Related papers: Optimal Haplotype Assembly from High-Throughput Ma…
A DNA palindrome is a segment of double-stranded DNA sequence with inver- sion symmetry which may form secondary structures conferring significant biolog- ical functions ranging from RNA transcription to DNA replication. To test if the…
Pairwise alignment of DNA sequencing data is a ubiquitous task in bioinformatics and typically represents a heavy computational burden. State-of-the-art approaches to speed up this task use hashing to identify short segments (k-mers) that…
Multi Expression Programming (MEP) is a Genetic Programming variant that uses a linear representation of chromosomes. MEP individuals are strings of genes encoding complex computer programs. When MEP individuals encode expressions, their…
Assessing the correctness of genome assemblies is an important step in any genome project. Several methods exist, but most are computationally intensive and, in some cases, inappropriate. Here I present baa.pl, a fast and easy-to-use…
We compute the homology of the matching complex $M(\Gamma)$, where $\Gamma$ is the complete hypergraph on $n\geq 2$ vertices, and analyse the $S_n$-representations carried by this homology. These results are achieved using standard…
Recent matrix completion based methods have not been able to properly model the Haplotype Assembly Problem (HAP) for noisy observations. To cope with such a case, in this letter we propose a new Minimum Error Correction (MEC) based matrix…
Although geographic isolation has been shown to play a key role in promoting reproductive isolation, it is now believed that speciation can also happen in sympatry and with considerable gene flow. Here we present a model of sympatric…
Recently, haplo-identical transplantation with multiple HLA mismatches has become a viable option for system cell transplants. Haplotype sharing detection requires imputation of donor and recipient. We show that even in high-resolution…
Background Nucleotide sequences contain multiple codes responsible for organism's functioning and structure. They can be investigated by various signal processing methods. These techniques are well suited for indication of frequently…
Motivation: Whole-genome high-coverage sequencing has been widely used for personal and cancer genomics as well as in various research areas. However, in the lack of an unbiased whole-genome truth set, the global error rate of variant calls…
Finding optimal evolutionary trees from sequence data is typically an intractable problem, and there is usually no way of knowing how close to optimal the best tree from some search truly is. The problem would seem to be particularly acute…
Meta-analysis of multiple genome-wide association studies (GWAS) is effective for detecting single or multi marker associations with complex traits. We develop a flexible procedure ("STAMP") based on mixture models to perform region based…
Background: Regions with copy number variations (in germline cells) or copy number alteration (in somatic cells) are of great interest for human disease gene mapping and cancer studies. They represent a new type of mutation and are…
De novo assembly is the process of reconstructing the genome sequence of an organism from sequencing reads. Genome sequences are essential to biology, and assembly has been a central problem in bioinformatics for four decades. Until…
Genetic interaction measures how different genes collectively contribute to a phenotype, and can reveal functional compensation and buffering between pathways under genetic perturbations. Recently, genome-wide screening for genetic…
Two proteins are homologous if they have a common evolutionary origin, and the binary classification problem is to identify proteins in a candidate set that are homologous to a particular native protein. The feature (explanatory) variables…
Given pointed cellular spaces $X$ and $Y$, $X$ compact, and an integer $r\ge0$, we define a relation $\overset r\approx$ on $[X,Y]$ and argue for the conjecture that it always coincides with the $r$-similarity $\overset r\sim$.
We consider a random fitness landscape on the space of haploid diallelic genotypes with n genetic loci, where each genotype is considered either inviable or viable depending on whether or not there are any incompatibilities among its allele…
In a population with haploid reproduction any individual has a single parent in the previous generation. If all genealogical distances among pairs of individuals (generations from the closest common ancestor) are known it is possible to…
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…