Related papers: Optimal Haplotype Assembly from High-Throughput Ma…
This paper aims at a newly raising task in visual surveillance: re-identifying people at a distance by matching body information, given several reference examples. Most of existing works solve this task by matching a reference template with…
Being able to store and transmit human genome sequences is an important part in genomic research and industrial applications. The complete human genome has 3.1 billion base pairs (haploid), and storing the entire genome naively takes about…
Large whole-genome sequencing projects have provided access to much of the rare variation in human populations, which is highly informative about population structure and recent demography. Here, we show how the age of rare variants can be…
To uncover the genetic basis of complex disease, individuals are often measured at a large number of genetic variants (usually SNPs) across the genome. GemTools provides computationally efficient tools for modeling genetic ancestry based on…
We study homomorphism polynomials, which are polynomials that enumerate all homomorphisms from a pattern graph $H$ to $n$-vertex graphs. These polynomials have received a lot of attention recently for their crucial role in several new…
Whole and targeted sequencing of human genomes is a promising, increasingly feasible tool for discovering genetic contributions to risk of complex diseases. A key step is calling an individual's genotype from the multiple aligned short read…
The human genome remains incomplete, with multi-megabase sized gaps representing the endogenous centromeres and other heterochromatic regions. These regions are commonly enriched with long arrays of near-identical tandem repeats, known as…
Due to the recent evolution of sequencing techniques, the number of available genomes is rising steadily, leading to the possibility to make large scale genomic comparison between sets of close species. An interesting question to answer is:…
Long reads produced by third-generation sequencing technologies are used to construct an assembly (i.e., the subject's genome), which is further used in downstream genome analysis. Unfortunately, long reads have high sequencing error rates…
Tumor cell populations can be thought of as being composed of homogeneous cell subpopulations, with each subpopulation being characterized by overlapping sets of single nucleotide variants (SNVs). Such subpopulations are known as subclones…
High read depth can be used to assemble short sequence repeats. The existing genome assemblers fail in repetitive regions of longer than average read. I propose a new algorithm for a DNA assembly which uses the relative frequency of reads…
We present several new results pertaining to haplotyping. These results concern the combinatorial problem of reconstructing haplotypes from incomplete and/or imperfectly sequenced haplotype fragments. We consider the complexity of the…
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…
We discuss two different ways of chromosomes' and genomes' evolution. Purifying selection dominates in large panmictic populations, where Mendelian law of independent gene assortment is valid. If the populations are small, recombination…
Many natural combinatorial quantities can be expressed by counting the number of homomorphisms to a fixed relational structure. For example, the number of 3-colorings of an undirected graph $G$ is equal to the number of homomorphisms from…
Real-world graphs exhibit increasing heterophily, where nodes no longer tend to be connected to nodes with the same label, challenging the homophily assumption of classical graph neural networks (GNNs) and impeding their performance.…
The problems of large-scale multiple testing are often encountered in modern scientific researches. Conventional multiple testing procedures usually suffer considerable loss of testing efficiency due to the lack of consideration of…
In the last few decades, the human allosomes are engrossed in an intensive attention among researchers. The allosomes are now already been sequenced and found there are about 2000 and 78 genes in human X and Y chromosomes respectively. The…
We consider a novel approach of measuring the homology of DNA sequences based of the variety of optimal alignments in the longest common subsequence sense. The proposed approach is compared with BLAST in measuring the homology of four…
A computationally simple genome-wide association study (GWAS) algorithm for estimating the main and epistatic effects of markers or single nucleotide polymorphisms (SNPs) is proposed. It is based on the intuitive assumption that changes of…