S
Susanna Repo
Researcher at University of California, Berkeley
Publications - 21
Citations - 1586
Susanna Repo is an academic researcher from University of California, Berkeley. The author has contributed to research in topics: Elixir (programming language) & Genome. The author has an hindex of 12, co-authored 21 publications receiving 1402 citations. Previous affiliations of Susanna Repo include Finnish Institute of Occupational Health & European Bioinformatics Institute.
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Journal ArticleDOI
A large-scale evaluation of computational protein function prediction
Predrag Radivojac,Wyatt T. Clark,Tal Ronnen Oron,Alexandra M. Schnoes,Tobias Wittkop,Artem Sokolov,Artem Sokolov,Kiley Graim,Christopher S. Funk,Karin Verspoor,Asa Ben-Hur,Gaurav Pandey,Gaurav Pandey,Jeffrey M. Yunes,Ameet Talwalkar,Susanna Repo,Susanna Repo,Michael L Souza,Damiano Piovesan,Rita Casadio,Zheng Wang,Jianlin Cheng,Hai Fang,Julian Gough,Patrik Koskinen,Petri Törönen,Jussi Nokso-Koivisto,Liisa Holm,Domenico Cozzetto,Daniel W. A. Buchan,Kevin Bryson,David T. Jones,Bhakti Limaye,Harshal Inamdar,Avik Datta,Sunitha K Manjari,Rajendra Joshi,Meghana Chitale,Daisuke Kihara,Andreas Martin Lisewski,Serkan Erdin,Eric Venner,Olivier Lichtarge,Robert Rentzsch,Haixuan Yang,Alfonso E. Romero,Prajwal Bhat,Alberto Paccanaro,Tobias Hamp,Rebecca Kaßner,Stefan Seemayer,Esmeralda Vicedo,Christian Schaefer,Dominik Achten,Florian Auer,Ariane Boehm,Tatjana Braun,Maximilian Hecht,Mark Heron,Peter Hönigschmid,Thomas A. Hopf,Stefanie Kaufmann,Michael Kiening,Denis Krompass,Cedric Landerer,Yannick Mahlich,Manfred Roos,Jari Björne,Tapio Salakoski,Andrew Wong,Hagit Shatkay,Hagit Shatkay,Fanny Gatzmann,Ingolf Sommer,Mark N. Wass,Michael J.E. Sternberg,Nives Škunca,Fran Supek,Matko Bošnjak,Panče Panov,Sašo Džeroski,Tomislav Šmuc,Yiannis A. I. Kourmpetis,Yiannis A. I. Kourmpetis,Aalt D. J. van Dijk,Cajo J. F. ter Braak,Yuanpeng Zhou,Qingtian Gong,Xinran Dong,Weidong Tian,Marco Falda,Paolo Fontana,Enrico Lavezzo,Barbara Di Camillo,Stefano Toppo,Liang Lan,Nemanja Djuric,Yuhong Guo,Slobodan Vucetic,Amos Marc Bairoch,Amos Marc Bairoch,Michal Linial,Patricia C. Babbitt,Steven E. Brenner,Christine A. Orengo,Burkhard Rost,Sean D. Mooney,Iddo Friedberg +107 more
TL;DR: Today's best protein function prediction algorithms substantially outperform widely used first-generation methods, with large gains on all types of targets, and there is considerable need for improvement of currently available tools.
Journal ArticleDOI
BODIL: a molecular modeling environment for structure-function analysis and drug design
Jukka V. Lehtonen,Dan-Johan Still,Ville-Veikko Rantanen,Jan Ekholm,Dag Björklund,Zuhair Iftikhar,Mikko Huhtala,Susanna Repo,Antti Jussila,Jussi Jaakkola,Olli T. Pentikäinen,Tommi Nyrönen,Tiina A. Salminen,Mats Gyllenberg,Mats Gyllenberg,Mark S. Johnson +15 more
TL;DR: BODIL is a molecular modeling environment geared to help the user to quickly identify key features of proteins critical to molecular recognition, especially in drug discovery applications, and to understand the structural basis for function.
Journal ArticleDOI
Association of gut microbiota with post-operative clinical course in Crohn's disease
TL;DR: In this article, the authors performed 16S ribosomal profiling using 101 base-pair single-end sequencing on the Illumina GAIIx platform with deep coverage, at an average depth of 1.3 million high quality reads per sample.
Journal ArticleDOI
Somatic Mutations of ErbB4 SELECTIVE LOSS-OF-FUNCTION PHENOTYPE AFFECTING SIGNAL TRANSDUCTION PATHWAYS IN CANCER
Denis Tvorogov,Maria Sundvall,Kari J. Kurppa,Maija Hollmén,Susanna Repo,Mark S. Johnson,Klaus Elenius,Klaus Elenius +7 more
TL;DR: It is demonstrated that 2 of 10 of the cancer-associated mutations of ErbB4 lead to loss of ErBB4 kinase activity due to disruption of functionally important structural features, suggesting that the somatic Erb b4 mutations have functional consequences and lead to selective changes in Erb B4 signaling.
Journal ArticleDOI
Reports from CAGI: The Critical Assessment of Genome Interpretation.
TL;DR: This paper presents a meta-analyses of the determinants of fungal establishment, establishment, and sporadically changes in response to E.coli found in the “silicon rainforest” using a probabilistic approach.