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
Evaluating Deep Learning models for predicting ALK-5 inhibition.
Gabriel Zarzana Espinoza,Rafaela Molina de Angelo,Patrícia R. Oliveira,Káthia Maria Honório,Káthia Maria Honório +4 more
TL;DR: In this article, the authors evaluated the performance of deep learning models in comparison to Random Forest, and Support Vector Regression for predicting the biological activity (pIC50) of ALK-5 inhibitors as candidates to treat cancer.
Journal ArticleDOI
Functional Identification of Serine Hydroxymethyltransferase as a Key Gene Involved in Lysostaphin Resistance and Virulence Potential of Staphylococcus aureus Strains
TL;DR: Genome-sequencing followed by subtractive and functional genomics revealed that serine hydroxymethyltransferase (glyA or shmT gene) plays a key role in lysostaphin resistance development and in determining the virulence potential of multiple drug-resistant S. aureus.
Journal ArticleDOI
Custom Hardware Architectures for Deep Learning on Portable Devices: A Review
TL;DR: In this article , the authors present a review of DL accelerators, as well as technologies with emerging devices, to highlight their architectural features in application-specific integrated circuit (IC) and field-programmable gate array (FPGA) platforms.
Journal ArticleDOI
Artificial Intelligence – Challenges and Chances for Europe
TL;DR: The contribution conveys insights into artificial intelligence’s basic methods and tools, its main achievements, its economic environment and the surrounding ethical and social issues and analyses the position of Europe in the global context.
Journal ArticleDOI
New marine-derived indolymethyl pyrazinoquinazoline alkaloids with promising antimicrobial profiles
Solida Long,Diana I. S. P. Resende,Andreia Palmeira,Anake Kijjoa,Artur M. S. Silva,Maria Elizabeth Tiritan,Patrícia Pereira-Terra,Joana Freitas-Silva,Sandra Barreiro,Renata Silva,Fernando Remião,Eugénia Pinto,Paulo Martins da Costa,Emília Sousa,Madalena Pinto +14 more
TL;DR: Inspired by marine alkaloids, a series of indolomethyl pyrazino [1,2-b]quinazoline-3,6-diones was prepared using a one-pot microwave-assisted multicomponent polycondensation of amino acids and evaluated for their antimicrobial activity against a panel of nine bacterial strains and five fungal strains.
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.