Search
Search Results
-
De-MISTED: Image-based classification of erroneous multiple sequence alignments using convolutional neural networks
The widespread use of high throughput genome sequencing technologies has resulted in a significant increase in the number of available sequences,...
-
SAM: cross-modal semantic alignments module for image-text retrieval
Cross-modal image-text retrieval has gained increasing attention due to its ability to combine computer vision with natural language processing....
-
Graph-Based Genome Inference from Hi-C Data
Three-dimensional chromosome structure plays an important role in fundamental genomic functions. Hi-C, a high-throughput, sequencing-based technique,...
-
CaReAl: capturing read alignments in a BAM file rapidly and conveniently
Some of the variants detected by high-throughput sequencing (HTS) are often not reproducible. To minimize the technical-induced artifacts, secondary...
-
Zoomable Heatmaps: Improving Manhattan Plots to Compare Multiple Genome-Wide Studies
Making comparisons between genome-wide association studies is a crucial practice in genetics. Despite this, conventional visualizations used in these...
-
Using alignment-free and pattern mining methods for SARS-CoV-2 genome analysis
Examining the genome sequences of the SARS-CoV-2 virus, that causes the respiratory disease known as coronavirus disease 2019 (COVID-19), play...
-
Fast and accurate bootstrap confidence limits on genome-scale phylogenies using little bootstraps
Felsenstein’s bootstrap approach is widely used to assess confidence in species relationships inferred from multiple sequence alignments. It...
-
COVID-19 Genome Analysis Using Alignment-Free Methods
Examining the genome sequences of the novel coronavirus (COVID-19) strains is critical to properly understand this disease and its functionalities....
-
Haplotype-Aware Sequence Alignment to Pangenome Graphs
Modern pangenome graphs are built using haplotype-resolved genome assemblies. While map** reads to a pangenome graph, prioritizing alignments that...
-
See Finer, See More: Implicit Modality Alignment for Text-Based Person Retrieval
Text-based person retrieval aims to find the query person based on a textual description. The key is to learn a common latent space map** between...
-
Time- and memory-efficient genome assembly with Raven
Whole genome sequencing technologies are unable to invariably read DNA molecules intact, a shortcoming that assemblers try to resolve by stitching...
-
Bi-alignments as Models of Incongruent Evolution of RNA Sequence and Secondary Structure
RNA molecules may be subject to independent selection pressures on sequence and structure. This can, in principle, lead to the preservation of...
-
Explainable deep neural networks for novel viral genome prediction
Viral infection causes a wide variety of human diseases including cancer and COVID-19. Viruses invade host cells and associate with host molecules,...
-
Scalable Reference Genome Assembly from Compressed Pan-Genome Index with Spark
High-throughput sequencing (HTS) technologies have enabled rapid sequencing of genomes and large-scale genome analytics with massive data sets....
-
Uncertainty Quantification Using Subsampling for Assembly-Free Estimates of Genomic Distance and Phylogenetic Relationships
Computing the distance between two genomes, often without using alignments or even access to assembled sequences, is fundamental to many downstream...
-
Irregular alignment of arbitrarily long DNA sequences on GPU
The use of Graphics Processing Units to accelerate computational applications is increasingly being adopted due to its affordability, flexibility and...
-
Generating Genomic Maps of Z-DNA with the Transformer Algorithm
Z-DNA and Z-RNA were shown to play an important role in various processes of genome functioning acting as flipons that launch or suppress genetic...
-
Gaps and Runs in Syntenic Alignments
Gene loss is the obverse of novel gene acquisition by a genome through a variety of evolutionary processes. It serves a number of functional and...
-
Sequence to Graph Alignment Using Gap-Sensitive Co-linear Chaining
Co-linear chaining is a widely used technique in sequence alignment tools that follow seed-filter-extend methodology. It is a mathematically rigorous...
-
Improved DNA-versus-Protein Homology Search for Protein Fossils
Protein fossils, i.e. noncoding DNA descended from coding DNA, arise frequently from transposable elements (TEs), decayed genes, and viral...