Genomics
Spatial multi-modal omics technology, highlighted by Nature Methods as an advanced biological technique in 2023, plays a critical role in resolving biological regulatory processes with spatial context. Recently, graph neural networks based…
With the rapid development of high-throughput sequencing platforms, an increasing number of omics technologies, such as genomics, metabolomics, and transcriptomics, are being applied to disease genetics research. However, biological data…
Liver cancer is a leading cause of cancer-related mortality worldwide, with its high genetic heterogeneity complicating diagnosis and treatment. This study introduces DLSOM, a deep learning framework utilizing stacked autoencoders to…
Summary: Accurate phenotype prediction from genomic sequences is a highly coveted task in biological and medical research. While machine-learning holds the key to accurate prediction in a variety of fields, the complexity of biological data…
Computational variant effect predictors (VEPs) are providing increasingly strong evidence to classify the pathogenicity of missense variants. Precision vs. recall analysis is useful in evaluating VEP performance, especially when adjusted…
The alignment between RNA sequences and structures in foundation models (FMs) has yet to be thoroughly investigated. Existing FMs have struggled to establish sequence-structure alignment, hindering the free flow of genomic information…
In unforeseen situations, such as nuclear power plant's or civilian radiation accidents, there is a need for effective and computationally inexpensive methods to determine the expression level of a selected gene panel, allowing for rough…
The advancement of novel combinatorial CRISPR screening technologies enables the identification of synergistic gene combinations on a large scale. This is crucial for developing novel and effective combination therapies, but the…
AI language models (LMs) show promise for biological sequence analysis. We re-engineered open-source LMs (GPT-2, BLOOM, DistilRoBERTa, ELECTRA, and Mamba, ranging from 70M to 12B parameters) for microbial sequence classification. The models…
This groundbreaking research extracted DNA from petroleum using nanoparticle affinity bead technology, yielding 3,159,020 petroleum DNA (pDNA) sequences, primarily environmental DNA. While most original in situ DNA (oriDNA) was lost,…
High quality ancient DNA (aDNA) is essential for molecular paleontology. Due to DNA degradation and contamination by environmental DNA (eDNA), current research is limited to fossils less than 1 million years old. The study successfully…
This article critically examines the methodologies applied in ancient DNA (aDNA) research, particularly those developed by Dr. P\"a\"abo's team, which have significantly influenced the field. The focus is on the challenges of distinguishing…
In cancer research, the term epigenetics was used in the 1970s in its modern sense encompassing non-genetic events modifying the chromatin state, mainly to oppose the emerging oncogene paradigm. However, starting from the establishment of…
The development of single-cell and spatial transcriptomics has revolutionized our capacity to investigate cellular properties, functions, and interactions in both cellular and spatial contexts. However, the analysis of single-cell and…
Mutational signatures connect characteristic mutational patterns in the genome with biological or chemical processes that take place in cancers. Analysis of mutational signatures can help elucidate tumor evolution, prognosis, and…
DNA sequence alignment involves assigning short DNA reads to the most probable locations on an extensive reference genome. This process is crucial for various genomic analyses, including variant calling, transcriptomics, and epigenomics.…
Motivation: The three-dimensional (3D) organization of the genome plays a critical role in regulating gene expression and maintaining cellular homeostasis. Disruptions in this spatial organization can result in abnormal chromatin…
The rise of complex multicellular ecosystems Neoproterozoic time was preceded by a microbial Proterozoic biosphere, where productivity may have been largely restricted to microbial mats made up of bacteria including oxygenic photosynthetic…
Building a general-purpose task model similar to ChatGPT has been an important research direction for gene large language models. Instruction fine-tuning is a key component in building ChatGPT, but existing instructions are primarily based…
Metastasis is a leading cause of cancer-related mortality and remains challenging to detect during early stages. Accurate identification of cancers likely to metastasize can improve treatment strategies and patient outcomes. This study…