A high-stringency blueprint of the human proteome

S Adhikari, EC Nice, EW Deutsch, L Lane… - Nature …, 2020 - nature.com
Abstract The Human Proteome Organization (HUPO) launched the Human Proteome Project
(HPP) in 2010, creating an international framework for global collaboration, data sharing …

Subcellular proteomics

JA Christopher, C Stadler, CE Martin… - Nature Reviews …, 2021 - nature.com
The eukaryotic cell is compartmentalized into subcellular niches, including membrane-
bound and membrane-less organelles. Proteins localize to these niches to fulfil their …

OpenCell: Endogenous tagging for the cartography of human cellular organization

NH Cho, KC Cheveralls, AD Brunner, K Kim… - Science, 2022 - science.org
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 …

Avoiding a replication crisis in deep-learning-based bioimage analysis

RF Laine, I Arganda-Carreras, R Henriques… - Nature …, 2021 - nature.com
Deep learning algorithms are powerful tools for analyzing, restoring and transforming
bioimaging data. One promise of deep learning is parameter-free one-click image analysis …

The human protein atlas—spatial localization of the human proteome in health and disease

A Digre, C Lindskog - Protein Science, 2021 - Wiley Online Library
For a complete understanding of a system's processes and each protein's role in health and
disease, it is essential to study protein expression with a spatial resolution, as the exact …

A multi-scale map of cell structure fusing protein images and interactions

Y Qin, EL Huttlin, CF Winsnes, ML Gosztyla, L Wacheul… - Nature, 2021 - nature.com
The cell is a multi-scale structure with modular organization across at least four orders of
magnitude. Two central approaches for mapping this structure—protein fluorescent imaging …

Self-supervised deep learning encodes high-resolution features of protein subcellular localization

H Kobayashi, KC Cheveralls, MD Leonetti, LA Royer - Nature methods, 2022 - nature.com
Explaining the diversity and complexity of protein localization is essential to fully understand
cellular architecture. Here we present cytoself, a deep-learning approach for fully self …

A sandbox for prediction and integration of DNA, RNA, and proteins in single cells

MD Luecken, DB Burkhardt, R Cannoodt… - Thirty-fifth conference …, 2021 - openreview.net
The last decade has witnessed a technological arms race to encode the molecular states of
cells into DNA libraries, turning DNA sequencers into scalable single-cell microscopes …

Image-based cell phenotyping with deep learning

A Pratapa, M Doron, JC Caicedo - Current opinion in chemical biology, 2021 - Elsevier
A cell's phenotype is the culmination of several cellular processes through a complex
network of molecular interactions that ultimately result in a unique morphological signature …

Mapping the nucleolar proteome reveals a spatiotemporal organization related to intrinsic protein disorder

L Stenström, D Mahdessian, C Gnann… - Molecular Systems …, 2020 - embopress.org
The nucleolus is essential for ribosome biogenesis and is involved in many other cellular
functions. We performed a systematic spatiotemporal dissection of the human nucleolar …