Fran Supek

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Tomislav ŠmucSenior scientist, Rudjer Boskovic Institute, Zagreb, CroatiaVerified email at irb.hr
Ben LehnerGenerative and Synthetic Genomics, Wellcome Sanger Institute; Systems and Synthetic Biology, CRGVerified email at sanger.ac.uk
Matko BošnjakGoogle DeepMindVerified email at deepmind.com
Anita KriskoUniversity Medical Center Goettingen, Department of Experimental NeurodegenerationVerified email at med.uni-goettingen.de
Rik GH LindeboomThe Netherlands Cancer Institute, Amsterdam, the NetherlandsVerified email at nki.nl
Toni GabaldonGroup Leader, Institute for Research in Biomedicine (IRB), Barcelona Supercomputing Centre (BSC)Verified email at crg.es
Marina SalvadoresIRB BarcelonaVerified email at irbbarcelona.org
Jurica LevaticPostdoc, Department of Knowledge Technologies, Jožef Stefan Institute, Ljubljana, SloveniaVerified email at ijs.si
David Mas-PontePostdoc, University of WashingtonVerified email at uw.edu
Vedrana VidulinPink Data AnalyticsVerified email at pinkdataanalytics.com
Marko MarjanovicRudjer Boskovic InstituteVerified email at irb.hr
Solip ParkCentre for Genomic RegulationVerified email at crg.eu
Saso DzeroskiJozef Stefan Institute, Dept. of Knowledge TechnologiesVerified email at ijs.si
Tobias WarneckeDepartment of Biochemistry, University of OxfordVerified email at bioch.ox.ac.uk
Belen MiñanaCenter for Genomic RegulationVerified email at crg.es
Juan ValcarcelICREA Research Professor, Center for Genomic RegulationVerified email at crg.eu
Josep BiaynaPostdoctoral researcher- ICR - Goethe University Frankfurt am MainVerified email at med.uni-frankfurt.de
Maria BrbićEPFLVerified email at cs.stanford.edu
Jelena ReparResearch associate at Ruder Boskovic Institute, CroatiaVerified email at irb.hr
Jose Espinosa-CarrascoPostdoctoral researcher, Center for Genomic Regulation (CRG)Verified email at crg.eu

Fran Supek

Genome Data Science lab PI, BRIC / University of Copenhagen professor, IRB Barcelona Group Leader

Verified email at irb.hr - Homepage

Genomics Cancer evolution Mutagenesis Gene function Machine learning


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REVIGO summarizes and visualizes long lists of gene ontology terms F Supek, M Bošnjak, N Škunca, T Šmuc PloS one 6 (7), e21800, 2011	6189	2011
A large-scale evaluation of computational protein function prediction P Radivojac, WT Clark, TR Oron, AM Schnoes, T Wittkop, A Sokolov, ... Nature methods 10 (3), 221-227, 2013	1111	2013
Synonymous mutations frequently act as driver mutations in human cancers F Supek, B Miñana, J Valcárcel, T Gabaldón, B Lehner Cell 156 (6), 1324-1335, 2014	633	2014
The rules and impact of nonsense-mediated mRNA decay in human cancers RGH Lindeboom, F Supek, B Lehner Nature genetics 48 (10), 1112-1118, 2016	475	2016
An expanded evaluation of protein function prediction methods shows an improvement in accuracy Y Jiang, TR Oron, WT Clark, AR Bankapur, D D’Andrea, R Lepore, ... Genome biology 17, 1-19, 2016	437	2016
The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens N Zhou, Y Jiang, TR Bergquist, AJ Lee, BZ Kacsoh, AW Crocker, ... Genome biology 20, 1-23, 2019	402	2019
Differential DNA mismatch repair underlies mutation rate variation across the human genome F Supek, B Lehner Nature 521 (7550), 81-84, 2015	401	2015
Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition B Rodriguez-Martin, EG Alvarez, A Baez-Ortega, J Zamora, F Supek, ... Nature genetics 52 (3), 306-319, 2020	389	2020
The impact of nonsense-mediated mRNA decay on genetic disease, gene editing and cancer immunotherapy RGH Lindeboom, M Vermeulen, B Lehner, F Supek Nature genetics 51 (11), 1645-1651, 2019	232	2019
Clustered Mutation Signatures Reveal that Error-Prone DNA Repair Targets Mutations to Active Genes F Supek, B Lehner Cell 130 (3), 534-547, 2017	213	2017
To NMD or not to NMD: nonsense-mediated mRNA decay in cancer and other genetic diseases F Supek, B Lehner, RGH Lindeboom Trends in Genetics 37 (7), 657-668, 2021	183	2021
Comparison of codon usage measures and their applicability in prediction of microbial gene expressivity F Supek, K Vlahoviček BMC bioinformatics 6, 1-15, 2005	168	2005
MUFFINN: cancer gene discovery via network analysis of somatic mutation data A Cho, JE Shim, E Kim, F Supek, B Lehner, I Lee Genome biology 17, 1-16, 2016	153	2016
INCA: synonymous codon usage analysis and clustering by means of self-organizing map F Supek, K Vlahoviček Bioinformatics 20 (14), 2329-2330, 2004	127	2004
The landscape of microbial phenotypic traits and associated genes M Brbić, M Piškorec, V Vidulin, A Kriško, T Šmuc, F Supek Nucleic acids research, gkw964, 2016	114	2016
Translational selection is ubiquitous in prokaryotes F Supek, N Škunca, J Repar, K Vlahoviček, T Šmuc PLoS genetics 6 (6), e1001004, 2010	92	2010
On Relevance of Codon Usage to Expression of Synthetic and Natural Genes in Escherichia coli F Supek, T \# 352; muc Genetics 185 (3), 1129-1134, 2010	90	2010
A synthesis of bacterial and archaeal phenotypic trait data JS Madin, DA Nielsen, M Brbic, R Corkrey, D Danko, K Edwards, ... Scientific data 7 (1), 170, 2020	87	2020
DNA mismatch repair promotes APOBEC3-mediated diffuse hypermutation in human cancers D Mas-Ponte, F Supek Nature genetics 52 (9), 958-968, 2020	85	2020
Antitumor potential of crown ethers: structure− activity relationships, cell cycle disturbances, and cell death studies of a series of ionophores M Marjanović, M Kralj, F Supek, L Frkanec, I Piantanida, T Šmuc, ... Journal of medicinal chemistry 50 (5), 1007-1018, 2007	78	2007

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