ArticleProceedings of the National Academy of Sciences of the United States of America2018
The in silico human surfaceome.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 238 papers, 1 of them a synthesis that pooled it.
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Who cites it
238 citing papers in PubMed, 1 synthesis or guideline pooled it, 407 citations in OpenAlex.
- Generation of human islet cell type-specific identity genesets.Nature communications · 2022Pooled it
- Unbiased, systematic surfaceome profiling of Acute Leukemia to identify novel immunotherapy targets.bioRxiv : the preprint server for biology · 2026Article
- Antibody-drug conjugate engineering: from design to efficacy and safety.Signal transduction and targeted therapy · 2026Review
- Cell-type-specific surfaceome profiling of 100-500 isolated cells using a droplet-based Magnetic Affinity Purification System.Nature communications · 2026Article
- Deciphering the mechanisms of macrophage polarization through comprehensive analysis of cellular and cell-surface protein glycosylation.Nature communications · 2026Article
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- Photosensitizer proximity labeling captures the lipid and protein interactomes.Nature chemical biology · 2026Article
- Protocol for N-glycoproteomic enrichment of cancer cell-surface proteins in patient-derived xenografts.STAR protocols · 2026Article
- A Framework for Benchmarking Pathway Reconstruction Algorithms.bioRxiv : the preprint server for biology · 2026Article
- GPNMB-directed CAR T cell therapy against MiT/TFE-family fusion-driven solid tumors.Nature cancer · 2026Article
- Genetic screening identifies WNT5A/RYK as a determinant of extracellular vesicle fate.Science advances · 2026Article
- Proteomic Profiling Identifies CLDN3 as a Tumor-Selective Therapeutic Target in Small Cell Lung Cancer.bioRxiv : the preprint server for biology · 2026Article
- IMMUNIA: A Reasoning-Centered Framework for Immunoregulatory Surfaceome Discovery.ACS pharmacology & translational science · 2026Article
- Endocytic turnover of endothelial cell-membrane proteins as a driver of rat blood-brain barrier specialization and dysfunction.iScience · 2026Article
- Bioinformatic pipeline to identify potential therapeutic targets with subsequent isolation and characterization of novel human anti- DDR1 antibodies.Scientific reports · 2026Article
- Decoding the Apical-Basal Surfaceome of Colon Epithelial Cells via Side-Selective Biotinylation.Biomolecules · 2026Article
- Surfaceome Capture by Multiplex Biotinylation Enables Enhanced Identification of Cell Surface Proteins by Mass Spectrometry.Molecular & cellular proteomics : MCP · 2026Article
- Inverse expression of Ten3 and Lphn2 across the developing mouse brain suggests a global strategy for circuit assembly.Current biology : CB · 2026Article
- Ten3-Lphn2-mediated target selection across the extended hippocampal network demonstrates a repeated strategy for circuit assembly.Current biology : CB · 2026Article
- Article
178 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Cell-surface proteins are of great biomedical importance, as demonstrated by the fact that 66% of approved human drugs listed in the DrugBank database target a cell-surface protein. Despite this biomedical relevance, there has been no comprehensive assessment of the human surfaceome, and only a fraction of the predicted 5,000 human transmembrane proteins have been shown to be located at the plasma membrane. To enable analysis of the human surfaceome, we developed the surfaceome predictor SURFY, based on machine learning. As a training set, we used experimentally verified high-confidence cell-surface proteins from the Cell Surface Protein Atlas (CSPA) and trained a random forest classifier on 131 features per protein and, specifically, per topological domain. SURFY was used to predict a human surfaceome of 2,886 proteins with an accuracy of 93.5%, which shows excellent overlap with known cell-surface protein classes (i.e., receptors). In deposited mRNA data, we found that between 543 and 1,100 surfaceome genes were expressed in cancer cell lines and maximally 1,700 surfaceome genes were expressed in embryonic stem cells and derivative lines. Thus, the surfaceome diversity depends on cell type and appears to be more dynamic than the nonsurface proteome. To make the predicted surfaceome readily accessible to the research community, we provide visualization tools for intuitive interrogation (wlab.ethz.ch/surfaceome). The in silico surfaceome enables the filtering of data generated by multiomics screens and supports the elucidation of the surfaceome nanoscale organization.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.