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BIOTIC: a Bayesian framework to integrate single-cell multi-omics for transcription factor activity inference and improve identity characterization of cells.
Brief Bioinform
November 2024
Department of Automation, Xiamen University, Xiang'an South Road, Xiang'an, 361102, Xiamen, Fujian, China.
Understanding cell destiny requires unraveling the intricate mechanism of gene regulation, where transcription factors (TFs) play a pivotal role. However, the actual contribution of TFs, that is TF activity, is not only determined by TF expression, but also accessibility of corresponding chromatin regions. Therefore, we introduce BIOTIC, an advanced Bayesian model with a well-established gene regulation structure that harnesses the power of single-cell multi-omics data to model the gene expression process under the control of regulatory elements, thereby defining the regulatory activity of TFs with variational inference.
View Article and Find Full Text PDFRho1 and Rgf1 establish a new actin-dependent signal to determine growth poles in yeast independently of microtubules and the Tea1-Tea4 complex.
PLoS Biol
November 2024
Instituto de Biología Funcional y Genómica (IBFG), CSIC/Universidad de Salamanca and Departamento de Microbiología y Genética, Universidad de Salamanca. C/ Zacarías González, Salamanca, Spain.
Cellular asymmetry begins with the selection of a discrete point on the cell surface that triggers Rho-GTPases activation and localized assembly of the cytoskeleton to establish new growth zones. The cylindrical shape of fission yeast is organized by microtubules (MT) that deliver the landmark Tea1-Tea4 complex at the cell tips to define the growth poles. However, only a few tea1Δ cells mistaken the direction of growth, indicating that they manage to detect their growth sites.
View Article and Find Full Text PDFMD-GNN: A mechanism-data-driven graph neural network for molecular properties prediction and new material discovery.
J Mol Graph Model
September 2023
QingGong College, North China University of Science and Technology, TangShan, Hebei, 064000, China.
Molecular properties prediction and new material discovery are significant for the pharmaceutical industry, food, chemistry, and other fields. The popular methods are theoretical mechanism calculation and machine learning. There is a deviation between the theoretical mechanism calculation results and the experimental data.
View Article and Find Full Text PDFSystems Biology Approach for Personalized Hemostasis Correction.
J Pers Med
November 2022
Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117198 Moscow, Russia.
The correction of blood coagulation impairments of a bleeding or thrombotic nature employs standard protocols where the type of drug, its dose and the administration regime are stated. However, for a group of patients, such an approach may be ineffective, and personalized therapy adjustment is needed. Laboratory hemostasis tests are used to control the efficacy of therapy, which is expensive and time-consuming.
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