewed; Journal article, 2014-10-14)
      Background: Research in cell biology is steadily contributing new knowledge about many aspects of physiological processes, both with respect to the involved molecular structures as well as their related function. Illustrations ...
    • RASflow: an RNA-Seq analysis workflow with Snakemake 

      Zhang, Xiaokang; Jonassen, Inge (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 ...
    • SBMLmod: a Python-based web application and web service for efficient data integration and model simulation 

      Schäuble, Sascha; Stavrum, Anne-Kristin; Bockwoldt, Mathias; Puntervoll, Pål; Heiland, Ines (Peer reviewed; Journal article, 2017-06-24)
      Background: Systems Biology Markup Language (SBML) is the standard model representation and description language in systems biology. Enriching and analysing systems biology models by integrating the multitude of available ...
    • A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB 

      Rayner, Tim F.; Rocca-Serra, Philippe; Spellman, Paul T.; Causton, Helen C.; Farne, Anna; Holloway, Ele; Irizarry, Rafael A.; Liu, Junmin; Maier, Donald S.; Miller, Michael; Petersen, Kjell; Quackenbush, John; Sherlock, Gavin; Stoeckert, Christian J. Jr; White, Joseph; Whetzel, Patricia L.; Wymore, Farrell; Parkinson, Helen; Sarkans, Ugis; Ball, Catherine A.; Brazma, Alvis (Peer reviewed; Journal article, 2006-11-06)
      Background: Sharing of microarray data within the research community has been greatly facilitated by the development of the disclosure and communication standards MIAME and MAGEML by the MGED Society. However, the complexity ...
    • TMM@: a web application for the analysis of transmembrane helix mobility 

      Skjærven, Lars; Jonassen, Inge; Reuter, Nathalie (Peer reviewed; Journal article, 2007-07-02)
      Background: To understand the mechanism by which a protein transmits a signal through the cell membrane, an understanding of the flexibility of its transmembrane (TM) region is essential. Normal Mode Analysis (NMA) has ...
    • Visual Cavity Analysis in Molecular Simulations 

      Parulek, Julius; Turkay, Cagatay; Reuter, Nathalie; Viola, Ivan (Peer reviewed; Journal article, 2013-11-12)
      Molecular surfaces provide a useful mean for analyzing interactions between biomolecules; such as identification and characterization of ligand binding sites to a host macromolecule. We present a novel technique, which ...
    • XHM: A system for detection of potential cross hybridizations in DNA microarrays 

      Flikka, Kristian; Yadetie, Fekadu; Lægreid, Astrid; Jonassen, Inge (Peer reviewed; Journal article, 2004-08-27)
      Background: Microarrays have emerged as the preferred platform for high throughput gene expression analysis. Cross-hybridization among genes with high sequence similarities can be a source of error reducing the reliability ...