Concept

Cladistics

Related publications (39)

Inferring transcript phylogenies

Alternative splicing, an unknown mechanism 20 years ago, is now recognized as a major mechanism for proteome and transcriptome diversity, particularly in mammals - some researchers conjecture that up to 90% of human genes are alternatively spliced. Despite ...

IEEE Press2011

Refining transcriptional regulatory networks using network evolutionary models and gene histories

Bernard Moret, Xiuwei Zhang

Background: Computational inference of transcriptional regulatory networks remains a challenging problem, in part due to the lack of strong network models. In this paper we present evolutionary approaches to improve the inference of regulatory networks for ...

2010

Fast and accurate phylogenetic reconstruction from high-resolution whole-genome data and a novel robustness estimator

Bernard Moret, Yu Lin, Vaibhav Rajan

The rapid accumulation of whole-genome data has renewed interest in the study of genomic rearrangements. Comparative genomics, evolutionary biology, and cancer research all require models and algorithms to elucidate the mechanisms, history, and consequence ...

Springer2010

On Exploring Genome Rearrangement Phylogenetic Patterns

Wei Xu

The study of genorne rearrangement is much harder than the corresponding problems on DNA and protein sequences, because of the occurrences of numerous combinatorial structures. By explicitly exploring these combinatorial structures, the recently developed ...

Springer-Verlag New York2010

Worst-case optimal approximation algorithms for maximizing triplet consistency within phylogenetic networks

This article concerns the following question arising in computational evolutionary biology. For a given subclass of phylogenetic networks, what is the maximum value of 0

2010

How many bootstrap replicates are necessary?

Bernard Moret, Alexandros Stamatakis

Phylogenetic bootstrapping (BS) is a standard technique for inferring confidence values on phylogenetic trees that is based on reconstructing many trees from minor variations of the input data, trees called replicates. BS is used with all phylogenetic reco ...

2010

Improving inference of transcriptional regulatory networks based on network evolutionary models

Bernard Moret, Xiuwei Zhang

Computational inference of transcriptional regulatory networks remains a challenging problem, in part due to the lack of strong network models. In this paper we present evolutionary approaches to improve the inference of regulatory networks for a family of ...

Springer2009

Maximum independent sets of commuting and noninterfering inversions

Bernard Moret, Krister Swenson

Background: Given three signed permutations, an inversion median is a fourth permutation that minimizes the sum of the pairwise inversion distances between it and the three others. This problem is NP-hard as well as hard to approximate. Yet median-based ap ...

2009

Assessing functional diversity in the field -methodology matters!

Aurélie Thébault

Interpreting the functional diversity of vegetation is important in unravelling the relationship between environmental change, community composition and ecosystem processes. Functional diversity is the range and distribution of functional trait values i ...

2008

Ribosomal RNA Genes Challenge the Monophyly of the Hyalospheniidae (Amoebozoa: Arcellinida)

Edward Mitchell, Mariusz Lamentowicz, Enrique Lara, Thierry Jean Heger

To date only five partial and two complete SSU rRNA gene sequences are available for the lobose testate amoebae (Arcellinida). Consequently, the phylogenetic relationships among taxa and the definition of species are still largely dependant on morphologica ...

2008

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