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A guide to machine learning for biologists

Nature reviews. Molecular cell biology, 2022-01, Vol.23 (1), p.40-55

2022

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Nontuberculous mycobacterial disease mortality in the United States, 1999-2010: a population-based comparative study

PloS one, 2014-03, Vol.9 (3), p.e91879

2014

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Deep learning extends de novo protein modelling coverage of genomes using iteratively predicted structural constraints

Nature communications, 2019-09, Vol.10 (1), p.3977-13, Article 3977

2019

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Differentiable simulation to develop molecular dynamics force fields for disordered proteins

Chemical science (Cambridge), 2024-03, Vol.15 (13), p.4897-499

Greener, Joe G

2024

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Differentiable molecular simulation can learn all the parameters in a coarse-grained force field for proteins

PloS one, 2021-09, Vol.16 (9), p.e0256990-e0256990

2021

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Design of metalloproteins and novel protein folds using variational autoencoders

Scientific reports, 2018-11, Vol.8 (1), p.16189-12, Article 16189

2018

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Commentary on Conde et al.: Evidence and gap map offer an important opportunity for dialogue and refinement of the gateway hypothesis controversy

Addiction (Abingdon, England), 2024-10, Vol.119 (10), p.1709-1710

2024

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Structure-based prediction of protein allostery

Current opinion in structural biology, 2018-06, Vol.50, p.1-8

2018

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Magnetic Coupling in Colloidal Clusters for Hierarchical Self-Assembly

ACS nano, 2021-03, Vol.15 (3), p.4989-4999

2021

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Development of a biomarker mortality risk model in acute respiratory distress syndrome

Critical care (London, England), 2019-12, Vol.23 (1), p.410-410, Article 410

2019

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Involvement of eNAMPT/TLR4 inflammatory signaling in progression of non‐alcoholic fatty liver disease, steatohepatitis, and fibrosis

The FASEB journal, 2023-03, Vol.37 (3), p.e22825-n/a

2023

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Asthma is Different in Women

Current allergy and asthma reports, 2015-06, Vol.15 (6), p.28-28, Article 28

2015

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A Razor's Edge: Vascular Responses to Acute Inflammatory Lung Injury/Acute Respiratory Distress Syndrome

Annual review of physiology, 2024-02, Vol.86 (1), p.505-529

2024

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Prediction of interresidue contacts with DeepMetaPSICOV in CASP13

Proteins, structure, function, and bioinformatics, 2019-12, Vol.87 (12), p.1092-1099

2019

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A Variant in the Promoter of MUC5B and Idiopathic Pulmonary Fibrosis

The New England journal of medicine, 2011-04, Vol.364 (16), p.1576-1577

2011

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NRF2 and Diabetes: The Good, the Bad, and the Complex

Diabetes (New York, N.Y.), 2022-12, Vol.71 (12), p.2463-2476

2022

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The Differing Roles of Flavins and Quinones in Extracellular Electron Transfer in Lactiplantibacillus plantarum

Applied and environmental microbiology, 2023-01, Vol.89 (1), p.e0131322

2023

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Novel Machine Learning Can Predict Acute Asthma Exacerbation

Chest, 2021-05, Vol.159 (5), p.1747-1757

2021

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Tissue ACE phenotyping in lung cancer

PloS one, 2019-12, Vol.14 (12), p.e0226553-e0226553

2019

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Essential role for paxillin tyrosine phosphorylation in LPS-induced mitochondrial fission, ROS generation and lung endothelial barrier loss

Scientific reports, 2021-09, Vol.11 (1), p.17546-17546, Article 17546

2021

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Genomic and Genetic Approaches to Deciphering Acute Respiratory Distress Syndrome Risk and Mortality

Antioxidants & redox signaling, 2019-11, Vol.31 (14), p.1027-1052

2019

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Association between the MUC5B promoter polymorphism and survival in patients with idiopathic pulmonary fibrosis

JAMA : the journal of the American Medical Association, 2013-06, Vol.309 (21), p.2232

2013

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Integrative omics provide biological and clinical insights into acute respiratory distress syndrome

Intensive care medicine, 2021-07, Vol.47 (7), p.761-771

2021

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Targeting NOX4 alleviates sepsis-induced acute lung injury via attenuation of redox-sensitive activation of CaMKII/ERK1/2/MLCK and endothelial cell barrier dysfunction

Redox biology, 2020-09, Vol.36, p.101638-101638, Article 101638

2020

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Imatinib attenuates inflammation and vascular leak in a clinically relevant two-hit model of acute lung injury

American journal of physiology. Lung cellular and molecular physiology, 2015-12, Vol.309 (11), p.L1294-L1304

2015

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A guide to machine learning for biologists

Nontuberculous mycobacterial disease mortality in the United States, 1999-2010: a population-based comparative study

Deep learning extends de novo protein modelling coverage of genomes using iteratively predicted structural constraints

Differentiable simulation to develop molecular dynamics force fields for disordered proteins

Differentiable molecular simulation can learn all the parameters in a coarse-grained force field for proteins

Design of metalloproteins and novel protein folds using variational autoencoders

Commentary on Conde et al.: Evidence and gap map offer an important opportunity for dialogue and refinement of the gateway hypothesis controversy

Structure-based prediction of protein allostery

Magnetic Coupling in Colloidal Clusters for Hierarchical Self-Assembly

Development of a biomarker mortality risk model in acute respiratory distress syndrome

Involvement of eNAMPT/TLR4 inflammatory signaling in progression of non‐alcoholic fatty liver disease, steatohepatitis, and fibrosis

Asthma is Different in Women

A Razor's Edge: Vascular Responses to Acute Inflammatory Lung Injury/Acute Respiratory Distress Syndrome

Prediction of interresidue contacts with DeepMetaPSICOV in CASP13

A Variant in the Promoter of MUC5B and Idiopathic Pulmonary Fibrosis

NRF2 and Diabetes: The Good, the Bad, and the Complex

The Differing Roles of Flavins and Quinones in Extracellular Electron Transfer in Lactiplantibacillus plantarum

Novel Machine Learning Can Predict Acute Asthma Exacerbation

Tissue ACE phenotyping in lung cancer

Essential role for paxillin tyrosine phosphorylation in LPS-induced mitochondrial fission, ROS generation and lung endothelial barrier loss

Genomic and Genetic Approaches to Deciphering Acute Respiratory Distress Syndrome Risk and Mortality

Association between the MUC5B promoter polymorphism and survival in patients with idiopathic pulmonary fibrosis

Integrative omics provide biological and clinical insights into acute respiratory distress syndrome

Targeting NOX4 alleviates sepsis-induced acute lung injury via attenuation of redox-sensitive activation of CaMKII/ERK1/2/MLCK and endothelial cell barrier dysfunction

Imatinib attenuates inflammation and vascular leak in a clinically relevant two-hit model of acute lung injury

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