Article
Plant Sciences
Mimi Luo, Xiaoxia Liu, Hongyan Su, Meiling Li, Mengfei Li, Jianhe Wei
Summary: A transcriptomic analysis was conducted on Angelica sinensis using RNA-seq, revealing key genes involved in flowering regulation during vernalization and providing new insights into the regulatory networks of flowering in Angelica sinensis.
Article
Genetics & Heredity
Zhigang Jia, Xiujun Zhang
Summary: In this work, a novel method called DDTG is presented to improve the accuracy of causality determination in gene regulatory network (GRN) inference by dissecting downstream target genes. The method determines the topology and hierarchy of GRNs using mutual information and conditional mutual information, and the regulatory directions of GRNs using Taylor formula-based regression. The method is validated on benchmark GRNs and outperforms popular GRN inference methods.
FRONTIERS IN GENETICS
(2022)
Article
Mathematics, Applied
J. Ritchie
Summary: This study focuses on pattern formation on directed networks and addresses the question of how to detect pattern formation when the Laplacian matrix is not diagonalizable. It also considers the related problem of pattern formation with non-local reaction kinetics and temporal networks.
COMMUNICATIONS IN NONLINEAR SCIENCE AND NUMERICAL SIMULATION
(2023)
Article
Plant Sciences
Lang Yan, Yan Li, Yuan Qing, Xiang Tao, Haiyan Wang, Xianjun Lai, Yizheng Zhang
Summary: This study investigated the transcriptionally regulated genes and functional pathways involved in the host response to Synchytrium endobioticum infection in potato. Through phenotypic and dual RNA-Seq analyses, the researchers identified 5,052 differentially expressed genes (DEGs) during the progression of the disease. They found that the number of DEGs increased with disease development, and identified important functional groups related to plant-pathogen interaction, fatty acid elongation, and phenylpropanoid biosynthesis. Gene coexpression networks revealed high interconnectivity of the induced response and identified several hub genes enriched at different stages of infection.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Cardiac & Cardiovascular Systems
Robin J. G. Hartman, Katie Owsiany, Lijiang Ma, Simon Koplev, Ke Hao, Lotte Slenders, Mete Civelek, Michal Mokry, Jason C. Kovacic, Gerard Pasterkamp, Gary Owens, Johan L. M. Bjorkegren, Hester M. den Ruijter
Summary: By comparing sex-specific gene regulatory networks (GRNs), clear sex differences in network activity within atherosclerotic tissues were observed. Genes more active in women were associated with mesenchymal cells and endothelial cells, while genes more active in men were associated with the immune system.
Article
Genetics & Heredity
Linzhuo Fan, Jinhong Hou, Guimin Qin
Summary: Breast cancer is a common malignant tumor in women. This study proposes a computational framework based on stage-specific gene regulatory networks to predict disease genes of breast cancer. Key genes specific to each stage were identified and shown to be significantly associated with breast cancer-related genes.
FRONTIERS IN GENETICS
(2021)
Article
Multidisciplinary Sciences
Surama Biswas, Santosh Manicka, Erik Hoel, Michael Levin
Summary: Studies have shown that gene regulatory networks possess various types of memory, which is important for understanding the variability and time-dependent changes of drug action. Defining and identifying memory through a computational framework is beneficial for the biomedical field. Timed stimuli offer a powerful alternative for controlling complex in vivo dynamics.
Article
Plant Sciences
Mengyao Li, Xiaoyan Li, Jin Zhou, Yue Sun, Jiageng Du, Zhuo Wang, Ya Luo, Yong Zhang, Qing Chen, Yan Wang, Yuanxiu Lin, Yunting Zhang, Wen He, Xiaorong Wang, Haoru Tang
Summary: This study systematically analyzed the TPS gene family in celery, revealing the functional diversity and biosynthesis pathways of terpenoids. It identified key candidate genes that regulate the biosynthesis of volatile compounds and provided a foundation for the development and utilization of terpenoids in celery.
FRONTIERS IN PLANT SCIENCE
(2022)
Review
Cell Biology
Isabella Schember, Marc S. Halfon
Summary: This study reviews two insect pigmentation gene regulatory networks (GRNs) and discusses common themes in GRN evolution, as well as the challenges of studying GRN changes across different evolutionary distances. The study finds that alterations in pigmentation GRNs in species like fruit flies and butterflies can occur through the co-option and rewiring of trans-acting factors.
Article
Cell Biology
Tobias Strunz, Martin Kellner, Christina Kiel, Bernhard H. F. Weber
Summary: This study identified clusters of co-regulated genes across multiple tissues using eQTL analysis and colocalization studies, highlighting the importance of understanding common effects on biological pathways and treatment implications when targeting co-regulated disease genes.
Review
Biochemistry & Molecular Biology
Magdalena Piotrowska, Mateusz Gliwinski, Piotr Trzonkowski, Dorota Iwaszkiewicz-Grzes
Summary: Regulatory T cells (Tregs) play a critical role in the immune system by exerting suppressive functions, and disturbances in their function can lead to autoimmune dysregulation. Apart from Foxp3, other genes are involved in Tregs development and function. Epigenetic changes, specifically DNA methylation, are believed to be crucial in determining Tregs function.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Plant Sciences
Zexue He, Mengqi Li, Xiucai Pan, Yulian Peng, Yining Shi, Qi Han, Manli Shi, Linwei She, Gennadii Borovskii, Xiaojun Chen, Xiaofeng Gu, Xuejiao Cheng, Wenli Zhang
Summary: This study investigates the role of R-loops in the regulation of gene transcription during COLD stress in rice. The findings show that COLD treatment leads to the reprogramming of R-loops across the genome, and R-loops can modulate the expression of COLD-responsive genes through the regulation of transcription factors and long non-coding RNAs. Moreover, the study validates the contrasting roles of two R-loop loci in the regulation of COLD-responsive gene expression.
Article
Computer Science, Artificial Intelligence
Zhenlong Xiao, Xin Wang, Lin Hong
Summary: Self-organized pattern formation enables swarm robots to autonomously interact with local environments and form complex structures without global knowledge. This study proposes a novel cellular reaction gene regulatory network (CR-GRN) for controlling pattern formation maneuvering. Simulation experiments demonstrate that CR-GRN can satisfy the requirements of turning curvature and maintain robot uniformity, allowing robots to effectively cope with complex environments and maintain stable formations during maneuvering.
FRONTIERS IN NEUROROBOTICS
(2022)
Article
Biology
Sona Charles, Jeyakumar Natarajan
Summary: The study utilized high throughput sequencing data to construct a multifactorial regulatory network associated with Dilated Cardiomyopathy (DCM), identifying key nodes and modules related to DCM, exploring potential associations with other diseases, and isolating probable targets for studying the mechanisms of DCM development and progression to heart failure.
COMPUTATIONAL BIOLOGY AND CHEMISTRY
(2021)
Article
Multidisciplinary Sciences
Wencheng Yin, Luis Mendoza, Jimena Monzon-Sandoval, Araxi O. Urrutia, Humberto Gutierrez
Summary: Transcriptomes self-organize into gene co-expression clusters where genes display coordinated expression patterns across samples. Highly co-expressed gene groups are enriched in common functions and processes. Widespread co-expression naturally emerges in regulatory networks and serves as a reliable indicator of active co-regulation in cellular contexts.
Article
Genetics & Heredity
Hongtao Chen, Michal Levo, Lev Barinov, Miki Fujioka, James B. Jaynes, Thomas Gregor
Article
Biochemistry & Molecular Biology
Mariela D. Petkova, Gasper Tkacik, William Bialek, Eric F. Wieschaus, Thomas Gregor
Article
Multidisciplinary Sciences
Alexander H. Morrison, Mark S. Diamond, Ceire A. Hay, Katelyn T. Byrne, Robert H. Vonderheide
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Biochemistry & Molecular Biology
Fernando W. Rossine, Ricardo Martinez-Garcia, Allyson E. Sgro, Thomas Gregor, Corina E. Tarnita
Review
Developmental Biology
Gasper Tkacik, Thomas Gregor
Summary: This article provides a brief historical perspective on the emergence of positional information concept and its influence in the field of developmental biology, highlighting a modern interpretation in terms of information theory. It emphasizes the importance of stochasticity in cell specification processes.
Editorial Material
Biochemistry & Molecular Biology
Michelle D. Wang, Mario Nicodemi, Nynke H. Dekker, Thomas Gregor, David Holcman, Antoine M. van Oijen, Suliana Manley
Article
Cell Biology
Marcelo Nollmann, Isma Bennabi, Markus Gotz, Thomas Gregor
Summary: In the past two decades, it has been increasingly recognized that the multiscale spatial and temporal organization of the genome plays a crucial role in nuclear function. This review focuses on recent advances in light microscopy and their contribution to our understanding of transcription. The authors discuss the spatial and temporal aspects that shape nuclear order and their impact on regulatory components, with a particular emphasis on genomic scales relevant to function. The emerging perspective suggests that spatiotemporal constraints add complexity to transcriptional regulation, posing new challenges in understanding how information is transmitted from molecular factors through the genome and space to generate functional outputs.
COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Marianne Bauer, Mariela D. Petkova, Thomas Gregor, Eric F. Wieschaus, William Bialek
Summary: In gene expression regulation, the concentration of transcription factor molecules represents information relevant to the organism, but there are physical limits to the precision of these measurements. Lower thresholds are more important for thresholded measurements, and fine tuning is not necessary for near-optimal information transmission. Information theoretic approach can help identify the optimal sensor for the entire gap gene network.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Michal Levo, Joao Raimundo, Xin Yang Bing, Zachary Sisco, Philippe J. Batut, Sergey Ryabichko, Thomas Gregor, Michael S. Levine
Summary: The prevailing view of metazoan gene regulation is challenged by recent findings that reveal physical and functional connections between genes separated by large genomic distances, providing new insights into gene regulation mechanisms.
Article
Cell Biology
Anand P. Singh, Ping Wu, Sergey Ryabichko, Joao Raimundo, Michael Swan, Eric Wieschaus, Thomas Gregor, Jared E. Toettcher
Summary: This study demonstrates that the kinetics of gene expression downstream of a developmental transcription factor can be revealed by combining fast optogenetic stimuli, real-time transcriptional reporters, and a simplified genetic background. This approach provides a powerful tool for studying developmental gene networks in vivo.
Article
Cell Biology
Lukas Voortman, Caitlin Anderson, Elizabeth Urban, Luorongxin Yuan, Sang Tran, Alexandra Neuhaus-Follini, Josh Derrick, Thomas Gregor, Robert J. Johnston Jr
Summary: Stochastic mechanisms play a role in diversifying cell fates during development, but the process of how cells randomly choose between different fates is still poorly understood. In the Drosophila eye, the expression of the transcription factor Spineless (Ss) determines the random mosaic of two R7 photoreceptor subtypes. The study reveals that the transcriptional activity and chromatin compaction at the ss gene locus are regulated by cis-regulatory elements and trans factors during R7 development.
DEVELOPMENTAL CELL
(2022)
Article
Multidisciplinary Sciences
Rabea Seyboldt, Juliette Lavoie, Adrien Henry, Jules Vanaret, Mariela D. Petkova, Thomas Gregor, Paul Francois
Summary: This study proposes a neural network-based approach for dimensionality reduction and analysis of biological gene expression data, using a genetic network in the early Drosophila embryo as a case study. The results show that the spatial positioning of gap genes can be controlled by maternally defined spatial modes, rather than the previously assumed intricate interactions.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Fernando W. Rossine, Gabriel T. Vercelli, Corina E. Tarnita, Thomas Gregor
Summary: This study reveals the foraging strategy of amoebae, a common protozoan predator in soil, and identifies amoebae mobility as the key determinant of predation efficiency. The findings provide insights into the role of protozoan predators in microbial soil ecosystems.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Transplantation
Alexander H. Morrison, Meera Gupta, Kelsey Lloyd, Jennifer Trofe-Clark, Mary Ann Lim, Christine Limonte, Matthew H. Levine, Deirdre Sawinski, Malek Kamoun, Paige M. Porrett
TRANSPLANTATION DIRECT
(2019)
Review
Oncology
Alexander H. Morrison, Katelyn T. Byrne, Robert H. Vonderheide