Related papers: Selscan: an efficient multi-threaded program to pe…
This paper presents an efficient program for checking Mendelian consistency in a pedigree. Since pedigrees may contain incomplete and/or erroneous information, geneticists need to pre-process them before performing linkage analysis.…
The maximal sensitivity of the Smith-Waterman (SW) algorithm has enabled its wide use in biological sequence database search. Unfortunately, the high sensitivity comes at the expense of quadratic time complexity, which makes the algorithm…
Motivation: The multiple sequence alignment (MSA) problem has been extensively studied, with numerous approaches developed over recent years. With the rapid growth of sequence data, there is an increasing need for fast and accurate MSA…
As the number of possible predictors generated by high-throughput experiments continues to increase, methods are needed to quickly screen out unimportant covariates. Model-based screening methods have been proposed and theoretically…
Assembling a gene from candidate exons is an important problem in computational biology. Among the most successful approaches to this problem is \emph{spliced alignment}, proposed by Gelfand et al., which scores different candidate exon…
This work suggests faster and space-efficient index construction algorithms for LSH for Euclidean distance (\textit{a.k.a.}~\ELSH) and cosine similarity (\textit{a.k.a.}~\SRP). The index construction step of these LSHs relies on grouping…
This paper proposes a novel approach for storing and retrieving massive DNA sequences.. The method is based on a perceptual hash function, commonly used to determine the similarity between digital images, that we adapted for DNA sequences.…
Background and Purpose: Colorectal cancer is a common fatal malignancy, the fourth most common cancer in men, and the third most common cancer in women worldwide. Timely detection of cancer in its early stages is essential for treating the…
Hyperspectral (HS) imaging presents itself as a non-contact, non-ionizing and non-invasive technique, proven to be suitable for medical diagnosis. However, the volume of information contained in these images makes difficult providing the…
Fetal ultrasound screening during pregnancy plays a vital role in the early detection of fetal malformations which have potential long-term health impacts. The level of skill required to diagnose such malformations from live ultrasound…
Crowd counting based on density maps is generally regarded as a regression task.Deep learning is used to learn the mapping between image content and crowd density distribution. Although great success has been achieved, some pedestrians far…
Results: We present an application that enables the quantitative analysis of multichannel 5-D (x, y, z, t, channel) and large montage confocal fluorescence microscopy images. The image sequences show stem cells together with blood vessels,…
Analysis of genomic segments shared identical-by-descent (IBD) between individuals is fundamental to many genetic applications, from demographic inference to estimating the heritability of diseases, but IBD detection accuracy in…
The single nucleotide polymorphism (SNP) is the most widely studied type of genetic variation. A haplotype is defined as the sequence of alleles at SNP sites on each haploid chromosome. Haplotype information is essential in unravelling the…
Motivation: Array Comparative Genomic Hybridization (aCGH) is used to scan the entire genome for variations in DNA copy number. A central task in the analysis of aCGH data is the segmentation into groups of probes sharing the same DNA copy…
Humans have $23$ pairs of homologous chromosomes. The homologous pairs are almost identical pairs of chromosomes. For the most part, differences in homologous chromosome occur at certain documented positions called single nucleotide…
HQC is one of the code-based finalists in the last round of the NIST post quantum cryptography standardization process. In this process, security and implementation efficiency are key metrics for the selection of the candidates. A critical…
Segmentation is an essential requirement in medicine when digital images are used in illness diagnosis, especially, in posterior tasks as analysis and disease identification. An efficient segmentation of brain Magnetic Resonance Images…
Embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs) derived from somatic cells (SCs) provide promising resources for regenerative medicine and medical research, leading to a daily identification of new cell lines.…
Homomorphic encryption (HE) enables computation on encrypted data, and hence it has a great potential in privacy-preserving outsourcing of computations to the cloud. Hardware acceleration of HE is crucial as software implementations are…