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Volume 12 Supplement 9

Proceedings of the Ninth Annual Research in Computational Molecular Biology (RECOMB) Satellite Workshop on Comparative Genomics

Proceedings

Edited by Aaron Darling and Cathal Seoighe

Ninth Annual Research in Computational Molecular Biology (RECOMB) Satellite Workshop on Comparative Genomics.

Galway, Ireland8-10 October 2011

  1. During evolution, large-scale genome rearrangements of chromosomes shuffle the order of homologous genome sequences ("synteny blocks") across species. Some years ago, a controversy erupted in genome rearrangem...

    Authors: Oliver Attie, Aaron E Darling and Sophia Yancopoulos
    Citation: BMC Bioinformatics 2011 12(Suppl 9):S1
  2. Tandemly Arrayed Gene (TAG) clusters are groups of paralogous genes that are found adjacent on a chromosome. TAGs represent an important repertoire of genes in eukaryotes. In addition to tandem duplication eve...

    Authors: Olivier Tremblay Savard, Denis Bertrand and Nadia El-Mabrouk
    Citation: BMC Bioinformatics 2011 12(Suppl 9):S2
  3. The lengths of 5’UTRs of multicellular eukaryotes have been suggested to be subject to stochastic changes, with upstream start codons (uAUGs) as the major constraint to suppress 5’UTR elongation. However, this...

    Authors: Chun-Hsi Chen, Hsuan-Yu Lin, Chia-Lin Pan and Feng-Chi Chen
    Citation: BMC Bioinformatics 2011 12(Suppl 9):S3
  4. Species phylogenies are not estimated directly, but rather through phylogenetic analyses of different gene datasets. However, true gene trees can differ from the true species tree (and hence from one another) ...

    Authors: Jimmy Yang and Tandy Warnow
    Citation: BMC Bioinformatics 2011 12(Suppl 9):S4
  5. Paralog reduction, the loss of duplicate genes after whole genome duplication (WGD) is a pervasive process. Whether this loss proceeds gene by gene or through deletion of multi-gene DNA segments is controversi...

    Authors: Baoyong Wang, Chunfang Zheng and David Sankoff
    Citation: BMC Bioinformatics 2011 12(Suppl 9):S5
  6. A gene tree for a gene family is often discordant with the containing species tree because of its complex evolutionary course during which gene duplication, gene loss and incomplete lineage sorting events migh...

    Authors: Taoyang Wu and Louxin Zhang
    Citation: BMC Bioinformatics 2011 12(Suppl 9):S7
  7. The distance between two genomes is often computed by comparing only the common markers between them. Some approaches are also able to deal with non-common markers, allowing the insertion or the deletion of su...

    Authors: Marília D V Braga, Raphael Machado, Leonardo C Ribeiro and Jens Stoye
    Citation: BMC Bioinformatics 2011 12(Suppl 9):S8
  8. The identification of functional regions contained in a given multiple sequence alignment constitutes one of the major challenges of comparative genomics. Several studies have focused on the identification of ...

    Authors: Dunarel Badescu, Alix Boc, Abdoulaye Baniré Diallo and Vladimir Makarenkov
    Citation: BMC Bioinformatics 2011 12(Suppl 9):S9
  9. Classical approaches to compute the genomic distance are usually limited to genomes with the same content, without duplicated markers. However, differences in the gene content are frequently observed and can r...

    Authors: Marília D V Braga, Raphael Machado, Leonardo C Ribeiro and Jens Stoye
    Citation: BMC Bioinformatics 2011 12(Suppl 9):S13
  10. Comparison of complete genomes of Bacteria and Archaea shows that gene content varies considerably and that genomes evolve quite rapidly via gene duplication and deletion and horizontal gene transfer. We analy...

    Authors: R Eric Collins, Hugh Merz and Paul G Higgs
    Citation: BMC Bioinformatics 2011 12(Suppl 9):S14
  11. Large-scale comparison of genomic sequences requires reliable tools for the search of local alignments. Practical local aligners are in general fast, but heuristic, and hence sometimes miss significant matches.

    Authors: Birte Kehr, David Weese and Knut Reinert
    Citation: BMC Bioinformatics 2011 12(Suppl 9):S15
  12. Changes in transcriptional orientation (“CTOs”) occur frequently in prokaryotic genomes. Such changes usually result from genomic inversions, which may cause a conflict between the directions of replication an...

    Authors: Chieh-Hua Lin, Chun-Yi Lian, Chao Agnes Hsiung and Feng-Chi Chen
    Citation: BMC Bioinformatics 2011 12(Suppl 9):S19
  13. Segmental duplications in genomes have been studied for many years. Recently, several studies have highlighted a biological phenomenon called breakpoint-duplication that apparently associates a significant propor...

    Authors: Antoine Thomas, Jean-Stéphane Varré and Aïda Ouangraoua
    Citation: BMC Bioinformatics 2011 12(Suppl 9):S20

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