Zobrazeno 1 - 10
of 271
pro vyhledávání: '"Tianshou Zhou"'
Autor:
Junya Wang, Yi-Jiao Zhang, Cong Xu, Jiaze Li, Jiachen Sun, Jiarong Xie, Ling Feng, Tianshou Zhou, Yanqing Hu
Publikováno v:
Nature Communications, Vol 15, Iss 1, Pp 1-11 (2024)
Abstract The evolution processes of complex systems carry key information in the systems’ functional properties. Applying machine learning algorithms, we demonstrate that the historical formation process of various networked complex systems can be
Externí odkaz:
https://doaj.org/article/7ab3508da09844f59fe78c1165052da2
Publikováno v:
PLoS Computational Biology, Vol 19, Iss 12, p e1011722 (2023)
Recent experimental evidence strongly supports that three-dimensional (3D) long-range enhancer-promoter (E-P) interactions have important influences on gene-expression dynamics, but it is unclear how the interaction information is translated into gen
Externí odkaz:
https://doaj.org/article/9e800cd99e6f4a9e9ea3ba6a8af60fe4
Publikováno v:
Mathematical Biosciences and Engineering, Vol 19, Iss 8, Pp 8426-8451 (2022)
Transcription involves gene activation, nuclear RNA export (NRE) and RNA nuclear retention (RNR). All these processes are multistep and biochemical. A multistep reaction process can create memories between reaction events, leading to non-Markovian ki
Externí odkaz:
https://doaj.org/article/a1f02bf17ff4474687f0d1628040a669
Autor:
Songhao Luo, Zhenquan Zhang, Zihao Wang, Xiyan Yang, Xiaoxuan Chen, Tianshou Zhou, Jiajun Zhang
Publikováno v:
Royal Society Open Science, Vol 10, Iss 4 (2023)
Gene expression has inherent stochasticity resulting from transcription's burst manners. Single-cell snapshot data can be exploited to rigorously infer transcriptional burst kinetics, using mathematical models as blueprints. The classical telegraph m
Externí odkaz:
https://doaj.org/article/99e47427ff81441fada2441766e33d6a
Publikováno v:
npj Systems Biology and Applications, Vol 8, Iss 1, Pp 1-9 (2022)
Abstract Although multistability is an important dynamic property of a wide range of complex systems, it is still a challenge to develop mathematical models for realising high order multistability using realistic regulatory mechanisms. To address thi
Externí odkaz:
https://doaj.org/article/403867e3806c403c8dc57d2e169ce332
Publikováno v:
Mathematical Biosciences and Engineering, Vol 19, Iss 2, Pp 2095-2119 (2022)
eRNAs as the products of enhancers can regulate gene expression via various possible ways, but which regulation way is more reasonable is debatable in biology, and in particular, how eRNAs impact gene expression remains unclear. Here we introduce a m
Externí odkaz:
https://doaj.org/article/a3a1c0cc531f448faca8c45ae1468e75
Publikováno v:
Mathematical Biosciences and Engineering, Vol 19, Iss 4, Pp 3313-3336 (2022)
While transcription often occurs in a bursty manner, various possible regulations can lead to complex promoter patterns such as promoter cycles, giving rise to an important question: How do promoter kinetics shape transcriptional bursting kinetics? H
Externí odkaz:
https://doaj.org/article/a2de209541bb402bbb5317f2c81a3ae2
Publikováno v:
Mathematical Biosciences and Engineering, Vol 18, Iss 4, Pp 4713-4730 (2021)
Gene transcription in single cells is inherently a probabilistic process. The relationship between variance ($ \sigma^{2} $) and mean expression ($ \mu $) is of paramount importance for investigations into the evolutionary origins and consequences of
Externí odkaz:
https://doaj.org/article/605d52e9a87c4710a99264784152b70f
DTFLOW: Inference and Visualization of Single-cell Pseudotime Trajectory Using Diffusion Propagation
Publikováno v:
Genomics, Proteomics & Bioinformatics, Vol 19, Iss 2, Pp 306-318 (2021)
One of the major challenges in single-cell data analysis is the determination of cellular developmental trajectories using single-cell data. Although substantial studies have been conducted in recent years, more effective methods are still strongly n
Externí odkaz:
https://doaj.org/article/6ba432b316d04ca8b6b67af3b350dcb3
Publikováno v:
Mathematical Biosciences and Engineering, Vol 17, Iss 5, Pp 5304-5325 (2020)
Gene expression is an inherently noisy process due to low copy numbers of mRNA or protein. The involved reaction events may happen in a Markov fashion but also in a non-Markov manner, depending on waiting-time distributions for the occurrence of reac
Externí odkaz:
https://doaj.org/article/5070bf42a2be4fa7a97deb85c5383982