Untitled

Protein coalitions in a core mammalian biochemical network linked by rapidly evolving proteins

“…Phylogenetic profiles [ 14 ] of human protein sequences involved in GSIS were estimated using BLAST searches [ 41 ] against 243 fully sequenced genomes from the COGENT database [ 42 , 43 ], including 197 Bacteria, 22 Archaea and 24 Eukaryota species, using an E-value cut-off of 10 (12,083 hits, of which 11,925 hits, or 98.7% of the total, had an E-value < 1). The classification process was non-hierarchical: proteins with hits to more than five prokaryote species are classified as universal [U]; the remaining proteins with at least a single hit to non-metazoan eukaryotes are classified as eukaryote-specific [E]; proteins with at least a single hit to non-mammalian metazoa are classified as metazoan-specific [M]; and, finally, proteins recognizing only other vertebrate proteins are classified as vertebrate-specific [V].…”

A polyphasic strategy incorporating genomic data for the taxonomic description of novel bacterial species

“…In the 1980s, the advent of DNA amplification and sequencing techniques, in particular of the 16S rRNA gene, constituted a major step forward by facilitating bacterial classification (Gürtler & Mayall, 2001; Coenye & Vandamme, 2004; Konstantinidis & Tiedje, 2007). Then, starting in the mid-1990s, whole-genome sequencing constituted a revolution by giving access to the complete genetic information of a strain (Janssen et al , 2003). Despite this tremendous progress and the various genome-based methods that were developed and proposed for taxonomic purposes, including multilocus sequence analysis and average nucleotide identity (ANI), whole-genome analysis (Stackebrandt et al , 2002; Rosselló-Mora, 2005; Goris et al , 2007; Konstantinidis & Tiedje, 2007; Yarza et al , 2008) has not as yet been accepted as a source of taxonomic information.…”

Establishment of computational biology in Greece and Cyprus: Past, present, and future

“…Around that time, a similar position was created at the University of Cyprus, heralding a new period with more support for the field through research and teaching programs at the undergraduate and graduate levels, later (2016) followed by a European Research Area (ERA)-Chair appointment at the Cyprus Institute of Neurology and Genetics. Aggregating around initiatives already formulated at the EMBL, such as EMBNet and the EBI (Research & Services) [28,29], including many training events for advanced graduates (bioinformatics workshop at Institute of Agrobiotechnology (INA)-CERTH 2006, ENFIN workshop 2007, and EMBO metagenomics workshop 2008), the field started receiving certain regional publicity and attracting the attention it deserved [30]. During this time, there was a general excitement worldwide, with investors willing to fund a range of start-up companies that became active in the fledgling industry [27].…”