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  • Yufeng Wu
  • Evolution; international journal of organic…
  • 2012
Incomplete lineage sorting can cause incongruence between the phylogenetic history of genes (the gene tree) and that of the species (the species tree), which can complicate the inference of phylogenies. In this article, I present a new coalescent-based algorithm for species tree inference with maximum likelihood. I first describe an improved method for(More)
MOTIVATION We are interested in studying the evolution of DNA single nucleotide polymorphism sequences which have undergone (meiotic) recombination. For a given set of sequences, computing the minimum number of recombinations needed to explain the sequences (with one mutation per site) is a standard question of interest, but it has been shown to be NP-hard,(More)
Detecting historical recombination is an important computational problem which has received great attention recently. Due to recombination, input sequences form a mosaic, where each input sequence is composed of segments from founder sequences. In this paper, we present improved algorithms for the problem of finding the minimum mosaic (a mosaic containing(More)
MOTIVATION Reticulate network is a model for displaying and quantifying the effects of complex reticulate processes on the evolutionary history of species undergoing reticulate evolution. A central computational problem on reticulate networks is: given a set of phylogenetic trees (each for some region of the genomes), reconstruct the most parsimonious(More)
MOTIVATION Structural variation (SV), such as deletion, is an important type of genetic variation and may be associated with diseases. While there are many existing methods for detecting SVs, finding deletions is still challenging with low-coverage short sequence reads. Existing deletion finding methods for sequence reads either use the so-called split(More)
  • Yufeng Wu
  • IEEE/ACM Transactions on Computational Biology…
  • 2010
Coalescent likelihood is the probability of observing the given population sequences under the coalescent model. Computation of coalescent likelihood under the infinite sites model is a classic problem in coalescent theory. Existing methods are based on either importance sampling or Markov chain Monte Carlo and are inexact. In this paper, we develop a(More)
The haplotype inference (HI) problem is the problem of inferring 2n haplotype pairs from n observed genotype vectors. This is a key problem that arises in studying genetic variation in populations, for example in the ongoing HapMap project [5]. In order to have a hope of finding the haplotypes that actually generated the observed genotypes, we must use some(More)
Large scale video copy detection task requires compact feature insensitive to various copy changes. Based on local feature trajectory behavior we discover invariant visual patterns for generating robust feature. Bag of Trajectory (BoT) technical is adopted for fast pattern matching. Our algorithm with lower cost is more robust compared to the state-of-art(More)
We quantify the importance of contracting frictions versus taxes for firms’ capital structures. We estimate a dynamic contracting model in which a firm seeks debt financing from an lender and is subject to taxation. Because the firm can renege on the financing contract, the optimal contract is self-enforcing. Collateral constraints arise endogenously. Using(More)