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computational biology

GeneTech 知识引擎共收录 775 篇相关科研实体，横跨 22 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）

• 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…
• 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…
• AI/ML-enabled multi-omics integration of host genetics, immunity, and the gut microbiome in Crohn’s disease: From diagnosis to theranostics
  2026 · AI 安全与对齐 · Crohn's disease is a long-term inflammatory disorder arising from the interaction of genetic risk factors, immune system dysfunction, and alterations in gut microbiota. Variability in clinical phenotypes and lack of biom…
• ARTIFICIAL INTELLIGENCE AND COMPUTATIONAL BIOLOGY IN HEALTHCARE: GENOMICS, PUBLIC HEALTH AND MICROBIOME
  2026 · 生物计算 · This book brings together pioneering research at the intersection of technology, health, and microbiology, showcasing how computational innovation and biological insight are reshaping our understanding of life and diseas…
• Organ cross-talk: molecular mechanisms, biological functions, and therapeutic interventions for diseases
  2026 · 生物计算 · Organ cross-talk, also known as the organ axis or organ interaction network, plays a vital role in maintaining physiological homeostasis and responding to environmental stimuli. This review comprehensively integrates cut…
• From 2D cultures to 3D systems: evolving cancer models at the interface of functional precision medicine and theranostics
  2026 · 仿生智能 · Advances in patient-derived cancer models are pushing precision oncology by linking functional testing directly to therapeutic decision-making.Traditional two-dimensional (2D) cancer cell culture systems have long served…
• Statewide surficial geologic map of Nebraska underscores Quaternary landscape evolution from the High Plains to the Central Lowland
  2026 · 脑科学 · Surficial geologic mapping in Nebraska has been conducted primarily at the 1:24,000 scale since the mid-1990s, although there have also been limited efforts to map generalized Quaternary and surficial geology within the …
• Statewide surficial geologic map of Nebraska underscores Quaternary landscape evolution from the High Plains to the Central Lowland
  2026 · 脑科学 · Surficial geologic mapping in Nebraska has been conducted primarily at the 1:24,000 scale since the mid-1990s, although there have also been limited efforts to map generalized Quaternary and surficial geology within the …
• 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…
• 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…
• 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…
• Developing an alternative medium for in-space biomanufacturing.
  2025 · 地外矿物 · In-space biomanufacturing provides a sustainable solution to facilitate long-term, self-sufficient human habitation in extraterrestrial environments. However, its dependence on Earth-supplied feedstocks renders in-space …
• Bacterial community profile of three Ethiopian hot springs based on 16S rRNA gene nanopore sequencing
  2025 · 地外矿物 · Ethiopia harbors a number of hot springs not yet well explored or studied using a metagenomic approach to reveal their bacterial diversity. Understanding the bacterial diversity of these ecosystems is valuable for uncove…
• Editorial: Deep subsurface microbiology and energetics
  2025 · 地外矿物 · In hyperalkaline fluids derived from serpentinization in the Samail Ophiolite, Howells et al. reveal that formate, rather than hydrogen or acetate, provides the most favorable energy source for methanogenesis under CO₂-l…
• DNA Molecular Computing with Weighted Signal Amplification for Cancer miRNA Biomarker Diagnostics.
  2025 · 生物计算 · The expression levels of microRNAs (miRNAs) are strongly linked to cancer progression, making them promising biomarkers for cancer detection. Enzyme-free signal amplification DNA circuits have facilitated the detection o…
• Genetic circuits in synthetic biology: broadening the toolbox of regulatory devices
  2025 · 生物计算 · Devices sensing inputs and generating outputs are fundamental regulatory units, and as such are the basis of more complex regulatory networks. We provide an overview of regulatory devices used as fundamental regulatory b…
• Algorithms and tools for data-driven omics integration to achieve multilayer biological insights: a narrative review
  2025 · 生物计算 · Systems biology is a holistic approach to biological sciences that combines experimental and computational strategies, aimed at integrating information from different scales of biological processes to unravel pathophysio…
• Current landscape of plasma proteomics from technical innovations to biological insights and biomarker discovery
  2025 · 生物计算 · Plasma is a rich source of biomolecules, including proteins, that reflect both health and disease. Due to their key roles in biological processes, proteins hold significant potential as biomarkers, fueling the rise of pl…
• The GSA Family in 2025: A Broadened Sharing Platform for Multi-omics and Multimodal Data
  2025 · 生物计算 · The Genome Sequence Archive family (GSA family) provides a comprehensive suite of database resources for archiving, retrieving, and sharing multi-omics data for the global academic and industrial communities. It currentl…
• MODOMICS: a database of RNA modifications and related information. 2025 update and 20th anniversary
  2025 · 生物计算 · MODOMICS is the reference database of RNA modifications and related information, integrating chemical, biochemical, structural, and functional data. In this 2025 update, marking the 20th anniversary of MODOMICS, the data…
• Contrastive-learning of language embedding and biological features for cross modality encoding and effector prediction
  2025 · 生物计算 · Identifying and characterizing virulence proteins secreted by Gram-negative bacteria are fundamental for deciphering microbial pathogenicity as well as aiding the development of therapeutic strategies. Effector predictor…
• Nanozymes expanding the boundaries of biocatalysis
  2025 · 生物计算 · Biocatalysis is fundamental to biological processes and sustainable applications. Over time, the understanding of biocatalysis has evolved considerably. Initially, protein enzymes were recognized as the primary biocataly…
• Deciphering the biological fate of mRNA-LNP-based biologics: A perspective from tissue to intracellular distribution
  2025 · 生物计算 · The remarkable clinical success of mRNA-lipid nanoparticle (mRNA-LNP) vaccines, particularly evidenced by their pandemic-era impact and subsequent 2023 Nobel Prize recognition, has intensified global efforts to expand th…
• Integrating Genomics and Proteomics Technologies in Biological Research: Advantages, Challenges, and Prospects
  2025 · 生物计算 · Introduction: The integration of genomics and proteomics, two cornerstone omics technologies, has transformed our understanding of biological systems, enabling deeper insights into disease mechanisms, biomarker discovery…
• Diagnosis of nontuberculous mycobacterial infections using genomics and artificial intelligence-machine learning approaches: scope, progress and challenges
  2025 · 医疗人工智能 · The nontuberculous mycobacterial (NTM) infections cause morbidity and mortality in individuals who are immunocompromised and those with lung conditions. The timely diagnosis of NTM infections is thus the need of the hour…
• Artificial Intelligence in Ovarian Cancer: A Systematic Review and Meta-Analysis of Predictive AI Models in Genomics, Radiomics, and Immunotherapy
  2025 · 医疗人工智能 · Background/Objectives: Artificial intelligence (AI) is increasingly influencing oncological research by enabling precision medicine in ovarian cancer through enhanced prediction of therapy response and patient stratifica…
• Spatial mapping of the brain metabolome lipidome and glycome
  2025 · 仿生智能 · Metabolites, lipids, and glycans are fundamental but interconnected classes of biomolecules that form the basis of the metabolic network. These molecules are dynamically channeled through multiple pathways that govern ce…
• Advancements in Single-Molecule Fluorescence Detection Techniques and Their Expansive Applications in Drug Discovery and Neuroscience
  2025 · 脑科学 · Single-molecule fluorescence technology stands at the forefront of scientific research as a sophisticated tool, pushing the boundaries of our understanding. This review comprehensively summarizes the technological advanc…
• Pluripotent stem-cell-derived therapies in clinical trial: A 2025 update
  2025 · 脑科学 · Since the first derivation of human pluripotent stem cells (hPSCs) 27 years ago, technologies to control their differentiation and manufacturing have advanced immensely, enabling increasing numbers of clinical trials wit…
• Established and emerging new approach methodologies in neuroscience
  2025 · 脑科学 · The increasing need for ethical, human-relevant, and efficient alternatives to animal testing is driving the development of New Approach Methodologies (NAMs) in safety assessment and drug development. However, the inhere…
• Cancer cell dormancy: An update to 2025
  2025 · 脑科学 · About 70 years ago, scientists first observed groups of cancer cells in a “temporary mitotic arrest,” a dormant state that complicates treatment and increases the risk of recurrence. Recent updates have provided novel in…
• 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…
• 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…
• Integrating Omics Data and AI for Cancer Diagnosis and Prognosis
  2024 · AI 驱动科学发现 · Cancer is one of the leading causes of death, making timely diagnosis and prognosis very important. Utilization of AI (artificial intelligence) enables providers to organize and process patient data in a way that can lea…
• Extremophiles and Extremophilic Behaviour-New Insights and Perspectives.
  2024 · 地外矿物 · Extremophiles, throughout evolutionary time, have evolved a plethora of unique strategies to overcome hardships associated with the environments they are found in. Modifying their genome, showing a bias towards certain a…
• Ancient environmental microbiomes and the cryosphere
  2024 · 地外矿物 · In this review, we delineate the unique set of characteristics associated with cryosphere environments (namely, ice and permafrost) which present both challenges and opportunities for studying ancient environmental micro…
• Naturally Occurring Microbiota-Accessible Borates: A Focused Minireview
  2024 · 地外矿物 · Recently, we discovered and proved the essentiality of organic boron species (OBS), such as borate–pectic polysaccharides and borate–phenolic esters, for healthy symbiosis (HS) between microbiota and human/animal (H/A) h…
• MEGA12: Molecular Evolutionary Genetic Analysis Version 12 for Adaptive and Green Computing
  2024 · 生物计算 · We introduce the 12th version of the Molecular Evolutionary Genetics Analysis (MEGA12) software. This latest version brings many significant improvements by reducing the computational time needed for selecting optimal su…
• Parallel molecular data storage by printing epigenetic bits on DNA
  2024 · 生物计算 · DNA storage has shown potential to transcend current silicon-based data storage technologies in storage density, longevity and energy consumption1–3. However, writing large-scale data directly into DNA sequences by de no…
• Challenges for error-correction coding in DNA data storage: photolithographic synthesis and DNA decay
  2024 · 生物计算 · Abstract Efficient error-correction codes are crucial for realizing DNA’s potential as a long-lasting, high-density storage medium for digital data. At the same time, new workflows promising low-cost, resilient DNA data …
• SwissDock 2024: major enhancements for small-molecule docking with Attracting Cavities and AutoDock Vina
  2024 · 生物计算 · Drug discovery aims to identify potential therapeutic compounds capable of modulating the activity of specific biological targets. Molecular docking can efficiently support this process by predicting binding interactions…
• WebGestalt 2024: faster gene set analysis and new support for metabolomics and multi-omics
  2024 · 生物计算 · Enrichment analysis, crucial for interpreting genomic, transcriptomic, and proteomic data, is expanding into metabolomics. Furthermore, there is a rising demand for integrated enrichment analysis that combines data from …
• Updated resources for exploring experimentally-determined PDB structures and Computed Structure Models at the RCSB Protein Data Bank
  2024 · 生物计算 · The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB, RCSB.org), the US Worldwide Protein Data Bank (wwPDB, wwPDB.org) data center for the global PDB archive, provides access to the PDB da…

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