Nature Search

A deep learning model for predicting next-generation sequencing depth from DNA sequence

DNA probes used in next generation sequencing (NGS) have variable hybridisation kinetics, resulting in non-uniform coverage. Here, the authors develop a deep learning model to predict NGS depth using DNA probe sequences and apply to human and non-human sequencing panels.

Jinny X. Zhang
Boyan Yordanov
David Yu Zhang
ResearchOpen Access19 Jul 2021
Nature Communications

Volume: 12, P: 1-10
A systematic approach to inserting split inteins for Boolean logic gate engineering and basal activity reduction

Split inteins are powerful tools for designing synthetic split proteins. Here the authors use a mini-Mu transposon screen to map split sites, enabling the development of protein-based logic gates and fine control of protein activity.

Trevor Y. H. Ho
Alexander Shao
Baojun Wang
ResearchOpen Access13 Apr 2021
Nature Communications

Volume: 12, P: 1-12
Stochastic pulsing of gene expression enables the generation of spatial patterns in Bacillus subtilis biofilms

Stochastic pulsing of gene expression can generate phenotypic diversity in a genetically identical population of cells. Here, the authors show that stochastic pulsing in the expression of a sigma factor enables the formation of spatial patterns in a multicellular system, Bacillus subtilis bacterial biofilms.

Eugene Nadezhdin
Niall Murphy
James C. W. Locke
ResearchOpen Access19 Feb 2020
Nature Communications

Volume: 11, P: 1-12
Interpretation of morphogen gradients by a synthetic bistable circuit

Morphogen gradients can be dynamic and transient yet give rise to stable cellular patterns. Here the authors show that a synthetic morphogen-induced mutual inhibition circuit produces stable boundaries when the spatial average of morphogens falls within the region of bistability.

Paul K. Grant
Gregory Szep
Andrew Phillips
ResearchOpen Access02 Nov 2020
Nature Communications

Volume: 11, P: 1-8
DNA-based communication in populations of synthetic protocells

Semipermeable proteinosome membranes allow complex DNA message communication through compartmentalization and protect the DNA circuits from degradation in a biological environment.

Alex Joesaar
Shuo Yang
Tom F. A. de Greef
Research04 Mar 2019
Nature Nanotechnology

Volume: 14, P: 369-378
A spatially localized architecture for fast and modular DNA computing

Fast and scalable molecular logic circuits can be created through the spatial organization of DNA hairpins on DNA origami scaffolds.

Gourab Chatterjee
Neil Dalchau
Georg Seelig
Research24 Jul 2017
Nature Nanotechnology

Volume: 12, P: 920-927
Programmable chemical controllers made from DNA

Chemical controllers made from DNA can be programmed to implement any dynamic behaviour compatible with chemical kinetics.

Yuan-Jyue Chen
Neil Dalchau
Georg Seelig
Research29 Sept 2013
Nature Nanotechnology

Volume: 8, P: 755-762
Predicting DNA hybridization kinetics from sequence

The rate constant of DNA hybridization varies over several orders of magnitude and is affected by temperature and DNA sequence. A machine-learning algorithm that is capable of accurately predicting hybridization rate constants has now been developed. Tests with this algorithm showed that over 90% of predictions were correct to within a factor of three.

Jinny X. Zhang
John Z. Fang
David Yu Zhang
Research06 Nov 2017
Nature Chemistry

Volume: 10, P: 91-98
Selector function of MHC I molecules is determined by protein plasticity

Alistair Bailey
Neil Dalchau
Tim Elliott
ResearchOpen Access20 Oct 2015
Scientific Reports

Volume: 5, P: 1-15
Noise Reduction in Complex Biological Switches

Luca Cardelli
Attila Csikász-Nagy
Max Tschaikowski
ResearchOpen Access08 Feb 2016
Scientific Reports

Volume: 6, P: 1-12
Host genotype and time dependent antigen presentation of viral peptides: predictions from theory

R. Charlotte Eccleston
Peter V. Coveney
Neil Dalchau
ResearchOpen Access30 Oct 2017
Scientific Reports

Volume: 7, P: 1-20

Search

A deep learning model for predicting next-generation sequencing depth from DNA sequence

A systematic approach to inserting split inteins for Boolean logic gate engineering and basal activity reduction

Stochastic pulsing of gene expression enables the generation of spatial patterns in Bacillus subtilis biofilms

Interpretation of morphogen gradients by a synthetic bistable circuit

DNA-based communication in populations of synthetic protocells

A spatially localized architecture for fast and modular DNA computing

Programmable chemical controllers made from DNA

Predicting DNA hybridization kinetics from sequence

Selector function of MHC I molecules is determined by protein plasticity

Noise Reduction in Complex Biological Switches

Host genotype and time dependent antigen presentation of viral peptides: predictions from theory

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