DepMicroDiff: Diffusion-Based Dependency-Aware Multimodal Imputation for Microbiome Data [0.03%]
基于扩散的依赖性感知多模态微生物组数据插补方法 DepMicroDiff
Rabeya Tus Sadia,Qiang Cheng
Rabeya Tus Sadia
Microbiome data analysis is essential for understanding host health and disease, yet its inherent sparsity and noise pose major challenges for accurate imputation, hindering downstream tasks such as biomarker discovery. Existing imputation ...
Ava E D Kelly,John S H Danial
Ava E D Kelly
High-order multiplexing in super-resolution microscopy is limited by trade-offs between spectral discrimination, imaging speed, and experimental complexity. Here, we show that red-green-blue (RGB) complementary metal oxide semiconductor (CM...
MetaphorPrompt2-A Structure and Function-Focused Approach for Extracting Causal Events from Biological Text [0.03%]
基于结构和功能的从生物文本中抽取因果事件的新方法
Parth Patel,Yu-Chiao Chiu,Yufei Huang et al.
Parth Patel et al.
Extracting molecular regulatory pathways (MRPs) from biomedical literature is crucial for building knowledge graphs that represent disease mechanisms and molecular regulation. However, even advanced large language models (LLMs) using in-con...
Microbiome-Metabolome Crosstalk in HPV Pathogenesis: From Ecosystem Dynamics to Translational Biomarkers [0.03%]
人乳头瘤病毒致病机制中的微生物组-代谢组相互作用：从生态系统动力学到底物标志物的转化
Mariano A Molina,Wenkui Dai
Mariano A Molina
High-risk human papillomavirus (hrHPV) infection alters the cervicovaginal microenvironment, driving metabolic reprogramming that influences viral persistence and progression to cervical cancer. This review adopts a systems-level perspectiv...
Michail Patsakis,Alexandros Margaris,Ioannis Mouratidis et al.
Michail Patsakis et al.
As synthetic genomics scales toward the construction of increasingly larger genomes, computational strategies are needed to address technical feasibility. We introduce an algorithmic framework for the minimum-cost synthetic genome planning ...
Functional Genomic Evidence for Candidate Small Viral RNA-Mediated Epigenetic Interference in SARS-CoV-1 and SARS-CoV-2 [0.03%]
功能基因组学证据表明SARS-CoV-1和SARS-CoV-2的小病毒RNA介导的表观遗传干扰的作用候选机制
Amber R Paulson,Vincent Montoya,Jeffrey B Joy
Amber R Paulson
Small viral RNAs (svRNAs) have emerged as key factors in host adaptation and virulence, with evidence of their presence in both SARS-CoV-2 and SARS-CoV-1. Here, using functional genomics, we identify 6 candidate svRNA-triplex-forming oligon...
From Pixels to Patterns: A Multidimensional Framework to Decode Cytoskeletal Organization [0.03%]
从像素到模式：解码细胞骨架组织的多维框架
Diogo Fróis Vieira,Joana Figueiredo,João Sanches
Diogo Fróis Vieira
The cytoskeleton is a dynamic filamentous network that supports essential cellular processes, from shape maintenance to cell division and migration. Advances in microscopy and computational image analysis now enable visualization and quanti...
A Large Concept Model for Mechanistic Simulation of Disease Trajectories: A Hypothesis-Generating Exemplar for Pediatric Acute Lymphoblastic Leukemia [0.03%]
一种用于疾病发展机制模拟的大规模概念模型：以儿童急性淋巴细胞白血病为例的假说生成方法
Wayne R Danter
Wayne R Danter
Background: Many diseases evolve through complex, nonlinear trajectories shaped by interacting genetic, cellular, and environmental factors over time. Such dynamics are difficult to represent using static risk models, particularly in biolog...
Adversarial Sequence Mutations in AlphaFold and ESMFold Reveal Nonphysical Structural Invariance, Confidence Failures, and Concerns for Protein Design [0.03%]
针对AlphaFold和ESMFold的对抗序列突变揭示了非物理结构不变性、置信度失败及蛋白质设计中的问题
Jonathan Feldman,Maximilian Brogi,Jeffrey Skolnick
Jonathan Feldman
AlphaFold has transformed structural biology and spawned an ecosystem of derivative tools for protein design, binding prediction, and drug discovery. However, whether AlphaFold has learned generalizable biophysical principles as opposed to ...
High-Throughput Prediction of Protein-Protein Interactions Uncovers Hidden Molecular Networks in Biosynthetic Gene Clusters [0.03%]
高通量预测蛋白质-蛋白质相互作用以揭开生物合成基因簇中的隐藏分子网络
Yoshitaka Moriwaki,Taro Shiraishi,Yohei Katsuyama et al.
Yoshitaka Moriwaki et al.
Biosynthetic gene clusters (BGCs) are contiguous genomic regions that encode diverse proteins responsible for natural product biosynthesis. These proteins collectively produce various secondary metabolites with complex chemical structure, i...