A5038899615- Genomics and Phylogenetic Studies
- Genomics and Chromatin Dynamics
- Chromosomal and Genetic Variations
- RNA and protein synthesis mechanisms
- Genomic variations and chromosomal abnormalities
- Explainable Artificial Intelligence (XAI)
- RNA Research and Splicing
- Bioinformatics and Genomic Networks
- Plant Reproductive Biology
- Cancer Genomics and Diagnostics
- Genetics, Aging, and Longevity in Model Organisms
- Cell Image Analysis Techniques
- Machine Learning and Data Classification
- Retinal Development and Disorders
- CRISPR and Genetic Engineering
- Gene expression and cancer classification
- Primate Behavior and Ecology
- Genetic factors in colorectal cancer
Carnegie Mellon University
2020-2025
China Agricultural University
2020
We present haplotype-resolved reference genomes and comparative analyses of six ape species, namely: chimpanzee, bonobo, gorilla, Bornean orangutan, Sumatran siamang. achieve chromosome-level contiguity with unparalleled sequence accuracy (<1 error in 500,000 base pairs), completely sequencing 215 gapless chromosomes telomere-to-telomere. resolve challenging regions, such as the major histocompatibility complex immunoglobulin loci, providing more in-depth evolutionary insights. Comparative...
Abstract The most dynamic and repetitive regions of great ape genomes have traditionally been excluded from comparative studies 1–3 . Consequently, our understanding the evolution species is incomplete. Here we present haplotype-resolved reference analyses six species: chimpanzee, bonobo, gorilla, Bornean orangutan, Sumatran orangutan siamang. We achieve chromosome-level contiguity with substantial sequence accuracy (<1 error in 2.7 megabases) completely 215 gapless chromosomes...
Modeling long-range DNA dependencies is crucial for understanding genome structure and function across a wide range of biological contexts. However, effectively capturing these extensive dependencies, which may span millions base pairs in tasks such as three-dimensional (3D) chromatin folding prediction, remains significant challenge. Furthermore, comprehensive benchmark suite evaluating that rely on notably absent. To address this gap, we introduce DNAL ong B ench , dataset encompassing...
Genome editing enzymes can introduce targeted changes to the DNA in living cells 1-4 , transforming biological research and enabling first approved gene therapy for sickle cell disease 5 . However, their genome-wide activity be altered by genetic variation at on- or off-target sites 6-8 potentially impacting both precision therapeutic safety. Due a lack of scalable methods measure from large populations diverse target libraries, frequency extent these variant effects on remains unknown....
Abstract Advances in machine learning (ML) have enabled the development of next-generation prediction models for complex computational biology problems. These developments spurred use interpretable (IML) to unveil fundamental biological insights through data-driven knowledge discovery. However, general, standards and guidelines IML usage not been well-characterized, representing a major gap toward fully realizing potential IML. Here, we introduce workflow on best practices using methods...
Abstract Motivation The accumulation of somatic mutations plays critical roles in cancer development and progression. However, the global patterns mutations, especially non-coding their defining molecular subtypes have not been well characterized due to computational challenges analysing complex mutational patterns. Results Here, we develop a new algorithm, called MutSpace, effectively extract patient-specific features using an embedding framework for larger sequence context. Our method is...
The spatial positioning of chromosomes relative to functional nuclear bodies is intertwined with genome functions such as transcription. However, the sequence patterns and epigenomic features that collectively influence chromatin in a genome-wide manner are not well understood. Here, we develop new transformer-based deep learning model called UNADON, which predicts cytological distance specific type body, measured by TSA-seq, using both signals. Evaluations UNADON four cell lines (K562, H1,...
Hormones play a crucial role both in plants and animals. As we all known, hormones work through specific receptors different organisms. Therefore, the hormone interaction between plant animal is an interesting question worth discussing. Recently, food safety has become common topic concerned by consumers. A widely discussed rumor such as “Fruit bulking agent some human reproductive hormones” leads us to consider whether did regulate growth. Based on large amount of previous research,...