Simulation-based inference of cell migration dynamics in complex spatial environments [0.03%]
基于模拟的复杂空间环境下的细胞迁移动力学的推理
Jonas Arruda,Emad Alamoudi,Robert Mueller et al.
Jonas Arruda et al.
To assess cell migration in complex spatial environments, microfabricated chips, such as mazes and pillar forests, are routinely used to impose spatial and mechanical constraints, and cell trajectories are followed within these structures b...
Dynamical network analysis reveals long-range residue couplings at the pMHC interface underlying enhanced immunogenicity [0.03%]
动态网络分析揭示了pMHC界面上的基本相互作用残基耦合，解释了增强的免疫原性现象
Tom Resink,Benedetta Maria Sala,Renhua Sun et al.
Tom Resink et al.
The interaction between a class I peptide-major histocompatibility complex (pMHC) and a T cell receptor (TCR) plays a central role in the elicitation of CD8+ T cell immune responses. As a result, considerable effort has been invested in und...
Spatial FBA reveals heterogeneous Warburg niches in renal tumors and lactate consumption in colorectal cancer [0.03%]
空间FBA揭示了肾肿瘤中的异质性瓦堡生态位和结直肠癌中的乳酸消耗
Davide Maspero,Giovanni Marteletto,Francesco Lapi et al.
Davide Maspero et al.
To investigate how spatial constraints shape cancer metabolism, we devised the spatial Flux Balance Analysis (spFBA) framework for the enrichment of spatial transcriptomics data with relative estimates of metabolic fluxes. Applying spFBA to...
Russell C Rockne,Morten Andersen,Alexander R A Anderson et al.
Russell C Rockne et al.
This perspective article discusses emerging advances at the interface of mechanistic modeling and data-driven machine learning, highlighting opportunities for AI to accelerate discovery, improve predictive modeling, and enhance clinical dec...
In silico modeling of anterior foregut endoderm differentiation towards lung epithelial progenitors [0.03%]
肺上皮祖细胞体外建模预测分析
Amirmahdi Mostofinejad,David A Romero,Dana Brinson et al.
Amirmahdi Mostofinejad et al.
Directed differentiation of human induced pluripotent stem cells (iPSCs) into anterior foregut endoderm (AFE) and lung progenitors (LPs) has wide-ranging implications for lung developmental biology, disease modeling, and regenerative medici...
Canalization as a stabilizing principle of gene regulatory networks: a discrete dynamical systems perspective [0.03%]
基因调控网络的 canalization 稳定机制：离散动力系统视角
Claus Kadelka
Claus Kadelka
Gene regulatory networks exhibit remarkable stability, maintaining functional phenotypes despite genetic and environmental perturbations. Discrete dynamical models, such as Boolean networks, provide systems biologists with a tractable frame...
Machine learning prediction for AML based on 3D genome selected circRNA [0.03%]
基于三维基因组选择的环状rna的机器学习在急性髓系白血病中的预测作用
Zhangli Yuan,Wenqian Yan,Ruoyao Wang et al.
Zhangli Yuan et al.
Acute myeloid leukemia (AML) is a clinically aggressive hematologic malignancy driven by complex genetic and epigenetic aberrations. Circular RNAs (circRNAs), characterized by covalently closed structures and exceptional stability, have eme...
Gene regulatory network transitions reveal the central transcription factors in lung adenocarcinoma progression [0.03%]
基因调控网络的转换揭示了肺腺癌进展中的中心转录因子
Upasana Ray,Adarsh Singh,Debabrata Samanta et al.
Upasana Ray et al.
Transcription factors play a central role in cancer growth, progression, and metastasis, and contribute to intratumor phenotypic plasticity that enable drug tolerance and cancer relapse. Changes in the regulatory activities of transcription...
Association of copy number alterations with the immune transcriptomic landscape in cancer [0.03%]
拷贝数改变与癌症免疫转录组图谱间的关联分析
Stefan Loipfinger,Arkajyoti Bhattacharya,Carlos G Urzúa-Traslaviña et al.
Stefan Loipfinger et al.
Tumors with high copy number alteration (CNA) burden often respond poorly to immune checkpoint inhibitor therapy. However, how CNAs affect the anti-cancer immune response remains unclear. To address this, we set out to capture the transcrip...
Asthma-mediated control of optic glioma growth via T cell-microglia interactions: A mathematical model [0.03%]
哮喘通过T细胞-小胶质细胞相互作用介导的视神经胶质瘤生长控制：一种数学模型
Donggu Lee,Sean Lawler,Yangjin Kim
Donggu Lee
Optic glioma, a slow-growing tumor, is associated with Neurofibromatosis type 1 (NF1) mutations and increased midkine (MDK) production. A connection between asthma and optic glioma has previously been observed, but the mechanisms are unclea...