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
Reads0
Chats0
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
Citations
More filters
Journal ArticleDOI
High accuracy barrier heights, enthalpies, and rate coefficients for chemical reactions
TL;DR: In this article , the authors used CCSD(T)-F12a/cc-pVDZ-F12//ωB97X-D3/def2-TZVP to obtain high-quality single point calculations for nearly 22,000 unique stable species and transition states.
Journal ArticleDOI
Digital Insights Into Nucleotide Metabolism and Antibiotic Treatment Failure.
TL;DR: In this paper, the authors review emerging technologies poised to transform understanding into why antibiotics may fail in the clinic and discuss how these technologies led to the discovery that nucleotide metabolism regulates antibiotic drug responses and why these are relevant to human infections.
Journal ArticleDOI
Machine Learning for Plant Stress Modeling: A Perspective towards Hormesis Management
Amanda Rico-Chavez,Jesus Alejandro Franco,Arturo A. Fernandez-Jaramillo,Luis Miguel Contreras-Medina,Ramón G. Guevara-González,Quetzalcoatl Hernandez-Escobedo +5 more
TL;DR: In this paper , the authors discuss the most recent ML and DL applications in plant stress science, focusing on their potential for improving the development of hormesis management protocols, and discuss how artificial intelligence tools, particularly Machine Learning (ML) and Deep Learning (DL), have become crucial for processing and interpreting data to accurately model plant stress responses such as genomic variation, gene and protein expression, and metabolite biosynthesis.
Proceedings ArticleDOI
Periodic Graph Transformers for Crystal Material Property Prediction
TL;DR: The proposed Matformer is designed to be invariant to periodicity and can capture repeating patterns explicitly and outperforms baseline methods consistently, demonstrating the importance of periodic invariance and explicit repeating pattern encoding for crystal representation learning.
Journal ArticleDOI
Human germline editing: Legal-ethical guidelines for South Africa
TL;DR: Five guiding principles are proposed to guide ethical and legal policy reform regarding human germline editing in South Africa: Given its potential to improve the lives of the people of South Africa, human germlines editing should be regulated, not banned.
References
More filters
Journal ArticleDOI
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
TL;DR: This work presents DESeq2, a method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates, which enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression.
Journal ArticleDOI
Fast and accurate short read alignment with Burrows–Wheeler transform
Heng Li,Richard Durbin +1 more
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.
Journal ArticleDOI
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
TL;DR: EdgeR as mentioned in this paper is a Bioconductor software package for examining differential expression of replicated count data, which uses an overdispersed Poisson model to account for both biological and technical variability and empirical Bayes methods are used to moderate the degree of overdispersion across transcripts, improving the reliability of inference.
Journal ArticleDOI
One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products
TL;DR: A simple and highly efficient method to disrupt chromosomal genes in Escherichia coli in which PCR primers provide the homology to the targeted gene(s), which should be widely useful, especially in genome analysis of E. coli and other bacteria.
Journal ArticleDOI
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.