4.7 Article

PHONEMeS: Efficient Modeling of Signaling Networks Derived from Large-Scale Mass Spectrometry Data

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 Biochemistry & Molecular Biology

Dynamic 3D proteomes reveal protein functional alterations at high resolution in situ

Valentina Cappelletti et al.

Summary: The global protein structural readout based on limited proteolysis-mass spectrometry (LiP-MS) can detect functional alterations in biological processes with high resolution and coverage simultaneously and in situ. Analysis of structural barcodes can capture changes in enzyme activity, phosphorylation, protein aggregation, complex formation, and more.
Article Biochemistry & Molecular Biology

Causal integration of multi-omics data with prior knowledge to generate mechanistic hypotheses

Aurelien Dugourd et al.

Summary: COSMOS is a method that integrates multiple omics datasets to provide mechanistic hypotheses for experimental observations through network-level causal reasoning and activity estimation. When applied to a ccRCC dataset, COSMOS successfully captures relevant crosstalks within and between different omics layers.

MOLECULAR SYSTEMS BIOLOGY (2021)

Article Biochemical Research Methods

Bringing data from curated pathway resources to Cytoscape with OmniPath

Francesco Ceccarelli et al.

BIOINFORMATICS (2020)

Article Biotechnology & Applied Microbiology

The functional landscape of the human phosphoproteome

David Ochoa et al.

NATURE BIOTECHNOLOGY (2020)

Article Biochemical Research Methods

Converting networks to predictive logic models from perturbation signalling data with CellNOpt

Enio Gjerga et al.

BIOINFORMATICS (2020)

Article Biochemistry & Molecular Biology

Proteogenomic Analysis of Human Colon Cancer Reveals New Therapeutic Opportunities

Suhas Vasaikar et al.

Article Biochemistry & Molecular Biology

Elucidating essential kinases of endothelin signalling by logic modelling of phosphoproteomics data

Alexander Schafer et al.

MOLECULAR SYSTEMS BIOLOGY (2019)

Article Mathematical & Computational Biology

From expression footprints to causal pathways: contextualizing large signaling networks with CARNIVAL

Anika Liu et al.

NPJ SYSTEMS BIOLOGY AND APPLICATIONS (2019)

Review Biochemical Research Methods

Characterizing disease-associated changes in post-translational modifications by mass spectrometry

Camilla Thygesen et al.

EXPERT REVIEW OF PROTEOMICS (2018)

Article Biochemical Research Methods

Network inference reveals novel connections in pathways regulating growth and defense in the yeast salt response

Matthew E. MacGilvray et al.

PLOS COMPUTATIONAL BIOLOGY (2018)

Article Cell Biology

Synthesizing Signaling Pathways from Temporal Phosphoproteomic Data

Ali Sinan Koksal et al.

CELL REPORTS (2018)

Article Biochemical Research Methods

Benchmarking substrate-based kinase activity inference using phosphoproteomic data

Claudia Hernandez-Armenta et al.

BIOINFORMATICS (2017)

Letter Biochemical Research Methods

OmniPath: guidelines and gateway for literature-curated signaling pathway resources

Denes Turei et al.

NATURE METHODS (2016)

Article Biochemistry & Molecular Biology

Elucidation of Signaling Pathways from Large-Scale Phosphoproteomic Data Using Protein Interaction Networks

Jan Daniel Rudolph et al.

CELL SYSTEMS (2016)

Article Biochemistry & Molecular Biology

limma powers differential expression analyses for RNA-sequencing and microarray studies

Matthew E. Ritchie et al.

NUCLEIC ACIDS RESEARCH (2015)

Article Multidisciplinary Sciences

Empirical inference of circuitry and plasticity in a kinase signaling network

Edmund H. Wilkes et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)

Article Multidisciplinary Sciences

Large-scale models of signal propagation in human cells derived from discovery phosphoproteomic data

Camille D. A. Terfve et al.

NATURE COMMUNICATIONS (2015)

Article Biochemistry & Molecular Biology

Systematic discovery of in vivo phosphorylation networks

Rune Linding et al.