Now showing items 38-57 of 649

    • Axis patterning by BMPs: cnidarian network reveals evolutionary constraints 

      Genikhovich, Grigory; Fried, Patrick; Prünster, M. Mandela; Schinko, Johannes B.; Gilles, Anna F.; Fredman, David; Meier, Karin; Iber, Dagmar; Technau, Ulrich (Peer reviewed; Journal article, 2015-03)
      BMP signaling plays a crucial role in the establishment of the dorso-ventral body axis in bilaterally symmetric animals. However, the topologies of the bone morphogenetic protein (BMP) signaling networks vary drastically ...
    • B-chromatic number: Beyond NP-hardness 

      Panolan, Fahad; Philip, Geevarghese; Saurabh, Saket (Conference object; 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 ...
    • 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 ...
    • 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 ...
    • 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 ...
    • 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 ...
    • 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 ...
    • 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 ...