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Despite significant strides in the field of 3D scene editing, current methods encounter substantial challenge, particularly in preserving 3D consistency in multi-view editing process. To tackle this challenge, we propose a progressive 3D…
"Epigenetic Tracking" is an evo-devo method to generate arbitrary 2d or 3d shapes; as such, it belongs to the field of "artificial embryology". In silico experiments have proved the effectiveness of the method in devo-evolving shapes of any…
The identification of disease-associated genes has recently gathered much attention for uncovering disease complex mechanisms that could lead to new insights into the treatment of diseases. For exploring disease-susceptible genes, not only…
The SARS-CoV-2 RNA pseudoknot is a promising target for antiviral intervention, as it regulates the efficiency of $-$1 programmed ribosomal frameshifting ($-$1 PRF), a mechanism that is essential for viral protein synthesis. The pseudoknot…
Stimulated Raman scattering (SRS) microscopy offers great potential to surpass fluorescent-based approaches, owing to the sharp linewidth of Raman vibrations amenable to super-multiplex cell imaging, but currently lacks one crucial…
Large-scale volumetric medical images with annotation are rare, costly, and time prohibitive to acquire. Self-supervised learning (SSL) offers a promising pre-training and feature extraction solution for many downstream tasks, as it only…
Being a dual purpose enzyme, the DNA polymerase is responsible for elongation of the newly formed DNA strand as well as cleaving the erroneous growth in case of a misincorporation. The efficiency of replication depends on the coordination…
Inspired by the success of unsupervised pre-training paradigms, researchers have applied these approaches to DNA pre-training. However, we argue that these approaches alone yield suboptimal results because pure DNA sequences lack sufficient…
DNA is not only the genetic material of life, but also a favorable material for a new computing model. Various research works based on DNA computing have been carried out in recent years. DNA sequence design is the foundation of such…
Eukaryotic DNA replication follows a specific temporal program, with some genomic regions consistently replicating earlier than others, yet what determines this program is largely unknown. Highly transcribed regions have been observed to…
Next generation sequencing technology rapidly produces massive volume of data and quality control of this sequencing data is essential to any genomic analysis. Here we present MEEPTOOLS, which is a collection of open-source tools based on…
Recent advancements in spatial transcriptomics technologies allow researchers to simultaneously measure RNA expression levels for hundreds to thousands of genes while preserving spatial information within tissues, providing critical…
Renaturation of complementary single strands of DNA is one of the important processes that requires better understanding in the view of molecular biology and biological physics. Here we develop a stochastic dynamical model on the DNA…
This paper is a partial reproduction of work by Soltani et al. which presented EvoCrash, a tool for replicating software failures in Java by reproducing stack traces. EvoCrash uses a guided genetic algorithm to generate JUnit test cases…
Spatial transcriptomics (ST) has emerged as an advanced technology that provides spatial context to gene expression. Recently, deep learning-based methods have shown the capability to predict gene expression from WSI data using ST data.…
Predicting how genetic variation affects phenotypic outcomes at the organismal, cellular, and molecular levels requires deciphering the cis-regulatory code, the sequence rules by which non-coding regions regulate genes. In this perspective,…
Next-generation sequencing (NGS) is a pivotal technique in genome sequencing due to its high throughput, rapid results, cost-effectiveness, and enhanced accuracy. Its significance extends across various domains, playing a crucial role in…
One of the notable fields in studying the genetics of cancer is disease gene identification which affects disease treatment and drug discovery. Many researches have been done in this field. Genome-wide association studies (GWAS) are one of…
The way to infer well-supported phylogenetic trees that precisely reflect the evolutionary process is a challenging task that completely depends on the way the related core genes have been found. In previous computational biology studies,…
Emerging evidence suggests that the introns and intergenic sequences of the genomes of higher eukaryotes (the ``junk'' DNA) codes for a vast, RNA-based, genetic regulatory network. It is believed that this network is responsible for the…