• The bio.tools registry of software tools and data resources for the life sciences 

      Ison, Jon; Ienasescu, Hans-Ioan; Chmura, Piotr; Rydza, Emil; Ménager, Hervé; Kalaš, Matúš; Schwämmle, Veit; Grüning, Björn A.; Beard, Niall; Lopez, Rodrigo; Duvaud, Severine; Stockinger, Heinz; Persson, Bengt; Svobodová Vařeková, Radka; Raček, Tomáš; Vondrášek, Jiří; Peterson, Hedi; Salumets, Ahto; Jonassen, Inge; et al., +18 authors (total 37) (Peer reviewed; Journal article, 2019-08-12)
      Bioinformaticians and biologists rely increasingly upon workflows for the flexible utilization of the many life science tools that are needed to optimally convert data into knowledge. We outline a pan-European enterprise ...
    • 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 (Peer reviewed; Journal article, 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 BioHackathons ...
    • Bioimage analysis workflows: community resources to navigate through a complex ecosystem [version 1; peer review: 2 approved] 

      Paul-Gilloteaux, Perrine; Tosi, Sébastien; Hériche, Jean-Karim; Gaignard, Alban; Ménager, Hervé; Marée, Raphaël; Baecker, Volker; Klemm, Anna; Kalaš, Matúš; Zhang, Chong; Miura, Kota; Colombelli, Julien (Journal article; Peer reviewed, 2021)
      Workflows are the keystone of bioimage analysis, and the NEUBIAS (Network of European BioImage AnalystS) community is trying to gather the actors of this field and organize the information around them. One of its most ...
    • Biomarker Discovery Using Statistical and Machine Learning Approaches on Gene Expression Data 

      Zhang, Xiaokang (Doctoral thesis, 2020-10-30)
      My PhD is affiliated with the dCod 1.0 project (https://www.uib.no/en/dcod): decoding the systems toxicology of Atlantic cod (Gadus morhua), which aims to better understand how cods adapt and react to the stressors in the ...
    • BioSimulators: a central registry of simulation engines and services for recommending specific tools 

      Shaikh, Bilal; Smith, Lucian P; Vasilescu, Dan; Marupilla, Gnaneswara; Wilson, Michael; Agmon, Eran; Agnew, Henry; Andrews, Steven S; Anwar, Azraf; Beber, Moritz E; Bergmann, Frank T; Brooks, David; Brusch, Lutz; Calzone, Laurence; Choi, Kiri; Cooper, Joshua; Detloff, John; Drawert, Brian; Dumontier, Michel; Ermentrout, G Bard; Faeder, James R; Freiburger, Andrew P; Fröhlich, Fabian; Funahashi, Akira; Garny, Alan; Gennari, John H; Gleeson, Padraig; Goelzer, Anne; Haiman, Zachary; Hasenauer, Jan; Hellerstein, Joseph L; Hermjakob, Henning; Hoops, Stefan; Ison, Jon C; Jahn, Diego; Jakubowski, Henry V; Jordan, Ryann; Kalaš, Matúš; König, Matthias; Liebermeister, Wolfram; Sheriff, Rahuman S. Malik; Mandal, Synchon; McDougal, Robert; Medley, J Kyle; Mendes, Pedro; Müller, Robert; Myers, Chris J; Naldi, Aurelien; Nguyen, Tung V. N; Nickerson, David P; Olivier, Brett G; Patoliya, Drashti; Paulevé, Loïc; Petzold, Linda R; Priya, Ankita; Rampadarath, Anand K; Rohwer, Johann M; Saglam, Ali S; Singh, Dilawar; Sinha, Ankur; Snoep, Jacky; Sorby, Hugh; Spangler, Ryan; Starruß, Jörn; Thomas, Payton J; Van Niekerk, David; Weindl, Daniel; Zhang, Fengkai; Zhukova, Anna; Goldberg, Arthur P; Schaff, James C; Blinov, Michael L; Sauro, Herbert M; Moraru, Ion I; Karr, Jonathan R (Journal article; Peer reviewed, 2022)
      Computational models have great potential to accelerate bioscience, bioengineering, and medicine. However, it remains challenging to reproduce and reuse simulations, in part, because the numerous formats and methods for ...
    • biotoolsSchema: a formalized schema for bioinformatics software description 

      Ison, Jon; Ienasescu, Hans; Rydza, Emil; Chmura, Piotr; Rapacki, Kristoffer; Gaignard, Alban; Schwämmle, Veit; van Helden, Jacques; Kalaš, Matúš; Ménager, Hervé (Journal article; Peer reviewed, 2021)
      Background Life scientists routinely face massive and heterogeneous data analysis tasks and must find and access the most suitable databases or software in a jungle of web-accessible resources. The diversity of information ...
    • 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 (Peer reviewed; Journal article, 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 ...
    • Bisection of Bounded Treewidth Graphs by Convolutions 

      Eiben, Eduard; Lokshtanov, Daniel; Mouawad, Amer E. (Journal article; Peer reviewed, 2019)
      In the Bisection problem, we are given as input an edge-weighted graph G. The task is to find a partition of V(G) into two parts A and B such that ||A| - |B|| <= 1 and the sum of the weights of the edges with one endpoint ...
    • A Bit-Vector Differential Model for the Modular Addition by a Constant 

      Azimi, Seyyed Arash; Ranea, Adrián; Salmasizadeh, Mahmoud; Mohajeri, Javad; Aref, Mohammad Reza; Rijmen, Vincent Stefaan (Journal article; Peer reviewed, 2020)
      ARX algorithms are a class of symmetric-key algorithms constructed by Addition, Rotation, and XOR, which achieve the best software performances in low-end microcontrollers. To evaluate the resistance of an ARX cipher against ...
    • 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 ...
    • Blockchain as a Technology to Facilitate Privacy and Better Health Record Management 

      Gebremedhin, Tsigab Angosom (Master thesis, 2018-09-01)
      Fear of stigmatization and discrimination from colleagues, friends and family drives patients with various type of mental health problems away from a traditional face-to-face therapy and enforces them to look for an ...
    • BlockDiploma – Decentralizing the Norwegian Diploma Registry using Blockchain Technology 

      Reite, Thomas Mårstøl (Master thesis, 2020-06-03)
      Academic diplomas are being falsified and potentially resulting in unqualified individuals getting the job, or a better candidate being bypassed by a forger. Secure and reliable verification mechanisms for academic diplomas ...
    • Bounds on the nonlinearity of differentially uniform functions by means of their image set size, and on their distance to affine functions 

      Carlet, Claude Michael (Journal article; Peer reviewed, 2021)
      We revisit and take a closer look at a (not so well known) result of a 2017 paper, showing that the differential uniformity of any vectorial function is bounded from below by an expression depending on the size of its image ...
    • Building large k-cores from sparse graphs 

      Fomin, Fedor; Sagunov, Danil; Simonov, Kirill (Journal article; Peer reviewed, 2020)
      A popular model to measure network stability is the k-core, that is the maximal induced subgraph in which every vertex has degree at least k. For example, k-cores are commonly used to model the unraveling phenomena in ...
    • Building Trust in Remote Internet Voting 

      Nestås, Lars Hopland (Master thesis, 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 ...
    • 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 ...
    • Case Studies in Constructive Mathematics 

      Parmann, Erik (Doctoral thesis, 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 finiteness ...
    • Causal inference in drug discovery and development 

      Michoel, Tom; Zhang, Jitao David (Journal article; Peer reviewed, 2023)
      To discover new drugs is to seek and to prove causality. As an emerging approach leveraging human knowledge and creativity, data, and machine intelligence, causal inference holds the promise of reducing cognitive bias and ...
    • 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 ...