医学 AI

ECKO: Explainable Clinical Knowledge for Oncology

Marta Contreiras Silva, Daniel Faria, Laura Balbi, Susana Nunes, Ana Filipa Rodrigues, Aleksander Palkowski, Michal Waleron, Emilia Daghir-Wojtkowiak, Ashwin Adrian Kallor, Christophe Battail, Federico Maria Corazza, Manuel Fiorelli, Armando Stellato, Javier Antonio Alfaro, Fabio Massimo Zanzotto, Catia Pesquita

专题命中 生物医学文本 ：biomedical(abstract)；分类 q-bio

Comments 18 pages, 9 figures

Mendelian randomization in a multi-ancestry world: reflections and practical advice

Amy M. Mason, Verena Zuber, Gibran Hemani, Elena Raffetti, Yu Xu, Amanda H. W Chong, Benjamin Woolf, Elias Allara, Dipender Gill, Opeyemi Soremekun, Stephen Burgess

专题命中 生物医学文本 ：biomedical(abstract)；分类 q-bio

Comments 20 pages, 2 figures

Recent Advances in Microfluidics and Bioelectronics for Three-Dimensional Organoid Interfaces

Caroline Ferguson, Yan Li, Yi Zhang, Xueju Wang

专题命中 生物医学文本 ：biomedical(abstract)；分类 q-bio

Contrastive Learning Enhances Language Model Based Cell Embeddings for Low-Sample Single Cell Transcriptomics

Luxuan Zhang, Douglas Jiang, Qinglong Wang, Haoqi Sun, Feng Tian

专题命中 生物医学文本 ：biomedical(abstract)；分类 q-bio

Comments 14 pages, 4 figures, 2 tables

Deep Clustering for Blood Cell Classification and Quantification

Mihaela Macarie-Ancau, Adrian Groza

专题命中 生物医学文本 ：biomedical(abstract)；分类 q-bio

InterFeat: A Pipeline for Finding Interesting Scientific Features

Dan Ofer, Michal Linial, Dafna Shahaf

机构 * The Hebrew University of Jerusalem（耶路撒冷希伯来大学） ； Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem（生物化学系、生命科学研究所、耶路撒冷希伯来大学） ； Department of Computer Science, The Hebrew University of Jerusalem（计算机科学系、耶路撒冷希伯来大学） 纠错

专题命中 生物医学文本 ：biomedical(abstract)；分类 q-bio

Harmonizing the Generation and Pre-publication Stewardship of FAIR Image Data

Nikki Bialy, Frank Alber, Brenda Andrews, Michael Angelo, Brian Beliveau, Lacramioara Bintu, Alistair Boettiger, Ulrike Boehm, Claire M. Brown, Mahmoud Bukar Maina, James J. Chambers, Beth A. Cimini, Kevin Eliceiri, Rachel Errington, Orestis Faklaris, Nathalie Gaudreault, Ronald N. Germain, Wojtek Goscinski, David Grunwald, Michael Halter, Dorit Hanein, John W. Hickey, Judith Lacoste, Alex Laude, Emma Lundberg, Jian Ma, Leonel Malacrida, Josh Moore, Glyn Nelson, Elizabeth Kathleen Neumann, Roland Nitschke, Shuichi Onami, Jaime A. Pimentel, Anne L. Plant, Andrea J. Radtke, Bikash Sabata, Denis Schapiro, Johannes Schöneberg, Jeffrey M. Spraggins, Damir Sudar, Wouter-Michiel Adrien Maria Vierdag, Niels Volkmann, Carolina Wählby, Siyuan, Wang, Ziv Yaniv, Caterina Strambio-De-Castillia

专题命中 生物医学文本 ：biomedical(abstract)；分类 q-bio

Comments This manuscript is published with a closely related companion entitled 'Enabling Global Image Data Sharing in the Life Sciences', which was initially made available on ArXiv (https://doi.org/10.48550/arXiv.2401.13023) and is now published on Nature Methods (https://doi.org/10.1038/s41592-024-02585-z)

AI-Driven Drug Repurposing through miRNA-mRNA Relation

Sharanya Manoharan, Balu Bhasuran, Oviya Ramalakshmi Iyyappan, Mohamed Saleem Abdul Shukkoor, Malathi Sellapan, Kalpana Raja

专题命中 生物医学文本 ：biomedical(abstract)；分类 q-bio

A Multi-Layered Framework for Modeling Human Biology: From Basic AI Agents to a Full-Body AI Agent

Aoqi Wang, Jiajia Liu, Jianguo Wen, Yangyang Luo, Zhiwei Fan, Liren Yang, Xi Hu, Ruihan Luo, Yankai Yu, Sophia Li, Weiling Zhao, Xiaobo Zhou

专题命中 生物医学文本 ：biomedical(abstract)；分类 q-bio

Dominant ionic currents in rabbit ventricular action potential dynamics

Zhechao Yang, Hao Gao, Godfrey L. Smith, Radostin D. Simitev

专题命中 生物医学文本 ：biomedical(abstract)；分类 q-bio

Journal ref PLoS One 20(7): e0328261. (2025)

Synthesis of nanoparticles from carboxymethyl cellulose using one-pot hydrothermal carbonization for Drug Entrapment Studies

Mohaddeseh Sharifi, S. Hajir Bahrami

专题命中 生物医学文本 ：biomedical(abstract)；分类 q-bio

Comments This article is currently under review in Carbon Trends

A novel approach for classifying Monoamine Neurotransmitters by applying Machine Learning on UV plasmonic-engineered Auto Fluorescence Time Decay Series (AFTDS)

Mohammad Mohammadi, Sima Najafzadehkhoei, George Vega Yon, Yunshan Wang

专题命中 生物医学文本 ：biomedical(abstract)；分类 q-bio

Nanoplasmonic Optical Fiber Sensing of SARS-CoV-2 Nucleocapsid Protein Using an Aptamer-DNA Tetrahedron Interface

Xu Pin, Cui Jingyu, Cheng Zhi, Simon Chi-Chin Shiu, Cui Jingxian, Li Yujian, Liu Yifan, Wang Lin, Ryan Ho Ping Siu, Julian A. Tanner, Yu Changyuan

专题命中 生物医学文本 ：diagnosis(abstract)；分类 q-bio

Accelerating Causal Network Discovery of Alzheimer Disease Biomarkers via Scientific Literature-based Retrieval Augmented Generation

Xiaofan Zhou, Liangjie Huang, Pinyang Cheng, Wenpen Yin, Rui Zhang, Wenrui Hao, Lu Cheng

专题命中 生物医学文本 ：diagnosis(abstract)；分类 q-bio

Comments 9 pages, under review

Assessing parameter identifiability of a hemodynamics PDE model using spectral surrogates and dimension reduction

Mitchel J. Colebank

专题命中 生物医学文本 ：biomedical(abstract)；分类 q-bio

Comments 30 pages, 12 figures

Causal knowledge graph analysis identifies adverse drug effects

Sumyyah Toonsi, Paul Schofield, Robert Hoehndorf

机构 * Computer, Electrical and Mathematical Sciences & Engineering（计算机、电气与数学科学与工程） ； King Abdullah University of Science and Technology（卡布斯科学技术大学） ； University of Cambridge（剑桥大学） ； SDAIA–KAUST Center of Excellence in Data Science and Artificial Intelligence（数据科学与人工智能卓越中心） ； KAUST Center of Excellence for Smart Health (KCSH)（智能健康卓越中心） 纠错

专题命中 生物医学文本 ：biomedical(abstract)；分类 q-bio

A Fourfold Pathogen Reference Ontology Suite

Shane Babcock, Carter Benson, Giacomo De Colle, Sydney Cohen, Alexander D. Diehl, Ram A. N. R. Challa, Ray Mavrovich, Joshua Billig, Anthony Huffman, Yongqun He, John Beverley

专题命中 生物医学文本 ：biomedical(abstract)；分类 q-bio

Comments 25 pages

Advances in Surrogate Modeling for Biological Agent-Based Simulations: Trends, Challenges, and Future Prospects

Kerri-Ann Norton, Daniel Bergman, Harsh Vardhan Jain, Trachette Jackson

专题命中 生物医学文本 ：biomedical(abstract)；分类 q-bio

Comments 38 pages, 3 figures, Review article

ProtoBERT-LoRA: Parameter-Efficient Prototypical Finetuning for Immunotherapy Study Identification

Shijia Zhang, Xiyu Ding, Kai Ding, Jacob Zhang, Kevin Galinsky, Mengrui Wang, Ryan P. Mayers, Zheyu Wang, Hadi Kharrazi

专题命中 生物医学文本 ：biomedical(abstract)；分类 q-bio

Comments Submitted to AMIA 2025 Annual Symposium

Variability of morphology in beat-to-beat photoplethysmographic waveform quantified with unsupervised wave-shape manifold learning for clinical assessment

Yu-Chieh Ho, Te-Sheng Lin, She-Chih Wang, Chen-Shi Chang, Yu-Ting Lin

专题命中 生物医学文本 ：biomedical(abstract)；分类 q-bio

Using Label-Free Raman Spectroscopy Integrated with Microfluidic Chips to Probe Ferroptosis Networks in Cells

Muhammad Muhammad, Chang-Sheng Shao, Raziq Nawaz, Amil Aligayev, Muhammad Hassan, Mona Alrasheed Bashir, Jamshed Iqbal, Jie Zhan, Qing Huang

专题命中 生物医学文本 ：biomedical(abstract)；分类 q-bio

Discovery of novel antimicrobial peptides with notable antibacterial potency by a LLM-based foundation model

Jike Wang, Jianwen Feng, Yu Kang, Peichen Pan, Jingxuan Ge, Yan Wang, Mingyang Wang, Zhenxing Wu, Xingcai Zhang, Jiameng Yu, Xujun Zhang, Tianyue Wang, Lirong Wen, Guangning Yan, Yafeng Deng, Hui Shi, Chang-Yu Hsieh, Zhihui Jiang, Tingjun Hou

专题命中 生物医学文本 ：biomedical(abstract)；分类 q-bio

Comments 43 pages, 6 figures, 5 tables. Due to the limitation "The abstract field cannot be longer than 1,920 characters", the abstract appearing here is slightly shorter than that in the PDF file

From FAIR to CURE: Guidelines for Computational Models of Biological Systems

Herbert M. Sauro, Eran Agmon, Michael L. Blinov, John H. Gennari, Joe Hellerstein, Adel Heydarabadipour, Peter Hunter, Bartholomew E. Jardine, Elebeoba May, David P. Nickerson, Lucian P. Smith, Gary D Bader, Frank Bergmann, Patrick M. Boyle, Andreas Drager, James R. Faeder, Song Feng, Juliana Freire, Fabian Frohlich, James A. Glazier, Thomas E. Gorochowski, Tomas Helikar, Stefan Hoops, Princess Imoukhuede, Sarah M. Keating, Matthias Konig, Reinhard Laubenbacher, Leslie M. Loew, Carlos F. Lopez, William W. Lytton, Andrew McCulloch, Pedro Mendes, Chris J. Myers, Jerry G. Myers, Lealem Mulugeta, Anna Niarakis, David D. van Niekerk, Brett G. Olivier, Alexander A. Patrie, Ellen M. Quardokus, Nicole Radde, Johann M. Rohwer, Sven Sahle, James C. Schaff, T. J. Sego, Janis Shin, Jacky L. Snoep, Rajanikanth Vadigepalli, H. Steve Wiley, Dagmar Waltemath, Ion Moraru

专题命中 生物医学文本 ：biomedical(abstract)；分类 q-bio

Synthetic Porous Microstructures: Automatic Design, Simulation, and Permeability Analysis

Thomas Lavigne, Camilo Andrés Suarez Afanador, Anas Obeidat, Stéphane Urcun

专题命中 生物医学文本 ：biomedical(abstract)；分类 q-bio

Frustration In Physiology And Molecular Medicine

R. Gonzalo Parra, Elizabeth A. Komives, Peter G. Wolynes, Diego U. Ferreiro

专题命中 生物医学文本 ：pathology(abstract)；分类 q-bio

Survey and Improvement Strategies for Gene Prioritization with Large Language Models

Matthew Neeley, Guantong Qi, Guanchu Wang, Ruixiang Tang, Dongxue Mao, Chaozhong Liu, Sasidhar Pasupuleti, Bo Yuan, Fan Xia, Pengfei Liu, Zhandong Liu, Xia Hu

专题命中 生物医学文本 ：diagnosis(abstract)；分类 q-bio

Comments 11 pages, 4 figures, 10 pages of supplementary figures

A technical review of multi-omics data integration methods: from classical statistical to deep generative approaches

Ana R. Baião, Zhaoxiang Cai, Rebecca C Poulos, Phillip J. Robinson, Roger R Reddel, Qing Zhong, Susana Vinga, Emanuel Gonçalves

专题命中 生物医学文本 ：biomedical(abstract)；分类 q-bio

Comments 43 pages, 4 figures

Mechanisms for bump state localization in two-dimensional networks of leaky Integrate-and-Fire neurons

A. Provata, J. Hizanidis, K. Anesiadis, O. E. Omel'chenko

专题命中 生物医学文本 ：biomedical(abstract)；分类 q-bio

Controllable Protein Sequence Generation with LLM Preference Optimization

Xiangyu Liu, Yi Liu, Silei Chen, Wei Hu

专题命中 生物医学文本 ：biomedical(abstract)；分类 q-bio

Comments Accepted in the 39th Annual AAAI Conference on Artificial Intelligence (AAAI 2025)

Detecting signal from science:The structure of research communities and prior knowledge improves prediction of genetic regulatory experiments

Alexander V. Belikov, Andrey Rzhetsky, James Evans

专题命中 生物医学文本 ：biomedical(abstract)；分类 q-bio

Comments 61 pages, 20 figures