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Quantitative Biology

Authors and titles for March 2025

Total of 426 entries : 1-50 51-100 101-150 151-200 ... 401-426
Showing up to 50 entries per page: fewer | more | all
[1] arXiv:2503.00008 [cn-pdf, pdf, html, other]
Title: An Efficient Algorithm for Determining the Equivalence of Zero-one Reaction Networks
Yue Jiao, Xiaoxian Tang
Subjects: Molecular Networks (q-bio.MN)
[2] arXiv:2503.00016 [cn-pdf, pdf, html, other]
Title: Time-Irreversible Quantum-Classical Dynamics of Molecular Models in the Brain
Alessandro Sergi, Antonino Messina, Rosalba Saija, Gabriella Martino, Maria Teresa Caccamo, Min-Fang Kuo, Michael A. Nitsche
Journal-ref: Symmetry 2025, 17, 285
Subjects: Neurons and Cognition (q-bio.NC) ; Disordered Systems and Neural Networks (cond-mat.dis-nn) ; Other Condensed Matter (cond-mat.other) ; Biological Physics (physics.bio-ph) ; Quantum Physics (quant-ph)
[3] arXiv:2503.00048 [cn-pdf, pdf, html, other]
Title: Dynamical analysis of an HIV infection model including quiescent cells and immune response
Ibrahim Nali, Attila Dénes, Abdessamad Tridane, Xueyong Zhou
Subjects: Populations and Evolution (q-bio.PE)
[4] arXiv:2503.00089 [cn-pdf, pdf, html, other]
Title: Protein Structure Tokenization: Benchmarking and New Recipe
Xinyu Yuan, Zichen Wang, Marcus Collins, Huzefa Rangwala
Comments: Accepted at ICML 2025
Subjects: Quantitative Methods (q-bio.QM) ; Artificial Intelligence (cs.AI) ; Machine Learning (cs.LG)
[5] arXiv:2503.00096 [cn-pdf, pdf, other]
Title: BixBench: a Comprehensive Benchmark for LLM-based Agents in Computational Biology
Ludovico Mitchener, Jon M Laurent, Alex Andonian, Benjamin Tenmann, Siddharth Narayanan, Geemi P Wellawatte, Andrew White, Lorenzo Sani, Samuel G Rodriques
Comments: 8 main text pages, 5 main figures
Subjects: Quantitative Methods (q-bio.QM) ; Artificial Intelligence (cs.AI)
[6] arXiv:2503.00143 [cn-pdf, pdf, html, other]
Title: RecCrysFormer: Refined Protein Structural Prediction from 3D Patterson Maps via Recycling Training Runs
Tom Pan, Evan Dramko, Mitchell D. Miller, George N. Phillips Jr., Anastasios Kyrillidis
Comments: 16 pages, 9 figures. To be published in Proceedings of CPAL 2025
Subjects: Quantitative Methods (q-bio.QM) ; Machine Learning (cs.LG) ; Optimization and Control (math.OC)
[7] arXiv:2503.00165 [cn-pdf, pdf, other]
Title: Leveraging Sequence Purification for Accurate Prediction of Multiple Conformational States with AlphaFold2
Enming Xing, Junjie Zhang, Shen Wang, Xiaolin Cheng
Subjects: Biomolecules (q-bio.BM)
[8] arXiv:2503.00197 [cn-pdf, pdf, html, other]
Title: Unveiling sex dimorphism in the healthy cardiac anatomy: fundamental differences between male and female heart shapes
Beatrice Moscoloni, Cameron Beeche, Julio A. Chirinos, Patrick Segers, Mathias Peirlinck
Subjects: Tissues and Organs (q-bio.TO)
[9] arXiv:2503.00648 [cn-pdf, pdf, html, other]
Title: T-cell receptor specificity landscape revealed through de novo peptide design
Gian Marco Visani, Michael N. Pun, Anastasia A. Minervina, Philip Bradley, Paul Thomas, Armita Nourmohammad
Subjects: Quantitative Methods (q-bio.QM) ; Machine Learning (cs.LG)
[10] arXiv:2503.00655 [cn-pdf, pdf, html, other]
Title: Implicit Generative Modeling by Kernel Similarity Matching
Shubham Choudhary, Paul Masset, Demba Ba
Comments: 37 Pages, 9 figures
Subjects: Neurons and Cognition (q-bio.NC) ; Signal Processing (eess.SP)
[11] arXiv:2503.00776 [cn-pdf, pdf, html, other]
Title: Validity of the total quasi-steady-state approximation in stochastic biochemical reaction networks
Yun Min Song, Kangmin Lee, Jae Kyoung Kim
Comments: 11 pages, 2 figures
Subjects: Molecular Networks (q-bio.MN) ; Probability (math.PR)
[12] arXiv:2503.00913 [cn-pdf, pdf, other]
Title: Applying computational protein design to therapeutic antibody discovery -- current state and perspectives
Weronika Bielska, Igor Jaszczyszyn, Pawel Dudzic, Bartosz Janusz, Dawid Chomicz, Sonia Wrobel, Victor Greiff, Ryan Feehan, Jared Adolf-Bryfogle, Konrad Krawczyk
Subjects: Biomolecules (q-bio.BM)
[13] arXiv:2503.01179 [cn-pdf, pdf, html, other]
Title: Algebraic approaches for the decomposition of reaction networks and the determination of existence and number of steady states
Joseph M. Sauder, Bruce P. Ayati, Ryan Kinser
Subjects: Quantitative Methods (q-bio.QM)
[14] arXiv:2503.01226 [cn-pdf, pdf, html, other]
Title: Dementia Insights: A Context-Based MultiModal Approach
Sahar Sinene Mehdoui, Abdelhamid Bouzid, Daniel Sierra-Sosa, Adel Elmaghraby
Subjects: Neurons and Cognition (q-bio.NC) ; Machine Learning (cs.LG)
[15] arXiv:2503.01250 [cn-pdf, pdf, html, other]
Title: A Study on the Specialist Predator with the Allee Effect on the Prey
Tanmay Das, Mahatsab Mandal
Comments: 15 pages, 5 figures
Subjects: Populations and Evolution (q-bio.PE) ; Dynamical Systems (math.DS)
[16] arXiv:2503.01376 [cn-pdf, pdf, html, other]
Title: Pushing the boundaries of Structure-Based Drug Design through Collaboration with Large Language Models
Bowen Gao, Yanwen Huang, Yiqiao Liu, Wenxuan Xie, Wei-Ying Ma, Ya-Qin Zhang, Yanyan Lan
Subjects: Biomolecules (q-bio.BM)
[17] arXiv:2503.01459 [cn-pdf, pdf, html, other]
Title: Primer C-VAE: An interpretable deep learning primer design method to detect emerging virus variants
Hanyu Wang, Emmanuel K. Tsinda, Anthony J. Dunn, Francis Chikweto, Alain B. Zemkoho
Subjects: Genomics (q-bio.GN) ; Machine Learning (cs.LG)
[18] arXiv:2503.01761 [cn-pdf, pdf, other]
Title: A comprehensive and reliable protocol for manual segmentation of the human claustrum using high-resolution MRI
Steven Seung-Suk Kang, Joseph Bodenheimer, Kayley Morris, Tracey Butler
Subjects: Neurons and Cognition (q-bio.NC)
[19] arXiv:2503.01834 [cn-pdf, pdf, other]
Title: Intercellular contact is sufficient to drive Fibroblast to Myofibroblast transitions
Vasuretha Chandar, Benjamin M. Goykadosh, Harikrishnan Parameswaran
Subjects: Cell Behavior (q-bio.CB)
[20] arXiv:2503.01910 [cn-pdf, pdf, html, other]
Title: dyAb: Flow Matching for Flexible Antibody Design with AlphaFold-driven Pre-binding Antigen
Cheng Tan, Yijie Zhang, Zhangyang Gao, Yufei Huang, Haitao Lin, Lirong Wu, Fandi Wu, Mathieu Blanchette, Stan. Z. Li
Comments: AAAI 2025 Oral
Subjects: Quantitative Methods (q-bio.QM) ; Artificial Intelligence (cs.AI)
[21] arXiv:2503.01994 [cn-pdf, pdf, other]
Title: Fungal Genetic Variants in Oceanic Environments
Sade A. Davenport (1), Scott H. Harrison (2) ((1) Intelligence Community Postdoctoral Research Fellowship Program and North Carolina Agricultural and Technical State University, (2) Department of Biology, North Carolina Agricultural and Technical State University)
Comments: 13 pages, 4 figures
Subjects: Populations and Evolution (q-bio.PE) ; Genomics (q-bio.GN)
[22] arXiv:2503.02058 [cn-pdf, pdf, html, other]
Title: RiboGen: RNA Sequence and Structure Co-Generation with Equivariant MultiFlow
Dana Rubin, Allan dos Santos Costa, Manvitha Ponnapati, Joseph Jacobson
Comments: 6 pages
Subjects: Biomolecules (q-bio.BM) ; Machine Learning (cs.LG)
[23] arXiv:2503.02351 [cn-pdf, pdf, html, other]
Title: MindSimulator: Exploring Brain Concept Localization via Synthetic FMRI
Guangyin Bao, Qi Zhang, Zixuan Gong, Zhuojia Wu, Duoqian Miao
Comments: 23 pages, ICLR 2025
Subjects: Neurons and Cognition (q-bio.NC) ; Artificial Intelligence (cs.AI)
[24] arXiv:2503.02486 [cn-pdf, pdf, html, other]
Title: Spatial competition and repulsion: pattern formation and the role of movement
Cristóbal López, Eduardo H. Colombo, Emilio Hernández-García, Ricardo Martinez-Garcia
Comments: 13 pages, 6 figures
Subjects: Populations and Evolution (q-bio.PE) ; Statistical Mechanics (cond-mat.stat-mech) ; Pattern Formation and Solitons (nlin.PS) ; Biological Physics (physics.bio-ph)
[25] arXiv:2503.02500 [cn-pdf, pdf, other]
Title: The Neural Basis of Groove Sensations: Implications for Music-Based Interventions and Dance Therapy in Parkinson's Disease
Chen-Gia Tsai, Chia-Wei Li
Comments: The 4th International Symposium on Music and Health Promotion, April 11-12, Hsinchu, Taiwan
Subjects: Neurons and Cognition (q-bio.NC)
[26] arXiv:2503.02523 [cn-pdf, pdf, other]
Title: Unlocking tropical forest complexity: How tree assemblages in secondary forests boost biodiversity conservation
Maïri Souza Oliveira, Maxime Lenormand, Sandra Luque, Nelson A. Zamora, Samuel Alleaume, Adriana C. Aguilar Porras, Marvin U. Castillo, Eduardo Chacón-Madrigal, Diego Delgado, Luis Gustavo Hernández Sánchez, Marie-Ange Ngo Bieng, Ruperto M. Quesada, Gilberth S. Solano, Pedro M. Zúñiga
Comments: 28 pages, 7 figures + Appendix
Subjects: Populations and Evolution (q-bio.PE) ; Quantitative Methods (q-bio.QM)
[27] arXiv:2503.02555 [cn-pdf, pdf, html, other]
Title: Proliferating active disks with game dynamical interaction
Alejandro Almodóvar, Tobias Galla, Cristóbal López
Subjects: Populations and Evolution (q-bio.PE) ; Statistical Mechanics (cond-mat.stat-mech)
[28] arXiv:2503.02569 [cn-pdf, pdf, other]
Title: Prediction of amino acid content in live black soldier fly larvae using near infrared spectroscopy
R.M. Zaalberg, L.B. Andersen, S.J. Noel, A.J. Buitenhuis, K. Jensen, G. Gebreyesus
Comments: 28 pages, 2 figures, 3 supplementary files
Subjects: Quantitative Methods (q-bio.QM)
[29] arXiv:2503.02618 [cn-pdf, pdf, other]
Title: ZAPBench: A Benchmark for Whole-Brain Activity Prediction in Zebrafish
Jan-Matthis Lueckmann, Alexander Immer, Alex Bo-Yuan Chen, Peter H. Li, Mariela D. Petkova, Nirmala A. Iyer, Luuk Willem Hesselink, Aparna Dev, Gudrun Ihrke, Woohyun Park, Alyson Petruncio, Aubrey Weigel, Wyatt Korff, Florian Engert, Jeff W. Lichtman, Misha B. Ahrens, Michał Januszewski, Viren Jain
Subjects: Neurons and Cognition (q-bio.NC) ; Computer Vision and Pattern Recognition (cs.CV) ; Machine Learning (cs.LG)
[30] arXiv:2503.02636 [cn-pdf, pdf, html, other]
Title: YARE-GAN: Yet Another Resting State EEG-GAN
Yeganeh Farahzadi, Morteza Ansarinia, Zoltan Kekecs
Subjects: Neurons and Cognition (q-bio.NC) ; Artificial Intelligence (cs.AI)
[31] arXiv:2503.02642 [cn-pdf, pdf, other]
Title: Weight transport through spike timing for robust local gradients
Timo Gierlich, Andreas Baumbach, Akos F. Kungl, Kevin Max, Mihai A. Petrovici
Comments: 19 pages, 9 figures
Subjects: Neurons and Cognition (q-bio.NC) ; Emerging Technologies (cs.ET) ; Machine Learning (cs.LG) ; Neural and Evolutionary Computing (cs.NE)
[32] arXiv:2503.02685 [cn-pdf, pdf, html, other]
Title: TReND: Transformer derived features and Regularized NMF for neonatal functional network Delineation
Sovesh Mohapatra, Minhui Ouyang, Shufang Tan, Jianlin Guo, Lianglong Sun, Yong He, Hao Huang
Comments: 10 Pages, 5 figures
Subjects: Neurons and Cognition (q-bio.NC) ; Computer Vision and Pattern Recognition (cs.CV) ; Signal Processing (eess.SP) ; Quantitative Methods (q-bio.QM)
[33] arXiv:2503.02726 [cn-pdf, pdf, html, other]
Title: Measurement noise scaling laws for cellular representation learning
Gokul Gowri, Peng Yin, Allon M. Klein
Subjects: Quantitative Methods (q-bio.QM) ; Information Theory (cs.IT)
[34] arXiv:2503.02781 [cn-pdf, pdf, html, other]
Title: Multimodal AI predicts clinical outcomes of drug combinations from preclinical data
Yepeng Huang, Xiaorui Su, Varun Ullanat, Intae Moon, Ivy Liang, Lindsay Clegg, Damilola Olabode, Ruthie Johnson, Nicholas Ho, Megan Gibbs, Megan Gibbs, Alexander Gusev, Bino John, Marinka Zitnik
Subjects: Quantitative Methods (q-bio.QM) ; Artificial Intelligence (cs.AI) ; Machine Learning (cs.LG)
[35] arXiv:2503.02792 [cn-pdf, pdf, html, other]
Title: Les Houches lectures on Theoretical Ecology: High-dimensional models and extreme events
Ada Altieri
Comments: Lectures given at Les Houches Summer School "Theory of Large Deviations and Applications" (July 2024)
Subjects: Populations and Evolution (q-bio.PE) ; Disordered Systems and Neural Networks (cond-mat.dis-nn) ; Statistical Mechanics (cond-mat.stat-mech)
[36] arXiv:2503.02794 [cn-pdf, pdf, html, other]
Title: Social hierarchy shapes foraging decisions
Lisa Blum Moyse, Ahmed El Hady
Comments: arXiv admin note: text overlap with arXiv:2412.02381
Subjects: Populations and Evolution (q-bio.PE)
[37] arXiv:2503.02981 [cn-pdf, pdf, other]
Title: Modeling Iodine Deficiency
Paul Fong, Albert Li, Zoe Meadows, Rati Pillai, Chelsea Proutt, Alex Schneider
Comments: 46 pages, 8 figures,
Subjects: Tissues and Organs (q-bio.TO) ; Biomolecules (q-bio.BM)
[38] arXiv:2503.02997 [cn-pdf, pdf, html, other]
Title: Enabling Fast, Accurate, and Efficient Real-Time Genome Analysis via New Algorithms and Techniques
Can Firtina
Comments: PhD Thesis submitted to ETH Zurich
Subjects: Genomics (q-bio.GN) ; Hardware Architecture (cs.AR) ; Data Structures and Algorithms (cs.DS) ; Emerging Technologies (cs.ET)
[39] arXiv:2503.03001 [cn-pdf, pdf, html, other]
Title: Multicellular self-organization in Escherichia coli
Devina Puri, Kyle R. Allison
Comments: 19 pages, 5 figures
Subjects: Cell Behavior (q-bio.CB)
[40] arXiv:2503.03131 [cn-pdf, pdf, html, other]
Title: Spatially-Structured Models of Viral Dynamics: A Scoping Review
Thomas Williams, James M. McCaw, James M. Osborne
Subjects: Quantitative Methods (q-bio.QM)
[41] arXiv:2503.03310 [cn-pdf, pdf, html, other]
Title: Optimal virulence strategies in epidemiological models with asymptomatic transmission
C. Brandon Ogbunugafor, Sudam Surasinghe
Subjects: Populations and Evolution (q-bio.PE)
[42] arXiv:2503.03503 [cn-pdf, pdf, html, other]
Title: Collaborative Expert LLMs Guided Multi-Objective Molecular Optimization
Jiajun Yu, Yizhen Zheng, Huan Yee Koh, Shirui Pan, Tianyue Wang, Haishuai Wang
Subjects: Biomolecules (q-bio.BM) ; Artificial Intelligence (cs.AI) ; Machine Learning (cs.LG)
[43] arXiv:2503.03773 [cn-pdf, pdf, html, other]
Title: A Phylogenetic Approach to Genomic Language Modeling
Carlos Albors, Jianan Canal Li, Gonzalo Benegas, Chengzhong Ye, Yun S. Song
Comments: 15 pages, 7 figures
Subjects: Genomics (q-bio.GN) ; Machine Learning (cs.LG)
[44] arXiv:2503.03783 [cn-pdf, pdf, html, other]
Title: Passive Heart Rate Monitoring During Smartphone Use in Everyday Life
Shun Liao, Paolo Di Achille, Jiang Wu, Silviu Borac, Jonathan Wang, Xin Liu, Eric Teasley, Lawrence Cai, Yuzhe Yang, Yun Liu, Daniel McDuff, Hao-Wei Su, Brent Winslow, Anupam Pathak, Shwetak Patel, James A. Taylor, Jameson K. Rogers, Ming-Zher Poh
Comments: Updated author list
Subjects: Tissues and Organs (q-bio.TO) ; Artificial Intelligence (cs.AI) ; Emerging Technologies (cs.ET) ; Human-Computer Interaction (cs.HC) ; Machine Learning (cs.LG)
[45] arXiv:2503.03784 [cn-pdf, pdf, html, other]
Title: Neural Models of Task Adaptation: A Tutorial on Spiking Networks for Executive Control
Ashwin Viswanathan Kannan, Madhumitha Ganesan
Comments: 6 pages
Subjects: Neurons and Cognition (q-bio.NC) ; Machine Learning (cs.LG) ; Neural and Evolutionary Computing (cs.NE)
[46] arXiv:2503.03786 [cn-pdf, pdf, html, other]
Title: Self is the Best Learner: CT-free Ultra-Low-Dose PET Organ Segmentation via Collaborating Denoising and Segmentation Learning
Zanting Ye, Xiaolong Niu, Xu Han, Xuanbin Wu, Wantong Lu, Yijun Lu, Hao Sun, Yanchao Huang, Hubing Wu, Lijun Lu
Comments: This work has been accepted by MICCAI2025; 9 pages, 5 figures
Subjects: Tissues and Organs (q-bio.TO) ; Computer Vision and Pattern Recognition (cs.CV) ; Image and Video Processing (eess.IV)
[47] arXiv:2503.03790 [cn-pdf, pdf, html, other]
Title: DDCSR: A Novel End-to-End Deep Learning Framework for Cortical Surface Reconstruction from Diffusion MRI
Chengjin Li, Yuqian Chen, Nir A. Sochen, Wei Zhang, Carl-Fredrik Westin, Rathi Yogesh, Lauren J. O'Donnell, Ofer Pasternak, Fan Zhang
Comments: 9 pages, 3 figures
Subjects: Tissues and Organs (q-bio.TO) ; Graphics (cs.GR) ; Image and Video Processing (eess.IV)
[48] arXiv:2503.03913 [cn-pdf, pdf, other]
Title: Proton Flows, Proton Gradients and Subcellular Architecture in Biological Energy Conversion
Luca Quaroni
Subjects: Subcellular Processes (q-bio.SC)
[49] arXiv:2503.03950 [cn-pdf, pdf, html, other]
Title: The Nature of Organization in Living Systems
Pedro Márquez-Zacarías, Andrés Ortiz-Muñoz, Emma P. Bingham
Comments: 22 pages, 7 figures
Subjects: Quantitative Methods (q-bio.QM) ; Populations and Evolution (q-bio.PE)
[50] arXiv:2503.03989 [cn-pdf, pdf, html, other]
Title: Integrating Protein Dynamics into Structure-Based Drug Design via Full-Atom Stochastic Flows
Xiangxin Zhou, Yi Xiao, Haowei Lin, Xinheng He, Jiaqi Guan, Yang Wang, Qiang Liu, Feng Zhou, Liang Wang, Jianzhu Ma
Comments: Accepted to ICLR 2025
Subjects: Biomolecules (q-bio.BM) ; Machine Learning (cs.LG)
Total of 426 entries : 1-50 51-100 101-150 151-200 ... 401-426
Showing up to 50 entries per page: fewer | more | all