Deep flanking sequence engineering for efficient promoter design using DeepSEED
Author
Abstract
Suggested Citation
DOI: 10.1038/s41467-023-41899-y
Download full text from publisher
References listed on IDEAS
- Maarten Van Brempt & Jim Clauwaert & Friederike Mey & Michiel Stock & Jo Maertens & Willem Waegeman & Marjan De Mey, 2020. "Predictive design of sigma factor-specific promoters," Nature Communications, Nature, vol. 11(1), pages 1-13, December.
- Fangjie Zhu & Lucas Farnung & Eevi Kaasinen & Biswajyoti Sahu & Yimeng Yin & Bei Wei & Svetlana O. Dodonova & Kazuhiro R. Nitta & Ekaterina Morgunova & Minna Taipale & Patrick Cramer & Jussi Taipale, 2018. "The interaction landscape between transcription factors and the nucleosome," Nature, Nature, vol. 562(7725), pages 76-81, October.
- Timothy C. Yu & Winnie L. Liu & Marcia S. Brinck & Jessica E. Davis & Jeremy Shek & Grace Bower & Tal Einav & Kimberly D. Insigne & Rob Phillips & Sriram Kosuri & Guillaume Urtecho, 2021. "Multiplexed characterization of rationally designed promoter architectures deconstructs combinatorial logic for IPTG-inducible systems," Nature Communications, Nature, vol. 12(1), pages 1-14, December.
- Jicong Cao & Eva Maria Novoa & Zhizhuo Zhang & William C. W. Chen & Dianbo Liu & Gigi C. G. Choi & Alan S. L. Wong & Claudia Wehrspaun & Manolis Kellis & Timothy K. Lu, 2021. "High-throughput 5′ UTR engineering for enhanced protein production in non-viral gene therapies," Nature Communications, Nature, vol. 12(1), pages 1-10, December.
- Ming-Ru Wu & Lior Nissim & Doron Stupp & Erez Pery & Adina Binder-Nissim & Karen Weisinger & Casper Enghuus & Sebastian R. Palacios & Melissa Humphrey & Zhizhuo Zhang & Eva Maria Novoa & Manolis Kelli, 2019. "A high-throughput screening and computation platform for identifying synthetic promoters with enhanced cell-state specificity (SPECS)," Nature Communications, Nature, vol. 10(1), pages 1-10, December.
- Jan Zrimec & Xiaozhi Fu & Azam Sheikh Muhammad & Christos Skrekas & Vykintas Jauniskis & Nora K. Speicher & Christoph S. Börlin & Vilhelm Verendel & Morteza Haghir Chehreghani & Devdatt Dubhashi & Ver, 2022. "Controlling gene expression with deep generative design of regulatory DNA," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
Most related items
These are the items that most often cite the same works as this one and are cited by the same works as this one.- Travis L. LaFleur & Ayaan Hossain & Howard M. Salis, 2022. "Automated model-predictive design of synthetic promoters to control transcriptional profiles in bacteria," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
- Qiuge Zhang & Samira M. Azarin & Casim A. Sarkar, 2022. "Model-guided engineering of DNA sequences with predictable site-specific recombination rates," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
- Pakavarin Louphrasitthiphol & Alessia Loffreda & Vivian Pogenberg & Sarah Picaud & Alexander Schepsky & Hans Friedrichsen & Zhiqiang Zeng & Anahita Lashgari & Benjamin Thomas & E. Elizabeth Patton & M, 2023. "Acetylation reprograms MITF target selectivity and residence time," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
- Marios G. Koliopoulos & Reyhan Muhammad & Theodoros I. Roumeliotis & Fabienne Beuron & Jyoti S. Choudhary & Claudio Alfieri, 2022. "Structure of a nucleosome-bound MuvB transcription factor complex reveals DNA remodelling," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
- Anna Berenson & Ryan Lane & Luis F. Soto-Ugaldi & Mahir Patel & Cosmin Ciausu & Zhaorong Li & Yilin Chen & Sakshi Shah & Clarissa Santoso & Xing Liu & Kerstin Spirohn & Tong Hao & David E. Hill & Marc, 2023. "Paired yeast one-hybrid assays to detect DNA-binding cooperativity and antagonism across transcription factors," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
- Amir Shahein & Maria López-Malo & Ivan Istomin & Evan J. Olson & Shiyu Cheng & Sebastian J. Maerkl, 2022. "Systematic analysis of low-affinity transcription factor binding site clusters in vitro and in vivo establishes their functional relevance," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
- Michaël Noë & Dimitrios Mathios & Akshaya V. Annapragada & Shashikant Koul & Zacharia H. Foda & Jamie E. Medina & Stephen Cristiano & Christopher Cherry & Daniel C. Bruhm & Noushin Niknafs & Vilmos Ad, 2024. "DNA methylation and gene expression as determinants of genome-wide cell-free DNA fragmentation," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
- Yafeng Wang & Guiquan Zhang & Qingzhou Meng & Shisheng Huang & Panpan Guo & Qibin Leng & Lingyun Sun & Geng Liu & Xingxu Huang & Jianghuai Liu, 2022. "Precise tumor immune rewiring via synthetic CRISPRa circuits gated by concurrent gain/loss of transcription factors," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
- Tianbao Li & Qi Liu & Zhong Chen & Kun Fang & Furong Huang & Xueqi Fu & Qianben Wang & Victor X. Jin, 2022. "Dynamic nucleosome landscape elicits a noncanonical GATA2 pioneer model," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
- Anushweta Asthana & Parameshwaran Ramanan & Alexander Hirschi & Keelan Z. Guiley & Tilini U. Wijeratne & Robert Shelansky & Michael J. Doody & Haritha Narasimhan & Hinrich Boeger & Sarvind Tripathi & , 2022. "The MuvB complex binds and stabilizes nucleosomes downstream of the transcription start site of cell-cycle dependent genes," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
- Evangelos-Marios Nikolados & Arin Wongprommoon & Oisin Mac Aodha & Guillaume Cambray & Diego A. Oyarzún, 2022. "Accuracy and data efficiency in deep learning models of protein expression," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
- Vivekanandan Ramalingam & Xinyang Yu & Brian D. Slaughter & Jay R. Unruh & Kaelan J. Brennan & Anastasiia Onyshchenko & Jeffrey J. Lange & Malini Natarajan & Michael Buck & Julia Zeitlinger, 2023. "Lola-I is a promoter pioneer factor that establishes de novo Pol II pausing during development," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
Corrections
All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-41899-y. See general information about how to correct material in RePEc.
If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.
If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .
If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.
For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .
Please note that corrections may take a couple of weeks to filter through the various RePEc services.