☆ 4.7 Article

Gene set proximity analysis: expanding gene set enrichment analysis through learned geometric embeddings, with drug-repurposing applications in COVID-19

BIOINFORMATICS (2023)

相关参考文献

注意：仅列出部分参考文献，下载原文获取全部文献信息。

Article Biochemical Research Methods

Deep graph representations embed network information for robust disease marker identification

Omar Maddouri et al.

Summary: GCNCC is a graph convolutional network-based approach that can identify highly effective and robust network-based disease markers. By integrating gene expression data with protein interaction data, GCNCC learns reproducible markers with consistently accurate prediction performance across different diseases and platforms.

BIOINFORMATICS (2022)

添加到收藏夹

Article Biochemistry & Molecular Biology

Identification of Required Host Factors for SARS-CoV-2 Infection in Human Cells

Zharko Daniloski et al.

Summary: Researchers conducted a genome-scale CRISPR screen to identify host factors crucial for SARS-CoV-2 infection, highlighting genes related to ATPase proton pump, Retromer, and Commander complexes. Validating these gene targets through multiple methods, they found shared transcriptional changes in cholesterol biosynthesis when top-ranked genes were lost. Loss of RAB7A was shown to reduce viral entry by sequestering the ACE2 receptor inside cells, underscoring its importance early in the viral infection process.

CELL (2021)

添加到收藏夹

Article Biochemistry & Molecular Biology

Genome-wide CRISPR Screens Reveal Host Factors Critical for SARS-CoV-2 Infection

Jin Wei et al.

Summary: Identification of essential host genes for SARS-CoV-2 infection, including ACE2 and Cathepsin L, and the discovery of pro-viral genes and pathways specific to SARS lineage and pan-coronavirus provide potential therapeutic targets and insights into pathogenesis of COVID-19. Small-molecule antagonists of these gene products inhibited SARS-CoV-2 infection across species, highlighting their conserved role in susceptibility to highly pathogenic CoVs.

CELL (2021)

添加到收藏夹

Article Biochemistry & Molecular Biology

Genome-Scale Identification of SARS-CoV-2 and Pan-coronavirus Host Factor Networks

William M. Schneider et al.

Summary: The study revealed the host factors and pathways involved in SARS-CoV-2 and seasonal coronavirus infections, providing a rich resource for developing therapeutic strategies for future coronavirus pandemics.

CELL (2021)

添加到收藏夹

Article Endocrinology & Metabolism

Metformin use is associated with a reduced risk of mortality in patients with diabetes hospitalised for COVID-19

Jean-Daniel Lalau et al.

Summary: Prior metformin use is associated with a lower risk of death in patients with diabetes hospitalized for COVID-19, suggesting potential benefits of metformin in this population.

DIABETES & METABOLISM (2021)

添加到收藏夹

Article Biochemistry & Molecular Biology

The Gene Ontology resource: enriching a GOld mine

Seth Carbon et al.

Summary: The Gene Ontology Consortium has made advancements in the last two years, such as improving the GO-CAM annotation framework, increasing the number of annotations and annotated gene products, and reviewing older annotations for consistency.

NUCLEIC ACIDS RESEARCH (2021)

添加到收藏夹

Article Endocrinology & Metabolism

Metformin Use Is Associated With Reduced Mortality in a Diverse Population With COVID-19 and Diabetes

Andrew B. Crouse et al.

Summary: The study found that Black/African-Americans, obesity, hypertension, and diabetes were associated with higher likelihood of contracting COVID-19. Diabetes was also linked to a dramatic increase in COVID-19-related mortality, but the use of metformin showed a significant reduction in mortality for diabetic individuals with COVID-19.

FRONTIERS IN ENDOCRINOLOGY (2021)

添加到收藏夹

Correction Multidisciplinary Sciences

Learning interpretable cellular and gene signature embeddings from single-cell transcriptomic data (vol 12, 5261, 2021)

Yifan Zhao et al.

NATURE COMMUNICATIONS (2021)

添加到收藏夹

Article Chemistry, Multidisciplinary

Potent Noncovalent Inhibitors of the Main Protease of SARS-CoV-2 from Molecular Sculpting of the Drug Perampanel Guided by Free Energy Perturbation Calculations

Chun-Hui Zhang et al.

Summary: Starting from known drugs, the study redesigned perampanel into potent noncovalent inhibitors of SARS-CoV-2 main protease with ca. 20 nM IC50 values. Free-energy perturbation calculations and high-resolution X-ray crystal structures guided the design efforts and rapid development of effective analogues. Cell-based antiviral assays confirmed the potential of the compounds for COVID-19 treatment, highlighting the power of computational chemistry in drug discovery.

ACS CENTRAL SCIENCE (2021)

添加到收藏夹

Article Biochemical Research Methods

PIGNON: a protein-protein interaction-guided functional enrichment analysis for quantitative proteomics

Rachel Nadeau et al.

Summary: The PIGNON method is proposed for detecting differentially expressed functional annotations without assessing individual protein expression significance. PIGNON maps protein expression levels onto a protein-protein interaction network to detect functional annotations where proteins are differentially expressed and clustered. The results complement state-of-the-art functional enrichment analyses and highlight functional annotations missed by standard approaches.

BMC BIOINFORMATICS (2021)

添加到收藏夹

Article Respiratory System

Outcomes for hospitalized patients with idiopathic pulmonary fibrosis treated with antifibrotic medications

Bryan T. Kelly et al.

Summary: The study aimed to determine the effect of nintedanib and pirfenidone on mortality following respiratory-related hospitalizations. While antifibrotic medications did not directly improve mortality during hospitalization or at 30 days, ongoing treatment post-discharge was associated with improved long-term survival for patients with Idiopathic Pulmonary Fibrosis.

BMC PULMONARY MEDICINE (2021)

添加到收藏夹

Review Medicine, General & Internal

Metformin in Patients With COVID-19: A Systematic Review and Meta-Analysis

Yin Li et al.

Summary: Metformin use in COVID-19 patients was associated with a reduced risk of mortality and hospitalization, but not with intubation and deterioration. Randomized controlled trials are needed to confirm the findings.

FRONTIERS IN MEDICINE (2021)

添加到收藏夹

Article Biotechnology & Applied Microbiology

GeneWalk identifies relevant gene functions for a biological context using network representation learning

Robert Ietswaart et al.

Summary: GeneWalk introduces a new method that aims to identify individual genes and their relevant functions in high-throughput functional genomics experiments, by automatically assembling experiment-specific gene regulatory networks and using representation learning to quantify the similarity between genes and GO annotations. By performing gene- and condition-specific functional analysis, GeneWalk converts a list of genes into data-driven hypotheses.

GENOME BIOLOGY (2021)

添加到收藏夹

Article Biochemical Research Methods

Toward a gold standard for benchmarking gene set enrichment analysis

Ludwig Geistlinger et al.

Summary: Researchers developed a framework for assessing enrichment methods based on defined criteria, evaluated 10 major enrichment methods using a curated compendium of expression datasets, and provided practical recommendations for efficient interpretation of results when applying these methods.

BRIEFINGS IN BIOINFORMATICS (2021)

添加到收藏夹

Article Public, Environmental & Occupational Health

Metformin Treatment Was Associated with Decreased Mortality in COVID-19 Patients with Diabetes in a Retrospective Analysis

Pan Luo et al.

AMERICAN JOURNAL OF TROPICAL MEDICINE AND HYGIENE (2020)

添加到收藏夹

Review Genetics & Heredity

Gene Set Analysis: Challenges, Opportunities, and Future Research

Farhad Maleki et al.

FRONTIERS IN GENETICS (2020)

添加到收藏夹

Article Computer Science, Artificial Intelligence

Gaussian embedding for large-scale gene set analysis

Sheng Wang et al.

NATURE MACHINE INTELLIGENCE (2020)

添加到收藏夹

Review Genetics & Heredity

Cancer transcriptome profiling at the juncture of clinical translation

Marcin Cieslik et al.

NATURE REVIEWS GENETICS (2018)

添加到收藏夹

Review Genetics & Heredity

Discerning molecular interactions: A comprehensive review on biomolecular interaction databases and network analysis tools

Sravan Kumar Miryala et al.

GENE (2018)

添加到收藏夹

Article Mathematical & Computational Biology

GSAE: an autoencoder with embedded gene-set nodes for genomics functional characterization

Hung-I Harry Chen et al.

BMC SYSTEMS BIOLOGY (2018)

添加到收藏夹

Article Biochemistry & Molecular Biology

The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible

Damian Szklarczyk et al.

NUCLEIC ACIDS RESEARCH (2017)

添加到收藏夹

Article Biochemistry & Molecular Biology

KEGG: new perspectives on genomes, pathways, diseases and drugs

Minoru Kanehisa et al.

NUCLEIC ACIDS RESEARCH (2017)

添加到收藏夹

Article Biochemical Research Methods

STAMS: STRING-assisted module search for genome wide association studies and application to autism

Sara Hillenmeyer et al.

BIOINFORMATICS (2016)

添加到收藏夹

Article Biochemical Research Methods

Bioconductor's EnrichmentBrowser: seamless navigation through combined results of set- & network-based enrichment analysis

Ludwig Geistlinger et al.

BMC BIOINFORMATICS (2016)

添加到收藏夹

Review Genetics & Heredity

The statistical properties of gene-set analysis

Christiaan A. de Leeuw et al.

NATURE REVIEWS GENETICS (2016)

添加到收藏夹

Article Cardiac & Cardiovascular Systems

Effectiveness and Safety of Dabigatran, Rivaroxaban, and Apixaban Versus Warfarin in Nonvalvular Atrial Fibrillation

Xiaoxi Yao et al.

JOURNAL OF THE AMERICAN HEART ASSOCIATION (2016)

添加到收藏夹

Article Biochemical Research Methods

DSigDB: drug signatures database for gene set analysis

Minjae Yoo et al.

BIOINFORMATICS (2015)

添加到收藏夹

Article Health Care Sciences & Services

Optum Labs: Building A Novel Node In The Learning Health Care System

Paul J. Wallace et al.

HEALTH AFFAIRS (2014)

添加到收藏夹

Article Biochemical Research Methods

A gene signature based method for identifying subtypes and subtype-specific drivers in cancer with an application to medulloblastoma

Peikai Chen et al.

BMC BIOINFORMATICS (2013)

添加到收藏夹

Article Multidisciplinary Sciences

A Comparison of Gene Set Analysis Methods in Terms of Sensitivity, Prioritization and Specificity

Adi L. Tarca et al.

PLOS ONE (2013)

添加到收藏夹

Article Biochemical Research Methods

EnrichNet: network-based gene set enrichment analysis

Enrico Glaab et al.

BIOINFORMATICS (2012)

添加到收藏夹

Article Biochemical Research Methods

Down-weighting overlapping genes improves gene set analysis

Adi Laurentiu Tarca et al.

BMC BIOINFORMATICS (2012)

添加到收藏夹

Article Biochemistry & Molecular Biology

Camera: a competitive gene set test accounting for inter-gene correlation

Di Wu et al.

NUCLEIC ACIDS RESEARCH (2012)

添加到收藏夹

Article Multidisciplinary Sciences

Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation

Daniele Merico et al.

PLOS ONE (2010)

添加到收藏夹

Article Biochemical Research Methods

A novel signaling pathway impact analysis

Adi Laurentiu Tarca et al.

BIOINFORMATICS (2009)

添加到收藏夹

Article Biochemical Research Methods

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

Da Wei Huang et al.

NATURE PROTOCOLS (2009)

添加到收藏夹

Article Biochemical Research Methods

Analyzing gene expression data in terms of gene sets:: methodological issues

Jelle J. Goeman et al.

BIOINFORMATICS (2007)

添加到收藏夹

Article Multidisciplinary Sciences

Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles

A Subramanian et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)

添加到收藏夹

Article Biochemical Research Methods

GO::TermFinder - open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes

EI Boyle et al.

BIOINFORMATICS (2004)

添加到收藏夹

Article Genetics & Heredity

PGC-1α-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes

VK Mootha et al.

NATURE GENETICS (2003)

添加到收藏夹

© Peeref 2019-2024. All rights reserved.