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Quantitative Biology

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Total of 89 entries : 1-50 51-89
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Fri, 22 Nov 2024 (showing 12 of 12 entries )

[1] arXiv:2411.14293 [pdf, other]
Title: Machine learning framework to predict the performance of lipid nanoparticles for nucleic acid delivery
Gaurav Kumar, Arezoo M. Ardekani
Comments: This is a preprint of a manuscript under review
Subjects: Biomolecules (q-bio.BM)
[2] arXiv:2411.14291 [pdf, other]
Title: Adaptive flexibility of cytoskeletal structures through nonequilibrium entropy production
Yuika Ueda, Shinji Deguchi
Subjects: Cell Behavior (q-bio.CB); Subcellular Processes (q-bio.SC)
[3] arXiv:2411.14157 [pdf, html, other]
Title: DrugGen: Advancing Drug Discovery with Large Language Models and Reinforcement Learning Feedback
Mahsa Sheikholeslami, Navid Mazrouei, Yousof Gheisari, Afshin Fasihi, Matin Irajpour, Ali Motahharynia
Comments: 20 pages, 5 figures, 3 tables, and 7 supplementary files. To use the model, see this https URL
Subjects: Quantitative Methods (q-bio.QM); Artificial Intelligence (cs.AI)
[4] arXiv:2411.14130 [pdf, other]
Title: Evidence of epigenetic oncogenesis: a turning point in cancer research
Jean-Pascal Capp, Benoît Aliaga, Vera Pancaldi
Subjects: Genomics (q-bio.GN)
[5] arXiv:2411.14107 [pdf, html, other]
Title: Inward rectifier potassium channels interact with calcium channels to promote robust and physiological bistability
Anaëlle De Worm, Guillaume Drion, Pierre Sacré
Subjects: Neurons and Cognition (q-bio.NC)
[6] arXiv:2411.14079 [pdf, other]
Title: Interpretable QSPR Modeling using Recursive Feature Machines and Multi-scale Fingerprints
Jiaxuan Shen, Haitao Zhang, Yunjie Wang, Yilong Wang, Song Tao, Bo Qiu, Ng Shyh-Chang
Subjects: Biomolecules (q-bio.BM)
[7] arXiv:2411.13796 [pdf, html, other]
Title: Re-examining aggregation in the Tallis-Leyton model of parasite acquisition
R. McVinish
Subjects: Populations and Evolution (q-bio.PE)
[8] arXiv:2411.13680 [pdf, html, other]
Title: Long-term predictive models for mosquito borne diseases: a narrative review
Marcio Maciel Bastos, Luiz Max Carvalho, Eduardo Correa Araujo, Flávio Codeço Coelho
Subjects: Quantitative Methods (q-bio.QM); Dynamical Systems (math.DS); Biological Physics (physics.bio-ph)
[9] arXiv:2411.13630 [pdf, html, other]
Title: Competitive binding of Activator-Repressor in Stochastic Gene Expression
Amit Kumar Das
Comments: 34 pages,47 figures
Subjects: Molecular Networks (q-bio.MN); Biological Physics (physics.bio-ph)
[10] arXiv:2411.13556 [pdf, other]
Title: gggenomes: effective and versatile visualizations for comparative genomics
Thomas Hackl (1), Markus Ankenbrand (2), Bart van Adrichem (1), David Wilkins (3), Kristina Haslinger (4) ((1) Groningen Institute for Evolutionary Life Sciences, University of Groningen, The Netherlands (2) Center for Computational and Theoretical Biology, Julius-Maximilians-Universität Würzburg, Germany (3) Discipline of General Practice, Adelaide Medical School, The University of Adelaide, Australia (4) Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, The Netherlands)
Comments: TH and MA contributed equally to this work. Corresponding author: Thomas Hackl
Subjects: Genomics (q-bio.GN)
[11] arXiv:2411.14242 (cross-list from cs.CE) [pdf, html, other]
Title: Approximate Constrained Lumping of Chemical Reaction Networks
Alexander Leguizamon-Robayo, Antonio Jiménez-Pastor, Micro Tribastone, Max Tschaikowski, Andrea Vandin
Subjects: Computational Engineering, Finance, and Science (cs.CE); Quantitative Methods (q-bio.QM)
[12] arXiv:2411.13688 (cross-list from cs.LG) [pdf, other]
Title: Investigating Graph Neural Networks and Classical Feature-Extraction Techniques in Activity-Cliff and Molecular Property Prediction
Markus Dablander
Comments: Doctoral Thesis (Mathematical Institute, University of Oxford)
Subjects: Machine Learning (cs.LG); Biomolecules (q-bio.BM); Machine Learning (stat.ML)

Thu, 21 Nov 2024 (showing 15 of 15 entries )

[13] arXiv:2411.13390 [pdf, html, other]
Title: Energy-based generative models for monoclonal antibodies
Paul Pereira, Hervé Minoux, Aleksandra M. Walczak, Thierry Mora
Subjects: Biomolecules (q-bio.BM)
[14] arXiv:2411.13380 [pdf, html, other]
Title: Bounds on the Treewidth of Level-k Rooted Phylogenetic Networks
Alexey Markin, Sriram Vijendran, Oliver Eulenstein
Subjects: Populations and Evolution (q-bio.PE); Combinatorics (math.CO)
[15] arXiv:2411.13280 [pdf, html, other]
Title: Structure-Based Molecule Optimization via Gradient-Guided Bayesian Update
Keyue Qiu, Yuxuan Song, Jie Yu, Hongbo Ma, Ziyao Cao, Zhilong Zhang, Yushuai Wu, Mingyue Zheng, Hao Zhou, Wei-Ying Ma
Comments: 27 pages, 17 figures
Subjects: Biomolecules (q-bio.BM); Artificial Intelligence (cs.AI)
[16] arXiv:2411.13263 [pdf, html, other]
Title: Estimating the tails of the spectrum of the Hessian of the log-likelihood for \textit{ab-initio} single-particle reconstruction in electron cryomicroscopy
Aaditya V. Rangan, Wai-Shing Tang, Pilar Cossio, Kexin Zhang, Nikolaus Grigorieff
Subjects: Quantitative Methods (q-bio.QM)
[17] arXiv:2411.13228 [pdf, other]
Title: A general relationship between population size and extinction risk
Thomas S Ball, Ben Balmford, Andrew Balmford, Daniele Rinaldo, Piero Visconti, Rhys Green
Subjects: Populations and Evolution (q-bio.PE)
[18] arXiv:2411.13189 [pdf, other]
Title: OpenMS WebApps: Building User-Friendly Solutions for MS Analysis
Tom David Müller (1 and 2), Arslan Siraj (1 and 2), Axel Walter (1 and 2), Jihyung Kim (1 and 2), Samuel Wein (1 and 2), Johannes von Kleist (1), Ayesha Feroz (1 and 2), Matteo Pilz (1 and 2), Kyowon Jeong (1 and 2), Justin Cyril Sing (3 and 4), Joshua Charkow (3 and 4), Hannes Luc Röst (3 and 4), Timo Sachsenberg (1 and 2) ((1) University of Tübingen, (2) Institute for Bioinformatics and Medical Informatics, (3) Donnelly Centre for Cellular and Biomolecular Research, (4) University of Toronto)
Comments: 19 pages, 5 figures
Subjects: Biomolecules (q-bio.BM); Human-Computer Interaction (cs.HC)
[19] arXiv:2411.13130 [pdf, html, other]
Title: The impact of recovery rate heterogeneity in achieving herd immunity
Gabriel Turinici
Subjects: Populations and Evolution (q-bio.PE); Dynamical Systems (math.DS)
[20] arXiv:2411.13048 [pdf, html, other]
Title: Conditional gene genealogies given the population pedigree for a diploid Moran model with selfing
Maximillian Newman, John Wakeley, Wai-Tong Louis Fan
Comments: 60 pages, 9 figures
Subjects: Populations and Evolution (q-bio.PE); Probability (math.PR)
[21] arXiv:2411.12957 [pdf, other]
Title: Computational and Experimental Exploration of Protein Fitness Landscapes: Navigating Smooth and Rugged Terrains
Mahakaran Sandhu (1,2), John Chen (1,5), Dana Matthews (1,2), Matthew A Spence (1,2), Sacha B Pulsford (1,2), Barnabas Gall (1,2), James Nichols (3), Nobuhiko Tokuriki (4), Colin J Jackson (1,2,3,5) ((1) Research School of Chemistry, Australian National University, (2) Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, (3) Research School of Biology, Australian National University, (4) Michael Smith Laboratories, University of British Columbia, (5) ARC Centre of Excellence in Synthetic Biology, Research School of Biology, Australian National University)
Comments: 16 pages, 4 figures, submitted to Biochemistry
Subjects: Populations and Evolution (q-bio.PE)
[22] arXiv:2411.12886 [pdf, html, other]
Title: NPGPT: Natural Product-Like Compound Generation with GPT-based Chemical Language Models
Koh Sakano, Kairi Furui, Masahito Ohue
Subjects: Biomolecules (q-bio.BM); Machine Learning (cs.LG); Quantitative Methods (q-bio.QM); Machine Learning (stat.ML)
[23] arXiv:2411.12784 [pdf, other]
Title: Cancer incidence estimation from mortality data: a validation study within a population-based cancer registry
Daniel Redondo-Sánchez, Miguel Rodríguez-Barranco, Alberto Ameijide, Francisco J. Alonso, Pablo Fernández-Navarro, Jose Juan Jiménez-Moleón, María-José Sánchez
Journal-ref: Population Health Metrics, Volume 19, 18, 2021
Subjects: Quantitative Methods (q-bio.QM)
[24] arXiv:2411.12779 [pdf, other]
Title: Chikungunya: The Silent Threat in the Shadows
Ambreen Talib, Rabbya Rayan Shah, Rameen Atique, Hafiza Arshi Saeed, Ayesha Haidar, Ayesha Nadeem, Areesha Naveed, Javeria Sharif, Abdul Samad
Subjects: Other Quantitative Biology (q-bio.OT)
[25] arXiv:2411.12769 [pdf, other]
Title: ukbFGSEA: an R Package for Applying Fast Preranked Gene Set Enrichment Analysis to UK Biobank Exome Data
Pengjun Guo, He Zhu
Subjects: Genomics (q-bio.GN)
[26] arXiv:2411.13326 (cross-list from cs.NE) [pdf, other]
Title: An Evolutional Neural Network Framework for Classification of Microarray Data
Maryam Eshraghi Evari, Md Nasir Sulaiman, Amir Rajabi Behjat
Subjects: Neural and Evolutionary Computing (cs.NE); Artificial Intelligence (cs.AI); Genomics (q-bio.GN)
[27] arXiv:2411.12853 (cross-list from cs.LG) [pdf, html, other]
Title: Integrating Secondary Structures Information into Triangular Spatial Relationships (TSR) for Advanced Protein Classification
Poorya Khajouie, Titli Sarkar, Krishna Rauniyar, Li Chen, Wu Xu, Vijay Raghavan
Subjects: Machine Learning (cs.LG); Biomolecules (q-bio.BM)

Wed, 20 Nov 2024 (showing 16 of 16 entries )

[28] arXiv:2411.12707 [pdf, html, other]
Title: Barttender: An approachable & interpretable way to compare medical imaging and non-imaging data
Ayush Singla, Shakson Isaac, Chirag J. Patel
Comments: Accepted to the Proceedings Track at Machine Learning for Health (ML4H 2024) conference, held on December 15-16, 2024 in Vancouver, Canada
Subjects: Quantitative Methods (q-bio.QM); Computer Vision and Pattern Recognition (cs.CV)
[29] arXiv:2411.12662 [pdf, html, other]
Title: bia-binder: A web-native cloud compute service for the bioimage analysis community
Craig T. Russell, Jean-Marie Burel, Awais Athar, Simon Li, Ugis Sarkans, Jason Swedlow, Alvis Brazma, Matthew Hartley, Virginie Uhlmann
Subjects: Quantitative Methods (q-bio.QM)
[30] arXiv:2411.12597 [pdf, html, other]
Title: GNNAS-Dock: Budget Aware Algorithm Selection with Graph Neural Networks for Molecular Docking
Yiliang Yuan, Mustafa Misir
Subjects: Biomolecules (q-bio.BM); Machine Learning (cs.LG)
[31] arXiv:2411.12370 [pdf, html, other]
Title: Rapid response to fast viral evolution using AlphaFold 3-assisted topological deep learning
JunJie Wee, Guo-Wei Wei
Comments: 21 pages, 4 figures
Subjects: Biomolecules (q-bio.BM); Populations and Evolution (q-bio.PE); Quantitative Methods (q-bio.QM)
[32] arXiv:2411.12332 [pdf, other]
Title: Silanization Strategies for Tailoring Peptide Functionalization on Silicon Surfaces: Implications for Enhancing Stem Cell Adhesion
Melissa Kosovari (CBMN), Thierry Buffeteau (ISM), Laurent Thomas (ISM), Andrée-Anne Guay Bégin (ULaval), Luc Vellutini (ISM), James Mcgettrick, Gaétan Laroche (ULaval), Marie-Christine Durrieu (CBMN)
Journal-ref: ACS Applied Materials & Interfaces, 2024, 16 (23), pp. 29770-29782
Subjects: Cell Behavior (q-bio.CB)
[33] arXiv:2411.12145 [pdf, other]
Title: Hierarchical Trait-State Model for Decoding Dyadic Social Interactions
Qianying Wu, Shigeki Nakauchi, Mohammad Shehata, Shinsuke Shimojo
Subjects: Neurons and Cognition (q-bio.NC); Quantitative Methods (q-bio.QM)
[34] arXiv:2411.12123 [pdf, other]
Title: Optimisation of locally advanced MSI-H/dMMR colorectal cancer treatment with neoadjuvant pembrolizumab using data-driven delay integro-differential equations
Georgio Hawi, Peter S. Kim, Peter P. Lee
Comments: 101 pages in total with 63 pages for the main body and 38 pages for the supporting information, 3 figures in the main body, 9 tables in the main body, 11 tables in the supporting information
Subjects: Cell Behavior (q-bio.CB); Dynamical Systems (math.DS); Tissues and Organs (q-bio.TO)
[35] arXiv:2411.12091 [pdf, html, other]
Title: Homogenized $\textit{C. elegans}$ Neural Activity and Connectivity Data
Quilee Simeon, Anshul Kashyap, Konrad P Kording, Edward S Boyden
Comments: The datasets are available for public access on Hugging Face: (1) calcium neural data: this https URL (2) connectome data: this https URL The code repository containing the preprocess and data modules can be accessed on GitHub: this https URL
Subjects: Neurons and Cognition (q-bio.NC)
[36] arXiv:2411.12087 [pdf, html, other]
Title: RatGene: Gene deletion-addition algorithms using growth to production ratio for growth-coupled production in constraint-based metabolic networks
Yier Ma, Takeyuki Tamura
Subjects: Molecular Networks (q-bio.MN); Quantitative Methods (q-bio.QM)
[37] arXiv:2411.12010 [pdf, html, other]
Title: Active learning for efficient discovery of optimal gene combinations in the combinatorial perturbation space
Jason Qin, Hans-Hermann Wessels, Carlos Fernandez-Granda, Yuhan Hao
Subjects: Genomics (q-bio.GN); Machine Learning (cs.LG)
[38] arXiv:2411.11915 [pdf, html, other]
Title: Phenome-wide causal proteomics enhance systemic lupus erythematosus flare prediction: A study in Asian populations
Liying Chen, Ou Deng, Ting Fang, Mei Chen, Xvfeng Zhang, Ruichen Cong, Dingqi Lu, Runrun Zhang, Qun Jin, Xinchang Wang
Subjects: Genomics (q-bio.GN); Machine Learning (cs.LG)
[39] arXiv:2411.11867 [pdf, html, other]
Title: Investigating synergies between chemical reaction networks (CRN) and mathematical epidemiology (ME), using the Mathematica package Epid-CRN
Florin Avram, Rim Adenane, Andrei D. Halanay, Matthew D. Johnson
Subjects: Molecular Networks (q-bio.MN)
[40] arXiv:2411.12656 (cross-list from physics.optics) [pdf, html, other]
Title: Flat Cell Imaging
Vahid Nasirimarekani, Zuzana Ditte, Eberhard Bodenschatz
Subjects: Optics (physics.optics); Quantitative Methods (q-bio.QM)
[41] arXiv:2411.12348 (cross-list from physics.soc-ph) [pdf, html, other]
Title: Environmental variability promotes the evolution of cooperation among geographically dispersed groups on dynamic networks
Masaaki Inaba, Eizo Akiyama
Subjects: Physics and Society (physics.soc-ph); Dynamical Systems (math.DS); Populations and Evolution (q-bio.PE)
[42] arXiv:2411.12232 (cross-list from math.AP) [pdf, html, other]
Title: Wavespeed selection of travelling wave solutions of a two-component reaction-diffusion model of cell invasion
Yuhui Chen, Michael C. Dallaston
Subjects: Analysis of PDEs (math.AP); Populations and Evolution (q-bio.PE)
[43] arXiv:2411.11875 (cross-list from cs.IR) [pdf, html, other]
Title: Exploring Optimal Transport-Based Multi-Grained Alignments for Text-Molecule Retrieval
Zijun Min, Bingshuai Liu, Liang Zhang, Jia Song, Jinsong Su, Song He, Xiaochen Bo
Comments: BIBM 2024 Regular Paper
Subjects: Information Retrieval (cs.IR); Artificial Intelligence (cs.AI); Computation and Language (cs.CL); Biomolecules (q-bio.BM)

Tue, 19 Nov 2024 (showing first 7 of 33 entries )

[44] arXiv:2411.11808 [pdf, html, other]
Title: Character-level Tokenizations as Powerful Inductive Biases for RNA Foundational Models
Adrián Morales-Pastor, Raquel Vázquez-Reza, Miłosz Wieczór, Clàudia Valverde, Manel Gil-Sorribes, Bertran Miquel-Oliver, Álvaro Ciudad, Alexis Molina
Comments: First version. Work in progress
Subjects: Quantitative Methods (q-bio.QM); Artificial Intelligence (cs.AI); Machine Learning (cs.LG); Biomolecules (q-bio.BM)
[45] arXiv:2411.11602 [pdf, html, other]
Title: Relating dynamics and structure of discrete and continuous time systems
Shuyun Jiao, David Waxman
Comments: 32 pages, 7 figures
Subjects: Populations and Evolution (q-bio.PE); Exactly Solvable and Integrable Systems (nlin.SI); Quantitative Methods (q-bio.QM)
[46] arXiv:2411.11513 [pdf, html, other]
Title: A Modular Open Source Framework for Genomic Variant Calling
Ankita Vaishnobi Bisoi, Bharath Ramsundar
Subjects: Quantitative Methods (q-bio.QM); Machine Learning (cs.LG)
[47] arXiv:2411.11366 [pdf, html, other]
Title: SCOP: A Sequence-Structure Contrast-Aware Framework for Protein Function Prediction
Runze Ma, Chengxin He, Huiru Zheng, Xinye Wang, Haiying Wang, Yidan Zhang, Lei Duan
Comments: Accepted as BIBM 2024 conference paper
Subjects: Biomolecules (q-bio.BM)
[48] arXiv:2411.11169 [pdf, html, other]
Title: Validating GWAS Findings through Reverse Engineering of Contingency Tables
Yuzhou Jiang, Erman Ayday
Subjects: Genomics (q-bio.GN); Cryptography and Security (cs.CR)
[49] arXiv:2411.11158 [pdf, html, other]
Title: Leveraging genomic deep learning models for non-coding variant effect prediction
Pooja Kathail, Ayesha Bajwa, Nilah M. Ioannidis
Subjects: Genomics (q-bio.GN)
[50] arXiv:2411.11143 [pdf, html, other]
Title: Integrated Ising Model with global inhibition for decision making
Olga Tapinova, Tal Finkelman, Tamar Reitich-Stolero, Rony Paz, Assaf Tal, Nir S. Gov
Comments: Main text: 14 pages; SI: 40 pages
Subjects: Neurons and Cognition (q-bio.NC); Biological Physics (physics.bio-ph)
Total of 89 entries : 1-50 51-89
Showing up to 50 entries per page: fewer | more | all