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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Predicting drug-target binding affinity through molecule representation block based on multi-head attention and skip connection
TL;DR: Wang et al. as mentioned in this paper presented a novel model named Molecule Representation Block-based Drug-Target binding Affinity prediction (MRBDTA), which is composed of embedding and positional encoding, molecule representation block and interaction learning module.
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Permeation of β-Lactamase Inhibitors through the General Porins of Gram-Negative Bacteria
Alessandro Pira,Mariano Andrea Scorciapino,Igor Bodrenko,Andrea Bosin,Silvia Acosta-Gutierrez,Matteo Ceccarelli +5 more
TL;DR: The results confirm the possibility to predict the permeability of molecules through porins by using a few molecular parameters and bolster the general model according to which the free energy increase is mostly due to the decrease of conformational entropy, and this can be compensated by a favorable alignment of the electric dipole with respect to the channel intrinsic electric field.
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Irritable bowel syndrome and microbiome; Switching from conventional diagnosis and therapies to personalized interventions
TL;DR: In this article , the authors proposed a new perspective on using data-driven approach and applying computational modelling and machine learning to design microbiome-aware personalized treatment for Irritable Bowel Syndrome (IBS).
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Irritable bowel syndrome and microbiome; Switching from conventional diagnosis and therapies to personalized interventions
TL;DR: In this paper , the authors proposed a new perspective on using data-driven approach and applying computational modelling and machine learning to design microbiome-aware personalized treatment for Irritable Bowel Syndrome (IBS).
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Septic acute kidney injury: a review of basic research.
TL;DR: This article reviews the basic research information that has been reported thus far on the subject of septic AKI, mainly from the viewpoint of functional dysregulation, including some knowledge acquired with multiphoton intravital imaging.
References
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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.