Related papers: PopIns: population-scale detection of novel sequen…
Traditional sequential recommendation methods assume that users' sequence data is clean enough to learn accurate sequence representations to reflect user preferences. In practice, users' sequences inevitably contain noise (e.g., accidental…
Accurate identification of haplotypes in sequenced human genomes can provide invaluable information about population demography and fine-scale correlations along the genome, thus empowering both population genomic and medical association…
Background Next Generation Sequencing (NGS) has dramatically enhanced our ability to sequence genomes, but not to assemble them. In practice, many published genome sequences remain in the state of a large set of contigs. Each contig…
De novo peptide sequencing from mass spectrometry data is an important method for protein identification. Recently, various deep learning approaches were applied for de novo peptide sequencing and DeepNovoV2 is one of the represetative…
Inverse design of short single-stranded RNA and DNA sequences (aptamers) is the task of finding sequences that satisfy a set of desired criteria. Relevant criteria may be, for example, the presence of specific folding motifs, binding to…
Ultrasound images are commonly formed by sequential acquisition of beam-steered scan-lines. Minimizing the number of required scan-lines can significantly enhance frame rate, field of view, energy efficiency, and data transfer speeds.…
The inner operations of the human brain as a biological processing system remain largely a mystery. Inspired by the function of the human brain and based on the analysis of simple neural network systems in other species, such as Drosophila,…
Identifying frequent subgraphs, also called network motifs, is crucial in analyzing and predicting properties of real-world networks. However, finding large commonly-occurring motifs remains a challenging problem not only due to its NP-hard…
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…
This paper focuses on drawing statistical inference based on a novel variant of maxima or minima nomination sampling (NS) designs. These sampling designs are useful for obtaining more representative sample units from the tails of the…
Analyses of targeted genomic sequencing data from next-generation-sequencing (NGS) technologies typically involves mapping reads to a reference sequence or clustering reads. For a number of species a reference genome is not available so the…
Microbes have a profound impact on our health and environment, but our understanding of the diversity and function of microbial communities is severely limited. Through DNA sequencing of microbial communities (metagenomics), DNA fragments…
Human parsing has recently attracted a lot of research interests due to its huge application potentials. However existing datasets have limited number of images and annotations, and lack the variety of human appearances and the coverage of…
DNA sequencing to identify genetic variants is becoming increasingly valuable in clinical settings. Assessment of variants in such sequencing data is commonly implemented through Bayesian heuristic algorithms. Machine learning has shown…
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…
De novo genome assembly, i.e., rebuilding the sequence of an unknown genome from redundant and erroneous short sequences, is a key but computationally intensive step in many genomics pipelines. The exponential growth of genomic data is…
Background: Advances in high throughput sequencing technologies provide a huge number of genomes to be analyzed. Thus, computational methods play a crucial role in analyzing and extracting knowledge from the data generated. Investigating…
Recent emergence of next-generation DNA sequencing technology has enabled acquisition of genetic information at unprecedented scales. In order to determine the genetic blueprint of an organism, sequencing platforms typically employ…
As sequencing technologies become more affordable and genomic databases expand continuously, the reuse of publicly available sequencing data emerges as a powerful strategy for studying microbial pathogens. Indeed, raw sequencing reads…
Metagenomics characterizes the taxonomic diversity of microbial communities by sequencing DNA directly from an environmental sample. One of the main challenges in metagenomics data analysis is the binning step, where each sequenced read is…