Related papers: On the Approximability of Comparing Genomes with D…
The problem of finding a maximum size matching in a graph (known as the maximum matching problem) is one of the most classical problems in computer science. Despite a significant body of work dedicated to the study of this problem in the…
In this paper we consider the problem of computing an mRNA sequence of maximal similarity for a given mRNA of secondary structure constraints, introduced by Backofen et al. in [BNS02] denoted as the MRSO problem. The problem is known to be…
We propose a metric for the space of multiple sequence alignments that can be used to compare two alignments to each other. In the case where one of the alignments is a reference alignment, the resulting accuracy measure improves upon…
A matching $M$ is a $\mathscr{P}$-matching if the subgraph induced by the endpoints of the edges of $M$ satisfies property $\mathscr{P}$. As examples, for appropriate choices of $\mathscr{P}$, the problems Induced Matching, Uniquely…
Suppose one desires to randomly sample a pair of objects such as socks, hoping to get a matching pair. Even in the simplest situation for sampling, which is sampling with replacement, the innocent phrase "the distribution of the color of a…
The de novo assembly of large, complex genomes is a significant challenge with currently available DNA sequencing technology. While many de novo assembly software packages are available, comparatively little attention has been paid to…
High-dimensional phenotypes hold promise for richer findings in association studies, but testing of several phenotype traits aggravates the grand challenge of association studies, that of multiple testing. Several methods have recently been…
An important problem in geometric computing is defining and computing similarity between two geometric shapes, e.g. point sets, curves and surfaces, etc. Important geometric and topological information of many shapes can be captured by…
This paper introduces the Gene Mover's Distance, a measure of similarity between a pair of cells based on their gene expression profiles obtained via single-cell RNA sequencing. The underlying idea of the proposed distance is to interpret…
We study the complexity of the problem of searching for a set of patterns that separate two given sets of strings. This problem has applications in a wide variety of areas, most notably in data mining, computational biology, and in…
In systems biology, it is becoming increasingly common to measure biochemical entities at different levels of the same biological system. Hence, data fusion problems are abundant in the life sciences. With the availability of a multitude of…
A distributed computing system is a collection of processors that communicate either by reading and writing from a shared memory or by sending messages over some communication network. Most prior biologically inspired distributed computing…
The task of estimating a matrix given a sample of observed entries is known as the \emph{matrix completion problem}. Most works on matrix completion have focused on recovering an unknown real-valued low-rank matrix from a random sample of…
In this paper we present a collection of results pertaining to haplotyping. The first set of results concerns the combinatorial problem of reconstructing haplotypes from incomplete and/or imperfectly sequenced haplotype data. More…
The NP-complete Permutation Pattern Matching problem asks whether a permutation P (the pattern) can be matched into a permutation T (the text). A matching is an order-preserving embedding of P into T. In the Generalized Permutation Pattern…
Frameshift mutations in protein-coding DNA sequences produce a drastic change in the resulting protein sequence, which prevents classic protein alignment methods from revealing the proteins' common origin. Moreover, when a large number of…
Meta-analysis is routinely performed in many scientific disciplines. This analysis is attractive since discoveries are possible even when all the individual studies are underpowered. However, the meta-analytic discoveries may be entirely…
Precision and Recall are two prominent metrics of generative performance, which were proposed to separately measure the fidelity and diversity of generative models. Given their central role in comparing and improving generative models,…
When an individual's DNA is sequenced, sensitive medical information becomes available to the sequencing laboratory. A recently proposed way to hide an individual's genetic information is to mix in DNA samples of other individuals. We…
Several processes in the cell, such as gene regulation, start when key proteins recognise and bind to short DNA sequences. However, as these sequences can be hundreds of million times shorter than the genome, they are hard to find by simple…