• An Atlas of the Human uORFome and its Regulation across Tissues 

      Tjeldnes, Håkon (Master thesis, 2018-06-19)
      Upstream open reading frames (uORFs) are in frame start and stop codons starting in the 5’ leader of mRNAs. They have been found to regulate gene expression, primarily through translational inhibition by hindering ribosomes ...
    • 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 ...
    • Detecting inosine in nanopore sequencing data with machine learning 

      Stautland, Thomas Kristoffer (Master thesis, 2021-08-13)
      Detecting modifications in DNA has been a long-standing challenge in understanding the workings of the genome, particularly with regards to regulatory function. The currently most widely used sequencing technology, NGS, ...
    • Shoelaces: An interactive tool for ribosome profiling processing and visualization 

      Birkeland, Åsmund; Chyzynska, Katarzyna; Valen, Eivind (Peer reviewed; Journal article, 2018-07-18)
      Background: The emergence of ribosome profiling to map actively translating ribosomes has laid the foundation for a diverse range of studies on translational regulation. The data obtained with different variations of this ...
    • Using registries to integrate bioinformatics tools and services into workbench environments 

      Ménager, Hervé; Kalaš, Matúš; Rapacki, Kristoffer; Ison, Jon (Peer reviewed; Journal article, 2015)
      The diversity and complexity of bioinformatics resources presents significant challenges to their localisation, deployment and use, creating a need for reliable systems that address these issues. Meanwhile, users demand ...
    • WSDL Workshop. Semantic web application in HTML5 for the discovery, construction and analysis of workflows 

      Nozal Canadas, Rafael Adolfo (Master thesis, 2013-11-20)
      WSDL-Workshop is a HTML5 web application for the discovery and exploration of web services and for analysing the compatibility between web services. This is the result of a mathematical model developed from WSDL1.1. The ...