Browsing by Author "Supek, Fran"

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  • Jiang, Yuxiang; Gabaldón Estevan, Juan Antonio, 1973-; Marcet Houben, Marina; Supek, Fran; Radivojac, Predrag (BioMed Central, 2016)
    Background: A major bottleneck in our understanding of the molecular underpinnings of life is the assignment of function to proteins. While molecular experiments provide the most reliable annotation of proteins, their ...
  • Supek, Fran; Lehner, Ben, 1978- (Elsevier, 2017)
    Many processes can cause the same nucleotide change in a genome, making the identification of the mechanisms causing mutations a difficult challenge. Here, we show that clustered mutations provide a more precise fingerprint ...
  • Supek, Fran; Lehner, Ben, 1978- (Nature Publishing Group, 2015)
    Cancer genome sequencing has revealed considerable variation in somatic mutation rates across the human genome, with mutation rates elevated in heterochromatic late replicating regions and reduced in early replicating ...
  • Vidulin, Vedrana; Šmuc, Tomislav; Supek, Fran (Oxford University Press, 2016)
    MOTIVATION: The number of sequenced genomes rises steadily but we still lack the knowledge about the biological roles of many genes. Automated function prediction (AFP) is thus a necessity. We hypothesized that AFP approaches ...
  • Brbić, Maria; Warnecke, Tobias; Krisko, Anita; Supek, Fran (Oxford University Press, 2015)
    The amino acid composition (AAC) of proteomes differs greatly between microorganisms and is associated with the environmental niche they inhabit, suggesting that these changes may be adaptive. Similarly, the oligonucleotide ...
  • Krisko, Anita; Copic, Tea; Gabaldón Estevan, Juan Antonio, 1973-; Lehner, Ben, 1978-; Supek, Fran (BioMed Central, 2014)
    Background: The genetic code is redundant, meaning that most amino acids can be encoded by more than one codon. Highly expressed genes tend to use optimal codons to increase the accuracy and speed of translation. Thus, ...
  • Cho, Ara; Shim, Jung; Kim, Eiru; Supek, Fran; Lehner, Ben, 1978-; Lee, Insuk (BioMed Central, 2016)
    A major challenge for distinguishing cancer-causing driver mutations from inconsequential passenger mutations is the long-tail of infrequently mutated genes in cancer genomes. Here, we present and evaluate a method for ...
  • Supek, Fran (Springer, 2016)
    Some mutations in gene coding regions exchange one synonymous codon for another, and thus do not alter the amino acid sequence of the encoded protein. Even though they are often called 'silent,' these mutations may exhibit ...
  • Brbić, Maria; Piškorec, Martija; Vidulin, Vedrana; Krisko, Anita; Šmuc, Tomislav; Supek, Fran (Oxford University Press, 2016)
    Bacteria and Archaea display a variety of phenotypic traits and can adapt to diverse ecological niches. However, systematic annotation of prokaryotic phenotypes is lacking. We have therefore developed ProTraits, a resource ...
  • Supek, Fran; Škunca, Nieves (Springer, 2017)
    Contemporary techniques in biology produce readouts for large numbers of genes simultaneously, the typical example being differential gene expression measurements. Moreover, those genes are often richly annotated using GO ...