Browsing by Author "Bork, Peer"

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  • Lloréns Rico, Verónica, 1989-; Cano, Jaime; Kamminga, Tjerko; Gil, Rosario; Latorre, Amparo; Chen, Wei-Hua; Bork, Peer; Glass, John I.; Serrano Pubull, Luis, 1982-; Lluch-Senar, Maria 1982- (American Association for the Advancement of Science (AAAS), 2016)
    cis-Encoded antisense RNAs (asRNAs) are widespread along bacterial transcriptomes. However, the role of most of these RNAs remains unknown, and there is an ongoing discussion as to what extent these transcripts are the ...
  • Noort, Vera van; Seebacher, Jan; Bader, Samuel; Mohammed, Shabaz; Vonkova, Ivana; Betts, Matthew J.; Kühner, Sebastian; Kumar, Runjun; Maier, Tobias; O'Flaherty, Martina; Rybin, Vladimir; Schmeisky, Arne; Yus, Eva; Stülke, Jörg; Serrano Pubull, Luis, 1982-; Russell, Robert B.; Heck, Albert J.R.; Bork, Peer; Gavin, Anne-Claude (Nature Publishing Group, 2012)
    Protein post-translational modifications (PTMs) represent important regulatory states that when combined have been hypothesized to act as molecular codes and to generate a functional diversity beyond genome and transcriptome. ...
  • Lluch-Senar, Maria 1982-; Delgado Blanco, Javier; Chen, Wei-Hua; Lloréns Rico, Verónica, 1989-; O’Reilly, Francis J.; Wodke, Judith A.H.; Unal, E. Besray; Yus, Eva; Martínez, Sira; Nichols, Robert J.; Ferrar, Tony; Vivancos Prellezo, Ana; Schmeisky, Arne; Stülke, Jörg; Noort, Vera van; Gavin, Anne-Claude; Bork, Peer; Serrano Pubull, Luis, 1982- (Wiley Blackwell, 2015)
    Identifying all essential genomic components is critical for the assembly of minimal artificial life. In the genome-reduced bacterium Mycoplasma pneumoniae, we found that small ORFs (smORFs; < 100 residues), accounting for ...
  • Powell, Sean; Forslund, Kristoffer; Szklarczyk, Damian; Trachana, Kalliopi; Roth, Alexander; Huerta Cepas, Jaime; Gabaldón Estevan, Juan Antonio, 1973-; Rattei, Thomas; Creevey, Chris; Kuhn, Michael; Jensen, Lars J.; Mering, Christian von; Bork, Peer (Oxford University Press, 2014)
    With the increasing availability of various 'omics data, high-quality orthology assignment is crucial for evolutionary and functional genomics studies. We here present the fourth version of the eggNOG database (available ...
  • Huerta Cepas, Jaime; Serra, François; Bork, Peer (Oxford University Press, 2016)
    The Environment for Tree Exploration (ETE) is a computational framework that simplifies the reconstruction, analysis, and visualization of phylogenetic trees and multiple sequence alignments. Here, we present ETE v3, ...
  • Boeckmann, Brigitte; Marcet Houben, Marina; Rees, Jonathan A.; Forslund, Kristoffer; Huerta Cepas, Jaime; Muffato, Matthieu; Yilmaz, Pelin; Xenarios, Ioannis; Bork, Peer; Lewis, Suzanna E.; Gabaldón Estevan, Juan Antonio, 1973-; Quest for Orthologs Species Tree Working Group (Oxford University Press, 2015)
    Quest for Orthologs (QfO) is a community effort with the goal to improve and benchmark orthology predictions. As quality assessment assumes prior knowledge on species phylogenies, we investigated the congruency between ...
  • Yus, Eva; Güell Cargol, Marc; Vivancos Prellezo, Ana; Chen, Wei-Hua; Lluch-Senar, Maria 1982-; Delgado Blanco, Javier; Gavin, Anne-Claude; Bork, Peer; Serrano Pubull, Luis, 1982- (Nature Publishing Group, 2012)
    Here, we report the genome-wide identification of small RNAs associated with transcription start sites (TSSs), termed tssRNAs, in Mycoplasma pneumoniae. tssRNAs were also found to be present in a different bacterial phyla, ...