相关论文: Fast Characterization of Segmental Duplications in…
Array-Based Comparative Genomic Hybridization (aCGH) is a method used to search for genomic regions with copy numbers variations. For a given aCGH profile, one challenge is to accurately segment it into regions of constant copy number.…
Short-read DNA sequencing instruments can yield over 1e+12 bases per run, typically composed of reads 150 bases long. Despite this high throughput, de novo assembly algorithms have difficulty reconstructing contiguous genome sequences using…
There is increasing realization in neuroscience that information is represented in the brain, e.g., neocortex, hippocampus, in the form sparse distributed codes (SDCs), a kind of cell assembly. Two essential questions are: a) how are such…
Motivation: Low-complexity (LC) DNA sequences are compositionally repetitive sequences that are often associated with spurious homologous matches and variant calling artifacts. While algorithms for identifying LC sequences exist, they…
DNA sequences are prone to creating secondary structures by folding back on themselves by non-specific hybridization among its nucleotides. The formation of secondary structures makes the sequences chemically inactive towards synthesis and…
Analyzing the properties of duplicate genes during evolution is useful to understand the development of new cell functions. The yeast S. cerevisiae is a useful testing ground for this problem, because its duplicated genes with different…
The paper addresses challenges in storing and retrieving sequences in contexts like anomaly detection, behavior prediction, and genetic information analysis. Associative Knowledge Graphs (AKGs) offer a promising approach by leveraging…
Motivation: High throughput DNA sequencing (HTS) technologies generate an excessive number of small DNA segments -- called short reads -- that cause significant computational burden. To analyze the entire genome, each of the billions of…
Bayesian model comparison frameworks can be used when fitting models to data in order to infer the appropriate model complexity in a data-driven manner. We aim to use them to detect the correct number of major episodes of star formation…
Next-generation wireless communication systems impose much stricter requirements for transmission rate, latency, and reliability. The peak data rate of 6G networks should be no less than 1 Tb/s, which is comparable to existing long-haul…
The nucleotide sequence representation of DNA can be inadequate for resolving protein-DNA binding sites and regulatory substrates, such as those involved in gene expression and horizontal gene transfer. Considering that sequence-like…
Single-strand breaks (SSBs) are the major DNA damage in the genome arising spontaneously as the outcome of genotoxins and intermediates of DNA transactions. SSBs play a crucial role in various biological processes and show a non-random…
Semantic Segmentation is an important module for autonomous robots such as self-driving cars. The advantage of video segmentation approaches compared to single image segmentation is that temporal image information is considered, and their…
Genome-wide association studies (GWAS) have led to the discovery of numerous single nucleotide polymorphisms (SNPs) associated with various phenotypes and complex diseases. However, the identified genetic variants do not fully explain the…
The Shortest Common Superstring (SCS) problem is a fundamental task in sequence analysis. In genome assembly, however, the double-stranded nature of DNA implies that each fragment may occur either in its original orientation or as its…
The Jaccard similarity index is an important measure of the overlap of two sets, widely used in machine learning, computational genomics, information retrieval, and many other areas. We design and implement SimilarityAtScale, the first…
One of the most computationally intensive tasks in computational biology is de novo genome assembly, the decoding of the sequence of an unknown genome from redundant and erroneous short sequences. A common assembly paradigm identifies…
Binary Code Similarity Detection (BCSD) is not only essential for security tasks such as vulnerability identification but also for code copying detection, yet it remains challenging due to binary stripping and diverse compilation…
Supervised learning algorithms based on Convolutional Neural Networks have become the benchmark for medical image segmentation tasks, but their effectiveness heavily relies on a large amount of labeled data. However, annotating medical…
During cancer progression, malignant cells accumulate somatic mutations that can lead to genetic aberrations. In particular, evolutionary events akin to segmental duplications or deletions can alter the copy-number profile (CNP) of a set of…