Related papers: GenHap: A Novel Computational Method Based on Gene…

This paper introduces a stochastic plug-and-play (PnP) sampling algorithm that leverages variable splitting to efficiently sample from a posterior distribution. The algorithm based on split Gibbs sampling (SGS) draws inspiration from the…

Single-cell RNA sequencing (scRNA-seq) is widely used to reveal heterogeneity in cells, which has given us insights into cell-cell communication, cell differentiation, and differential gene expression. However, analyzing scRNA-seq data is a…

A quadratic assignment problem (QAP) is a combinatorial optimization problem that belongs to the class of NP-hard ones. So, it is difficult to solve in the polynomial time even for small instances. Research on the QAP has thus focused on…

Single-cell RNA-seq data are challenging because of the sparseness of the read counts, the tiny expression of many relevant genes, and the variability in the efficiency of RNA extraction for different cells. We consider a simple…

DNA sequencing is the physical/biochemical process of identifying the location of the four bases (Adenine, Guanine, Cytosine, Thymine) in a DNA strand. As semiconductor technology revolutionized computing, modern DNA sequencing technology…

A major challenge in next-generation genome sequencing (NGS) is to assemble massive overlapping short reads that are randomly sampled from DNA fragments. To complete assembling, one needs to finish a fundamental task in many leading…

Discovering all the genetic causes of a phenotype is an important goal in functional genomics. In this paper we combine an experimental design for multiple independent detections of the genetic causes of a phenotype, with a high-throughput…

Homomorphic encryption (HE) is a promising technique used for privacy-preserving computation. Since HE schemes only support primitive polynomial operations, homomorphic evaluation of polynomial approximations for non-polynomial functions…

Motivation: Genomic data analyses such as Genome-Wide Association Studies (GWAS) or Hi-C studies are often faced with the problem of partitioning chromosomes into successive regions based on a similarity matrix of high-resolution,…

Applications such as megaregional planning require efficient methods for solving traffic assignment problems (TAPs) on large-scale networks. We propose a decomposition heuristic that generates approximate TAP solutions by partitioning the…

$\textbf{Motivation:}$ Small $p$-values are often required to be accurately estimated in large-scale genomic studies for the adjustment of multiple hypothesis tests and the ranking of genomic features based on their statistical…

The Genographic Project is an international effort using genetic data to chart human migratory history. The project is non-profit and non-medical, and through its Legacy Fund supports locally led efforts to preserve indigenous and…

A new optimization design is proposed for matrix completion by weighting the measurements and deriving the corresponding error bound. Accordingly, the Haplotype reconstruction using nuclear norm minimization with Weighted Constraint…

This paper presents a novel optical processing approach for exploring genome sequences built upon optical correlator for global alignment and extended DV-curve method for local alignment. To overcome the problem of traditional DV-curve…

Accurate segmentation and classification of nuclei in histology images is critical but challenging due to nuclei heterogeneity, staining variations, and tissue complexity. Existing methods often struggle with limited dataset variability,…

The haplotype resolution from xor-genotype data has been recently formulated as a new model for genetic studies. The xor-genotype data is a cheaply obtainable type of data distinguishing heterozygous from homozygous sites without…

We present the Scalable Nucleotide Alignment Program (SNAP), a new short and long read aligner that is both more accurate (i.e., aligns more reads with fewer errors) and 10-100x faster than state-of-the-art tools such as BWA. Unlike recent…

In this paper, we utilize structured learning to simultaneously address two intertwined problems: human pose estimation (HPE) and garment attribute classification (GAC), which are valuable for a variety of computer vision and multimedia…

Studying phenotype-gene association can uncover mechanism of diseases and develop efficient treatments. In complex disease where multiple phenotypes are available and correlated, analyzing and interpreting associated genes for each…

In forensic genetics, short tandem repeats (STRs) are used for human identification (HID). Degraded biological trace samples with low amounts of short DNA fragments (low-quality DNA samples) pose a challenge for STR typing. Predefined…