Now showing items 12-31 of 322

    • B-chromatic number: Beyond NP-hardness 

      Panolan, Fahad; Philip, Geevarghese; Saurabh, Saket (Dagstuhl Publishing, 2015)
      The b-chromatic number of a graph G, chi_b(G), is the largest integer k such that G has a k-vertex coloring with the property that each color class has a vertex which is adjacent to at least one vertex in each of the other ...
      Conference object
    • Binding Leverage as a Molecular Basis for Allosteric Regulation 

      Mitternacht, Simon; Berezovsky, Igor N. (Public Library of Science, 2011-09-15)
      Allosteric regulation involves conformational transitions or fluctuations between a few closely related states, caused by the binding of effector molecules. We introduce a quantity called binding leverage that measures ...
      Peer reviewedJournal article
    • BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains 

      Katayama, Toshiaki; Wilkinson, Mark D.; Aoki-Kinoshita, Kiyoko F.; Kawashima, Shuichi; Yamamoto, Yasunori; Yamaguchi, Atsuko; Okamoto, Shinobu; Kawano, Shin; Kim, Jin-Dong; Wang, Yue; Wu, Hongyan; Kano, Yoshinobu; Ono, Hiromasa; Bono, Hidemasa; Kocbek, Simon; Aerts, Jan; Akune, Yukie; Antezana, Erick; Arakawa, Kazuharu; Aranda, Bruno; Baran, Joachim; Bolleman, Jerven; Bonnal, Raoul J. P.; Buttigieg, Pier Luigi; Campbell, Matthew P.; Chen, Yi-an; Chiba, Hirokazu; Cock, Peter J. A.; Cohen, K. Bretonnel; Constantin, Alexandru; Duck, Geraint; Dumontier, Michel; Fujisawa, Takatomo; Fujiwara, Toyofumi; Goto, Naohisa; Hoehndorf, Robert; Igarashi, Yoshinobu; Itaya, Hidetoshi; Ito, Maori; Iwasaki, Wataru; Kalaš, Matúš; Katoda, Takeo; Kim, Taehong; Kokubu, Anna; Komiyama, Yusuke; Kotera, Masaaki; Laibe, Camille; Lapp, Hilmar; Lütteke, Thomas; Marshall, M. Scott; Mori, Takaaki; Mori, Hiroshi; Morita, Mizuki; Murakami, Katsuhiko; Nakao, Mitsuteru; Narimatsu, Hisashi; Nishide, Hiroyo; Nishimura, Yosuke; Nyström-Persson, Johan; Ogishima, Soichi; Okamura, Yasunobu; Okuda, Shujiro; Oshita, Kazuki; Packer, Nicki H; Prins, Pjotr; Ranzinger, Rene; Rocca-Serra, Philippe; Sansone, Susanna; Sawaki, Hiromichi; Shin, Sung-Ho; Splendiani, Andrea; Strozzi, Francesco; Tadaka, Shu; Toukach, Philip; Uchiyama, Ikuo; Umezaki, Masahito; Vos, Rutger; Whetzel, Patricia L.; Yamada, Issaku; Yamasaki, Chisato; Yamashita, Riu; York, William S.; Zmasek, Christian M.; Kawamoto, Shoko; Takagi, Toshihisa (BioMed Central, 2014-02-05)
      Abstract The application of semantic technologies to the integration of biological data and the interoperability of bioinformatics analysis and visualization tools has been the common theme of a series of annual ...
      Journal article
    • BioXSD: the common data-exchange format for everyday bioinformatics web services 

      Kalaš, Matúš; Puntervoll, Pål; Joseph, Alexandre; Bartaševičiūtė, Edita; Töpfer, Armin; Venkataraman, Prabakar; Pettifer, Steve; Bryne, Jan Christian; Ison, Jon; Blanchet, Christophe; Rapacki, Kristoffer; Jonassen, Inge (Oxford University Press, 2010)
      Motivation: The world-wide community of life scientists has access to a large number of public bioinformatics databases and tools, which are developed and deployed using diverse technologies and designs. More and more of ...
      Journal article
    • Blind search for post-translational modifications and amino acid substitutions using peptide mass fingerprints from two proteases 

      Barsnes, Harald; Mikalsen, Svein-Ole; Eidhammer, Ingvar (BioMed Central, 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 ...
      Journal articlePeer reviewed
    • Building Trust in Remote Internet Voting 

      Nestås, Lars Hopland (The University of Bergen, 2010-05-27)
      During the past decades, a lot of research has been done to create voting protocols and election systems that facilitate voting via the Internet. Many universities and private organizations are now using such systems for ...
      Master thesis
    • Case Studies in Constructive Mathematics 

      Parmann, Erik (The University of Bergen, 2016-01-22)
      The common theme in this thesis is the study of constructive provability: in particular we investigate aspects of finite sets and Kan simplicial sets from a constructive perspective. There are numerous definitions of ...
      Doctoral thesis
    • CCZ-equivalence of bent vectorial functions and related constructions 

      Budaghyan, Lilya; Carlet, Claude (Springer, 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 ...
      Peer reviewedJournal article
    • Characteristics of 454 pyrosequencing data—enabling realistic simulation with flowsim 

      Balzer, Susanne Mignon; Malde, Ketil; Lanzén, Anders; Sharma, Animesh; Jonassen, Inge (Oxford University Press, 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 ...
      Peer reviewedJournal article
    • Characteristics of Pyrosequencing Data – Analysis, Methods, and Tools 

      Balzer, Susanne Mignon (The University of Bergen, 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 ...
      Doctoral thesis
    • Choice of parameter for DP-based FPT algorithms: four case studies 

      Sæther, Sigve Hortemo (The University of Bergen, 2015-09-07)
      This thesis studies dynamic programming algorithms and structural parameters used when solving computationally hard problems. In particular, we look at algorithms that make use of structural decompositions to overcome ...
      Doctoral thesis
    • Chromatin and epigenetic features of long-range gene regulation 

      Harmston, Nathan; Lenhard, Boris (Oxford University Press (OUP), 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. ...
      Journal article
    • Classification of protein structures 

      Sætre, Narve (The University of Bergen, 1999-12)
      Master thesis
    • Classifying and Measuring Student Problems and Misconceptions 

      Rosbach, Alexander Hoem; Bagge, Anya Helene (Akademika forlag, 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 ...
    • Coding for passive RFID communication 

      Yang, Guang (The University of Bergen, 2012-08-31)
      This dissertation elaborates on channel coding for reliable communication in passive RFID systems. RFID applications have been developed and used widely. Since a passive RFID tag has no power requirements, passive RFID ...
      Doctoral thesis
    • Coherent Conformational Degrees of Freedom as a Structural Basis for Allosteric Communication 

      Mitternacht, Simon; Berezovsky, Igor N. (Public Library of Science, 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 ...
      Peer reviewedJournal article
    • Colluding Tags Attack on the ECC-based Grouping Proofs for Rfids 

      Abyaneh, Mohammad Reza Sohizadeh (The author, 2012)
      Recently, a new privacy-preserving elliptic curve based grouping proof protocol with colluding tag prevention( CTP) has been proposed. The CTP protocol is claimed to be resistant against colluding tags attacks in which ...
      Conference object
    • Combining Aspect-Oriented and Strategic Programming 

      Kalleberg, Karl Trygve; Visser, Eelco (Elsevier, 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 ...
      Journal article
    • Community Detection in Social Networks 

      Fasmer, Erlend Eindride (The University of Bergen, 2015-05-01)
      Social networks usually display a hierarchy of communities and it is the task of community detection algorithms to detect these communities and preferably also their hierarchical relationships. One common class of ...
      Master thesis
    • 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. (BioMed Central, 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 ...
      Journal article