Related papers: Widespread remote introgression in the grass genom…

Detecting and discovering new gene interactions based on known gene expressions and gene interaction data presents a significant challenge. Various statistical and deep learning methods have attempted to tackle this challenge by leveraging…

Motivation: Seed filtering is critical in DNA read mapping, a process where billions of DNA fragments (reads) sampled from a donor are mapped onto a reference genome to identify genomic variants of the donor. Read mappers 1) quickly…

Gene regulatory network inference uses genome-wide transcriptome measurements in response to genetic, environmental or dynamic perturbations to predict causal regulatory influences between genes. We hypothesized that evolution also acts as…

Retrieving gene functional networks from knowledge databases presents a challenge due to the mismatch between disease networks and subtype-specific variations. Current solutions, including statistical and deep learning methods, often fail…

Understanding how genes influence phenotype across species is a fundamental challenge in genetic engineering, which will facilitate advances in various fields such as crop breeding, conservation biology, and personalized medicine. However,…

Causal discovery in multi-omic datasets is crucial for understanding the bigger picture of gene regulatory mechanisms, but remains challenging due to high dimensionality, differentiation of direct from indirect relationships, and hidden…

We have developed a novel method to rapidly obtain homologous genomic data for phylogenetics directly from next-generation sequencing reads without the use of a reference genome. This software, called SISRS, avoids the time consuming steps…

Populations of isogenic embryonic stem cells or clonal bacteria often exhibit extensive phenotypic heterogeneity which arises from stochastic intrinsic dynamics of cells. The internal state of the cell can be transmitted epigenetically in…

Understanding the dynamics of genome rearrangements is a major issue of phylogenetics. Phylogenetics is the study of species evolution. A major goal of the field is to establish evolutionary relationships within groups of species, in order…

Weed management plays an important role in many modern agricultural applications. Conventional weed control methods mainly rely on chemical herbicides or hand weeding, which are often cost-ineffective, environmentally unfriendly, or even…

Recent technological advances coupled with large sample sets have uncovered many factors underlying the genetic basis of traits and the predisposition to complex disease, but much is left to discover. A common thread to most genetic…

Motivation The genotype assignment problem consists of predicting, from the genotype of an individual, which of a known set of populations it originated from. The problem arises in a variety of contexts, including wildlife forensics,…

Genomic selection (GS), as a critical crop breeding strategy, plays a key role in enhancing food production and addressing the global hunger crisis. The predominant approaches in GS currently revolve around employing statistical methods for…

Repetitive DNA sequences underpin genome architecture and evolutionary processes, yet they remain challenging to classify accurately. Terrier is a deep learning model designed to overcome these challenges by classifying repetitive DNA…

Phylogenetic networks which are, as opposed to trees, suitable to describe processes like hybridization and horizontal gene transfer, play a substantial role in evolutionary research. However, while non-treelike events need to be taken into…

Precision agriculture relies heavily on effective weed management to ensure robust crop yields. This study presents RoWeeder, an innovative framework for unsupervised weed mapping that combines crop-row detection with a noise-resilient deep…

With the strength of deep generative models, 3D pose transfer regains intensive research interests in recent years. Existing methods mainly rely on a variety of constraints to achieve the pose transfer over 3D meshes, e.g., the need for…

We present a technique to characterize differentially expressed genes in terms of their position in a high-dimensional co-expression network. The set-up of Gaussian graphical models is used to construct representations of the co-expression…

We develop a model for speciation due to postzygotic incompatibility generated by autoimmune reactions. The model is based on predator-prey interactions between a host plants and their pathogens. Such interactions are often…

Rhizomes play fundamental roles in plant evolution, persistence, and environmental adaptation by enabling clonal propagation, resource storage, and stress resilience. Despite their ecological and agronomic importance across diverse plant…