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Aug 11, 2026 20:03
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Editor And Guide Design
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abCRISPR: deep learning-based design of abasic gRNA sequences for specific CRISPR-Cas genome editing.
★10 · Bioinformatics (Oxford, England)
Reversing cancer cell behavior using AI-guided CRISPR and quantum nanobiology: a systems-based approach to epigenetic reprogramming.
★10 · Gene therapy
Structure and evolution-guided design of minimal RNA-guided nucleases.
★10 · Science (New York, N.Y.)
CrisprFusion: A feature fusion model with multi-type input features for sgRNA activity prediction.
★9 · Computational biology and chemistry
De novo design of potent CRISPR-Cas13 inhibitors.
★9 · Nature chemical biology
Systematic Benchmarking of CRISPR-Cas9 Off-Target Prediction Tools Reveals Limitations and Implications for Preclinical Assessment.
★9 · Human gene therapy
Regulatory And Expression Design
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Self-sufficient killing of malignant tumors by an engineered cancer-selective gene circuit.
★10 · Cell reports. Medicine
Distribution-Constrained Optimization for Reliable ML-Guided 5'UTR Sequence Design
★10
Unconditional de novo generation and functional validation of synthetic promoters with a diffusion model.
★9 · Synthetic and systems biotechnology
An encyclopedia of human enhancer-gene regulatory interactions.
★9 · Nature
Decoding promoter activity from DNA sequence using pre-trained language models.
★9 · Scientific reports
Engineering short-sequence elements for condensate-like assemblies by de novo design.
★9 · Synthetic and systems biotechnology
scReGAT: Leveraging Knowledge of Regulatory Interactions to Predict Long-range Gene Regulation at Single-cell Resolution.
★8 · Genomics, proteomics & bioinformatics
Foundation model reveals the shared organization of transcription and topologically associating domains
★8
Wiz regulates clustered protocadherin genes by restricting CTCF/cohesin loop extrusion in a genomic-distance biased manner.
★7 · PLoS genetics
Chromatin topology and distal elements underlie divergent cell-type-specific regulation of 9p21 locus cell cycle genes
★7
Protein And Sequence Models
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Property guidance for protein sequence generative models with ProteinGuide.
★10 · Nature biotechnology
Leveraging protein language model for maturation of high-affinity peptide ligand in the purification of an adeno‒associated virus vector.
★10 · Journal of chromatography. A
A distribution-aware and functionally relevant novel framework for generation and discovery of bioactive peptides
★10
Interpreting embeddings from genome and protein language models.
★9 · Biotechnology advances
Modified heated dynamics and deep mutational scanning enhance anti-CXCR2 antibody affinity.
★9 · Journal of biomolecular structure & dynamics
Evolutionary Curriculum Learning Improves Biological Sequence Modeling
★9
Evaluating SARS-CoV-2 antibody resilience via prediction and design of escape viral variants
★9
High-throughput machine learning-aided antibody discovery for cell surface antigens
★9
Causal intervention validation of gene regulatory signals in scGPT.
★8 · Journal of biomedical informatics
Systematic evaluation of single-cell foundation model interpretability: attention-derived edge scores add no incremental value over gene-level features for perturbation-target prediction.
★8 · BMC genomics
Scalable Extraction of Information on Protein-Protein Interactions using Topological Data Analysis
★8
A map of human protein-protein interaction embeddings for functional discovery
★8
Trajectory forecasting lifts the femtosecond ceiling in molecular simulation
★7
What Makes a Good Vaccine Antigen Target? Defining Key Features and Predicting Candidates in the Staphylococcus aureus Proteome
★7
Scop3P-Toolkit: executable structure-aware workflows linking PTMs, peptides, and mutations to protein function
★7
Immunoinformatics-Driven Design of a Multiepitope Vaccine for Rustrela Virus-Induced Neurological Diseases: A New Frontier in Encephalitis and Meningoencephalitis Prevention.
★6 · Viral immunology
Delivery And Formulation
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High-throughput microfluidics and machine learning-assisted screening of lipid nanoparticle formulations for siRNA delivery.
★9 · Materials today. Bio
Bacteriophage nanoparticles: an emerging modular delivery platform.
★8 · Current opinion in biotechnology
Branched Ionizable Lipids Drive Cholesterol Domain Formation and pH-Dependent Remodeling in Lipid Nanoparticles.
★7 · Journal of chemical theory and computation
Target And Variant Discovery
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Deciphering protein mutation-phenotype linkages from CRISPR-based tiling mutagenesis screens
★9
Virtual-cell verification enables self-auditing AI discovery for immune rejuvenation
★9
Assessing Computational Models for Pharmacogenomic Variant Interpretation
★9
Integrating single-cell sQTL mapping with deep-learning splicing prediction identifies causal variants under influenza infection.
★8 · Genome biology
Synonymous variants in IRX4 and their association with congenital heart disease: an in-silico functional assessment.
★8 · Molecular biology reports
VOICE: A Vision-Omics Foundation Model Integrating Direct and Retrieval-Based Prediction of In-situ Single-Cell Gene Expression
★8
nf-cavalier: A Nextflow Pipeline for Rare Disease Variant Prioritization and Reporting
★8
Agentic Artificial Intelligence-Driven Explainable Deep Learning for Deciphering Noncoding Pathogenic Mechanisms of Delirium Through Genomic Big Data Integration.
★7 · Big data
Missense mutations in MKRN3 and central precocious puberty: a mutational approach to understanding protein function.
★7 · Current opinion in pediatrics
Single-Cell Virtual Perturbation Screening Identifies STAT3 as a Key Regulator of Dentinogenesis.
★7 · Cell proliferation
Shared Genetic Architecture of Epilepsy and Glioma Revealed by Mendelian Randomization: Identifying Prognostic Biomarkers and Therapeutic Targets.
★7 · Current cancer drug targets
AI-driven multi-omics deciphering of extrachromosomal circular DNA rescues hidden targets in colorectal cancer.
★7 · Cell communication and signaling : CCS
Exploratory multi-omics links CCL2/TIMP1 axis to immunosuppressive TME in glioblastoma.
★7 · Cell cycle (Georgetown, Tex.)
Immune regulatory mechanisms and potential microbiota-associated targets in Kawasaki disease: an integrative multi-omics and network pharmacology study.
★7 · Artificial cells, nanomedicine, and biotechnology
DetectGxT: detecting gene-by-treatment interactions on molecular count phenotypes accounting for allelic additivity
★7
Uncovering High-Order Epistatic Interactions in GWAS via a Machine Learning-Based Feature Engineering Framework
★7
De novo transformer modeling improves recovery of genetic cell types from sparse single-cell RNA sequencing
★7
Integrated pan-cancer systems biology and structure-based simulation identifies Annona muricata-derived natural scaffolds as putative IDO1 modulators for cancer immunotherapy.
★6 · Computational biology and chemistry
Vector And Capsid Design
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Novel VSV-G Variants with Enhanced Blinding for Targeted Delivery of Lentiviral Vectors.
★7 · Human gene therapy