Related papers: Pan-genome Analysis of Angiosperm Plastomes using …
Investigating the genetic architecture of complex diseases is challenging due to the multifactorial and interactive landscape of genomic and environmental influences. Although genome-wide association studies (GWAS) have identified thousands…
In cancer research, high-throughput profiling has been extensively conducted. In recent studies, the integrative analysis of data on multiple cancer patient groups/subgroups has been conducted. Such analysis has the potential to reveal the…
Background. Models of ancestral gene order reconstruction have progressively integrated different evolutionary patterns and processes such as unequal gene content, gene duplications, and implicitly sequence evolution via reconciled gene…
Single-cell RNA-seq data allow the quantification of cell type differences across a growing set of biological contexts. However, pinpointing a small subset of genomic features explaining this variability can be ill-defined and…
Cells of diatoms and related algae with complex plastids of red algal origin are highly compartmentalized. These plastids are surrounded by four envelope membranes, which also define the periplastidic compartment (PPC), the space between…
In the fourth \emph{Fermi} Large Area Telescope source catalog (4FGL), 5064 $\gamma$-ray sources are reported, including 3207 active galactic nuclei (AGNs), 239 pulsars, 1336 unassociated sources, 92 sources with weak association with…
Provenance analysis based on system audit data has emerged as a fundamental approach for investigating Advanced Persistent Threat (APT) attacks. Due to the high concealment and long-term persistence of APT attacks, they are only represented…
This paper presents a method for large corpus analysis to semantically classify an entire clause. In particular, we use cooccurrence statistics among similar clauses to determine the aspectual class of an input clause. The process examines…
Motivation: Multi-omics integration can improve cancer subtyping, but modality informativeness and noise vary across cancer types and patients. Existing graph-based methods optimize modality weights jointly with the classification objective…
In this article we are describing a new algorithm for detecting and validating partial horizontal gene transfers (HGT). The presented algorithm is based on a sliding window procedure which analyzes fragments of the given multiple sequence…
Conjugated organic molecules represent an important area of materials chemistry for both fundamental scientific exploration and technological applications. Using a genetic algorithm to computationally screen up to ~25-50 million molecules…
Objectives: Pancreatic cancer is a lethal disease, hard to diagnose and usually results in poor prognosis and high mortality. Developing an artificial intelligence (AI) algorithm to accurately and universally predict the early cancer risk…
Background: It is well known that the development of cancer is caused by the accumulation of somatic mutations within the genome. For oncogenes specifically, current research suggests that there is a small set of "driver" mutations that are…
A prespecified set of genes may be enriched, to varying degrees, for genes that have altered expression levels relative to two or more states of a cell. Knowing the enrichment of gene sets defined by functional categories, such as gene…
The genotype-phenotype map is an essential object in our understanding of organismal complexity and adaptive properties, determining at once genomic plasticity and those constraints that may limit the ability of genomes to attain…
Identifying phenotypes plays an important role in furthering our understanding of disease biology through practical applications within healthcare and the life sciences. The challenge of dealing with the complexities and noise within…
In several recent papers new gene-detection algorithms were proposed for detecting protein-coding regions without requiring learning dataset of already known genes. The fact that unsupervised gene-detection is possible closely connected to…
The genome-wide recombination rate ($RR$) of a species is often described by one parameter, the ratio between total genetic map length ($G$) and physical map length ($P$), measured in centiMorgans per Megabase (cM/Mb). The value of this…
While deep learning has revolutionized the prediction of rigid protein structures, modelling the conformational ensembles of Intrinsically Disordered Proteins (IDPs) remains a key frontier. Current AI paradigms present a trade-off: Protein…
Recently, the EAGL-I system was developed to rapidly create massive labeled datasets of plants intended to be commonly used by farmers and researchers to create AI-driven solutions in agriculture. As a result, a publicly available plant…