Article
Biochemical Research Methods
Allen W. Lynch, Christina Theodoris, Henry Long, Myles Brown, X. Shirley Liu, Clifford A. Meyer
Summary: MIRA is a comprehensive methodology that compares gene expression and chromatin accessibility in single cells to infer regulatory mechanisms driving cell fate transitions. It models cell states and regulatory potential of gene loci to represent cell states in an efficient and interpretable latent space, and reveals the variable influence of local accessibility on transcription at different gene loci.
Article
Genetics & Heredity
Yoonjee Kang, Denis Thieffry, Laura Cantini
Summary: Networks are powerful tools for studying biological systems, with specific algorithms developed for inferring regulatory interactions from functional genomics data. While benchmarks for single-cell network inference are often based on simulated data, real data tests show that GENIE3 and GRNBoost2 are the most reproducible methods with better alignment to true biological interactions.
FRONTIERS IN GENETICS
(2021)
Review
Immunology
Shubham Tripathi, John S. Tsang, Kyemyung Park
Summary: Regulatory T cells have crucial roles in immune homeostasis and response. A systems immunology approach can advance our understanding of Treg function and identify general principles of immune regulation.
TRENDS IN IMMUNOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Xuezhu Wang, Yucheng Dong, Yongchang Zheng, Yang Chen
Summary: Genetic, epigenetic, and metabolic alterations are key features of cancer development. By establishing a conceptual in silico metabolic and epigenetic regulatory network (MER-Net) based on high-throughput methods, new potential biomarkers and therapeutic targets can be revealed through integration and analysis of large multiomics networks.
JOURNAL OF GENETICS AND GENOMICS
(2021)
Review
Microbiology
Ashwini Sunkavalli, Ryan McClure, Caroline Genco
Summary: This article describes the transcriptional regulators and genes of Neisseria gonorrhoeae and their role in infection, as well as the influence of the genital tract microbiome on gonococcal survival and gene regulation. The understanding of N. gonorrhoeae's strategies in gene regulation and their impact on the pathogen's characteristics during infection has the potential to identify new strategies for the treatment and prevention of gonorrhea.
Article
Immunology
Vinicius M. de Lima, Bianca B. Batista, Jose F. da Silva Neto
Summary: In this study, the researchers characterized the ChuPRSTUV heme utilization system employed by Chromobacterium violaceum to explore an important iron reservoir in mammalian hosts, free heme and hemoproteins. The study revealed that all genes of the chu operon, except chuS, are required for heme and hemoglobin utilization in C. violaceum. Additionally, the researchers demonstrated that ChuP acts as a positive regulator of chuR and vbuA, connecting heme and siderophore utilization.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Physics, Multidisciplinary
Yan Yan, Feng Jiang, Xinan Zhang, Tianhai Tian
Summary: This study developed a new algorithm to solve the dependence on variable order in datasets for inferring regulatory networks between genes and proteins, and successfully inferred the regulatory networks.
Review
Immunology
Shohei Hori, Ryuichi Murakami
Summary: Regulatory T (Treg) cells expressing Foxp3 are crucial for maintaining immune and tissue homeostasis, interacting with a molecular network to differentiate and function effectively. They can exert anti-inflammatory and protective functions in various tissues and immune environments, adapting to diverse and changing conditions by integrating external cues with intrinsic molecular networks.
INTERNATIONAL IMMUNOLOGY
(2021)
Article
Multidisciplinary Sciences
Kenji Kobayashi, Kazuki Maeda, Miki Tokuoka, Atsushi Mochizuki, Yutaka Satou
Summary: Linkage logic theory provides a mathematical criterion for controlling network dynamics by manipulating a subset of network nodes. By using this theory, missing edges in experimental networks can be found, the information content of reconstituted networks can be evaluated, and cell fate can be reprogrammed accordingly.
SCIENTIFIC REPORTS
(2021)
Article
Business
Shiyi Ying, Youlin Huang, Lixian Qian, Jinzhu Song
Summary: Social networking services (SNSs) have raised significant privacy concerns by collecting and analyzing users' personal data for personalization and customization purposes. This study investigates the psychological mechanisms that support or discourage mobile SNS users from enabling location tracking, considering the privacy paradox. Based on a survey of young internet users in China, the analysis shows that reasons against location tracking are negatively related to the intention, while reasons for location tracking are insignificant. The study contributes to understanding the antecedents of the reasoning process and offers practical suggestions for SNS providers and policymakers.
TECHNOLOGICAL FORECASTING AND SOCIAL CHANGE
(2023)
Article
Agriculture, Multidisciplinary
Xin Zhao, Zhangjiang He, Yifei Gao, Yanze Kan, Yufei Jiao, Yunxia Liu, Shuaishuai Huang, Zhibing Luo, Yongjun Zhang
Summary: In the insect fungal pathogen, Beauveria bassiana, BbSre1 regulates oxidative stress response, peroxisome division, and redox homeostasis. Gene disruption inhibits peroxisome division, affects redox homeostasis, and impairs lipid/fatty acid metabolism and sterol biosynthesis. These findings broaden our understanding of the role of Sre1 in regulating oxidative stress and lipid metabolism.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2023)
Article
Physics, Mathematical
Jun Du, Di Liu
Summary: Based on Transition Path Theory, a general approach is developed to identify and calculate Transition States in stochastic chemical reacting networks using probability currents and constraint optimization. An alternative scheme for computing transition pathways through topological sorting is introduced, which is proven to be highly efficient.
COMMUNICATIONS IN COMPUTATIONAL PHYSICS
(2021)
Review
Cell Biology
Shiwen Ma, Yao Mawulikplimi Adzavon, Xiaohu Wen, Pengxiang Zhao, Fei Xie, Mengyu Liu, Xuemei Ma
Summary: Ferroptosis is a newly defined programmed cell death process that differs from other types of programmed cell death. It can be regulated by antioxidants and iron-chelating agents, and it affects cancer progression by influencing iron ion deposition and lipid peroxidation. Significant progress has been made in understanding the molecular mechanism of ferroptosis.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Biology
Brenda Delamonica, Gabor Balazsi, Michael Shub
Summary: Researchers propose a mathematical concept for modeling metastatic breast cancer systems and investigate the state transitions of the system using bifurcation theory. The study reveals that two-parameter bifurcations can separate different cell state transition modalities, providing a new perspective for defining such transitions based on mathematical theory.
JOURNAL OF THEORETICAL BIOLOGY
(2023)
Article
Nutrition & Dietetics
Cheng-Fang Tsai, Guan-Wei Chen, Yen-Chang Chen, Ching-Kai Shen, Dah-Yuu Lu, Liang-Yo Yang, Jia-Hong Chen, Wei-Lan Yeh
Summary: Macrophage polarization plays essential roles in various diseases, and the natural compound quercetin has been found to inhibit inflammation and enhance M2 macrophage polarization and antioxidant expression. These findings are important for the potential use of quercetin as a drug for the treatment of inflammatory disorders in the central nervous system.
Article
Ecology
Steven A. Frank
ECOLOGY AND EVOLUTION
(2017)
Review
Physics, Multidisciplinary
Steven A. Frank
Article
Ecology
S. A. Frank
JOURNAL OF EVOLUTIONARY BIOLOGY
(2014)
Article
Multidisciplinary Sciences
Steven A. Frank
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2018)
Review
Physics, Multidisciplinary
Steven A. Frank
Article
Biology
Steven A. Frank
JOURNAL OF THEORETICAL BIOLOGY
(2019)
Article
Biology
Steven A. Frank
JOURNAL OF THEORETICAL BIOLOGY
(2019)
Article
Microbiology
Steven A. Frank, Paul Schmid-Hempel
Article
Biology
Steven A. Frank
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2020)
Article
Ecology
Steven A. Frank
FRONTIERS IN ECOLOGY AND EVOLUTION
(2020)
Article
Physics, Multidisciplinary
Steven A. Frank, Frank J. Bruggeman
Article
Biology
Steven A. Frank
Summary: This article introduces a computational method to optimize transcription factor (TF) networks and discusses the role of TFs in cellular function and how cells process information through their TF networks.
Article
Mathematics, Applied
Steven A. Frank
Summary: Multicellular organisms start as a single cell and develop through cell division. Mutations occurring during development are inherited by all descendant cells, leading to a variable number of mutant cells in the body. This article discusses the quantitative principles of estimating the number of mutant cells and the variability between individuals using a Frechet distribution approximation. It also examines the implications of somatic mutational mosaicism for understanding diseases like cancer, neurodegeneration, and atherosclerosis.
Article
Ecology
Steven A. Frank
Summary: Robustness protects organisms by reducing trait variation caused by perturbations and minimizing the consequences of bad situations. This article demonstrates that both types of robustness increase the heritability of protected traits and diseases. The natural tendency for organisms to exhibit robustness may contribute to the high heritability of certain diseases.
Article
Psychology, Multidisciplinary
Steven A. Frank
BEHAVIORAL SCIENCES
(2019)
Article
Biology
Iain Hunter, Raz Leib
Summary: Natural movement is related to health, but it is difficult to measure. Existing methods cannot capture the full range of natural movement. Comparing movement across different species helps identify common biomechanical and computational principles. Developing a system to quantify movement in freely moving animals in natural environments and relating it to life quality is crucial. This study proposes a theoretical framework based on movement ability and validates it in Drosophila.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Andy Gardner
Summary: Fisher's geometric model is a useful tool for predicting key properties of Darwinian adaptation, and here it is applied to predict differences between the evolution of altruistic versus nonsocial phenotypes. The results suggest that the effect size maximizing probability of fixation is smaller in the context of altruism and larger in the context of nonsocial phenotypes, leading to lower overall probability of fixation for altruism and higher overall probability of fixation for nonsocial phenotypes.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Thomas F. Pak, Joe Pitt-Francis, Ruth E. Baker
Summary: Cell competition is a process where cells interact in multicellular organisms to determine a winner or loser status, with loser cells being eliminated through programmed cell death. The winner cells then populate the tissue. The outcome of cell competition is context-dependent, as the same cell type can win or lose depending on the competing cell type. This paper proposes a mathematical framework to study the emergence of winner or loser status, highlighting the role of active cell death and identifying the factors that drive cell competition in a cell-based modeling context.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Haruto Tomizuka, Yuuya Tachiki
Summary: Batesian mimicry is a strategy in which palatable prey species resemble unpalatable prey species to avoid predation. The evolution of this mimicry plays a crucial role in protecting the unpalatable species from extinction.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Jason W. Olejarz, Martin A. Nowak
Summary: Gene drive technology shows potential for population control, but its release may have unpredictable consequences. The study suggests that the failure of suppression is a natural outcome, and there are complex dynamics among wild populations.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Hamid Ravaee, Mohammad Hossein Manshaei, Mehran Safayani, Javad Salimi Sartakhti
Summary: Gene expression analysis is valuable for cancer classification and phenotype identification. IP3G, based on Generative Adversarial Networks, enhances gene expression data and discovers phenotypes in an unsupervised manner. By converting gene expression profiles into images and utilizing IP3G, new phenotype profiles can be generated, improving classification accuracy.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Beatrix Rahnsch, Leila Taghizadeh
Summary: This study forecasts the evolution of the COVID-19 pandemic in Germany using a network-based inference method and compares it with other approaches. The results show that the network-inference based approach outperforms other methods in short-to mid-term predictions, even with limited information about the new disease. Furthermore, predictions based on the estimation of the reproduction number in Germany can yield more reliable results with increasing data availability, but still cannot surpass the network-inference based algorithm.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Rongsheng Huang, Qiaojun Situ, Jinzhi Lei
Summary: Maintaining tissue homeostasis requires appropriate regulation of stem cell differentiation. Random inheritance of epigenetic states plays a pivotal role in stem cell differentiation. This computational model provides valuable insights into the intricate mechanism governing stem cell differentiation and cell reprogramming, offering a promising path for enhancing the field of regenerative medicine.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Patrick Vincent N. Lubenia, Eduardo R. Mendoza, Angelyn R. Lao
Summary: This study compares insulin signaling in healthy and type 2 diabetes states using reaction network analysis. The results show similarities and differences between the two conditions, providing insights into the mechanisms of insulin resistance, including the involvement of other complexes, less restrictive interplay between species, and loss of concentration robustness in GLUT4.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Nuverah Mohsin, Heiko Enderling, Renee Brady-Nicholls, Mohammad U. Zahid
Summary: Mathematical modeling is crucial in understanding radiobiology and designing treatment approaches in radiotherapy for cancer. This study compares three tumor volume dynamics models and analyzes the implications of model selection. A new metric, the point of maximum reduction of tumor volume (MRV), is introduced to quantify the impact of radiotherapy. The results emphasize the importance of caution in selecting models of response to radiotherapy due to the artifacts imposed by each model.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Armindo Salvador
Summary: Michael Savageau's Biochemical Systems Analysis papers have had a significant impact on Systems Biology, generating core concepts and tools. This article provides a brief summary of these papers and discusses the most relevant developments in Biochemical Systems Theory since their publication.
JOURNAL OF THEORETICAL BIOLOGY
(2024)