Related papers: Shotgun DNA sequencing evidence: sample-specific a…
Motivation: Alternative splicing is an important mechanism in which the regions of pre-mRNAs are differentially joined in order to form different transcript isoforms. Alternative splicing is involved in the regulation of normal…
Phylogenetic trait evolution models allow for the estimation of evolutionary correlations between a set of traits observed in a sample of related organisms. By directly modeling the evolution of the traits along an estimable phylogenetic…
Motivation: Whole-genome high-coverage sequencing has been widely used for personal and cancer genomics as well as in various research areas. However, in the lack of an unbiased whole-genome truth set, the global error rate of variant calls…
Intercellular heterogeneity serves as both a confounding factor in studying individual clones and an information source in characterizing any heterogeneous tissues, such as blood, tumor systems. Due to inevitable sequencing errors and other…
Predicting genetic perturbations enables the identification of potentially crucial genes prior to wet-lab experiments, significantly improving overall experimental efficiency. Since genes are the foundation of cellular life, building gene…
A flood of reliable seismic data will soon arrive. The migration to larger telescopes on the ground may free up 4-m class instruments for multi-site campaigns, and several forthcoming satellite missions promise to yield nearly uninterrupted…
Nearest neighbor (NN) sampling provides more semantic variations than pre-defined transformations for self-supervised learning (SSL) based image recognition problems. However, its performance is restricted by the quality of the support set,…
An off-the-shelf model as a commercial service could be stolen by model stealing attacks, posing great threats to the rights of the model owner. Model fingerprinting aims to verify whether a suspect model is stolen from the victim model,…
DNA storage is now being considered as a new archival storage method for its durability and high information density, but still facing some challenges like high costs and low throughput. By reducing sequencing sample size for decoding…
In 2016, the European Network of Forensic Science Institutes (ENFSI) published guidelines for the evaluation, interpretation and reporting of scientific evidence. In the guidelines, ENFSI endorsed the use of the likelihood ratio (LR) as a…
Given genetic variations and various phenotypical traits, such as Magnetic Resonance Imaging (MRI) features, we consider two important and related tasks in biomedical research: i)to select genetic and phenotypical markers for disease…
Positive and negative association prediction between gene and phenotype helps to illustrate the underlying mechanism of complex traits in organisms. The transcription and regulation activity of specific genes will be adjusted accordingly in…
Biological sequence analysis relies on the ability to denoise the imprecise output of sequencing platforms. We consider a common setting where a short sequence is read out repeatedly using a high-throughput long-read platform to generate…
Kidney stones are a common and debilitating health issue, and genetic factors play a crucial role in determining susceptibility. While Genome-Wide Association Studies (GWAS) have identified numerous single nucleotide polymorphisms (SNPs)…
The shotgun sequencing process involves fragmenting a long DNA sequence (input string) into numerous shorter, unordered, and overlapping segments (referred to as \emph{reads}). The reads are sequenced, and later aligned to reconstruct the…
Sequencing by tunneling is a next-generation approach to read single-base information using electronic tunneling transverse to the single-stranded DNA (ssDNA) backbone while the latter is translocated through a narrow channel. The original…
Significant volumes of knowledge have been accumulated in recent years linking subtle genetic variations to a wide variety of medical disorders from Cystic Fibrosis to mental retardation. Nevertheless, there are still great challenges in…
A fundamental property of DNA is that the reverse complement (RC) of a sequence often carries identical biological meaning. However, state-of-the-art DNA language models frequently fail to capture this symmetry, producing inconsistent…
Segmental duplications (SDs), or low-copy repeats (LCR), are segments of DNA greater than 1 Kbp with high sequence identity that are copied to other regions of the genome. SDs are among the most important sources of evolution, a common…
The decreasing costs and increasing speed and accuracy of DNA sample collection, preparation, and sequencing has rapidly produced an enormous volume of genetic data. However, fast and accurate analysis of the samples remains a bottleneck.…