A Deep Learning Approach to Antibiotic Discovery
Jonathan M. Stokes,Kevin Yang,Kyle Swanson,Wengong Jin,Andres Cubillos-Ruiz,Nina M. Donghia,Craig R. MacNair,Shawn French,Lindsey A. Carfrae,Zohar Bloom-Ackermann,Victoria M. Tran,Anush Chiappino-Pepe,Ahmed H. Badran,Ian W. Andrews,Ian W. Andrews,Ian W. Andrews,Emma J. Chory,George M. Church,Eric D. Brown,Tommi S. Jaakkola,Regina Barzilay,James J. Collins +21 more
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TLDR
A deep neural network capable of predicting molecules with antibacterial activity is trained and a molecule from the Drug Repurposing Hub-halicin- is discovered that is structurally divergent from conventional antibiotics and displays bactericidal activity against a wide phylogenetic spectrum of pathogens.About:
This article is published in Cell.The article was published on 2020-02-20 and is currently open access. It has received 1002 citations till now.read more
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Synthetic biology-inspired strategies and tools for engineering of microbial natural product biosynthetic pathways.
TL;DR: In this article, the authors discussed recent advances in synthetic biology-inspired strategies, including bioinformatics and genetic engineering tools and approaches for identification, cloning, editing/refactoring of candidate biosynthetic pathways, construction of heterologous expression hosts, fitness optimization between target pathways and hosts and detection of NP production.
Journal Article
Deep Graph Neural Networks with Shallow Subgraph Samplers
Hanqing Zeng,Muhan Zhang,Yinglong Xia,Ajitesh Srivastava,Rajgopal Kannan,Viktor K. Prasanna,Long Jin,Andrey Malevich,Ren Chen +8 more
TL;DR: A simple "deep GNN, shallow sampler" design principle is proposed to improve both the GNN accuracy and efficiency -- to generate representation of a target node, a deep GNN is used to pass messages only within a shallow, localized subgraph.
Proceedings ArticleDOI
One Transformer Can Understand Both 2D & 3D Molecular Data
TL;DR: Transformer-M as discussed by the authors uses the standard Transformer as the backbone architecture, and develops two separated channels to encode 2D and 3D structural information and incorporate them with the atom features in the network modules.
Journal ArticleDOI
Deep learning to design nuclear-targeting abiotic miniproteins
Carly K. Schissel,Somesh Mohapatra,Justin M. Wolfe,Colin M. Fadzen,Colin M. Fadzen,Kamela Bellovoda,Chia-Ling Wu,Jenna A. Wood,Annika B. Malmberg,Andrei Loas,Rafael Gómez-Bombarelli,Bradley L. Pentelute +11 more
TL;DR: In this article, the authors combined high-throughput experimentation with a directed evolution-inspired deep learning approach in which the molecular structures of natural and unnatural residues are represented as topological fingerprints.
Journal ArticleDOI
Electrochemical Deposition of Cu Metal-Organic Framework Films for the Dual Analysis of Pathogens.
Zhaowei Sun,Ying Peng,Minghui Wang,Yuxin Lin,Mohammed Jalalah,Saeed A. Alsareii,Farid A. Harraz,Jie Yang,Genxi Li,Genxi Li +9 more
TL;DR: In this paper, an electrochemical biosensor was proposed for the dual detection of Staphylococcus aureus based on the electrodeposition of Cu metal-organic framework (Cu-MOF) thin films.
References
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TL;DR: Burrows-Wheeler Alignment tool (BWA) is implemented, a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps.
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One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products
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Extended-Connectivity Fingerprints
David Rogers,Mathew Hahn +1 more
TL;DR: A description of their implementation has not previously been presented in the literature, and ECFPs can be very rapidly calculated and can represent an essentially infinite number of different molecular features.