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Publications

-Publications at Yale-

 

2024

80.       Rosenberger G, Li W, Turunen M, He J, Subramaniam PS, Pampou S, Griffin AT, Karan C, Kerwin P, Murray D, Honig B, Liu Y*, Califano A*. Network-based elucidation of colon cancer drug resistance mechanisms by phosphoproteomic time-series analysis. Nature Communications 2024, 15: 3909. PMID: 38724493, DOI: 10.1038/s41467-024-47957-3.

79.       Gui Y, Fu H, Palanza Z, Tao J, Lin YH, Min W, Qiao Y, Bonin C, Hargis G, Wang Y, Yang P, Kreutzer DL, Wang Y, Liu Y, Yu Y, Liu Y, Zhou D. Fibroblast expression of transmembrane protein smoothened governs microenvironment characteristics after acute kidney injury. J Clin Invest 2024 PMID: 38713523, DOI: 10.1172/JCI165836.

78.       Ke S, Dang F, Wang L, Chen JY, Naik MT, Li W, Thavamani A, Kim N, Naik NM, Sui H, Tang W, Qiu C, Koikawa K, Batalini F, Stern Gatof E, Isaza DA, Patel JM, Wang X, Clohessy JG, Heng YJ, Lahav G, Liu Y, Gray NS, Zhou XZ, Wei W, Wulf GM, Lu KP. Reciprocal antagonism of PIN1-APC/C(CDH1) governs mitotic protein stability and cell cycle entry. Nature Communications 2024, 15: 3220. PMID: 38622115, DOI: 10.1038/s41467-024-47427-w.

77.      Hu Z, Chen PH, Li W, Krone M, Zheng S, Saarbach J, Velasco IU, Hines J, Liu Y, Crews CM. EGFR targeting PhosTACs as a dual inhibitory approach reveals differential downstream signaling. Science Advances 2024, 10: eadj7251. PMID: 38536914, DOI: 10.1126/sciadv.adj7251.

76.       Liu Q, Zhang J, Guo C, Wang M, Wang C, Yan Y, Sun L, Wang D, Zhang L, Yu H, Hou L, Wu C, Zhu Y, Jiang G, Zhu H, Zhou Y, Fang S, Zhang T, Hu L, Li J, Liu Y, Zhang H, Zhang B, Ding L, Robles AI, Rodriguez H, Gao D, Ji H, Zhou H, Zhang P. Proteogenomic characterization of small cell lung cancer identifies biological insights and subtype-specific therapeutic strategies.  Cell  2024 4;187(1):184-203.e28. doi: 10.1016/j.cell.2023.12.004. PMID: 38181741

75.      Liao X, Li W, Zhou H, Rajendran BK, Li A, Ren J, Luan Y, Calderwood DA, Turk B, Tang W*, Liu Y*, Wu D*,  The CUL5 E3 ligase complex negatively regulates central signaling pathways in CD8+ T cells.  Nature Communications 2024 19;15(1):603. doi: 10.1038/s41467-024-44885-0. PMID: 38242867

74.      Luan Y, Hu J, Wang Q, Wang X, Li W, Qu R, Yang C, Rajendran BK, Zhou H, Liu P, Zhang N, Shi Y, Liu Y*, Tang W*, Lu J*, Wu D*. Wnt5 controls splenic myelopoiesis and neutrophil functional ambivalency during DSS-induced colitis. Cell Reports 2024, 43: 113934. PMID: 38461416, DOI: 10.1016/j.celrep.2024.113934.

 

2023

73.     Huang X, Gan Z, Cui H, Lan T, Liu Y, Caron E, Shao W. The SysteMHC Atlas v2.0, an updated resource for mass spectrometry-based immunopeptidomics. Nucleic Acids Res 2023 PMID: 38000392, DOI: 10.1093/nar/gkad1068.

 

72.     Di Y, Li W, Salovska B, Ba Q, Hu Z, Wang S, Liu Y. A basic phosphoproteomic-DIA workflow integrating precise quantification of phosphosites in systems biology. Biophysics Reports 2023, 9: 82-98. PMID: 37753060, PMCID: PMC10518521, DOI: 10.52601/bpr.2023.230007.

71.      Gui Y, Palanza Z, Gupta PR, Li H, Pan Y, Wang Y, Hargis GR, Kreutzer DL, Wang Y, Bastacky SI, Liu Y, Liu S, Zhou D. Calponin 2 regulates ketogenesis to mitigate acute kidney injury. JCI Insight 2023 PMID: 37751293, DOI: 10.1172/jci.insight.170521.

70.       Reilly L, Lara E, Ramos D, Li Z, Pantazis CB, Stadler J, Santiana M, Roberts J, Faghri F, Hao Y, Nalls MA, Narayan P, Liu Y, Singleton AB, Cookson MR, Ward ME, Qi YA. A fully automated FAIMS-DIA mass spectrometry-based proteomic pipeline. Cell Rep Methods 2023, 100593. PMID: 37729920, DOI: 10.1016/j.crmeth.2023.100593.

69.       Girish V, Lakhani AA, Thompson SL, Scaduto CM, Brown LM, Hagenson RA, Sausville EL, Mendelson BE, Kandikuppa PK, Lukow DA, Yuan ML, Stevens EC, Lee SN, Schukken KM, Akalu SM, Vasudevan A, Zou C, Salovska B, Li W, Smith JC, Taylor AM, Martienssen RA, Liu Y, Sun R, Sheltzer JM. Oncogene-like addiction to aneuploidy in human cancers. Science 2023, eadg4521. PMID: 37410869, DOI: 10.1126/science.adg4521.

68.       Zhou W, Li W, Wang S, Salovska B, Hu Z, Tao B, Di Y, Punyamurtula U, Turk BE, Sessa WC, Liu Y. An optogenetic-phosphoproteomic study reveals dynamic Akt1 signaling profiles in endothelial cells. Nature Communications 2023, 14: 3803. PMID: 37365174, DOI: 10.1038/s41467-023-39514-1.

67.       Chen Y, Ge Y, Han X, Hao L, Huan T, Li L, Li L, Li W, Liang X, Lin Y, Liu X, Liu Y, Ma S, Peng J, Shou W, Sun L, Tao WA, Tian Y, Wang YK, Wang Y, Wu R, Wu S, Xia J, Yang Z, Zhang H, Zhang H, Zhao S, Weng N, Huang L. Meeting Report on the 2(nd) Chinese American Society for Mass Spectrometry (CASMS) Conference Advancing Biological and Pharmaceutical Mass Spectrometry. Mol Cell Proteomics 2023, 100559. PMID: 37105363, DOI: 10.1016/j.mcpro.2023.100559.

66.       Perez-Pepe M, Desotell A, Li H, Li W, Han B, Lin Q, Klein D, Liu Y, Goodarzi H, Alarcón C. 7SK methylation by METTL3 promotes transcriptional activity Science Advances 2023, 9: eade7500. PMID: 37163588, PMCID: PMC10171809, DOI: 10.1126/sciadv.ade7500.

65.       Salovska B, Liu Y. Post-translational modification and phenotype. Proteomics 2023 23(3-4):e2200535. doi: 10.1002/pmic.202200535.

64.       Salovska B, Gao  E, Müller-Dott S, Li  W, Cordon  CC, Wang S, Dugourd  A, Rosenberger  G, Saez-Rodriguez  J, Liu Y. Phosphoproteomic analysis of metformin signaling in colorectal cancer cells elucidates mechanism of action and potential therapeutic opportunities. Clinical and Translational Medicine 2023 Feb;13(2):e1179. doi: 10.1002/ctm2.1179.

63.       Hu  Z, Chen PH, Li W, Douglas  T, Hines J, Liu Y, Crews CM. Targeted Dephosphorylation of Tau by Phosphorylation Targeting Chimeras (PhosTACs) as a Therapeutic Modality.  J Am Chem Soc 2023 Feb 8. doi: 10.1021/jacs.2c11706.

2022

 

62.       Li W, Salovska B, Fornasiero  EF, Liu Y. Towards a hypothesis-free understanding of how Phosphorylation dynamically impacts protein turnover. Proteomics 2022 Nov 24;e2100387.
doi: 10.1002/pmic.202100387.

61.      Ma X, Dighe A, Maziarz J, Neumann E, Erkenbrack E, Hei Y, Liu Y, Suhail Y, Kshitiz, Pak I,  Levchenko A., Wagner GP. Evolution of higher mesenchymal CD44 expression in the human lineage: A gene linked to cancer malignancy. Evol Med Public Health 2022 Aug 30;10(1):447-462. doi: 10.1093/emph/eoac036.

 

60.       Ba Q, Hei Y, Dighe A, Li W, Maziarz J, Pak I, Wang S, Wagner GP, Liu Y. Proteotype coevolution and quantitative diversity across 11 mammalian species. Science Advances 2022 Sep 9;8(36):eabn0756. doi: 10.1126/sciadv.abn0756. Epub 2022 Sep 9. (IF=14.957)

59.    Cai W L, Chen JF,  Chen H, Wingrove E, Kurley SJ, Chan LH, Zhang M, Arnal-Estape A, Zhao M, Balabaki A, Li W, Yu X, Krop ED, Dou Y, Liu Y, Jin J, Westbrook TF, Nguyen DX, Yan Q. eLife 2022, 11.

2022 Aug 31;11:e78163. doi: 10.7554/eLife.78163.

 

2021

58. Jeong J., Shin J. , Li  W., Hong J., Lim  J., Hwang J., Chung J., Yan Q., Liu Y., Choi J., Wysolmerski J.  MAL2 mediates the formation of stable HER2 signaling complexes within lipid raft-rich membrane protrusions in breast cancer cells, Cell Reports 2021 Dec 28;37(13):110160.doi: 10.1016/j.celrep.2021.110160.

57. Liu Y. A peptidoform based proteomic strategy for studying functions of post-translational modifications, Proteomics 2021 Dec 8;e2100316. doi: 10.1002/pmic.202100316.

56. Yu C., Wang X., Li W., Liu Y., Huang L., Developing a Bimolecular Affinity Purification Strategy to Isolate 26S Proteasome Holocomplexes for Complex-Centric Proteomic Analysis, Analytical Chemistry 2021, 93, 39, 13407–13413

55. Gao E., Li W., Wu C., Shao W., Di Y., Liu Y., Data-independent Acquisition-based Proteome and Phosphoproteome Profiling across Six Melanoma Cell Lines Reveals Determinants of Proteotypes, Molecular Omics 2021 doi: 10.1039/d0mo00188k

54. Salovska B., Li W., Di Y., Liu Y., BoxCarmax: a high-selectivity data-independent acquisition mass spectrometry method for the analysis of protein turnover and complex samples, Analytical Chemistry https://doi.org/10.1021/acs.analchem.0c04293 (IF=8.008)

53. Pangou E., Bielska O., Guerber L., Schmucker S., Agote-Arán A., Ye T., Liao Y., Puig-Gamez M., Grandgirard E., Kleiss C., Liu Y., Compe E., Zhang Z, Aebersold R., Ricci R., Sumara I., A PKD-MFF signaling axis couples mitochondrial fission to mitotic progression, Cell Reports Volume 35, Issue 7, 109129 https://doi.org/10.1016/j.celrep.2021.109129

52. Zhou X., Li W., Liu Y., Amon A., Cross-compartment signal propagation in the mitotic exit network, Elife 2021 Jan 22;10: e63645. doi: 10.7554/eLife.63645.

51. Wu C.*, Ba Q*, Lu D. Li W., Salovska B., Hou P., Mueller T., Rosenberger G., Gao E., Di Y., Zhou H. Fornasiero E.F., Liu Y. Global and Site-Specific Effect of Phosphorylation on Protein Turnover. Developmental Cell  2021 Jan 11;56(1):111-124.e6. doi: 10.1016/j.devcel.2020.10.025.

(IF=13.417)

2020

50. Rosenberger G., Heusel M., Bludau I., Collins B., Martelli C. Williams E., Xue P., Liu Y., Aebersold R. Califano A. SECAT: Quantifying Protein Complex Dynamics across Cell States by Network-Centric Analysis of SEC-SWATH-MS Profiles. Cell Systems 2020 Volume 11, Issue 6, 16 December 2020, Pages 589-607.e8

49. Suzuki Y., Kuzina E., An SJ., Tome F., Mohanty J., Li W. , Lee S., Liu Y, Lax I., Schlessinger J. FGF23 contains two distinct high-affinity binding sites enabling bivalent interactions with α-Klotho.

Proc Natl Acad Sci U S A 2020 Nov 30;202018554. doi: 10.1073/pnas.2018554117.

 

48. Wang S., Li W., Hu L., Cheng J., Yang H., Liu Y. NAguideR: performing and prioritizing missing value imputations for consistent bottom-up proteomic analyses. Nucleic Acids Research 2020 doi:1093/nar/gkaa498 (IF=19.1160)

47. 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 2020, 16:e9170 https://doi.org/10.152/msb.20199170 (IF=13.068)

46. Gao X., Li Q., Liu Y., Zeng R. Multi-in-One: Multiple-proteases, One-hour-shot Strategy for Fast and High-coverage Phosphoproteomic Investigation.  Analytical Chemistry 2020 https://pubs.acs.org/doi/10.1021/acs.analchem.0c00906

45. Tsai T., Choi M., Banfai B, Liu Y., MacLean B., Dunkley T., Vitek O. Selection of features with consistent profiles improves relative protein quantification in mass spectrometry experiments. Molecular & Cellular Proteomics March 31, 2020, mcp.RA119.001792; https://doi.org/10.1074/mcp.RA119.001792

44. Poulos R., Hains P., Shah R., Lucas N., Xavier D., Manda S., Anees A., Koh J., Mahboob S., Wittman M., Williams S., Sykes E., Hecker M, Dausmann M., Wouters M., Ashman K., Yang J., Wild P., deFazio A.  Balleine R., Tully B., Aebersold R., Speed T., Liu Y, Reddel R, Robinson P., & Zhong Q. Strategies to enable large-scale proteomics for reproducible research. Nature Communications, 11, Article number: 3793 (2020)

https://www.nature.com/articles/s41467-020-17641-3

43. 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)

42. 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

41. 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.

 

40. 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.

39. 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) (IF=68.164)

38. Wang S, Cai Y, Cheng J, Li W, Liu Y#, Yang H#, motifeR: An Integrated Web Software for Identification and Visualization of Protein Posttranslational Modification Motifs. Proteomics 19 (23), 190024512019 (# co-corresponding author)

37. 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

 

36. 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

 

35. 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

 

34. 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

 

33. 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

 

32. 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.

 

31. 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

30. 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.

 

 

-Publications before Yale-

 

2017

 

29. 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 cells, Nature Communications, 2017 Oct. doi:10.1038/s41467-017-01422-6.

 

28. 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.

 

27. 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.

 

26. 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.

 

25. 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.

 

24. 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.

 

23. 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.

 

22. 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

 

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

 

20. 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.

 

19. Liu Y, Aebersold R (2016) The interdependence of transcript and protein abundance: new data-new complexities. Molecular systems biology 12: 856

 

18. 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)

 

17. 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

 

16. 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

 

15. 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

14. 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

 

13. 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

 

12. 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

 

11. 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

10. 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

 

9. 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

 

8. 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

 

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

 

 

Before 2013

 

6. 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

 

5. 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

 

4. 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

 

3. 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

2. 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

1. 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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