Related papers: Estimating phylogenetic distances between genomic …
Phylogenetic networks extend phylogenetic trees to model non-vertical inheritance, by which a lineage inherits material from multiple parents. The computational complexity of estimating phylogenetic networks from genome-wide data with…
Background: Alignment of biological sequences such as DNA, RNA or proteins is one of the most widely used tools in computational bioscience. All existing alignment algorithms rely on heuristic scoring schemes based on biological expertise.…
Understanding the dynamics of genome rearrangements is a major issue of phylogenetics. Phylogenetics is the study of species evolution. A major goal of the field is to establish evolutionary relationships within groups of species, in order…
The number of extant individuals within a lineage, as exemplified by counts of species numbers across genera in a higher taxonomic category, is known to be a highly skewed distribution. Because the sublineages (such as genera in a clade)…
Given a set of aligned sequences of independent noisy observations, we are concerned with detecting intervals where the mean values of the observations change simultaneously in a subset of the sequences. The intervals of changed means are…
DNA sequence alignment involves assigning short DNA reads to the most probable locations on an extensive reference genome. This process is crucial for various genomic analyses, including variant calling, transcriptomics, and epigenomics.…
Much of the on-going statistical analysis of DNA sequences is focused on the estimation of characteristics of coding and non-coding regions that would possibly allow discrimination of these regions. In the current approach, we concentrate…
Discrepancy measures between probability distributions are at the core of statistical inference and machine learning. In many applications, distributions of interest are supported on different spaces, and yet a meaningful correspondence…
This paper presents a new approach to statistical similarity assessment based on sequence alignment. The algorithm performs mutual matching of two random sequences by successively searching for common elements and by applying sequence…
Some genes can change their relative locations in a genome. Thus for different individuals of the same species, the orders of genes might be different. Such jumping genes are called transposons. A practical problem is to determine…
Domain shifts are ubiquitous in machine learning, and can substantially degrade a model's performance when deployed to real-world data. To address this, distribution alignment methods aim to learn feature representations which are invariant…
We introduce a scale-free method for testing the proportionality of branch lengths between two phylogenetic trees that have the same topology and contain the same set of taxa. This method scales both trees to a total length of 1 and sums up…
Considering the optimal alignment of two i.i.d. random sequences of length $n$, we show that when the scoring function is chosen randomly, almost surely the empirical distribution of aligned letter pairs in all optimal alignments converges…
The flexibility of short DNA chains is investigated via computation of the average correlation function between dimers which defines the persistence length. Path integration techniques have been applied to confine the phase space available…
Consider a string of $n$ positions, i.e. a discrete string of length $n$. Units of length $k$ are placed at random on this string in such a way that they do not overlap, and as often as possible, i.e. until all spacings between neighboring…
Mixing dependency lengths from sequences of different length is a common practice in language research. However, the empirical distribution of dependency lengths of sentences of the same length differs from that of sentences of varying…
In evolutionary biology, genetic sequences carry with them a trace of the underlying tree that describes their evolution from a common ancestral sequence. The question of how many sequence sites are required to recover this evolutionary…
This paper describes a new asynchronous algorithm and implementation for the problem of k-mer counting (KC), which concerns quantifying the frequency of length k substrings in a DNA sequence. This operation is common to many computational…
When the same set of genes appear in two top ranking gene lists in two different studies, it is often of interest to estimate the probability for this being a chance event. This overlapping probability is well known to follow the…
Much evolutionary information is stored in the fluctuations of protein length distributions. The genome size and non-coding DNA content can be calculated based only on the protein length distributions. So there is intrinsic relationship…