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computational biology

GeneTech 知识引擎共收录 5223 篇相关科研实体，横跨 30 个垂直领域。数据来自 OpenAlex、arXiv、Crossref、PubMed、Europe PMC 等公开学术源，全部可溯源到原文。

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代表性文献（按质量分排序，前 60 条）

• Next-Generation Target Discovery in ESKAPE Pathogens: An AI-Driven Framework from Omics-Based to Systems-Level Modeling and Clinical Translation
  2026 · AI 安全与对齐 · Background: Antimicrobial resistance (AMR) among ESKAPE pathogens—Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.—represents a ma…
• DELPHAI, AI Agent for Predicting Drug Response and Resistance
  2025 · AI Agent 生态 · Abstract Patient-derived organoids preserve critical tumor features and drug sensitivity patterns that mirror patient clinical responses, enabling single-cell RNA sequencing analysis of drug responses. Analyzing these pe…
• LongevityLLM: A Function-Driven AI Agent for End-to-End Protein and Aging Research
  2025 · AI Agent 生态 · Recent advances in large language models (LLMs) have unlocked new possibilities for scientific discovery, yet most remain limited to text summarization or hallucination-prone dialogue. Here, we present LongevityLLM—a fun…
• TransAgent: Dynamizing Transcriptional Regulation Analysis via Multi-omics-Aware AI Agent
  2025 · AI Agent 生态 · Abstract Transcriptional regulation research, as a core area of life sciences, faces challenges such as scattered multi-omics data, complex joint analysis, and difficulties in integrating data processing tools. To addres…
• Viral Sentry AI (VirSentAI) - Automated Zoonotic Surveillance & Drug Repurposing Agent
  2025 · AI Agent 生态 · Abstract Zoonotic viruses capable of jumping from animal reservoirs into human populations represent a persistent and unpredictable menace to global health. To confront this challenge, we developed Viral Sentry AI (VirSe…
• Uncovering Complicated Plant Biological Networks through the Assistance of Artificial Intelligence Tools
  2026 · 智慧农业 · Plant biological networks, comprising gene regulatory, protein–protein interaction (PPI), and metabolic pathways, are intricate systems fundamental to understanding plant development and physiology. The advent of artific…
• Sequence-based generative AI design of versatile tryptophan synthases
  2026 · AI 安全与对齐 · Enzymes are powerful and sustainable catalysts, but their widespread application is limited by the difficulty of identifying functional starting points for optimization, creating a major bottleneck in early- stage biocat…
• HEAL-KGGen: A Hierarchical Multi-Agent LLM Framework with Knowledge Graph Enhancement for Genetic Biomarker-Based Medical Diagnosis
  2025 · AI Agent 生态 · ABSTRACT The discovery and validation of genetic biomarkers across diverse diseases demand intelligent systems capable of integrating complex multi-omics data with clinical relevance. We introduce HEAL-KGGen, an end-to-e…
• Role of Artificial Intelligence Tools in CRISPR-Cas9 Genomic Editing Technique for Precision Agriculture
  2025 · 智慧农业 · CRISPR-Cas9 is a groundbreaking technology that has revolutionized genetic engineering by allowing precise and efficient genome editing. Despite its potential, the complexity and variability of genomic data present signi…
• Clone-Robust AI Alignment
  2025 · AI 安全与对齐 · A key challenge in training Large Language Models (LLMs) is properly aligning them with human preferences. Reinforcement Learning with Human Feedback (RLHF) uses pairwise comparisons from human annotators to train reward…
• Charting γ-secretase substrates by explainable AI
  2025 · AI 安全与对齐 · Proteases recognize substrates by decoding sequence information-an essential cellular process elusive when recognition motifs are absent. Here, we unravel this problem for γ-secretase, an intramembrane-cleaving protease …
• PromptBio: A Multi-Agent AI Platform for Bioinformatics Data Analysis
  2025 · AI 安全与对齐 · Abstract PromptBio is a modular AI platform for scalable, reproducible, and user-adaptable bioinformatics analysis, powered by generative AI and natural language interaction. It supports three complementary modes of anal…
• The Evolution of Anticancer 3D In Vitro Models: The Potential Role of Machine Learning and AI in the Next Generation of Animal-Free Experiments
  2025 · AI 安全与对齐 · The development of anticancer therapies has increasingly relied on advanced 3D in vitro models, which more accurately mimic the tumor microenvironment compared to traditional 2D cultures. This review describes the evolut…
• AlphaFold3: An Overview of Applications and Performance Insights
  2025 · AI 安全与对齐 · AlphaFold3, the latest release of AlphaFold developed by Google DeepMind and Isomorphic Labs, was designed to predict protein structures with remarkable accuracy. AlphaFold3 enhances our ability to model not only single …
• Bridging Sequence-Structure Alignment in RNA Foundation Models
  2025 · AI 安全与对齐 · 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 seamless flow of g…
• AI-driven discovery of dual antiaging and anti-AD therapeutics via PROTAC target deconvolution of a super-enhancer–regulated axis
  2025 · AI 安全与对齐 · The lack of safe, durable therapeutics that act against both biological aging and Alzheimer's disease is an unmet clinical need. To bridge this gap, we devised an artificial intelligence (AI)-enabled approach that pairs …
• Industrial applications of large language models
  2025 · AI 安全与对齐 · Large language models (LLMs) are artificial intelligence (AI) based computational models designed to understand and generate human like text. With billions of training parameters, LLMs excel in identifying intricate lang…
• In silico generation of synthetic cancer genomes using generative AI
  2025 · AI 安全与对齐 · Understanding how genomic alterations drive cancer is key to advancing precision oncology. To detect these alterations, accurate algorithms are used; however, due to privacy concerns, few deeply sequenced cancer genomes …
• Improving prediction accuracy in chimeric proteins with windowed multiple sequence alignment
  2025 · AI 安全与对齐 · A key step in protein structure prediction involves the detection of co-evolving pairs of residues, a signal for spatial proximity. This information is gleaned from multiple sequence alignment and underscores Alphafold's…
• Alignment-driven Cross-Graph Modeling for 3D RNA Inverse Folding
  2025 · AI 安全与对齐 · Abstract The 3D RNA inverse folding task aims to design RNA sequences that can fold into a target tertiary structure. This task is complicated by the inherent structural complexity and flexibility of RNA molecules. Consi…
• Quest for Orthologs in the era of Data Deluge and AI: Challenges and Innovations in Orthology Prediction and Data Integration
  2025 · AI 安全与对齐 · The rapid advancement of DNA sequencing technologies and computational algorithms has led to an unprecedented surge in genomic data, driven by several large-scale sequencing projects worldwide. Orthology plays a crucial …
• Spatial omics at the forefront: emerging technologies, analytical innovations, and clinical applications
  2025 · AI 安全与对齐 · Spatial omics transforms our understanding of cancer by revealing how tumor cells and the microenvironment are organized, interact, and evolve within tissues. Here, we synthesize advances in spatial technologies that map…
• Evaluation Beyond Goodness of Fit: Biophysical Alignment of AI Models for Kinase-Centric Drug Discovery
  2025 · AI 安全与对齐 · The potential of machine learning (ML) to accelerate modern drug discovery is widely recognized, especially when using ML to reason about the binding of small drug-like molecules to proteins. In order to assess whether s…
• SAND: a comprehensive annotation of class D β-lactamases using structural alignment-based numbering
  2025 · AI 安全与对齐 · Class D β-lactamases are a diverse group of enzymes that contribute to antibiotic resistance by inactivating β-lactam antibiotics. Examination of class D β-lactamases has evolved significantly over the years, with advanc…
• Regulating the AI-enabled ecosystem for human therapeutics
  2025 · AI 安全与对齐 · Recent advances in artificial intelligence (AI) tools and techniques can revolutionize the discovery, development, manufacturing, and delivery of new medicines by reducing the time and cost involved. The biopharmaceutica…
• Empowering biomedical discovery with AI agents
  2024 · AI Agent 生态 · We envision "AI scientists" as systems capable of skeptical learning and reasoning that empower biomedical research through collaborative agents that integrate AI models and biomedical tools with experimental platforms. …
• Improvements in viral gene annotation using large language models and soft alignments
  2024 · AI 安全与对齐 · BACKGROUND: The annotation of protein sequences in public databases has long posed a challenge in molecular biology. This issue is particularly acute for viral proteins, which demonstrate limited homology to known protei…
• PPB-Affinity: Protein-Protein Binding Affinity dataset for AI-based protein drug discovery
  2024 · AI 安全与对齐 · Prediction of protein-protein binding (PPB) affinity plays an important role in large-molecular drug discovery. Deep learning (DL) has been adopted to predict the changes of PPB binding affinities upon mutations, but the…
• Predicting gene sequences with AI to study codon usage patterns
  2024 · AI 安全与对齐 · Selective pressure acts on the codon use, optimizing multiple, overlapping signals that are only partially understood. We trained AI models to predict codons given their amino acid sequence in the eukaryotes Saccharomyce…
• Accelerating whole-genome alignment in the age of complete genome assemblies
  2024 · AI 安全与对齐 · Abstract Recent advancements in long-read sequencing and assembly methods have ushered in an era of high-quality genome assemblies. Modern assemblies commonly feature megabase-long sequences frequently spanning entire ch…
• Challenges in data-driven geospatial modeling for environmental research and practice
  2024 · AI 安全与对齐 · Machine learning-based geospatial applications offer unique opportunities for environmental monitoring due to domains and scales adaptability and computational efficiency. However, the specificity of environmental data i…
• tcrBLOSUM: an amino acid substitution matrix for sensitive alignment of distant epitope-specific TCRs
  2024 · AI 安全与对齐 · Deciphering the specificity of T-cell receptor (TCR) repertoires is crucial for monitoring adaptive immune responses and developing targeted immunotherapies and vaccines. To elucidate the specificity of previously unseen…
• Implementation of Banded Smith-Waterman Sequence Alignment Algorithm on CPU and FPGA
  2024 · AI 安全与对齐 · Abstract Sequence alignment(SA) is a fundamental aspect in the field of bioinformatics, crucial for various applications such as DNA sequencing and protein structure prediction. It involves the process of comparing a new…
• Comparison of different EC-mapping sensors
  2023 · 智慧农业 · Digital Soil Mapping becomes more and more important not only in Precision Farming. In the past, miscellaneous technologies and sensors, including geophysical techniques were tested to get information about the spatial v…
• UCSF ChimeraX : Tools for structure building and analysis
  2023 · AI 安全与对齐 · Advances in computational tools for atomic model building are leading to accurate models of large molecular assemblies seen in electron microscopy, often at challenging resolutions of 3-4 Å. We describe new methods in th…
• Kuhfeldrf/UniProt_Search: Librarian Agent v1.0.0 - Automated Bioactive Peptide Literature Search and MBPDB Update Tool
  2026 · AI Agent 生态 · Librarian Agent: Automated Bioactive Peptide Literature Search and MBPDB Update Tool Version 1.0.0 — Initial public release Overview This tool automates the discovery and documentation of milk-derived bioactive peptides …
• Kuhfeldrf/UniProt_Search: Librarian Agent v1.0.0 - Automated Bioactive Peptide Literature Search and MBPDB Update Tool
  2026 · AI Agent 生态 · Librarian Agent: Automated Bioactive Peptide Literature Search and MBPDB Update Tool Version 1.0.0 — Initial public release Overview This tool automates the discovery and documentation of milk-derived bioactive peptides …
• Toward Precision Bioconjugation: Chemical Strategies for Site-Selective Cysteine Conjugation
  2026 · 智慧农业 · The ability to access atomically tailored complex peptides and proteins provides powerful opportunities for dissecting molecular functions and advancing applications in chemical biology, therapeutics, and (bio)-materials…
• AI-Driven Multi-Omics Integration for Enhanced Drug Discovery Pipelines
  2025 · AI Agent 生态 · Integration of multi-omics data-genomics, transcriptomics, proteomics, and metabolomics-has become a crucial approach in the recent era for accelerating drug discovery. Artificial Intelligence synthesizes this multifario…
• THE INNER WORKINGS OF RIPENING: PHYSIOLOGY, BIOCHEMISTRY, AND MOLECULAR INSIGHTs
  2025 · 智慧农业 · Abstract : Fruit ripening is a complex, finely regulated developmental process that transitions fruit from growth to senescence, resulting in enhanced sensory and nutritional attributes. These changes are orchestrated th…
• THE INNER WORKINGS OF RIPENING: PHYSIOLOGY, BIOCHEMISTRY, AND MOLECULAR INSIGHTs
  2025 · 智慧农业 · Abstract : Fruit ripening is a complex, finely regulated developmental process that transitions fruit from growth to senescence, resulting in enhanced sensory and nutritional attributes. These changes are orchestrated th…
• SMILES alignment: a dynamic programming approach for the alignment of metabolites and other small organic molecules
  2025 · AI 安全与对齐 · Abstract Background There is a need for computational approaches to compare small organic molecules based on chemical similarity or for evaluating biochemical transformations. No tool currently exists to generate global …
• eLife Assessment: Minus the Error: Testing for Positive Selection in the Presence of Residual Alignment Errors
  2025 · AI 安全与对齐 · Positive selection is an evolutionary process which increases the frequency of advantageous mutations because they confer a fitness benefit. Inferring the past action of positive selection on protein-coding sequences is …
• Severe deviation in protein fold prediction by advanced AI: a case study
  2025 · AI 安全与对齐 · Artificial intelligence (AI) and deep learning are making groundbreaking strides in protein structure prediction. AlphaFold is remarkable in this arena for its outstanding accuracy in modelling proteins fold based solely…
• A Tool for Pair-Wise Alignment Algorithm
  2025 · AI 安全与对齐 · Bioinformatics is the application of computational techniques to the management and analysis of biological information. The relationship between a query sequence, commonly termed as probe and o he sequence, known as subj…
• Author comment: Microtubule flexibility, microtubule-based nucleation and ROP pattern co-alignment enhance protoxylem microtubule patterning — R0/PR1
  2025 · AI 安全与对齐 · The development of the water transporting xylem tissue in plants involves an intricate interplay of Rho-of-Plants (ROP) proteins and cortical microtubules to generate highly functional secondary cell wall patterns, such …
• Protein–protein interaction prediction methods: from docking-based to AI-based approaches
  2022 · AI 安全与对齐 · Protein-protein interactions (PPIs), such as protein-protein inhibitor, antibody-antigen complex, and supercomplexes play diverse and important roles in cells. Recent advances in structural analysis methods, including cr…
• Analysis of multipartite bacterial genomes using alignment free and alignment-based pipelines
  2022 · AI 安全与对齐 · Since the discovery of second chromosome in Rhodobacter sphaeroides 2.4.1 in 1989, multipartite genomes have been reported in over three hundred bacterial species under nine different phyla. This has shattered the unipar…
• Using molecular dynamics simulations to prioritize and understand AI-generated cell penetrating peptides
  2021 · AI 安全与对齐 · Cell-penetrating peptides have important therapeutic applications in drug delivery, but the variety of known cell-penetrating peptides is still limited. With a promise to accelerate peptide development, artificial intell…
• ATSE: a peptide toxicity predictor by exploiting structural and evolutionary information based on graph neural network and attention mechanism
  2021 · AI 安全与对齐 · MOTIVATION: Peptides have recently emerged as promising therapeutic agents against various diseases. For both research and safety regulation purposes, it is of high importance to develop computational methods to accurate…
• Determining leaf stomatal properties in citrus trees utilizing machine vision and artificial intelligence
  2020 · 智慧农业 · Identifying and quantifying the number and size of stomata on leaf surfaces is useful for a wide range of plant ecophysiological studies, specifically those related to water-use efficiency of different plant species or a…
• TANA: efficient approach for predicting protein functions by transferring annotation via alignment networks
  2020 · AI 安全与对齐 · Abstract Background: One of the challenges of the post-genomic era is to provide accurate function annotations for orphan and unannotated protein sequences. With the recent availability of huge protein-protein interactio…
• TANA: efficient approach for predicting protein functions by transferring annotation via alignment networks
  2020 · AI 安全与对齐 · Abstract Background: One of the challenges of the post-genomic era is to provide accurate function annotations for orphan and unannotated protein sequences. With the recent availability of huge PPIs networks for many mod…
• ATACdb: a comprehensive human chromatin accessibility database
  2020 · AI 安全与对齐 · Accessible chromatin is a highly informative structural feature for identifying regulatory elements, which provides a large amount of information about transcriptional activity and gene regulatory mechanisms. Human ATAC-…
• The Technique of Orchestration
  2024 · AI Agent 生态 · The Technique of Orchestration, Seventh Edition, is the definitive textbook on the study of orchestration, offering a concise, straight-to-the-point approach that prepares students to score their own compositions with co…
• PairK: Pairwise k-mer alignment for quantifying protein motif conservation in disordered regions
  2024 · AI 安全与对齐 · ABSTRACT Protein-protein interactions are often mediated by a modular peptide recognition domain binding to a short linear motif (SLiM) in the disordered region of another protein. The ability to predict domain-SLiM inte…
• Human scRNA-seq Alignment Pipeline Version 1.0 v1
  2024 · AI 安全与对齐 · The Morrisey and Basil Labs at the University of Pennsylvania use a specific protocol for scRNA-seq (single-cell RNA sequencing) alignment that involves the STARsolo tool (version 2.9.7a) to generate outputs comparable t…
• Protein Embedding based Alignment
  2023 · AI 安全与对齐 · Despite of the many progresses with alignment algorithms, aligning divergent protein sequences including those sharing less than 20-35% pairwise identity (so called “twilight zone”) remains a difficult problem. Many alig…
• RMalign: an RNA structural alignment tool based on a novel scoring function RMscore
  2019 · AI 安全与对齐 · BACKGROUND: RNA-protein 3D complex structure prediction is still challenging. Recently, a template-based approach PRIME is proposed in our team to build RNA-protein 3D complex structure models with a higher success rate …
• Mapping and characterizing N6-methyladenine in eukaryotic genomes using single-molecule real-time sequencing
  2018 · AI 安全与对齐 · N6-Methyladenine (m6dA) has been discovered as a novel form of DNA methylation prevalent in eukaryotes; however, methods for high-resolution mapping of m6dA events are still lacking. Single-molecule real-time (SMRT) sequ…

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