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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Open Graph Benchmark: Datasets for Machine Learning on Graphs
Weihua Hu,Matthias Fey,Marinka Zitnik,Yuxiao Dong,Hongyu Ren,Bowen Liu,Michele Catasta,Jure Leskovec +7 more
TL;DR: The OGB datasets are large-scale, encompass multiple important graph ML tasks, and cover a diverse range of domains, ranging from social and information networks to biological networks, molecular graphs, source code ASTs, and knowledge graphs, indicating fruitful opportunities for future research.
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TUDataset: A collection of benchmark datasets for learning with graphs.
Christopher Morris,Nils M. Kriege,Franka Bause,Kristian Kersting,Petra Mutzel,Marion Neumann +5 more
TL;DR: The TUDataset for graph classification and regression is introduced, which consists of over 120 datasets of varying sizes from a wide range of applications and provides Python-based data loaders, kernel and graph neural network baseline implementations, and evaluation tools.
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A guide to machine learning for biologists.
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Towards the sustainable discovery and development of new antibiotics
Marcus Miethke,Marco Pieroni,Tilmann Weber,Mark Brönstrup,Peter Hammann,Ludovic Halby,Paola B. Arimondo,Philippe Glaser,Bertrand Aigle,Helge B. Bode,Helge B. Bode,Rui Moreira,Yanyan Li,Andriy Luzhetskyy,Marnix H. Medema,Jean-Luc Pernodet,Marc Stadler,José R. Tormo,Olga Genilloud,Andrew W. Truman,Kira J. Weissman,Eriko Takano,Stefano Sabatini,Evi Stegmann,Heike Brötz-Oesterhelt,Wolfgang Wohlleben,Myriam Seemann,Martin Empting,Anna K. H. Hirsch,Brigitta Loretz,Claus-Michael Lehr,Alexander Titz,Jennifer Herrmann,Timo Jaeger,Silke Alt,Thomas Hesterkamp,Mathias Winterhalter,Andrea Schiefer,Kenneth Pfarr,Achim Hoerauf,Heather Graz,Michael Graz,Mika Lindvall,Savithri Ramurthy,Anders Karlén,Maarten van Dongen,Hrvoje Petković,Andreas Keller,Frédéric Peyrane,Stefano Donadio,Laurent Fraisse,Laura J. V. Piddock,Ian H. Gilbert,Heinz E. Moser,Rolf Müller +54 more
TL;DR: In this paper, the authors present a strategic blueprint to substantially improve our ability to discover and develop new antibiotics, and propose both short-term and long-term solutions to overcome the most urgent limitations in the various sectors of research and funding.
References
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Journal ArticleDOI
Global Challenge of Multidrug-Resistant Acinetobacter baumannii
Federico Perez,Andrea M. Hujer,Kristine M. Hujer,Brooke K. Decker,Philip N. Rather,Robert A. Bonomo,Robert A. Bonomo +6 more
TL;DR: This review summarizes the worldwide emergence of antibiotic-resistant A. baumannii as a nosocomial pathogen and focuses on its mechanisms of resistance against selected antibiotics.
Journal ArticleDOI
Systematic review of intestinal microbiota transplantation (fecal bacteriotherapy) for recurrent Clostridium difficile infection.
TL;DR: Effectiveness varied by route of instillation, relationship to stool donor, volume of IMT given, and treatment before infusion, but findings can guide physicians interested in implementing the procedure until better designed studies are conducted to confirm best practices.
Journal ArticleDOI
Reverse transcriptase template switching: a SMART approach for full-length cDNA library construction.
TL;DR: A fast, simple method for constructing full-length cDNA libraries using SMART technology, which uses the template-switching activity of Moloney murine leukemia virus reverse transcriptase to synthesize and anchor first-strand cDNA in one step.
Journal ArticleDOI
Mechanism of Interaction of Different Classes of Cationic Antimicrobial Peptides with Planar Bilayers and with the Cytoplasmic Membrane of Escherichia coli
TL;DR: It was demonstrated that individual peptides varied widely in their ability to depolarize the cytoplasmic membrane potential of E. coli, with certain peptides such as the loop peptide bactenecin and the alpha-helical peptide CP26 being unable to cause depolarization at the minimal inhibitory concentration (MIC), and others like gramicidin S causing maximal depolarized below the MIC.
Journal ArticleDOI
Definitions and guidelines for research on antibiotic persistence
Naomi N.Q. Balaban,Sophie Helaine,Kim Lewis,Martin Ackermann,Martin Ackermann,Bree B. Aldridge,Dan I. Andersson,Mark P. Brynildsen,Dirk Bumann,Andrew Camilli,James J. Collins,James J. Collins,James J. Collins,Christoph Dehio,Sarah M. Fortune,Jean-Marc Ghigo,Wolf-Dietrich Hardt,Alexander Harms,Matthias Heinemann,Deborah T. Hung,Urs Jenal,Bruce R. Levin,Jan Michiels,Gisela Storz,Man-Wah Tan,Tanel Tenson,Laurence Van Melderen,Annelies S. Zinkernagel +27 more
TL;DR: Scientists working on the response of bacteria to antibiotics define antibiotic persistence and provide practical guidance on how to study bacterial persister cells, and provide a guide to measuring persistence.