- 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. [Epub ahead of print] 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)

- 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.

 


-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.

 

- 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.

 

- 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.

 

 

- 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.

 

 

- 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

 

 

- 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

 

 

- 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