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quantitative biology methods

GeneTech 知识引擎共收录 291 篇相关科研实体，横跨 20 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）

• GenAI-Net: A Generative AI Framework for Automated Biomolecular Network Design
  2026 · 合成生物与生物制造 · Biomolecular networks underpin emerging technologies in synthetic biology-from robust biomanufacturing and metabolic engineering to smart therapeutics and cell-based diagnostics-and also provide a mechanistic language fo…
• DeepSeq: High-Throughput Single-Cell RNA Sequencing Data Labeling via Web Search-Augmented Agentic Generative AI Foundation Models
  2025 · AI 驱动科学发现 · Generative AI foundation models offer transformative potential for processing structured biological data, particularly in single-cell RNA sequencing, where datasets are rapidly scaling toward billions of cells. We propos…
• AI-powered virtual tissues from spatial proteomics for clinical diagnostics and biomedical discovery
  2025 · 生命科学 · Spatial proteomics technologies have transformed our understanding of complex tissue architecture in cancer but present unique challenges for computational analysis. Each study uses a different marker panel and protocol,…
• idMotif: An Interactive Motif Identification in Protein Sequences
  2024 · AI 驱动科学发现 · This article introduces idMotif, a visual analytics framework designed to aid domain experts in the identification of motifs within protein sequences. Motifs, short sequences of amino acids, are critical for understandin…
• A Foundation Model for Wearable Movement Data in Mental Health Research
  2024 · AI 驱动科学发现 · Wearable movement data is collected by nearly all commercially available smartwatches and is a valuable resource for mental health research, reflecting fine-grained temporal behavioral trends. Despite its promise, the de…
• L+M-24: Building a Dataset for Language + Molecules @ ACL 2024
  2024 · 地外矿物 · Language-molecule models have emerged as an exciting direction for molecular discovery and understanding. However, training these models is challenging due to the scarcity of molecule-language pair datasets. At this poin…
• How to Build the Virtual Cell with Artificial Intelligence: Priorities and Opportunities
  2024 · 医疗人工智能 · The cell is arguably the most fundamental unit of life and is central to understanding biology. Accurate modeling of cells is important for this understanding as well as for determining the root causes of disease. Recent…
• Hybrid deep learning-based strategy for the hepatocellular carcinoma cancer grade classification of H&E stained liver histopathology images
  2024 · 深海科技 · Hepatocellular carcinoma (HCC) is a common type of liver cancer whose early-stage diagnosis is a common challenge, mainly due to the manual assessment of hematoxylin and eosin-stained whole slide images, which is a time-…
• Geneverse: A collection of Open-source Multimodal Large Language Models for Genomic and Proteomic Research
  2024 · 生命科学 · The applications of large language models (LLMs) are promising for biomedical and healthcare research. Despite the availability of open-source LLMs trained using a wide range of biomedical data, current research on the a…
• Enhancing the Protein Tertiary Structure Prediction by Multiple Sequence Alignment Generation
  2023 · AI 驱动科学发现 · The field of protein folding research has been greatly advanced by deep learning methods, with AlphaFold2 (AF2) demonstrating exceptional performance and atomic-level precision. As co-evolution is integral to protein str…
• Revolutionizing Genomics with Reinforcement Learning Techniques
  2023 · 生命科学 · In recent years, Reinforcement Learning (RL) has emerged as a powerful tool for solving a wide range of problems, including decision-making and genomics. The exponential growth of raw genomic data over the past two decad…
• The Multi-modality Cell Segmentation Challenge: Towards Universal Solutions
  2023 · 合成生物与生物制造 · Cell segmentation is a critical step for quantitative single-cell analysis in microscopy images. Existing cell segmentation methods are often tailored to specific modalities or require manual interventions to specify hyp…
• The Essential Role Of Ribosomal Feedback In Bacterial Cell Growth And Metabolic Load -- A Systems Biology Approach For Unveiling Shared Resources Regulation Within Synthetic Genetic Circuits
  2026 · 生物计算 · Modeling growth in bacterial cells is a major issue in systems and synthetic biology. Despite several growth rate functions proposed in the literature, most focus on nutrient composition without explicitly accounting for…
• Artificial Intelligence Can Match Domain Experts in Evidence Extraction and Critical Appraisal of Microbial Oncogenesis Research Publications
  2026 · 生物计算 · Confirmed oncogenic microbes contribute significantly to cancer burden. Identifying novel microbial oncogenicity could yield strategies that will reduce disease burdens. However, relevant evidence is dispersed and infeas…
• Tracing protein and proteome history with chronologies and networks: folding recapitulates evolution
  2026 · 生命科学 · Introduction: While the origin and evolution of proteins remain mysterious, advances in evolutionary genomics and systems biology are facilitating the historical exploration of the structure, function and organization of…
• Spatial proteomics guided by H&E-based AI reveals recurrence-risk niches in triple-negative breast cancer
  2026 · 生命科学 · Deep learning models can predict cancer recurrence from H&E stained slides, but the localized molecular states underlying these predictions remain largely obscured. Here, we developed an outcome informed spatial path…
• scpFormer: A Foundation Model for Unified Representation and Integration of the Single-Cell Proteomics
  2026 · 生命科学 · The integration of single-cell proteomic data is often hindered by the fragmented nature of targeted antibody panels. To address this limitation, we introduce scpFormer, a transformer-based foundation model designed for …
• DIA-CLIP: a universal representation learning framework for zero-shot DIA proteomics
  2026 · 生命科学 · Data-independent acquisition mass spectrometry (DIA-MS) has established itself as a cornerstone of proteomic profiling and large-scale systems biology, offering unparalleled depth and reproducibility. Current DIA analysi…
• A Quantum Reservoir for Neurodynamical Forecasting
  2026 · 量子计算 · Forecasting neural activity from short recordings remains a fundamental challenge. Reservoir computing may offer an efficient paradigm for temporal prediction, however classical reservoirs typically underperform in small…
• Automated multi-dataset INST $^{13}$C metabolic flux analysis at microliter scale reveals robust fluxes but variable metabolite pools in $Corynebacterium~glutamicum$
  2026 · 合成生物与生物制造 · Isotopically non-stationary metabolic flux analysis (INST $^{13}$C-MFA) provides unique insights into cellular physiology but is typically limited by low throughput and high experimental costs. Here, we present a miniatu…
• Knowledge-Driven Agentic Scientific Corpus Distillation Framework for Biomedical Large Language Models Training
  2025 · AI Agent 生态 · Corpus distillation for biomedical large language models (LLMs) seeks to address the pressing challenge of insufficient quantity and quality in open-source annotated scientific corpora, which remains a bottleneck for eff…
• Evaluating New AI Cell Foundation Models on Challenging Kidney Pathology Cases Unaddressed by Previous Foundation Models
  2025 · AI 安全与对齐 · Accurate cell nuclei segmentation is critical for downstream tasks in kidney pathology and remains a major challenge due to the morphological diversity and imaging variability of renal tissues. While our prior work has e…
• Emerging AI Approaches for Cancer Spatial Omics
  2025 · AI 安全与对齐 · Technological breakthroughs in spatial omics and artificial intelligence (AI) have the potential to transform the understanding of cancer cells and the tumor microenvironment. Here we review the role of AI in spatial omi…
• Mass Balance Approximation of Unfolding Improves Potential-Like Methods for Protein Stability Predictions
  2025 · AI 驱动科学发现 · The prediction of protein stability changes following single-point mutations plays a pivotal role in computational biology, particularly in areas like drug discovery, enzyme reengineering, and genetic disease analysis. A…
• Domain Knowledge Infused Conditional Generative Models for Accelerating Drug Discovery
  2025 · AI 驱动科学发现 · The role of Artificial Intelligence (AI) is growing in every stage of drug development. Nevertheless, a major challenge in drug discovery AI remains: Drug pharmacokinetic (PK) and Drug-Target Interaction (DTI) datasets c…
• Automating Care by Self-maintainability for Full Laboratory Automation
  2025 · AI 驱动科学发现 · The automation of experiments in life sciences and chemistry has significantly advanced with the development of various instruments and AI technologies. However, achieving full laboratory automation, where experiments co…
• Physiological and Transcriptional Responses of Arabidopsis thaliana to Simulated Lunar and Martian Regolith Substrates
  2025 · 地外矿物 · The integration of plant-based bioregenerative life support systems is a central objective in NASA's Moon to Mars strategy. Arabidopsis thaliana, a model organism with extensive genomic resources, serves as a key species…
• MIDOG 2025 Track 2: A Deep Learning Model for Classification of Atypical and Normal Mitotic Figures under Class and Hardness Imbalances
  2025 · 地外矿物 · Motivation: Accurate classification of mitotic figures into normal and atypical types is crucial for tumor prognostication in digital pathology. However, developing robust deep learning models for this task is challengin…
• Histo-Miner: Deep learning based tissue features extraction pipeline from H&E whole slide images of cutaneous squamous cell carcinoma
  2025 · 地外矿物 · Recent advancements in digital pathology have enabled comprehensive analysis of Whole-Slide Images (WSI) from tissue samples, leveraging high-resolution microscopy and computational capabilities. Despite this progress, t…
• YH-MINER: Multimodal Intelligent System for Natural Ecological Reef Metric Extraction
  2025 · 地外矿物 · Coral reefs, crucial for sustaining marine biodiversity and ecological processes (e.g., nutrient cycling, habitat provision), face escalating threats, underscoring the need for efficient monitoring. Coral reef ecological…
• TEDDY: A Family Of Foundation Models For Understanding Single Cell Biology
  2025 · 生物计算 · Understanding the biological mechanisms of disease is crucial for medicine, and in particular, for drug discovery. AI-powered analysis of genome-scale biological data holds great potential in this regard. The increasing …
• Towards Electrophysiological and Histological Mapping of Upper Limb Nerves in Pigs Using Epineural Stimulation
  2025 · 仿生智能 · Understanding the relationship between nerve anatomy and the functional outcomes of electrical stimulation is critical for optimizing neural interface design. In this study, we conducted acute experiments on four pigs in…
• A Bayesian approach to model uncertainty in single-cell genomic data
  2025 · 脑科学 · Network models provide a powerful framework for analysing single-cell count data, facilitating the characterisation of cellular identities, disease mechanisms, and developmental trajectories. However, uncertainty modelin…
• Assimilation of machine learning-predicted nitrate to improve the quality of phytoplankton forecasting in the shelf sea environment
  2025 · 深海科技 · We demonstrate that assimilating Neural Network (NN)-predicted surface nitrate leads to a major improvement in phytoplankton short-range (1-5 day) dynamical model forecasts for the North-West European Shelf (NWES) seas. …
• TEDDY: A Family Of Foundation Models For Understanding Single Cell Biology
  2025 · 生命科学 · Understanding the biological mechanisms of disease is crucial for medicine, and in particular, for drug discovery. AI-powered analysis of genome-scale biological data holds great potential in this regard. The increasing …
• Neural Proteomics Fields for Super-resolved Spatial Proteomics Prediction
  2025 · 生命科学 · Spatial proteomics maps protein distributions in tissues, providing transformative insights for life sciences. However, current sequencing-based technologies suffer from low spatial resolution, and substantial inter-tiss…
• Subcellular proteome niche discovery using semi-supervised functional clustering
  2025 · 生命科学 · Intracellular compartmentalization of proteins underpins their function and the metabolic processes they sustain. Various mass spectrometry-based proteomics methods (subcellular spatial proteomics) now allow high through…
• Towards Scalable Proteomics: Opportunistic SMC Samplers on HTCondor
  2025 · 生命科学 · Quantitative proteomics plays a central role in uncovering regulatory mechanisms, identifying disease biomarkers, and guiding the development of precision therapies. These insights are often obtained through complex Baye…
• Phospho-Proteomics Method Optimization and Application to Stimulated Jurkat Cells
  2025 · 生命科学 · In clinical proteomics, available input is often limited. In addition, phospho-proteomics is of particular interest since the dysregulation of these post-translational modifications (PTMs) has been implicated in various …
• A graph-based approach for modification site assignment in proteomics
  2025 · 生命科学 · Background In proteomics, the most probable localizations of post-translational modifications are assessed by localization scores evaluating the likelihood of a given modification to occupy a site on a peptide sequence. …
• Leveraging Retrieval-Augmented Generation and Large Language Models to Predict SERCA-Binding Protein Fragments from Cardiac Proteomics Data
  2025 · 生命科学 · Large language models (LLMs) have shown promise in various natural language processing tasks, including their application to proteomics data to classify protein fragments. In this study, we curated a limited mass spectro…
• Accurate de novo sequencing of the modified proteome with OmniNovo
  2025 · 生命科学 · Post-translational modifications (PTMs) serve as a dynamic chemical language regulating protein function, yet current proteomic methods remain blind to a vast portion of the modified proteome. Standard database search al…
• MIDOG 2025 Track 2: A Deep Learning Model for Classification of Atypical and Normal Mitotic Figures under Class and Hardness Imbalances
  2025 · 量子计算 · Motivation: Accurate classification of mitotic figures into normal and atypical types is crucial for tumor prognostication in digital pathology. However, developing robust deep learning models for this task is challengin…
• TEDDY: A Family Of Foundation Models For Understanding Single Cell Biology
  2025 · 合成生物与生物制造 · Understanding the biological mechanisms of disease is crucial for medicine, and in particular, for drug discovery. AI-powered analysis of genome-scale biological data holds great potential in this regard. The increasing …
• A Symbolic and Statistical Learning Framework to Discover Bioprocessing Regulatory Mechanism: Cell Culture Example
  2025 · 合成生物与生物制造 · Bioprocess mechanistic modeling is essential for advancing intelligent digital twin representation of biomanufacturing, yet challenges persist due to complex intracellular regulation, stochastic system behavior, and limi…
• Lessons Learned from Deploying Adaptive Machine Learning Agents with Limited Data for Real-time Cell Culture Process Monitoring
  2025 · 合成生物与生物制造 · This study explores the deployment of three machine learning (ML) approaches for real-time prediction of glucose, lactate, and ammonium concentrations in cell culture processes, using Raman spectroscopy as input features…
• AI-Enabled Lung Cancer Prognosis
  2024 · AI 安全与对齐 · Lung cancer is the primary cause of cancer-related mortality, claiming approximately 1.79 million lives globally in 2020, with an estimated 2.21 million new cases diagnosed within the same period. Among these, Non-Small …
• Machine Learning Applied to the Detection of Mycotoxin in Food: A Review
  2024 · AI 安全与对齐 · Mycotoxins, toxic secondary metabolites produced by certain fungi, pose significant threats to global food safety and public health. These compounds can contaminate a variety of crops, leading to economic losses and heal…
• M$^{3}$-20M: A Large-Scale Multi-Modal Molecule Dataset for AI-driven Drug Design and Discovery
  2024 · AI 驱动科学发现 · This paper introduces M$^{3}$-20M, a large-scale Multi-Modal Molecule dataset that contains over 20 million molecules, with the data mainly being integrated from existing databases and partially generated by large langua…
• Drug Discovery SMILES-to-Pharmacokinetics Diffusion Models with Deep Molecular Understanding
  2024 · AI 驱动科学发现 · Artificial intelligence (AI) is increasingly used in every stage of drug development. One challenge facing drug discovery AI is that drug pharmacokinetic (PK) datasets are often collected independently from each other, o…
• Analysing control-theoretic properties of nonlinear synthetic biology circuits
  2024 · 生物计算 · Synthetic biology is a recent area of biological engineering, whose aim is to provide cells with novel functionalities. A number of important results regarding the development of control circuits in synthetic biology hav…
• Live-cell imaging powered by computation
  2024 · 生物计算 · The proliferation of microscopy methods for live-cell imaging offers many new possibilities for users but can also be challenging to navigate. We focus here on computational methods that promise to boost live-cell fluore…
• covSTATIS: a multi-table technique for network neuroscience
  2024 · 脑科学 · Similarity analyses between multiple correlation or covariance tables constitute the cornerstone of network neuroscience. Here, we introduce covSTATIS, a versatile, linear, unsupervised multi-table method designed to ide…
• Efficient gPC-based quantification of probabilistic robustness for systems in neuroscience
  2024 · 脑科学 · Robustness analysis is very important in biology and neuroscience, to unravel behavioural patterns of systems that are conserved despite large parametric uncertainties. To make studies of probabilistic robustness more ef…
• Boosting Skull-Stripping Performance for Pediatric Brain Images
  2024 · 脑科学 · Skull-stripping is the removal of background and non-brain anatomical features from brain images. While many skull-stripping tools exist, few target pediatric populations. With the emergence of multi-institutional pediat…
• Automating Exploratory Proteomics Research via Language Models
  2024 · 生命科学 · With the development of artificial intelligence, its contribution to science is evolving from simulating a complex problem to automating entire research processes and producing novel discoveries. Achieving this advanceme…
• TraianProt: a user-friendly R shiny application for wide format proteomics data downstream analysis
  2024 · 生命科学 · Mass spectrometry based proteomics enables large-scale identification, quantification, and characterization of proteins, post-translational modifications, and dynamic expression changes, providing critical insights into …
• Analysing control-theoretic properties of nonlinear synthetic biology circuits
  2024 · 合成生物与生物制造 · Synthetic biology is a recent area of biological engineering, whose aim is to provide cells with novel functionalities. A number of important results regarding the development of control circuits in synthetic biology hav…
• Digital Twin Calibration for Biological System-of-Systems: Cell Culture Manufacturing Process
  2024 · 合成生物与生物制造 · Biomanufacturing innovation relies on an efficient Design of Experiments (DoEs) to optimize processes and product quality. Traditional DoE methods, ignoring the underlying bioprocessing mechanisms, often suffer from a la…
• Protein 3D Graph Structure Learning for Robust Structure-based Protein Property Prediction
  2023 · AI 驱动科学发现 · Protein structure-based property prediction has emerged as a promising approach for various biological tasks, such as protein function prediction and sub-cellular location estimation. The existing methods highly rely on …

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