Synthetic promoter design in Escherichia coli based on multinomial diffusion model

Autor: Qixiu Du, May Nee Poon, Xiaocheng Zeng, Pengcheng Zhang, Zheng Wei, Haochen Wang, Ye Wang, Lei Wei, Xiaowo Wang

Publikováno v: iScience, Vol 27, Iss 11, Pp 111207- (2024)

Summary: Generative design of promoters has enhanced the efficiency of de novo creation of functional sequences. Though several deep generative models have been employed in biological sequence generation, including variational autoencoder (VAE) or Wa

Externí odkaz: https://doaj.org/article/adac8f097edc43f198e1100c142fd735

Nearly maximal information gain due to time integration in central dogma reactions

Autor: Swarnavo Sarkar, Jayan Rammohan

Publikováno v: iScience, Vol 26, Iss 6, Pp 106767- (2023)

Summary: Living cells process information about their environment through the central dogma processes of transcription and translation, which drive the cellular response to stimuli. Here, we study the transfer of information from environmental input

Externí odkaz: https://doaj.org/article/2b645929e102449eaf453d2d6832b9cd

Physical Modeling of a Sliding Clamp Mechanism for the Spreading of ParB at Short Genomic Distance from Bacterial Centromere Sites

Autor: Jean-Charles Walter, Jérôme Rech, Nils-Ole Walliser, Jérôme Dorignac, Frédéric Geniet, John Palmeri, Andrea Parmeggiani, Jean-Yves Bouet

Publikováno v: iScience, Vol 23, Iss 12, Pp 101861- (2020)

Summary: Bacterial ParB partitioning proteins involved in chromosomes and low-copy-number plasmid segregation are cytosine triphosphate (CTP)-dependent molecular switches. CTP-binding converts ParB dimers to DNA clamps, allowing unidimensional diffus

Externí odkaz: https://doaj.org/article/60f8b707193c430e877ac0d0ff508e17

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Synthetic promoter design in Escherichia coli based on multinomial diffusion model.

Autor: Du Q; Ministry of Education Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Bioinformatics Division, Beijing National Research Center for Information Science and Technology, Department of Automation, Tsinghua University, Beijing 100084, China., Poon MN; Ministry of Education Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Bioinformatics Division, Beijing National Research Center for Information Science and Technology, Department of Automation, Tsinghua University, Beijing 100084, China., Zeng X; Ministry of Education Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Bioinformatics Division, Beijing National Research Center for Information Science and Technology, Department of Automation, Tsinghua University, Beijing 100084, China., Zhang P; Ministry of Education Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Bioinformatics Division, Beijing National Research Center for Information Science and Technology, Department of Automation, Tsinghua University, Beijing 100084, China., Wei Z; Ministry of Education Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Bioinformatics Division, Beijing National Research Center for Information Science and Technology, Department of Automation, Tsinghua University, Beijing 100084, China., Wang H; Ministry of Education Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Bioinformatics Division, Beijing National Research Center for Information Science and Technology, Department of Automation, Tsinghua University, Beijing 100084, China., Wang Y; Ministry of Education Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Bioinformatics Division, Beijing National Research Center for Information Science and Technology, Department of Automation, Tsinghua University, Beijing 100084, China., Wei L; Ministry of Education Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Bioinformatics Division, Beijing National Research Center for Information Science and Technology, Department of Automation, Tsinghua University, Beijing 100084, China., Wang X; Ministry of Education Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Bioinformatics Division, Beijing National Research Center for Information Science and Technology, Department of Automation, Tsinghua University, Beijing 100084, China.

Publikováno v: IScience [iScience] 2024 Oct 18; Vol. 27 (11), pp. 111207. Date of Electronic Publication: 2024 Oct 18 (Print Publication: 2024).