Related papers: Template-based eukaryotic genome editing directed …
Motivation: Next generation methods of DNA sequencing produce relatively high rate of reading errors, which interfere with de novo genome assembly of newly sequenced organisms and particularly affect the quality of SNP detection important…
Syntax-guided synthesis is a paradigm in program synthesis in which the search space of candidate solutions is constrained by a syntactic template in the form of a grammar. These syntactic constraints serve two purposes: constraining the…
DNA methylation is an epigenetic mechanism that regulates gene expression by adding methyl groups to DNA. Abnormal methylation patterns can disrupt gene expression and have been linked to cancer development. To quantify DNA methylation,…
We present the Star-Based Automated Single-locus and Epistasis analysis tool - Genetic Programming (StarBASE-GP), an automated framework for discovering meaningful genetic variants associated with phenotypic variation in large-scale genomic…
Accurately reconstructing Gene Regulatory Networks (GRNs) is crucial for understanding gene functions and disease mechanisms. Single-cell RNA sequencing (scRNA-seq) technology provides vast data for computational GRN reconstruction. Since…
Cellular reprogramming, the conversion of one cell type to another, has fundamentally transformed our conception of cell types. Cellular reprogramming induces global changes in gene expression involving hundreds of transcription factors and…
Text guided 3D medical image segmentation offers a flexible alternative to class based and spatial prompt based models by allowing users to specify regions of interest directly in natural language. This paradigm avoids reliance on…
Recent advancements in single-cell genomics necessitate precision in gene panel selection to interpret complex biological data effectively. Those methods aim to streamline the analysis of scRNA-seq data by focusing on the most informative…
Spatial transcriptomics (ST) is essential for understanding diseases and developing novel treatments. It measures gene expression of each fine-grained area (i.e., different windows) in the tissue slide with low throughput. This paper…
Enzymatic DNA labeling is a powerful tool with applications in biochemistry, molecular biology, biotechnology, medical science, and genomic research. This paper contributes to the evolving field of DNA-based data storage by presenting a…
Single-cell-resolution spatial transcriptomics profiles gene expression at cellular locations in native tissues, yet accurate cell-type annotation remains challenging: imaging-based platforms are constrained by targeted gene panels, whereas…
The modeling of genomic sequences presents unique challenges due to their length and structural complexity. Traditional sequence models struggle to capture long-range dependencies and biological features inherent in DNA. In this work, we…
The investigation of plant transcriptional regulation constitutes a fundamental basis for crop breeding, where cis-regulatory elements (CREs), as the key factor determining gene expression, have become the focus of crop genetic improvement…
Virtual screening (VS) is an essential technique for understanding biomolecular interactions, particularly, drug design and discovery. The best-performing VS models depend vitally on three-dimensional (3D) structures, which are not…
Designing novel proteins with desired characteristics remains a significant challenge due to the large sequence space and the complexity of sequence-function relationships. Efficient exploration of this space to identify sequences that meet…
3D Gaussian Splatting (GS) is one of the most promising novel 3D representations that has received great interest in computer graphics and computer vision. While various systems have introduced editing capabilities for 3D GS, such as those…
We formulate a kinetic model of DNA replication that quantitatively describes recent results on DNA replication in the in vitro system of Xenopus laevis prior to the mid-blastula transition. The model describes well a large amount of…
Inspired by the effectiveness of genetic algorithms and the importance of synthesizability in molecular design, we present SynGA, a simple genetic algorithm that operates directly over synthesis routes. Our method features custom crossover…
Background: Advances in high throughput sequencing technologies provide a huge number of genomes to be analyzed. Thus, computational methods play a crucial role in analyzing and extracting knowledge from the data generated. Investigating…
The accurate retinal vessel segmentation (RVS) is of great significance to assist doctors in the diagnosis of ophthalmology diseases and other systemic diseases. Manually designing a valid neural network architecture for retinal vessel…