• B-chromatic number: Beyond NP-hardness 

      Panolan, Fahad; Philip, Geevarghese; Saurabh, Saket (Peer reviewed; Journal article, 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 ...
    • b-Coloring Parameterized by Clique-Width 

      Jaffke, Lars; Lima, Paloma Thome de; Lokshtanov, Daniel (Journal article; Peer reviewed, 2021)
      We provide a polynomial-time algorithm for b-Coloring on graphs of constant clique-width. This unifies and extends nearly all previously known polynomial-time results on graph classes, and answers open questions posed by ...
    • b-Coloring Parameterized by Clique-Width 

      Jaffke, Lars; Lima, Paloma T.; Lokshtanov, Daniel (Journal article; Peer reviewed, 2023)
      We provide a polynomial-time algorithm for b- Coloring on graphs of constant clique-width. This unifies and extends nearly all previously known polynomial time results on graph classes, and answers open questions posed by ...
    • Balanced judicious bipartition is fixed-parameter tractable 

      Lokshtanov, Daniel; Saurabh, Saket; Sharma, Roohani; Zehavi, Meirav (Journal article; Peer reviewed, 2019)
      The family of judicious partitioning problems, introduced by Bollobás and Scott to the field of extremal combinatorics, has been extensively studied from a structural point of view for over two decades. This rich realm of ...
    • Balancing the Game: Comparative Analysis of Single Heuristics and Adaptive Heuristic Approaches for Sports Scheduling Problem 

      Alesahebfosoul, Seyed Erfan (Master thesis, 2023-10-02)
      Sport timetabling problems are Combinatorial Optimization problems which involve the creation of schedules that determine when and where teams compete against each other. One specific type of sports scheduling, the double ...
    • Belief Propagation in Self-Dual F4-Additive Codes Utilizing Local Complementaion 

      Hammer, Åsmund (Master thesis, 2019-06-27)
      Developing algorithms for belief propagation in self-dual GF(4)-additive codes utilizing local complementation in order to improve decoding performance.
    • Beyond the question of fixed-parameter tractability 

      Dregi, Markus Fanebust (Doctoral thesis, 2017-01-06)
      Multivariate complexity is a prominent field that over the last decades has developed a rich toolbox, not only to tackle seemingly intractable problems, but also to describe the boundaries of tractability in a richer and ...
    • Bidimensionality and Kernels 

      Fomin, Fedor; Lokshtanov, Daniel; Saurabh, Saket; Thilikos, Dimitrios (Journal article; Peer reviewed, 2020)
      Bidimensionality theory was introduced by [E. D. Demaine et al., J. ACM, 52 (2005), pp. 866--893] as a tool to obtain subexponential time parameterized algorithms on H-minor-free graphs. In [E. D. Demaine and M. Hajiaghayi, ...
    • Bifurcation and sensitivity analysis reveal key drivers of multistability in a model of macrophage polarization 

      Frank, Anna-Simone; Larripa, Kamila; Ryu, Hwayeon; Snodgrass, Ryan; Röblitz, Susanna (Journal article; Peer reviewed, 2020)
      In this paper, we present and analyze a mathematical model for polarization of a single macrophage which, despite its simplicity, exhibits complex dynamics in terms of multistability. In particular, we demonstrate that an ...
    • Binary domain classification for Norwegian language in task-oriented dialogue systems 

      Evensen, Adrian Tvilde (Master thesis, 2022-09-01)
      Dialogue systems have gained more attention in recent years and have been called “the new app”. This is much due to the advancement in deep learning, more precisely in Natural Language Processing (NLP). An additional factor ...
    • Binary Linear Codes With Few Weights From Two-to-One Functions 

      Li, Kangquan; Li, Chunlei; Helleseth, Tor; Qu, Longjiang (Journal article; Peer reviewed, 2021)
      In this paper, we apply two-to-one functions over b F 2n in two generic constructions of binary linear codes. We consider two-to-one functions in two forms: (1) generalized quadratic functions; and (2) (x 2t +x) e with ...
    • Binding Leverage as a Molecular Basis for Allosteric Regulation 

      Mitternacht, Simon; Berezovsky, Igor N. (Peer reviewed; Journal article, 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 the ...
    • 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 ...