Key papers

• AuraGenome: An LLM-Powered Framework for On-the-Fly Reusable and Scalable Circular Genome Visualizations (2025)
  Chi Zhang et al.
  5.82
• GeneMamba: An Efficient and Effective Foundation Model on Single Cell Data (2025)
  Cong Qi et al.
  4.87
• AnnotateMissense: a genome-wide annotation and benchmarking framework for missense pathogenicity prediction (2026)
  Muhammad Muneeb et al.
  4.27
• UniPTMs: The First Unified Multi-type PTM Site Prediction Model via Master-Slave Architecture-Based Multi-Stage Fusion Strategy and Hierarchical Contrastive Loss (2025)
  Yiyu Lin et al.
  3.81
• PACE: Geometry-Aware Bridge Transport for Single-Cell Trajectory Inference (2026)
  Chenglei Yu et al.
  3.39
• Alz-QNet: A Quantum Regression Network for Studying Alzheimer's Gene Interactions (2025)
  Debanjan Konar and Neerav Sreekumar and Richard Jiang and Vaneet Aggarwal
  2.99
• Inferring genotype-phenotype maps using attention models (2025)
  Krishna Rijal et al.
  2.76
• Multi-megabase scale genome interpretation with genetic language models (2025)
  Frederik Tr\"auble et al.
  2.60
• GraphRareBench: An Auditable Graph-Evidence Benchmark for Phenotype-Driven Rare-Disease Diagnosis (2026)
  Guiling Guo et al.
  2.00
• Contrastive Representation Learning of Longitudinal Disease Trajectories on Temporal Graphs (2026)
  Bastian Pfeifer
  2.00
• AI-driven peptide discovery for endometrial cancer: deep generative modeling and molecular simulation in the big data era (2026)
  Israr Fatima et al.
  1.94
• Entropy, Disagreement, and the Limits of Foundation Models in Genomics (2026)
  Maxime Rochkoulets et al.
  1.83
• Discovery of a Hematopoietic Manifold in scGPT Yields a Method for Extracting Performant Algorithms from Biological Foundation Model Internals (2026)
  Ihor Kendiukhov
  1.78
• SynLeaF: A Dual-Stage Multimodal Fusion Framework for Synthetic Lethality Prediction Across Pan- and Single-Cancer Contexts (2026)
  Zheming Xing et al.
  1.78
• Lingshu-Cell: A generative cellular world model for transcriptome modeling toward virtual cells (2026)
  Han Zhang et al.
  1.78
• ScDiVa: Masked Discrete Diffusion for Joint Modeling of Single-Cell Identity and Expression (2026)
  Mingxuan Wang et al.
  1.72
• AntigenLM: Structure-Aware DNA Language Modeling for Influenza (2026)
  Yue Pei et al.
  1.72
• STRAND: Sequence-Conditioned Transport for Single-Cell Perturbations (2026)
  Boyang Fu et al.
  1.72
• scPilot: Large Language Model Reasoning Toward Automated Single-Cell Analysis and Discovery (2026)
  Yiming Gao et al.
  1.72
• AgriVariant: Variant Effect Prediction using DeepChem-Variant for Precision Breeding in Rice (2026)
  Ankita Vaishnobi Bisoi et al.
  1.72
• PanFoMa: A Lightweight Foundation Model and Benchmark for Pan-Cancer (2025)
  Xiaoshui Huang et al.
  1.61
• Sequence-to-Image Transformation for Sequence Classification Using Rips Complex Construction and Chaos Game Representation (2025)
  Sarwan Ali et al.
  1.61
• Murmur2Vec: A Hashing Based Solution For Embedding Generation Of COVID-19 Spike Sequences (2025)
  Sarwan Ali et al.
  1.61
• CellStream: Dynamical Optimal Transport Informed Embeddings for Reconstructing Cellular Trajectories from Snapshots Data (2025)
  Yue Ling et al.
  1.56
• A Hybrid Computational Intelligence Framework for scRNA-seq Imputation: Integrating scRecover and Random Forests (2025)
  Ali Anaissi et al.
  1.56
• MoRE: Batch-Robust Multi-Omics Representations from Frozen Pre-trained Transformers (2025)
  Audrey Pei-Hsuan Chen
  1.56
• Cross-Platform DNA Methylation Classifier for the Eight Molecular Subtypes of Group 3 & 4 Medulloblastoma (2025)
  Omer Abid and Gholamreza Rafiee
  1.50
• Knowledge Graph Sparsification for GNN-based Rare Disease Diagnosis (2025)
  Premt Cara et al.
  1.50
• Incorporating LLM Embeddings for Variation Across the Human Genome (2025)
  Hongqian Niu et al.
  1.44
• MOTGNN: Interpretable Graph Neural Networks for Multi-Omics Disease Classification (2025)
  Tiantian Yang et al.
  1.39
• Graph Structure Learning for Tumor Microenvironment with Cell Type Annotation from non-spatial scRNA-seq data (2025)
  Yu-An Huang et al.
  1.06
• A robust and lightweight deep attention multiple instance learning algorithm for predicting genetic alterations (2022)
  Bangwei Guo et al.
  —
• Bayesian tensor factorization for predicting clinical outcomes using integrated human genetics evidence (2022)
  Onuralp Soylemez
  —
• CustOmics: A versatile deep-learning based strategy for multi-omics integration (2022)
  Hakim Benkirane et al.
  —
• Graph Coloring via Neural Networks for Haplotype Assembly and Viral Quasispecies Reconstruction (2022)
  Hansheng Xue et al.
  —
• iEnhancer-ELM: improve enhancer identification by extracting position-related multiscale contextual information based on enhancer language models (2022)
  Jiahao Li et al.
  —
• UNADON: Transformer-based model to predict genome-wide chromosome spatial position (2023)
  Muyu Yang and Jian Ma
  —
• regulAS: A Bioinformatics Tool for the Integrative Analysis of Alternative Splicing Regulome using RNA-Seq data (2023)
  Sofya Lipnitskaya
  —
• XVir: A Transformer-Based Architecture for Identifying Viral Reads from Cancer Samples (2023)
  Shorya Consul et al.
  —
• Embed-Search-Align: DNA Sequence Alignment using Transformer Models (2023)
  Pavan Holur et al.
  —
• Multi-View Variational Autoencoder for Missing Value Imputation in Untargeted Metabolomics (2023)
  Chen Zhao et al.
  —
• Defining Reference Sequences for Nocardia Species by Similarity and Clustering Analyses of 16S rRNA Gene Sequence Data (2023)
  Manal Helal et al.
  —
• Interpretable deep learning in single-cell omics (2024)
  Manoj M Wagle et al.
  —
• $\Gamma$-VAE: Curvature regularized variational autoencoders for uncovering emergent low dimensional geometric structure in high dimensional data (2024)
  Jason Z. Kim et al.
  —
• scRDiT: Generating single-cell RNA-seq data by diffusion transformers and accelerating sampling (2024)
  Shengze Dong et al.
  —
• An Autoencoder and Generative Adversarial Networks Approach for Multi-Omics Data Imbalanced Class Handling and Classification (2024)
  Ibrahim Al-Hurani et al.
  —
• CAVACHON: a hierarchical variational autoencoder to integrate multi-modal single-cell data (2024)
  Ping-Han Hsieh et al.
  —
• DYNA: Disease-Specific Language Model for Variant Pathogenicity (2024)
  Huixin Zhan et al.
  —
• CellAgent: An LLM-driven Multi-Agent Framework for Automated Single-cell Data Analysis (2024)
  Yihang Xiao et al.
  —
• Single-cell Curriculum Learning-based Deep Graph Embedding Clustering (2024)
  Huifa Li et al.
  —
• PRAGA: Prototype-aware Graph Adaptive Aggregation for Spatial Multi-modal Omics Analysis (2024)
  Xinlei Huang et al.
  —