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Quantitative Biology

Authors and titles for recent submissions

[ total of 83 entries: 1-25 | 26-50 | 51-75 | 76-83 ]
[ showing 25 entries per page: fewer | more | all ]

Mon, 6 May 2024

[1]  arXiv:2405.02136 [pdf, other]
Title: bio2Byte Tools deployment as a Python package and Galaxy tool to predict protein biophysical properties
Authors: Jose Gavalda-Garcia, Adrian Diaz, Wim Vranken
Subjects: Quantitative Methods (q-bio.QM)
[2]  arXiv:2405.02117 [pdf, ps, other]
Title: Multi-grid reaction-diffusion master equation: applications to morphogen gradient modelling
Authors: Radek Erban, Stefanie Winkelmann
Subjects: Quantitative Methods (q-bio.QM); Biological Physics (physics.bio-ph)
[3]  arXiv:2405.02076 [pdf, other]
Title: SCIMAP: A Python Toolkit for Integrated Spatial Analysis of Multiplexed Imaging Data
Authors: Ajit J. Nirmal, Peter K. Sorger
Comments: 6 pages, 1 figure
Subjects: Quantitative Methods (q-bio.QM); Tissues and Organs (q-bio.TO)
[4]  arXiv:2405.02038 [pdf, other]
Title: Dimensionality reduction of neuronal degeneracy reveals two interfering physiological mechanisms
Authors: Arthur Fyon, Alessio Franci, Pierre Sacré, Guillaume Drion
Subjects: Neurons and Cognition (q-bio.NC); Mathematical Physics (math-ph); Cell Behavior (q-bio.CB)
[5]  arXiv:2405.01896 [pdf, ps, other]
Title: A Step Test to Evaluate the Susceptibility to Severe High-Altitude Illness in Field Conditions
Authors: Eric Hermand (URePSSS, H&P), Léo Lesaint, Laura Denis (H&P), Jean-Paul Richalet (INSEP), François Lhuissier (H&P)
Comments: High Altitude Medicine and Biology, 2024
Subjects: Tissues and Organs (q-bio.TO)
[6]  arXiv:2405.01715 [pdf, other]
Title: Identification of SNPs in genomes using GRAMEP, an alignment-free method based on the Principle of Maximum Entropy
Authors: Matheus Henrique Pimenta-Zanon, André Yoshiaki Kashiwabara, André Luís Laforga Vanzela, Fabricio Martins Lopes
Subjects: Genomics (q-bio.GN); Information Theory (cs.IT); Applications (stat.AP)
[7]  arXiv:2405.01703 [pdf, other]
Title: Fluid-structure interaction simulations for the prediction of fractional flow reserve in pediatric patients with anomalous aortic origin of a coronary artery
Authors: Charles Puelz, Craig G. Rusin, Dan Lior, Shagun Sachdeva, Tam T. Doan, Lindsay F. Eilers, Dana Reaves-O'Neal, Silvana Molossi
Subjects: Tissues and Organs (q-bio.TO); Medical Physics (physics.med-ph)
[8]  arXiv:2405.01664 [pdf, ps, other]
Title: Stress-induced Eukaryotic Translational Regulatory Mechanisms
Authors: Dilawar Ahmad Mir, Zhengxin Ma, Jordan Horrocks, Aric N Rogers
Comments: 37 Pages, Figures 7, Review Article
Subjects: Molecular Networks (q-bio.MN)
[9]  arXiv:2405.01616 [pdf, other]
Title: Generative Active Learning for the Search of Small-molecule Protein Binders
Authors: Maksym Korablyov, Cheng-Hao Liu, Moksh Jain, Almer M. van der Sloot, Eric Jolicoeur, Edward Ruediger, Andrei Cristian Nica, Emmanuel Bengio, Kostiantyn Lapchevskyi, Daniel St-Cyr, Doris Alexandra Schuetz, Victor Ion Butoi, Jarrid Rector-Brooks, Simon Blackburn, Leo Feng, Hadi Nekoei, SaiKrishna Gottipati, Priyesh Vijayan, Prateek Gupta, Ladislav Rampášek, Sasikanth Avancha, Pierre-Luc Bacon, William L. Hamilton, Brooks Paige, Sanchit Misra, Stanislaw Kamil Jastrzebski, Bharat Kaul, Doina Precup, José Miguel Hernández-Lobato, Marwin Segler, Michael Bronstein, Anne Marinier, Mike Tyers, Yoshua Bengio
Subjects: Biomolecules (q-bio.BM); Artificial Intelligence (cs.AI); Machine Learning (cs.LG)
[10]  arXiv:2405.02003 (cross-list from cond-mat.stat-mech) [pdf, ps, other]
Title: Smoothly vanishing density in the contact process by an interplay of disorder and long-distance dispersal
Authors: R. Juhász, I. A. Kovács
Comments: 8 pages, 6 figures
Subjects: Statistical Mechanics (cond-mat.stat-mech); Disordered Systems and Neural Networks (cond-mat.dis-nn); Populations and Evolution (q-bio.PE)
[11]  arXiv:2405.01989 (cross-list from math.OC) [pdf, other]
Title: Parameter estimation in ODEs: assessing the potential of local and global solvers
Authors: M. Fernández de Dios, Ángel M. González-Rueda, Julio R. Banga, Julio González-Díaz, David R. Penas
Subjects: Optimization and Control (math.OC); Quantitative Methods (q-bio.QM)
[12]  arXiv:2405.01983 (cross-list from cs.AI) [pdf, other]
Title: Model-based reinforcement learning for protein backbone design
Authors: Frederic Renard, Cyprien Courtot, Alfredo Reichlin, Oliver Bent
Subjects: Artificial Intelligence (cs.AI); Biomolecules (q-bio.BM)
[13]  arXiv:2405.01974 (cross-list from cs.LG) [pdf, other]
Title: Multitask Extension of Geometrically Aligned Transfer Encoder
Authors: Sung Moon Ko, Sumin Lee, Dae-Woong Jeong, Hyunseung Kim, Chanhui Lee, Soorin Yim, Sehui Han
Comments: 7 pages, 3 figures, 2 tables
Subjects: Machine Learning (cs.LG); Artificial Intelligence (cs.AI); Quantitative Methods (q-bio.QM)
[14]  arXiv:2405.01960 (cross-list from cond-mat.soft) [pdf, other]
Title: Proliferation-driven mechanical feedback regulates cell dynamics in growing tissues
Authors: Sumit Sinha, Xin Li, Abdul N Malmi-Kakkada, D. Thirumalai
Comments: 5 figures. arXiv admin note: text overlap with arXiv:2202.04806
Subjects: Soft Condensed Matter (cond-mat.soft); Statistical Mechanics (cond-mat.stat-mech); Biological Physics (physics.bio-ph); Cell Behavior (q-bio.CB)
[15]  arXiv:2405.01554 (cross-list from cs.LG) [pdf, other]
Title: Early-stage detection of cognitive impairment by hybrid quantum-classical algorithm using resting-state functional MRI time-series
Authors: Junggu Choi, Tak Hur, Daniel K. Park, Na-Young Shin, Seung-Koo Lee, Hakbae Lee, Sanghoon Han
Comments: 28 pages, 10 figures
Subjects: Machine Learning (cs.LG); Artificial Intelligence (cs.AI); Neurons and Cognition (q-bio.NC)

Fri, 3 May 2024 (showing first 10 of 19 entries)

[16]  arXiv:2405.01385 [pdf, other]
Title: Anti-seizure medication tapering is associated with delta band power reduction in a dose, region and time-dependent manner
Authors: Guillermo M. Besne, Nathan Evans, Mariella Panagiotopoulou, Billy Smith, Fahmida A Chowdhury, Beate Diehl, John S Duncan, Andrew W McEvoy, Anna Miserocchi, Jane de Tisi, Mathew Walker, Peter N. Taylor, Chris Thornton, Yujiang Wang
Subjects: Neurons and Cognition (q-bio.NC)
[17]  arXiv:2405.01148 [pdf, other]
Title: Qualia and the Formal Structure of Meaning
Authors: Xerxes D. Arsiwalla
Comments: 28 pages
Subjects: Neurons and Cognition (q-bio.NC); Artificial Intelligence (cs.AI); Category Theory (math.CT); History and Philosophy of Physics (physics.hist-ph)
[18]  arXiv:2405.01012 [pdf, other]
Title: Correcting Biased Centered Kernel Alignment Measures in Biological and Artificial Neural Networks
Authors: Alex Murphy, Joel Zylberberg, Alona Fyshe
Comments: ICLR 2024 Re-Align Workshop
Subjects: Neurons and Cognition (q-bio.NC); Computer Vision and Pattern Recognition (cs.CV)
[19]  arXiv:2405.00838 [pdf, other]
Title: Cross-modality Matching and Prediction of Perturbation Responses with Labeled Gromov-Wasserstein Optimal Transport
Authors: Jayoung Ryu, Romain Lopez, Charlotte Bunne, Aviv Regev
Comments: 16 pages, 4 figures, correspondence to Aviv Regev and Romain Lopez
Subjects: Genomics (q-bio.GN); Optimization and Control (math.OC)
[20]  arXiv:2405.00810 [pdf, other]
Title: A Simple Comparison of Biochemical Systems Theory and Metabolic Control Analysis
Authors: Herbert M Sauro
Subjects: Molecular Networks (q-bio.MN); Quantitative Methods (q-bio.QM); Subcellular Processes (q-bio.SC)
[21]  arXiv:2405.00753 [pdf, other]
Title: HMAMP: Hypervolume-Driven Multi-Objective Antimicrobial Peptides Design
Authors: Li Wang, Yiping Li, Xiangzheng Fu, Xiucai Ye, Junfeng Shi, Gary G. Yen, Xiangxiang Zeng
Subjects: Quantitative Methods (q-bio.QM); Artificial Intelligence (cs.AI)
[22]  arXiv:2405.00751 [pdf, other]
Title: F$^3$low: Frame-to-Frame Coarse-grained Molecular Dynamics with SE(3) Guided Flow Matching
Authors: Shaoning Li, Yusong Wang, Mingyu Li, Jian Zhang, Bin Shao, Nanning Zheng, Jian Tang
Comments: Accepted by ICLR 2024 GEM workshop
Subjects: Quantitative Methods (q-bio.QM); Artificial Intelligence (cs.AI); Machine Learning (cs.LG)
[23]  arXiv:2405.00702 [pdf, ps, other]
Title: Cold plasma treatment boosts barley germination and seedling vigor: Insights into soluble sugar, starch, and protein modifications
Authors: Mohamed Ali Benabderrahim, Imen Bettaieb, Hédia Hannachi, Mokhtar Rejili, Thierry Dufour
Journal-ref: Journal of Cereal Science, Vol. 116, 103852 (2024)
Subjects: Other Quantitative Biology (q-bio.OT)
[24]  arXiv:2405.01437 (cross-list from cs.GT) [pdf, other]
Title: Two competing populations with a common environmental resource
Authors: Keith Paarporn, James Nelson
Comments: Submission to CDC 24
Subjects: Computer Science and Game Theory (cs.GT); Systems and Control (eess.SY); Populations and Evolution (q-bio.PE)
[25]  arXiv:2405.01155 (cross-list from cs.LG) [pdf, other]
Title: SynFlowNet: Towards Molecule Design with Guaranteed Synthesis Pathways
Authors: Miruna Cretu, Charles Harris, Julien Roy, Emmanuel Bengio, Pietro Liò
Comments: Presented at ICLR 2024 GEM Workshop
Subjects: Machine Learning (cs.LG); Biomolecules (q-bio.BM)
[ total of 83 entries: 1-25 | 26-50 | 51-75 | 76-83 ]
[ showing 25 entries per page: fewer | more | all ]

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