Dr. Yansheng Liu

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Yansheng Liu

Dr. Yansheng Liu

ETH Zurich

Professur für Systembiologie

Dr. Yansheng Liu

HPT E 55

Auguste-Piccard-Hof 1

8093 Zürich


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Yansheng was born in 1982, Anhui Province China. He studied Biology at Beijing Forestry University for his Bachelor. Yansheng got his Master's degree and PhD (of Biomedical Sciences) in the Key Laboratory of Systems Biology at Shanghai Institute for Biological Sciences (SIBS), Chinese Academy of Sciences (CAS), where he worked in the field of biomarker discovery using mass spectrometry based proteomics.

Yansheng joined Prof. Ruedi Aebersold’s group in May 2011. His research includes the development of SWATH mass spectrometry (SWATH-MS) and its application in human plasma proteomics and N-linked glycoproteomics, for the purpose of systems biology studies and cancer biomarker discovery. The current research further involves in revealing the impact of genetics such as copy number variations (CNVs) at the translational and post-translational levels through human twin samples, rare genetic disease models, and human cancers.



  • Liu Y, Beyer A, Aebersold R (2016) On the dependency of cellular protein levels on mRNA abundance, Cell 2016. 165: 535-550
  • Rosenberger G*, Liu Y*, Rost HL, Ludwig C, Buil A, Bensimon A, Soste M, Spector TD, Dermitzakis ET, Collins BC, Malmstrom L, Aebersold, R. (2017) Inference and quantification of peptidoforms in large sample cohorts by SWATH-MS, Nature biotechnology 2017 Jun 12. doi: 10.1038/nbt.3908.
  • Liu Y, Gonzàlez-Porta M, Santos S, Brazma A, Marioni JC, Aebersold R, Venkitaraman AR, Wickramasinghe VO. (2017) Impact of Alternative Splicing on the Human Proteome. Cell reports 20, 1229-1241.
  • Collins B*, Hunter LC*, Liu Y*, Schilling B, Rosenberger G, Bader SL, Chan DW, Gibson BW, Gingras A, Held JM, Kurogi MH, Hou G, Krisp C, Larsen B, Lin L, Liu S, Molloy MP, Moritz RL, Ohtsuki S, Schlapbach R, Selevsek N, Thomas SN, Tzeng S, Zhang H, and Aebersold R, Multi-site assessment of quantitative and qualitative performance of SWATH mass spectrometry. Nature Communications in press.
  • Röst H, Liu Y, D'Agostino G, Zanella M, Navarro P, Rosenberger G, Collins B, Gillet L, Testa G, Malmstrom L, Aebersold R (2016) TRIC: an automated alignment strategy for reproducible protein quantification in targeted proteomics, Nature Methods doi: 10.1038/nmeth.3954.
  • Liu Y, Aebersold R (2016) The interdependence of transcript and protein abundance: new data-new complexities. Molecular systems biology 12: 856
  • Liu Y, Buil A, Collins BC, Gillet LC, Blum LC, Cheng LY, Vitek O, Mouritsen J, Lachance G, Spector TD, Dermitzakis ET, Aebersold R (2015) Quantitative variability of 342 plasma proteins in a human twin population. Molecular systems biology 11: 786
  • Liu Y, Chen J, Sethi A, Li QK, Chen L, Collins B, Gillet LC, Wollscheid B, Zhang H, Aebersold R (2014) Glycoproteomic analysis of prostate cancer tissues by SWATH mass spectrometry discovers N-acylethanolamine acid amidase and protein tyrosine kinase 7 as signatures for tumor aggressiveness. Molecular & cellular proteomics: MCP 13: 1753-1768
  • Tan SLW, Chadha S, Liu Y, Gabasova E, Perera D, Ahmed K, Constantinou S, Renaudin X, Lee M, Aebersold R, Venkitaraman AR (2017) A Class of Environmental and Endogenous Toxins Induces BRCA2 Haploinsufficiency and Genome Instability, Cell 169, 1105-1118 e15.
  • Liu Y, Huttenhain R, Surinova S, Gillet LC, Mouritsen J, Brunner R, Navarro P, Aebersold R (2013) Quantitative measurements of N-linked glycoproteins in human plasma by SWATH-MS. Proteomics 13: 1247-1256
  • Liu Y, Huttenhain R, Collins B, Aebersold R (2013) Mass spectrometric protein maps for biomarker discovery and clinical research. Expert review of molecular diagnostics 13: 811-825
  • Liu Y, Luo XY, Li QR, Li H, Li C, Ni H, Li RX, Wang R, Hu HC, Pan YJ, Chen HQ, Zeng R (2012) Shotgun and targeted proteomics reveal that pre-surgery serum levels of LRG1, SAA, and C4BP may refine prognosis of resected squamous cell lung cancer. Journal of molecular cell biology 4: 344-347
  • Liu Y, Luo X, Hu H, Wang R, Sun Y, Zeng R, Chen H (2012) Integrative proteomics and tissue microarray profiling indicate the association between overexpressed serum proteins and non-small cell lung cancer. PloS one 7: e51748
  • Liu Y, Li C, Xing Z, Yuan X, Wu Y, Xu M, Tu K, Li Q, Wu C, Zhao M, Zeng R (2010) Proteomic mining in the dysplastic liver of WHV/c-myc mice--insights and indicators for early hepatocarcinogenesis. The FEBS journal 277: 4039-4053
  • Luo X*, Liu Y*, Wang R, Hu H, Zeng R, Chen H (2011) A high-quality secretome of A549 cells aided the discovery of C4b-binding protein as a novel serum biomarker for non-small cell lung cancer. Journal of proteomics 74: 528-538
  • Li C*, Ruan HQ*, Liu Y*, Xu MJ, Dai J, Sheng QH, Tan YX, Yao ZZ, Wang HY, Wu JR, Zeng R (2012) Quantitative proteomics reveal up-regulated protein expression of the SET complex associated with hepatocellular carcinoma. Journal of proteome research 11: 871-885
  • Sajic T, Liu Y, Aebersold R (2015) Using data-independent, high-resolution mass spectrometry in protein biomarker research: perspectives and clinical applications. Proteomics Clinical applications 9: 307-321
  • Zhang Z, Meszaros G, He WT, Xu Y, de Fatima Magliarelli H, Mailly L, Mihlan M, Liu Y, Puig Gámez M, Goginashvili A, Pasquier A, Bielska O, Neven B, Quartier P, Aebersold R, Baumert TF, Georgel P, Han J, Ricci. R (2017).Protein kinase D at the Golgi controls NLRP3 inflammasome activation. The Journal of Experimental Medicine: JEM 2017 Jul 17. pii: jem.20162040. doi: 10.1084/jem.20162040.
  • Faktor J, Sucha R, Paralova V, Liu Y, Bouchal P. (2017) Comparison of targeted proteomics approaches for detecting and quantifying proteins derived from human cancer tissues, Proteomics 17.
  • Yu C, Gao J, Zhou Y, Chen X, Xiao R, Zheng J, Liu Y, Zhou H (2016) Deep Phosphoproteomic Measurements Pinpointing Drug Induced Protective Mechanisms in Neuronal Cells, Frontiers in Physiology 7, 635.
  • Zhong Q, Rüschoff J, Guo T, Gabrani M, Schüffler P, Rechsteiner M, Liu Y, Fuchs T, Rupp N, Fankhauser C, Buhmann J, Perner S, Poyet C, Blattner M, Soldini D, Moch H, Rubin M, Noske A, Rüschoff J, Haffner M, Jochum W, Wild P (2016) Image-based computational quantification and visualization of genetic alterations and tumour heterogeneity, Scientific Reports, 6: 24146.
  • Thomas SN, Harlan R, Chen J, Aiyetan P, Liu Y, Sokoll LJ, Aebersold R, Chan DW, Zhang H (2015) Multiplexed Targeted Mass Spectrometry-Based Assays for the Quantification of N-Linked Glycosite-Containing Peptides in Serum. Analytical chemistry 87: 10830-10838
  • Surinova S, Choi M, Tao S, Schuffler PJ, Chang CY, Clough T, Vyslouzil K, Khoylou M, Srovnal J, Liu Y, Matondo M, Huttenhain R, Weisser H, Buhmann JM, Hajduch M, Brenner H, Vitek O, Aebersold R (2015) Prediction of colorectal cancer diagnosis based on circulating plasma proteins. EMBO molecular medicine 7: 1166-1178
  • Cheng L, Liu Y, Chang C., Röst H, Aebersold R, Vitek O (2015) Statistical elimination of spectral features with large between-run variation enhances quantitative protein-level conclusions in experiments with data-independent spectral acquisition, BMC Bioinformatics 16 (Suppl 2), A4.
  • Rosenberger G, Koh CC, Guo T, Rost HL, Kouvonen P, Collins BC, Heusel M, Liu Y, Caron E, Vichalkovski A, Faini M, Schubert OT, Faridi P, Ebhardt HA, Matondo M, Lam H, Bader SL, Campbell DS, Deutsch EW, Moritz RL et al (2014) A repository of assays to quantify 10,000 human proteins by SWATH-MS. Scientific data 1: 140031
  • Gillet L, Liu Y, Ebhardt A, Aebersold, R (2013) Acquisition of protein signatures using SWATH-MS. Hospital Healthcare Europe HHE epub: 181-183
  • Li Y, Chi H, Wang LH, Wang HP, Fu Y, Yuan ZF, Li SJ, Liu Y, Sun RX, Zeng R, He SM (2010) Speeding up tandem mass spectrometry based database searching by peptide and spectrum indexing. Rapid communications in mass spectrometry 24: 807-814

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