Quantitative Biology

Authors and titles for Feb 2023

[1]  arXiv:2302.00104 [pdf, ps, other]

Title: NetMoST: A network-based machine learning approach for subtyping schizophrenia using polygenic SNP allele biomarkers

Authors: Xinru Wei, Shuai Dong, Zhao Su, Lili Tang, Pengfei Zhao, Chunyu Pan, Fei Wang, Yanqing Tang, Weixiong Zhang, Xizhe Zhang

Comments: 21 pages,4 figures

Subjects: Molecular Networks (q-bio.MN)

[2]  arXiv:2302.00142 [pdf, other]

Title: Leveraging Interactions in Microfluidic Droplets for Enhanced Biotechnology Screens

Authors: Carolus Vitalis, Tobias Wenzel

Comments: 10 pages, 3 figures

Journal-ref: Current Opinion in Biotechnology, August 2023, Volume 82, 102966

Subjects: Quantitative Methods (q-bio.QM); Biological Physics (physics.bio-ph)

[3]  arXiv:2302.00146 [pdf, other]

Title: Gyri vs. Sulci: Disentangling Brain Core-Periphery Functional Networks via Twin-Transformer

Authors: Xiaowei Yu, Lu Zhang, Haixing Dai, Lin Zhao, Yanjun Lyu, Zihao Wu, Tianming Liu, Dajiang Zhu

Comments: 13 pages, 4 figures

Subjects: Neurons and Cognition (q-bio.NC)

[4]  arXiv:2302.00203 [pdf, other]

Title: End-to-End Full-Atom Antibody Design

Authors: Xiangzhe Kong, Wenbing Huang, Yang Liu

Comments: Accepted to ICML 2023

Subjects: Biomolecules (q-bio.BM); Machine Learning (cs.LG)

[5]  arXiv:2302.00582 [pdf, ps, other]

Title: Habitat transition in the evolution of bacteria and archaea

Authors: Alexander L. Jaffe, Cindy J. Castelle, Jillian F. Banfield

Comments: Accepted for publication in the Annual Review of Microbiology, Volume 77

Subjects: Populations and Evolution (q-bio.PE); Genomics (q-bio.GN)

[6]  arXiv:2302.00587 [pdf, other]

Title: Molecular Graph Generation by Decomposition and Reassembling

Authors: Masatsugu Yamada, Mahito Sugiyama

Subjects: Biomolecules (q-bio.BM); Artificial Intelligence (cs.AI); Machine Learning (cs.LG)

[7]  arXiv:2302.00652 [pdf, other]

Title: Breathing cluster in complex neuron-astrocyte networks

Authors: Ya Wang, Liang Wang, Huawei Fan, Jun Ma, Hui Cao, Xingang Wang

Comments: 14 pages, 6 figures

Subjects: Neurons and Cognition (q-bio.NC); Pattern Formation and Solitons (nlin.PS)

[8]  arXiv:2302.00767 [pdf, other]

Title: ImageNomer: description of a functional connectivity and omics analysis tool and case study identifying a race confound

Authors: Anton Orlichenko, Grant Daly, Ziyu Zhou, Anqi Liu, Hui Shen, Hong-Wen Deng, Yu-Ping Wang

Comments: 11 pages

Subjects: Populations and Evolution (q-bio.PE); Machine Learning (cs.LG); Neurons and Cognition (q-bio.NC)

[9]  arXiv:2302.00772 [pdf, other]

Title: Meta-Analytic Operation of Threshold-independent Filtering (MOTiF) Reveals Sub-threshold Genomic Robustness in Trisomy

Authors: Roy Siegelmann, Hava Siegelmann

Comments: 20 pages including bibliography, tables, appendices, and five figures

Subjects: Quantitative Methods (q-bio.QM)

[10]  arXiv:2302.00826 [pdf, ps, other]

Title: Existence of exact solution of the Susceptible-Exposed-Infectious-Recovered (SEIR) epidemic model

Authors: Norio Yoshida

Comments: 40 pages, 9 figures

Journal-ref: J. Differential Equations 355(2023), 103-143

Subjects: Populations and Evolution (q-bio.PE)

[11]  arXiv:2302.00855 [pdf, other]

Title: Molecular Geometry-aware Transformer for accurate 3D Atomic System modeling

Authors: Zheng Yuan, Yaoyun Zhang, Chuanqi Tan, Wei Wang, Fei Huang, Songfang Huang

Subjects: Molecular Networks (q-bio.MN); Artificial Intelligence (cs.AI); Machine Learning (cs.LG)

[12]  arXiv:2302.00863 [pdf, ps, other]

Title: The Challenges and Opportunities in Creating an Early Warning System for Global Pandemics

Authors: David C. Danko, James Golden, Charles Vorosmarty, Anthony Cak, Fabio Corsi, Christopher E. Mason, Rafael Maciel-de-Freitas, Dorottya Nagy-Szakal, Niamh B. OHara

Subjects: Quantitative Methods (q-bio.QM); Computers and Society (cs.CY)

[13]  arXiv:2302.00887 [pdf, ps, other]

Title: Kainate receptor modulation by NETO2

Authors: Lingli He, Jiahui Sun, Yiwei Gao, Bin Li, Yuhang Wang, Yanli Dong, Weidong An, Hang Li, Bei Yang, Yuhan Ge, Xuejun Cai Zhang, Yun Stone Shi, Yan Zhao

Journal-ref: Nature, 599(7884), 325-329 (2021)

Subjects: Biomolecules (q-bio.BM)

[14]  arXiv:2302.00960 [pdf, other]

Title: Quantifying optimal resource allocation strategies for controlling epidemics

Authors: Biplab Maity, Swarnendu Banerjee, Abhishek Senapati, Joydev Chattopadhyay

Comments: 44 Pages, 10 Figures

Subjects: Populations and Evolution (q-bio.PE)

[15]  arXiv:2302.01019 [pdf, other]

Title: Biophysical aspects of neurocognitive modeling with long-term sustained temperature variations

Authors: Serge Kernbach, Olga Kernbach, Andreas Kernbach

Subjects: Neurons and Cognition (q-bio.NC); Biological Physics (physics.bio-ph); Medical Physics (physics.med-ph)

[16]  arXiv:2302.01076 [pdf, other]

Title: Convergence to the Equilibrium State in an Outbreak: When Can Growth Rates Accurately be Measured?

Authors: Adam Mielke, Lasse Engbo Christiansen

Comments: 4 pages, 1 figure

Subjects: Populations and Evolution (q-bio.PE)

[17]  arXiv:2302.01117 [pdf, other]

Title: PASSerRank: Prediction of Allosteric Sites with Learning to Rank

Authors: Hao Tian, Sian Xiao, Xi Jiang, Peng Tao

Subjects: Quantitative Methods (q-bio.QM)

[18]  arXiv:2302.01140 [pdf, ps, other]

Title: The big challenge for livestock genomics is to make sequence data pay

Authors: M. Johnsson (Swedish University of Agricultural Sciences)

Subjects: Genomics (q-bio.GN)

[19]  arXiv:2302.01187 [pdf, other]

Title: A Semi-Parametric Model for Decision Making in High-Dimensional Sensory Discrimination Tasks

Authors: Stephen Keeley, Benjamin Letham, Chase Tymms, Craig Sanders, Michael Shvartsman

Subjects: Neurons and Cognition (q-bio.NC)

[20]  arXiv:2302.01270 [pdf, other]

Title: Robust Perfect Adaptation of Reaction Fluxes Ensured by Network Topology

Authors: Yuji Hirono, Hyukpyo Hong, Jae Kyoung Kim

Comments: 5 pages, 2 figures (Supplemental Material: 14 pages, 1 figure)

Subjects: Molecular Networks (q-bio.MN); Biological Physics (physics.bio-ph)

[21]  arXiv:2302.01337 [pdf, ps, other]

Title: Comprehensive and user-analytics-friendly cancer patient database for physicians and researchers

Authors: Ali Firooz, Avery T. Funkhouser, Julie C. Martin, W. Jeffery Edenfield, Homayoun Valafar, Anna V. Blenda

Comments: 7 pages, 12 figures, peer reviewed and accepted in "International Conference on Computational Science and Computational Intelligence (CSCI 22)"

Journal-ref: Proceedings of the 2022 International Conference on Computational Science and Computational Intelligence (CSCI)

Subjects: Quantitative Methods (q-bio.QM); Computers and Society (cs.CY)

[22]  arXiv:2302.01449 [pdf, other]

Title: Transport-based morphometry of nuclear structures of digital pathology images in cancers

Authors: Mohammad Shifat E Rabbi, Natasha Ironside, John A Ozolek, Rajendra Singh, Liron Pantanowitz, Gustavo K Rohde

Subjects: Quantitative Methods (q-bio.QM)

[23]  arXiv:2302.01657 [pdf, ps, other]

Title: Made to measure: an introduction to quantification in microscopy data

Authors: Siân Culley, Alicia Cuber Caballero, Jemima J Burden, Virginie Uhlmann

Comments: 23 pages, 5 figures, 2 tables

Subjects: Quantitative Methods (q-bio.QM)

[24]  arXiv:2302.01694 [pdf, ps, other]

Title: Coevolving Boolean and Multi-Valued Regulatory Networks

Authors: Larry Bull

Comments: arXiv admin note: text overlap with arXiv:2102.11667

Subjects: Molecular Networks (q-bio.MN); Neural and Evolutionary Computing (cs.NE)

[25]  arXiv:2302.01924 [pdf, ps, other]

Title: Self-supervised enhancement of stimulus-evoked brain response data

Authors: Bernd Accou, Hugo Van hamme, Tom Francart

Comments: Submission to ICASSP 2023

Subjects: Neurons and Cognition (q-bio.NC); Signal Processing (eess.SP)