Machine learning for integrating data in biology and medicine: Principles, practice, and opportunities
New technologies have enabled the investigation of biology and human health at an
unprecedented scale and in multiple dimensions. These dimensions include a myriad of …
unprecedented scale and in multiple dimensions. These dimensions include a myriad of …
Mass spectrometry‐based protein–protein interaction networks for the study of human diseases
AL Richards, M Eckhardt, NJ Krogan - Molecular systems biology, 2021 - embopress.org
A better understanding of the molecular mechanisms underlying disease is key for
expediting the development of novel therapeutic interventions. Disease mechanisms are …
expediting the development of novel therapeutic interventions. Disease mechanisms are …
OpenCell: Endogenous tagging for the cartography of human cellular organization
Elucidating the wiring diagram of the human cell is a central goal of the postgenomic era.
We combined genome engineering, confocal live-cell imaging, mass spectrometry, and data …
We combined genome engineering, confocal live-cell imaging, mass spectrometry, and data …
[HTML][HTML] Dual proteome-scale networks reveal cell-specific remodeling of the human interactome
Thousands of interactions assemble proteins into modules that impart spatial and functional
organization to the cellular proteome. Through affinity-purification mass spectrometry, we …
organization to the cellular proteome. Through affinity-purification mass spectrometry, we …
STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets
Proteins and their functional interactions form the backbone of the cellular machinery. Their
connectivity network needs to be considered for the full understanding of biological …
connectivity network needs to be considered for the full understanding of biological …
CORUM: the comprehensive resource of mammalian protein complexes—2019
M Giurgiu, J Reinhard, B Brauner… - Nucleic acids …, 2019 - academic.oup.com
CORUM is a database that provides a manually curated repository of experimentally
characterized protein complexes from mammalian organisms, mainly human (67%), mouse …
characterized protein complexes from mammalian organisms, mainly human (67%), mouse …
[HTML][HTML] High-density proximity mapping reveals the subcellular organization of mRNA-associated granules and bodies
JY Youn, WH Dunham, SJ Hong, JDR Knight… - Molecular cell, 2018 - cell.com
Summary mRNA processing, transport, translation, and ultimately degradation involve a
series of dedicated protein complexes that often assemble into large membraneless …
series of dedicated protein complexes that often assemble into large membraneless …
Massive mining of publicly available RNA-seq data from human and mouse
RNA sequencing (RNA-seq) is the leading technology for genome-wide transcript
quantification. However, publicly available RNA-seq data is currently provided mostly in raw …
quantification. However, publicly available RNA-seq data is currently provided mostly in raw …
Proteomic and interactomic insights into the molecular basis of cell functional diversity
I Bludau, R Aebersold - Nature Reviews Molecular Cell Biology, 2020 - nature.com
The ability of living systems to adapt to changing conditions originates from their capacity to
change their molecular constitution. This is achieved by multiple mechanisms that modulate …
change their molecular constitution. This is achieved by multiple mechanisms that modulate …
KEA3: improved kinase enrichment analysis via data integration
Phosphoproteomics and proteomics experiments capture a global snapshot of the cellular
signaling network, but these methods do not directly measure kinase state. Kinase …
signaling network, but these methods do not directly measure kinase state. Kinase …