eccDNAMamba: A Pre-Trained Model for Ultra-Long eccDNA Sequence Analysis
Fuente:
arXiv
Saved in:
| Main Authors: | Liu, Zhenke, Li, Jien, Zhang, Ziqi |
|---|---|
| Format: | Preprint |
| Published: |
2025
|
| Subjects: | |
| Online Access: | |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
Similar Items
Embed-Search-Align: DNA Sequence Alignment using Transformer Models
by: Holur, Pavan, et al.
Published: (2023)
by: Holur, Pavan, et al.
Published: (2023)
DiscDiff: Latent Diffusion Model for DNA Sequence Generation
by: Li, Zehui, et al.
Published: (2024)
by: Li, Zehui, et al.
Published: (2024)
HybriDNA: A Hybrid Transformer-Mamba2 Long-Range DNA Language Model
by: Ma, Mingqian, et al.
Published: (2025)
by: Ma, Mingqian, et al.
Published: (2025)
scUnified: An AI-Ready Standardized Resource for Single-Cell RNA Sequencing Analysis
by: Xu, Ping, et al.
Published: (2025)
by: Xu, Ping, et al.
Published: (2025)
Dy-mer: An Explainable DNA Sequence Representation Scheme using Dictionary Learning
by: Peng, Zhiyuan, et al.
Published: (2024)
by: Peng, Zhiyuan, et al.
Published: (2024)
VQDNA: Unleashing the Power of Vector Quantization for Multi-Species Genomic Sequence Modeling
by: Li, Siyuan, et al.
Published: (2024)
by: Li, Siyuan, et al.
Published: (2024)
GeneZip: Region-Aware Compression for Long Context DNA Modeling
by: Zhao, Jianan, et al.
Published: (2026)
by: Zhao, Jianan, et al.
Published: (2026)
How Private Are DNA Embeddings? Inverting Foundation Model Representations of Genomic Sequences
by: Ouaari, Sofiane, et al.
Published: (2026)
by: Ouaari, Sofiane, et al.
Published: (2026)
EnTao-GPM: DNA Foundation Model for Predicting the Germline Pathogenic Mutations
by: Lin, Zekai, et al.
Published: (2025)
by: Lin, Zekai, et al.
Published: (2025)
Helix-mRNA: A Hybrid Foundation Model For Full Sequence mRNA Therapeutics
by: Wood, Matthew, et al.
Published: (2025)
by: Wood, Matthew, et al.
Published: (2025)
scCluBench: Comprehensive Benchmarking of Clustering Algorithms for Single-Cell RNA Sequencing
by: Xu, Ping, et al.
Published: (2025)
by: Xu, Ping, et al.
Published: (2025)
Interpretable DNA Sequence Classification via Dynamic Feature Generation in Decision Trees
by: Huynh, Nicolas, et al.
Published: (2026)
by: Huynh, Nicolas, et al.
Published: (2026)
JEPA-DNA: Grounding Genomic Foundation Models through Joint-Embedding Predictive Architectures
by: Larey, Ariel, et al.
Published: (2026)
by: Larey, Ariel, et al.
Published: (2026)
scInterpreter: Training Large Language Models to Interpret scRNA-seq Data for Cell Type Annotation
by: Li, Cong, et al.
Published: (2024)
by: Li, Cong, et al.
Published: (2024)
MergeDNA: Context-aware Genome Modeling with Dynamic Tokenization through Token Merging
by: Li, Siyuan, et al.
Published: (2025)
by: Li, Siyuan, et al.
Published: (2025)
FGBERT: Function-Driven Pre-trained Gene Language Model for Metagenomics
by: Duan, ChenRui, et al.
Published: (2024)
by: Duan, ChenRui, et al.
Published: (2024)
CRC-Screen: Certified DNA-Synthesis Hazard Screening Under Taxonomic Shift
by: Hasan, Najmul
Published: (2026)
by: Hasan, Najmul
Published: (2026)
Celler:A Genomic Language Model for Long-Tailed Single-Cell Annotation
by: Zhao, Huan, et al.
Published: (2025)
by: Zhao, Huan, et al.
Published: (2025)
Exploring the Potentials and Challenges of Using Large Language Models for the Analysis of Transcriptional Regulation of Long Non-coding RNAs
by: Wang, Wei, et al.
Published: (2024)
by: Wang, Wei, et al.
Published: (2024)
Omni-DNA: A Unified Genomic Foundation Model for Cross-Modal and Multi-Task Learning
by: Li, Zehui, et al.
Published: (2025)
by: Li, Zehui, et al.
Published: (2025)
Cross-Platform DNA Methylation Classifier for the Eight Molecular Subtypes of Group 3 & 4 Medulloblastoma
by: Abid, Omer, et al.
Published: (2025)
by: Abid, Omer, et al.
Published: (2025)
Full Field Transmission Tomography (FFOTT) for imaging extrachromosomal circular DNA (eccDNA) in cancer cell nuclei
by: Boccara, Nathan, et al.
Published: (2024)
by: Boccara, Nathan, et al.
Published: (2024)
scPilot: Large Language Model Reasoning Toward Automated Single-Cell Analysis and Discovery
by: Gao, Yiming, et al.
Published: (2026)
by: Gao, Yiming, et al.
Published: (2026)
WTKO-CNN: Deep Learning Reveals Sequence Motifs Distinguishing Wild-Type and Knockout ATAC-seq Peaks
by: Dey, Lopamudra
Published: (2026)
by: Dey, Lopamudra
Published: (2026)
Absorb & Escape: Overcoming Single Model Limitations in Generating Genomic Sequences
by: Li, Zehui, et al.
Published: (2024)
by: Li, Zehui, et al.
Published: (2024)
Multimodal 3D Genome Pre-training
by: Yang, Minghao, et al.
Published: (2025)
by: Yang, Minghao, et al.
Published: (2025)
Artificial Intelligence and Deep Learning Algorithms for Epigenetic Sequence Analysis: A Review for Epigeneticists and AI Experts
by: Tahir, Muhammad, et al.
Published: (2025)
by: Tahir, Muhammad, et al.
Published: (2025)
BSM: Small but Powerful Biological Sequence Model for Genes and Proteins
by: Xiang, Weixi, et al.
Published: (2024)
by: Xiang, Weixi, et al.
Published: (2024)
Multimodal Modeling of CRISPR-Cas12 Activity Using Foundation Models and Chromatin Accessibility Data
by: Amirabad, Azim Dehghani, et al.
Published: (2025)
by: Amirabad, Azim Dehghani, et al.
Published: (2025)
Machine Learning-Based Genomic Linguistic Analysis (Gene Sequence Feature Learning): A Case Study on Predicting Heavy Metal Response Genes in Rice
by: Yang, Ruiqi, et al.
Published: (2025)
by: Yang, Ruiqi, et al.
Published: (2025)
SeqMate: A Novel Large Language Model Pipeline for Automating RNA Sequencing
by: Mondal, Devam, et al.
Published: (2024)
by: Mondal, Devam, et al.
Published: (2024)
scSiameseClu: A Siamese Clustering Framework for Interpreting single-cell RNA Sequencing Data
by: Xu, Ping, et al.
Published: (2025)
by: Xu, Ping, et al.
Published: (2025)
Beyond Conditional Computation: Retrieval-Augmented Genomic Foundation Models with Gengram
by: Xu, Huinan, et al.
Published: (2026)
by: Xu, Huinan, et al.
Published: (2026)
DYNA: Disease-Specific Language Model for Variant Pathogenicity
by: Zhan, Huixin, et al.
Published: (2024)
by: Zhan, Huixin, et al.
Published: (2024)
Survey and Improvement Strategies for Gene Prioritization with Large Language Models
by: Neeley, Matthew, et al.
Published: (2025)
by: Neeley, Matthew, et al.
Published: (2025)
Life-Code: Central Dogma Modeling with Multi-Omics Sequence Unification
by: Liu, Zicheng, et al.
Published: (2025)
by: Liu, Zicheng, et al.
Published: (2025)
Enhanced Gene Selection in Single-Cell Genomics: Pre-Filtering Synergy and Reinforced Optimization
by: Zhang, Weiliang, et al.
Published: (2024)
by: Zhang, Weiliang, et al.
Published: (2024)
Analysis of multiple‐herbicide resistant Amaranthus palmeri populations from Spain points to an introduction of the eccDNA from America
by: Alfredo Manicardi, et al.
Published: (2025)
by: Alfredo Manicardi, et al.
Published: (2025)
Ctrl-DNA: Controllable Cell-Type-Specific Regulatory DNA Design via Constrained RL
by: Chen, Xingyu, et al.
Published: (2025)
by: Chen, Xingyu, et al.
Published: (2025)
NABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction
by: Li, Zhongmin, et al.
Published: (2025)
by: Li, Zhongmin, et al.
Published: (2025)
Similar Items
-
Embed-Search-Align: DNA Sequence Alignment using Transformer Models
by: Holur, Pavan, et al.
Published: (2023) -
DiscDiff: Latent Diffusion Model for DNA Sequence Generation
by: Li, Zehui, et al.
Published: (2024) -
HybriDNA: A Hybrid Transformer-Mamba2 Long-Range DNA Language Model
by: Ma, Mingqian, et al.
Published: (2025) -
scUnified: An AI-Ready Standardized Resource for Single-Cell RNA Sequencing Analysis
by: Xu, Ping, et al.
Published: (2025) -
Dy-mer: An Explainable DNA Sequence Representation Scheme using Dictionary Learning
by: Peng, Zhiyuan, et al.
Published: (2024)