Publications

biorxiv

- Wu C.*, Ba Q.*, Li W., Salovska B., Hou P., Mueller T., Rosenberger G.,  Gao E., Di. Y, Liu Y.

Global impact of phosphorylation on protein endurance. Biorxiv. 2020 doi: https://doi.org/10.1101/2020.03.12.989467

2020

- Salovska B., Zhu H.,  Gandhi T., Frank M., Li W., Rosenberger G., Wu C., Germain P.L., Zhou H., Hodny Z., Reiter L., Liu Y. Isoform‐resolved correlation analysis between mRNA abundance regulation and protein level degradation. Molecular Systems Biology 202016:e9170https://doi.org/10.152/msb.20199170

- Hausmann A, Russo G, Grossmann J, Zünd M, Schwank G, Aebersold R, Liu Y#, Sellin ME#, Hardt WD#. Germ-Free and Microbiota-Associated Mice yield Small Intestinal Epithelial Organoids with Equivalent and Robust Transcriptome/Proteome Expression Phenotypes. Cell Microbiol. 2020 Feb 18:e13191. doi: 10.1111/cmi.13191. (# co-corresponding author)

- Heusel M, Frank M, Köhler M, Amon S, Frommelt F, Rosenberger G, Bludau I, Aulakh S, Linder M, Liu Y, Collins B, et al. A global screen for assembly state changes of the mitotic proteome by SEC-SWATH-MS. Cell Systems 2020/02/05 https://www.sciencedirect.com/science/article/pii/S2405471220300016.

 

2019

- Mehnert M*, Li W*, Wu C, Salovska B, Liu Y. Combining Rapid Data Independent Acquisition and CRISPR Gene Deletion for Studying Potential Protein Functions: A Case of HMGN1. Proteomics. 2019 Mar 22;:e1800438. doi: 10.1002/pmic.201800438. PubMed PMID: 30901150.

 

- Li W, Chi H, Salovska B, Wu C, Sun L, Rosenberger G, Liu Y. Assessing the Relationship Between Mass Window Width and Retention Time Scheduling on Protein Coverage for Data-Independent Acquisition. J Am Soc Mass Spectrom. 2019 May 30;. doi: 10.1007/s13361-019-02243-1. [Epub ahead of print] PubMed PMID: 31147889.

 

- Liu Y#, Y. Mi, T. Mueller, S. Kreibich, E.G. Williams, A. Drogen, C. Borel, M.Frank, PL. Germain, I. Bludau, M. Mehnert, M. Seifert, M. Emmenlauer, I. Sorg, F. Bezrukov, F. Bena, H. Zhou, C. Dehio, G. Testa, J. Saez-Rodriguez, S.E. Antonarakis, W. Hardt & R. Aebersold, Multi-omic measurements of heterogeneity in HeLa cells across laboratories, Nature Biotechnology (2019) (# co-corresponding author)

 

- Gao Q, Zhu H, Dong L, Shi W, Chen R, Song Z, Huang C, Li J, Dong X, Zhou Y, Liu Q, Ma L, Wang X, Zhou J, Liu Y, Boja E, Robles AI, Ma W, Wang P, Li Y, Ding L, Wen B, Zhang B, Rodriguez H, Gao D, Zhou H, Fan J. Integrated Proteogenomic Characterization of HBV-Related Hepatocellular Carcinoma. Cell. (2019) 179(2):561-577

 

- McCool E, Chen D, Li W, Liu Y, Sun L. Capillary zone electrophoresis-tandem mass spectrometry with ultraviolet photodissociation (213 nm) for large-scale top–down proteomics, Analytical Methods (2019), 11, 2855-2861

 

- Bouchal P, Schubert OT, Faktor J, Capkova L, Imrichova H, Zoufalova K, Paralova V, Hrstka R, Liu Y, Ebhardt HA, Budinska E, Nenutil R, Aebersold R: Breast Cancer Classification Based on Proteotypes Obtained by SWATH Mass Spectrometry. Cell Reports. 2019 Jul 16. PMID: 31315058

 

- Shao W, Guo T, Toussaint NC, Xue P, Wagner U, Li L, Charmpi K, Zhu Y, Wu J, Buljan M, Sun R, Rutishauser D, Hermanns T, Fankhauser CD, Poyet C, Ljubicic J, Rupp N, Rüschoff JH, Zhong Q, Beyer A, Ji J, Collins BC, Liu Y, Rätsch G, Wild PJ, Aebersold R. Comparative analysis of mRNA and protein degradation in prostate tissues indicates high stability of proteins. Nature Communications, 2019 7;10(1):2524. doi: 10.1038/s41467-019-10513-5. PubMed PMID: 31175306.

 

 

 

 

2018

-B Yang*, H Wu*, PD Schnier*, Liu Y*, J Liu, N Wang, WF DeGrado, L Wang (2018), Proximity-enhanced SuFEx chemical cross-linker for specific and multitargeting cross-linking mass spectrometry, Proceedings of the National Academy of Sciences 115 (44), 11162-11167

 

-Forchelet D, Béguin S, Sajic T, Bararpour N, Pataky Z, Frias M, Grabherr S, Augsburger M,

 Liu Y, Charnley M, Déglon J, Aebersold R, Thomas A, Renaud P (2018), Separation of blood microsamples by exploiting sedimentation at the microscale, Scientific reports 20;8(1):14101. doi: 10.1038/s41598-018-32314-4.

 

-Ebhardt H, Root A, Liu Y, Gauthier NP, Sander C, Aebersold R (2018), Systems pharmacology using mass spectrometry identifies critical response nodes in prostate cancer, npj Systems Biology and Applications 2018 July 2 https://www.nature.com/articles/s41540-018-0064-1

-Sajic T*, Liu Y*, Arvaniti E, Surinova S, Sethi A, Huttenhain R, Williams EG, Schiess R, Blattmann P, Friedrich B, Omlin A, Gillessen S, Claassen M, Aebersold R (2018), Similarities and differences of blood N-glycoproteins in five solid carcinomas at localized clinical stage analyzed by SWATH-mass spectrometry, Cell Reports, 23(9):2819-2831.e5.

 

 

 

2017

-Liu Y, Borel C, Li L, Müller T, Williams EG., Germain PL, Buljan M, Sajic T, Boersema PJ, Shao W, Faini M, Testa G,  Beyer A, Antonarakis SE & Aebersold R (2017), Systematic proteome and proteostasis profiling in human Trisomy 21 fibroblast cellsNature Communications, 2017 Oct. doi:10.1038/s41467-017-01422-6.

 

- 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  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 ProteomeCell reports 20, 1229-1241.

 

- 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.

 

- 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. (2017) Multi-site assessment of quantitative and qualitative performance of SWATH mass spectrometry. Nature communications 8, 291.

 

- Rosenberger G, Bludau I, Schmitt U, Heusel M, Hunter CL, Liu Y, MacCoss MJ, MacLean BX, Nesvizhskii AI, Pedrioli PGA, Reiter L, Röst HL, Tate S, Ting YS, Collins BC, Aebersold R. (2017) Statistical control of peptide and protein error rates in large-scale targeted data-independent acquisition analyses. Nature methods 2017 Aug 21. doi: 10.1038/nmeth.4398.

 

- 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(5).

 

 

2016

 

- Liu Y*, Beyer A*, Aebersold R (2016) On the dependency of cellular protein levels on mRNA abundance. Cell 165: 535-550

(# co-corresponding author)

 

- 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

 

- 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.

(# co-corresponding author)

 

- 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.

 

 

2015

 

- 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

 

- 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
 

- 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.

 

 

2014

 

- 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
 

- 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

 

 

2013

 

- 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

 

- Gillet L, Liu Y, Ebhardt A, Aebersold, R (2013) Acquisition of protein signatures using SWATH-MS. Hospital Healthcare Europe HHE epub: 181-183

 

 

2012

 

- 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

 

- 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

 

 

Before 2012

 

- 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

 

- 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

 

- 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