全部文献期刊学位论文会议报纸专利标准年鉴图书|学者科研项目
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作者:Yun Deng , David Fernández-Baca
来源:[J].Algorithms for Molecular Biology(IF 1.606), 2017, Vol.12 (1)Springer
摘要:Semi-labeled trees generalize ordinary phylogenetic trees, allowing internal nodes to be labeled by higher-order taxa. Taxonomies are examples of semi-labeled trees. Suppose we are given collection \(\mathcal {P}\) of semi-labeled trees over various subsets of a set of taxa. The ...
作者:Marc Hellmuth
来源:[J].Algorithms for Molecular Biology(IF 1.606), 2017, Vol.12 (1)Springer
摘要:The history of gene families—which are equivalent to event-labeled gene trees—can be reconstructed from empirically estimated evolutionary event-relations containing pairs of orthologous, paralogous or xenologous genes. The question then arises as whether inferred event-labe...
作者:Laurent Noé
来源:[J].Algorithms for Molecular Biology(IF 1.606), 2017, Vol.12 (1)Springer
摘要:Spaced seeds , also named gapped q-grams, gapped k-mers, spaced q-grams , have been proven to be more sensitive than contiguous seeds ( contiguous q-grams, contiguous k-mers ) in nucleic and amino-acid sequences analysis. Initially proposed to detect sequence similarities an...
作者:Daniel Doerr , Metin Balaban , Pedro Feijão ...
来源:[J].Algorithms for Molecular Biology(IF 1.606), 2017, Vol.12 (1)Springer
摘要:The gene family-free framework for comparative genomics aims at providing methods for gene order analysis that do not require prior gene family assignment, but work directly on a sequence similarity graph. We study two problems related to the breakpoint median of three genomes, w...
作者:Emna Ben Abdallah , Maxime Folschette , Olivier Roux ...
来源:[J].Algorithms for Molecular Biology(IF 1.606), 2017, Vol.12 (1)Springer
摘要:This paper addresses the problem of finding attractors in biological regulatory networks. We focus here on non-deterministic synchronous and asynchronous multi-valued networks, modeled using automata networks (AN). AN is a general and well-suited formalism to study complex intera...
作者:Daniel Bork , Ricson Cheng , Jincheng Wang ...
来源:[J].Algorithms for Molecular Biology(IF 1.606), 2017, Vol.12 (1)Springer
摘要:Phylogenetic tree reconciliation is a widely-used method for inferring the evolutionary histories of genes and species. In the duplication-loss-coalescence (DLC) model, we seek a reconciliation that explains the incongruence between a gene and species tree using gene duplication,...
作者:Riccardo Dondi , Manuel Lafond , Nadia El-Mabrouk
来源:[J].Algorithms for Molecular Biology(IF 1.606), 2017, Vol.12 (1)Springer
摘要:Given a gene family, the relations between genes (orthology/paralogy), are represented by a relation graph, where edges connect pairs of orthologous genes and “missing” edges represent paralogs. While a gene tree directly induces a relation graph, the converse is not always ...
作者:Dan DeBlasio , John Kececioglu
来源:[J].Algorithms for Molecular Biology(IF 1.606), 2017, Vol.12 (1)Springer
摘要:In a computed protein multiple sequence alignment, the coreness of a column is the fraction of its substitutions that are in so-called core columns of the gold-standard reference alignment of its proteins. In benchmark suites of protein reference alignments, the core columns of t...
作者:Christopher Schröder , Sven Rahmann
来源:[J].Algorithms for Molecular Biology(IF 1.606), 2017, Vol.12 (1)Springer
摘要:Mixtures of beta distributions are a flexible tool for modeling data with values on the unit interval, such as methylation levels. However, maximum likelihood parameter estimation with beta distributions suffers from problems because of singularities in the log-likelihood functio...
作者:Guillaume Fertin , Géraldine Jean , Eric Tannier
来源:[J].Algorithms for Molecular Biology(IF 1.606), 2017, Vol.12 (1)Springer
摘要:Combinatorial works on genome rearrangements have so far ignored the influence of intergene sizes, i.e. the number of nucleotides between consecutive genes, although it was recently shown decisive for the accuracy of inference methods (Biller et al. in Genome Biol Evol 8:142...

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