Ruedi Aebersold - Publications

Affiliations: 
Systems biology ETH Zürich, Zürich, ZH, Switzerland 
Area:
Proteomics
Website:
http://en.wikipedia.org/wiki/Ruedi_Aebersold

468 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Schäfer A, Gjerga E, Welford RW, Renz I, Lehembre F, Groenen PM, Saez-Rodriguez J, Aebersold R, Gstaiger M. Elucidating essential kinases of endothelin signalling by logic modelling of phosphoproteomics data. Molecular Systems Biology. 15: e8828. PMID 31464372 DOI: 10.15252/msb.20198828  0.32
2019 Celis-Gutierrez J, Blattmann P, Zhai Y, Jarmuzynski N, Ruminski K, Grégoire C, Ounoughene Y, Fiore F, Aebersold R, Roncagalli R, Gstaiger M, Malissen B. Quantitative Interactomics in Primary T Cells Provides a Rationale for Concomitant PD-1 and BTLA Coinhibitor Blockade in Cancer Immunotherapy. Cell Reports. 27: 3315-3330.e7. PMID 31189114 DOI: 10.1016/j.celrep.2019.05.041  0.32
2019 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, ... ... Aebersold R, et al. Comparative analysis of mRNA and protein degradation in prostate tissues indicates high stability of proteins. Nature Communications. 10: 2524. PMID 31175306 DOI: 10.1038/s41467-019-10513-5  0.52
2019 Iacobucci C, Piotrowski C, Aebersold R, Amaral BC, Andrews PC, Bernfur K, Borchers CH, Brodie NI, Bruce JE, Cao Y, Chaignepain S, Chavez JD, Claverol S, Cox J, Davis TN, et al. The First Community-Wide, Comparative Cross-linking Mass Spectrometry Study. Analytical Chemistry. PMID 31045356 DOI: 10.1021/acs.analchem.9b00658  1
2019 Romanov N, Kuhn M, Aebersold R, Ori A, Beck M, Bork P. Disentangling Genetic and Environmental Effects on the Proteotypes of Individuals. Cell. PMID 31031010 DOI: 10.1016/j.cell.2019.03.015  0.56
2019 Gestaut D, Roh SH, Ma B, Pintilie G, Joachimiak LA, Leitner A, Walzthoeni T, Aebersold R, Chiu W, Frydman J. The Chaperonin TRiC/CCT Associates with Prefoldin through a Conserved Electrostatic Interface Essential for Cellular Proteostasis. Cell. PMID 30955883 DOI: 10.1016/j.cell.2019.03.012  0.36
2019 Liu Y, Mi Y, Mueller T, Kreibich S, Williams EG, Van Drogen A, Borel C, Frank M, Germain PL, Bludau I, Mehnert M, Seifert M, Emmenlauer M, Sorg I, Bezrukov F, ... ... Aebersold R, et al. Multi-omic measurements of heterogeneity in HeLa cells across laboratories. Nature Biotechnology. PMID 30778230 DOI: 10.1038/s41587-019-0037-y  0.4
2019 Wang P, Zuo Y, Sun J, Zuo T, Zhang S, Guo S, Shi X, Liang M, Zhou P, Zhang L, Wang X. Structural and functional definition of a vulnerable site on the hemagglutinin of highly pathogenic avian influenza A virus H5N1. The Journal of Biological Chemistry. PMID 30737282 DOI: 10.1074/jbc.RA118.007008  0.36
2019 Sendoel A, Subasic D, Ducoli L, Keller M, Michel E, Kohler I, Singh KD, Zheng X, Brümmer A, Imig J, Kishore S, Wu Y, Kanitz A, Kaech A, Mittal N, ... ... Aebersold R, et al. MINA-1 and WAGO-4 are part of regulatory network coordinating germ cell death and RNAi in C. elegans. Cell Death and Differentiation. PMID 30728462 DOI: 10.1038/s41418-019-0291-z  0.36
2019 Zhang X, Zhang S, Zhang L, Lu J, Zhao C, Luo F, Li D, Li X, Liu C. Heat shock protein 104 (HSP104) chaperones soluble Tau via a mechanism distinct from its disaggregase activity. The Journal of Biological Chemistry. PMID 30718279 DOI: 10.1074/jbc.RA118.005980  0.32
2019 Heusel M, Bludau I, Rosenberger G, Hafen R, Frank M, Banaei-Esfahani A, van Drogen A, Collins BC, Gstaiger M, Aebersold R. Complex-centric proteome profiling by SEC-SWATH-MS. Molecular Systems Biology. 15: e8438. PMID 30642884 DOI: 10.15252/msb.20188438  0.48
2018 Ludwig C, Gillet L, Rosenberger G, Amon S, Collins BC, Aebersold R. Data-independent acquisition-based SWATH-MS for quantitative proteomics: a tutorial. Molecular Systems Biology. 14: e8126. PMID 30104418  0.48
2018 Guo T, Li L, Zhong Q, Rupp NJ, Charmpi K, Wong CE, Wagner U, Rueschoff JH, Jochum W, Fankhauser CD, Saba K, Poyet C, Wild PJ, Aebersold R, Beyer A. Multi-region proteome analysis quantifies spatial heterogeneity of prostate tissue biomarkers. Life Science Alliance. 1. PMID 30090875 DOI: 10.26508/lsa.201800042  0.52
2018 Schuster H, Shao W, Weiss T, Pedrioli PGA, Roth P, Weller M, Campbell DS, Deutsch EW, Moritz RL, Planz O, Rammensee HG, Aebersold R, Caron E. A tissue-based draft map of the murine MHC class I immunopeptidome. Scientific Data. 5: 180157. PMID 30084848 DOI: 10.1038/sdata.2018.157  0.48
2018 Sajic T, Liu Y, Arvaniti E, Surinova S, Williams EG, Schiess R, Hüttenhain R, Sethi A, Pan S, Brentnall TA, Chen R, Blattmann P, Friedrich B, Niméus E, Malander S, ... ... Aebersold R, et al. Similarities and Differences of Blood N-Glycoproteins in Five Solid Carcinomas at Localized Clinical Stage Analyzed by SWATH-MS. Cell Reports. 23: 2819-2831.e5. PMID 29847809 DOI: 10.1016/j.celrep.2018.04.114  1
2018 Hülsmann J, Kravic B, Weith M, Gstaiger M, Aebersold RH, Collins BC, Meyer H. AP-SWATH reveals direct involvement of VCP/p97 in integrated stress response signaling through facilitating CReP/PPP1R15B degradation. Molecular & Cellular Proteomics : McP. PMID 29599191 DOI: 10.1074/mcp.RA117.000471  0.32
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. Systematic proteome and proteostasis profiling in human Trisomy 21 fibroblast cells. Nature Communications. 8: 1212. PMID 29089484 DOI: 10.1038/s41467-017-01422-6  0.52
2017 Shao W, Pedrioli PGA, Wolski W, Scurtescu C, Schmid E, Vizcaíno JA, Courcelles M, Schuster H, Kowalewski D, Marino F, Arlehamn CSL, Vaughan K, Peters B, Sette A, Ottenhoff THM, ... ... Aebersold R, et al. The SysteMHC Atlas project. Nucleic Acids Research. PMID 28985418 DOI: 10.1093/nar/gkx664  0.48
2017 Schwenk JM, Omenn GS, Sun Z, Campbell DS, Baker MS, Overall CM, Aebersold R, Moritz RL, Deutsch EW. The Human Plasma Proteome Draft of 2017: Building on the Human Plasma PeptideAtlas from Mass Spectrometry and Complementary Assays. Journal of Proteome Research. PMID 28938075 DOI: 10.1021/acs.jproteome.7b00467  0.48
2017 Collins BC, Hunter CL, Liu Y, Schilling B, Rosenberger G, Bader SL, Chan DW, Gibson BW, Gingras AC, Held JM, Hirayama-Kurogi M, Hou G, Krisp C, Larsen B, Lin L, ... ... Aebersold R, et al. Multi-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH-mass spectrometry. Nature Communications. 8: 291. PMID 28827567 DOI: 10.1038/s41467-017-00249-5  0.52
2017 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, et al. Statistical control of peptide and protein error rates in large-scale targeted data-independent acquisition analyses. Nature Methods. PMID 28825704 DOI: 10.1038/nmeth.4398  0.64
2017 Rosenberger G, Liu Y, Röst HL, Ludwig C, Buil A, Bensimon A, Soste M, Spector TD, Dermitzakis ET, Collins BC, Malmström L, Aebersold R. Inference and quantification of peptidoforms in large sample cohorts by SWATH-MS. Nature Biotechnology. PMID 28604659 DOI: 10.1038/nbt.3908  0.64
2017 Schubert OT, Röst HL, Collins BC, Rosenberger G, Aebersold R. Quantitative proteomics: challenges and opportunities in basic and applied research. Nature Protocols. 12: 1289-1294. PMID 28569762 DOI: 10.1038/nprot.2017.040  0.64
2017 Caron E, Roncagalli R, Hase T, Wolski WE, Choi M, Menoita MG, Durand S, García-Blesa A, Fierro-Monti I, Sajic T, Heusel M, Weiss T, Malissen M, Schlapbach R, Collins BC, ... ... Aebersold R, et al. Precise Temporal Profiling of Signaling Complexes in Primary Cells Using SWATH Mass Spectrometry. Cell Reports. 18: 3219-3226. PMID 28355572 DOI: 10.1016/j.celrep.2017.03.019  0.32
2017 Yadav L, Tamene F, Göös H, van Drogen A, Katainen R, Aebersold R, Gstaiger M, Varjosalo M. Systematic Analysis of Human Protein Phosphatase Interactions and Dynamics. Cell Systems. PMID 28330616 DOI: 10.1016/j.cels.2017.02.011  0.32
2017 Wang X, Cimermancic P, Yu C, Schweitzer A, Chopra N, Engel JL, Greenberg CH, Huszagh AS, Beck F, Sakata E, Yang Y, Novitsky EJ, Leitner A, Nanni P, Kahraman A, ... ... Aebersold R, et al. Molecular Details Underlying Dynamic Structures and Regulation of the Human 26S Proteasome. Molecular & Cellular Proteomics : McP. PMID 28292943 DOI: 10.1074/mcp.M116.065326  0.44
2017 Röst HL, Aebersold R, Schubert OT. Automated SWATH Data Analysis Using Targeted Extraction of Ion Chromatograms. Methods in Molecular Biology (Clifton, N.J.). 1550: 289-307. PMID 28188537 DOI: 10.1007/978-1-4939-6747-6_20  0.64
2017 Zolg DP, Wilhelm M, Schnatbaum K, Zerweck J, Knaute T, Delanghe B, Bailey DJ, Gessulat S, Ehrlich HC, Weininger M, Yu P, Schlegl J, Kramer K, Schmidt T, Kusebauch U, ... ... Aebersold R, et al. Building ProteomeTools based on a complete synthetic human proteome. Nature Methods. PMID 28135259 DOI: 10.1038/nmeth.4153  0.48
2016 Ciuffa R, Caron E, Leitner A, Uliana F, Gstaiger M, Aebersold R. Contribution of Mass Spectrometry-Based Proteomics to the Understanding of TNF-α Signaling. Journal of Proteome Research. PMID 27762135 DOI: 10.1021/acs.jproteome.6b00728  0.32
2016 Hauri S, Comoglio F, Seimiya M, Gerstung M, Glatter T, Hansen K, Aebersold R, Paro R, Gstaiger M, Beisel C. A High-Density Map for Navigating the Human Polycomb Complexome. Cell Reports. 17: 583-595. PMID 27705803 DOI: 10.1016/j.celrep.2016.08.096  0.32
2016 Navarro P, Kuharev J, Gillet LC, Bernhardt OM, MacLean B, Röst HL, Tate SA, Tsou CC, Reiter L, Distler U, Rosenberger G, Perez-Riverol Y, Nesvizhskii AI, Aebersold R, Tenzer S. A multicenter study benchmarks software tools for label-free proteome quantification. Nature Biotechnology. PMID 27701404 DOI: 10.1038/nbt.3685  0.64
2016 Okada H, Ebhardt HA, Vonesch SC, Aebersold R, Hafen E. Proteome-wide association studies identify biochemical modules associated with a wing-size phenotype in Drosophila melanogaster. Nature Communications. 7: 12649. PMID 27582081 DOI: 10.1038/ncomms12649  0.36
2016 Röst HL, Sachsenberg T, Aiche S, Bielow C, Weisser H, Aicheler F, Andreotti S, Ehrlich HC, Gutenbrunner P, Kenar E, Liang X, Nahnsen S, Nilse L, Pfeuffer J, Rosenberger G, ... ... Aebersold R, et al. OpenMS: a flexible open-source software platform for mass spectrometry data analysis. Nature Methods. 13: 741-748. PMID 27575624 DOI: 10.1038/nmeth.3959  0.64
2016 Van Eyk JE, Corrales FJ, Aebersold R, Cerciello F, Deutsch EW, Roncada P, Sanchez JC, Yamamoto T, Yang P, Zhang H, Omenn GS. Highlights of the Biology and Disease-driven Human Proteome Project, 2015-2016. Journal of Proteome Research. 15: 3979-3987. PMID 27573249 DOI: 10.1021/acs.jproteome.6b00444  0.48
2016 Aebersold R, Bensimon A, Collins BC, Ludwig C, Sabido E. Applications and Developments in Targeted Proteomics: From SRM to DIA/SWATH. Proteomics. 16: 2065-7. PMID 27542680 DOI: 10.1002/pmic.201600203  0.36
2016 Deutsch EW, Overall CM, Van Eyk JE, Baker MS, Paik YK, Weintraub ST, Lane L, Martens L, Vandenbrouck Y, Kusebauch U, Hancock WS, Hermjakob H, Aebersold R, Moritz RL, Omenn GS. Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 2.1. Journal of Proteome Research. 15: 3961-3970. PMID 27490519 DOI: 10.1021/acs.jproteome.6b00392  0.48
2016 Röst HL, Liu Y, D'Agostino G, Zanella M, Navarro P, Rosenberger G, Collins BC, Gillet L, Testa G, Malmström L, Aebersold R. TRIC: an automated alignment strategy for reproducible protein quantification in targeted proteomics. Nature Methods. PMID 27479329 DOI: 10.1038/nmeth.3954  0.64
2016 Kusebauch U, Campbell DS, Deutsch EW, Chu CS, Spicer DA, Brusniak MY, Slagel J, Sun Z, Stevens J, Grimes B, Shteynberg D, Hoopmann MR, Blattmann P, Ratushny AV, Rinner O, ... ... Aebersold R, et al. Human SRMAtlas: A Resource of Targeted Assays to Quantify the Complete Human Proteome. Cell. PMID 27453469 DOI: 10.1016/j.cell.2016.06.041  1
2016 Williams EG, Wu Y, Jha P, Dubuis S, Blattmann P, Argmann CA, Houten SM, Amariuta T, Wolski W, Zamboni N, Aebersold R, Auwerx J. Systems proteomics of liver mitochondria function. Science (New York, N.Y.). 352: aad0189. PMID 27284200 DOI: 10.1126/science.aad0189  1
2016 Groner AC, Cato L, de Tribolet-Hardy J, Bernasocchi T, Janouskova H, Melchers D, Houtman R, Cato AC, Tschopp P, Gu L, Corsinotti A, Zhong Q, Fankhauser C, Fritz C, Poyet C, ... ... Aebersold R, et al. TRIM24 Is an Oncogenic Transcriptional Activator in Prostate Cancer. Cancer Cell. PMID 27238081 DOI: 10.1016/j.ccell.2016.04.012  1
2016 Kim D, Setiaputra D, Jung T, Chung J, Leitner A, Yoon J, Aebersold R, Hebert H, Yip CK, Song JJ. Molecular Architecture of  Yeast Chromatin Assembly Factor 1. Scientific Reports. 6: 26702. PMID 27221973 DOI: 10.1038/srep26702  1
2016 Zhang H, Ryu D, Wu Y, Gariani K, Wang X, Luan P, D'Amico D, Ropelle ER, Lutolf MP, Aebersold R, Schoonjans K, Menzies KJ, Auwerx J. NAD+ repletion improves mitochondrial and stem cell function and enhances life span in mice. Science (New York, N.Y.). PMID 27127236 DOI: 10.1126/science.aaf2693  0.56
2016 Shao S, Guo T, Gross V, Lazarev A, Koh CC, Gillessen S, Joerger M, Jochum W, Aebersold R. Reproducible Tissue Homogenization and Protein Extraction for Quantitative Proteomics using MicroPestle-assisted Pressure Cycling Technology. Journal of Proteome Research. PMID 27098501 DOI: 10.1021/acs.jproteome.5b01136  1
2016 Mosadeghi R, Reichermeier KM, Winkler M, Schreiber A, Reitsma JM, Zhang Y, Stengel F, Cao J, Kim M, Sweredoski MJ, Hess S, Leitner A, Aebersold R, Peter M, Deshaies RJ, et al. Structural and kinetic analysis of the COP9-Signalosome activation and the cullin-RING ubiquitin ligase deneddylation cycle. Elife. 5. PMID 27031283 DOI: 10.7554/eLife.12102  1
2016 Vijayvargia R, Epand R, Leitner A, Jung TY, Shin B, Jung R, Lloret A, Singh Atwal R, Lee H, Lee JM, Aebersold R, Hebert H, Song JJ, Seong IS. Huntingtin's spherical solenoid structure enables polyglutamine tract-dependent modulation of its structure and function. Elife. 5. PMID 27003594 DOI: 10.7554/eLife.11184  1
2016 Liu Y, Aebersold R. The interdependence of transcript and protein abundance: new data-new complexities. Molecular Systems Biology. 12: 856. PMID 26792872 DOI: 10.15252/msb.20156720  1
2016 Mithoe SC, Ludwig C, Pel MJ, Cucinotta M, Casartelli A, Mbengue M, Sklenar J, Derbyshire P, Robatzek S, Pieterse CM, Aebersold R, Menke FL. Attenuation of pattern recognition receptor signaling is mediated by a MAP kinase kinase kinase. Embo Reports. PMID 26769563 DOI: 10.15252/embr.201540806  0.56
2016 Hoofnagle AN, Whiteaker JR, Carr SA, Kuhn E, Liu T, Massoni SA, Thomas SN, Townsend RR, Zimmerman LJ, Boja E, Chen J, Crimmins DL, Davies SR, Gao Y, Hiltke TR, ... ... Aebersold R, et al. Recommendations for the Generation, Quantification, Storage, and Handling of Peptides Used for Mass Spectrometry-Based Assays. Clinical Chemistry. 62: 48-69. PMID 26719571 DOI: 10.1373/clinchem.2015.250563  1
2016 Faridi P, Aebersold R, Caron E. A first dataset toward a standardized community-driven global mapping of the human immunopeptidome Data in Brief. 7: 201-205. DOI: 10.1016/j.dib.2016.02.016  1
2015 Greber BJ, Gerhardy S, Leitner A, Leibundgut M, Salem M, Boehringer D, Leulliot N, Aebersold R, Panse VG, Ban N. Insertion of the Biogenesis Factor Rei1 Probes the Ribosomal Tunnel during 60S Maturation. Cell. PMID 26709046 DOI: 10.1016/j.cell.2015.11.027  1
2015 Goh WW, Guo T, Aebersold R, Wong L. Quantitative proteomics signature profiling based on network contextualization. Biology Direct. 10: 71. PMID 26666224 DOI: 10.1186/s13062-015-0098-x  1
2015 Leitner A, Faini M, Stengel F, Aebersold R. Crosslinking and Mass Spectrometry: An Integrated Technology to Understand the Structure and Function of Molecular Machines. Trends in Biochemical Sciences. PMID 26654279 DOI: 10.1016/j.tibs.2015.10.008  1
2015 Schmidt A, Kochanowski K, Vedelaar S, Ahrné E, Volkmer B, Callipo L, Knoops K, Bauer M, Aebersold R, Heinemann M. The quantitative and condition-dependent Escherichia coli proteome. Nature Biotechnology. PMID 26641532 DOI: 10.1038/nbt.3418  1
2015 Schubert OT, Aebersold R. Microbial Proteome Profiling and Systems Biology: Applications to Mycobacterium tuberculosis. Advances in Experimental Medicine and Biology. 883: 235-54. PMID 26621471 DOI: 10.1007/978-3-319-23603-2_13  1
2015 Röst HL, Malmström L, Aebersold R. Reproducible quantitative proteotype data matrices for systems biology. Molecular Biology of the Cell. 26: 3926-31. PMID 26543201 DOI: 10.1091/mbc.E15-07-0507  1
2015 Walzthoeni T, Joachimiak LA, Rosenberger G, Röst HL, Malmström L, Leitner A, Frydman J, Aebersold R. xTract: software for characterizing conformational changes of protein complexes by quantitative cross-linking mass spectrometry. Nature Methods. PMID 26501516 DOI: 10.1038/nmeth.3631  1
2015 Ciferri C, Chandramouli S, Leitner A, Donnarumma D, Cianfrocco MA, Gerrein R, Friedrich K, Aggarwal Y, Palladino G, Aebersold R, Norais N, Settembre EC, Carfi A. Antigenic Characterization of the HCMV gH/gL/gO and Pentamer Cell Entry Complexes Reveals Binding Sites for Potently Neutralizing Human Antibodies. Plos Pathogens. 11: e1005230. PMID 26485028 DOI: 10.1371/journal.ppat.1005230  1
2015 Thomas S, Harlan R, Chen J, Aiyetan P, Liu Y, Sokoll LJ, Aebersold R, Chan DW, Zhang H. Multiplexed targeted mass spectrometry-based assays for the quantification of N-linked glycosite-containing peptides in serum. Analytical Chemistry. PMID 26451657 DOI: 10.1021/acs.analchem.5b02063  1
2015 Esterhuyse MM, Weiner J, Caron E, Loxton AG, Iannaccone M, Wagman C, Saikali P, Stanley K, Wolski WE, Mollenkopf HJ, Schick M, Aebersold R, Linhart H, Walzl G, Kaufmann SH. Epigenetics and Proteomics Join Transcriptomics in the Quest for Tuberculosis Biomarkers. Mbio. 6. PMID 26374119 DOI: 10.1128/mBio.01187-15  1
2015 Shao S, Guo T, Koh CC, Gillessen S, Joerger M, Jochum W, Aebersold R. Minimal sample requirement for highly multiplexed protein quantification in cell lines and tissues by PCT-SWATH mass spectrometry. Proteomics. PMID 26287124 DOI: 10.1002/pmic.201500161  1
2015 Chen L, Li J, Guo T, Ghosh S, Koh SK, Tian D, Zhang L, Jia D, Beuerman RW, Aebersold R, Chan EC, Zhou L. Global Metabonomic and Proteomic Analysis of Human Conjunctival Epithelial Cells (IOBA-NHC) in Response to Hyperosmotic Stress. Journal of Proteome Research. PMID 26260330 DOI: 10.1021/acs.jproteome.5b00443  0.56
2015 Surinova S, Choi M, Tao S, Schüffler PJ, Chang CY, Clough T, Vysloužil K, Khoylou M, Srovnal J, Liu Y, Matondo M, Hüttenhain R, Weisser H, Buhmann JM, Hajdúch M, ... ... Aebersold R, et al. Prediction of colorectal cancer diagnosis based on circulating plasma proteins. Embo Molecular Medicine. PMID 26253081 DOI: 10.15252/emmm.201404873  1
2015 Surinova S, Radová L, Choi M, Srovnal J, Brenner H, Vitek O, Hajdúch M, Aebersold R. Non-invasive prognostic protein biomarker signatures associated with colorectal cancer. Embo Molecular Medicine. 7: 1153-65. PMID 26253080 DOI: 10.15252/emmm.201404874  1
2015 Nillegoda NB, Kirstein J, Szlachcic A, Berynskyy M, Stank A, Stengel F, Arnsburg K, Gao X, Scior A, Aebersold R, Guilbride DL, Wade RC, Morimoto RI, Mayer MP, Bukau B. Crucial HSP70 co-chaperone complex unlocks metazoan protein disaggregation. Nature. 524: 247-51. PMID 26245380 DOI: 10.1038/nature14884  1
2015 Subasic D, Brümmer A, Wu Y, Pinto SM, Imig J, Keller M, Jovanovic M, Lightfoot HL, Nasso S, Götze S, Brunner E, Hall J, Aebersold R, Zavolan M, Hengartner M. Cooperative target mRNA destabilization and translation inhibition by miR-58 microRNA family in C. elegans. Genome Research. PMID 26232411 DOI: 10.1101/gr.183160.114  1
2015 Parker SJ, Rost H, Rosenberger G, Collins BC, Malmström L, Amodei D, Venkatraman V, Raedschelders K, Van Eyk JE, Aebersold R. Identification of a Set of Conserved Eukaryotic Internal Retention Time Standards for Data-independent Acquisition Mass Spectrometry. Molecular & Cellular Proteomics : McP. 14: 2800-13. PMID 26199342 DOI: 10.1074/mcp.O114.042267  0.64
2015 Caron E, Espona L, Kowalewski DJ, Schuster H, Ternette N, Alpízar A, Schittenhelm RB, Ramarathinam SH, Lindestam Arlehamn CS, Chiek Koh C, Gillet LC, Rabsteyn A, Navarro P, Kim S, Lam H, ... ... Aebersold R, et al. An open-source computational and data resource to analyze digital maps of immunopeptidomes. Elife. 4. PMID 26154972 DOI: 10.7554/eLife.07661  1
2015 Marcon E, Jain H, Bhattacharya A, Guo H, Phanse S, Pu S, Byram G, Collins BC, Dowdell E, Fenner M, Guo X, Hutchinson A, Kennedy JJ, Krastins B, Larsen B, ... ... Aebersold R, et al. Assessment of a method to characterize antibody selectivity and specificity for use in immunoprecipitation. Nature Methods. PMID 26121405 DOI: 10.1038/nmeth.3472  1
2015 Ebhardt HA, Root A, Sander C, Aebersold R. Applications of targeted proteomics in systems biology and translational medicine. Proteomics. PMID 26097198 DOI: 10.1002/pmic.201500004  1
2015 Schubert OT, Ludwig C, Kogadeeva M, Zimmermann M, Rosenberger G, Gengenbacher M, Gillet LC, Collins BC, Röst HL, Kaufmann SH, Sauer U, Aebersold R. Absolute Proteome Composition and Dynamics during Dormancy and Resuscitation of Mycobacterium tuberculosis. Cell Host & Microbe. 18: 96-108. PMID 26094805 DOI: 10.1016/j.chom.2015.06.001  1
2015 Hofmann A, Thiesler T, Gerrits B, Behnke S, Sobotzki N, Omasits U, Bausch-Fluck D, Bock T, Aebersold R, Moch H, Tinguely M, Wollscheid B. Surfaceome of classical Hodgkin and non-Hodgkin lymphoma. Proteomics. Clinical Applications. PMID 26076441 DOI: 10.1002/prca.201400146  0.56
2015 Sjöström M, Ossola R, Breslin T, Rinner O, Malmström L, Schmidt A, Aebersold R, Malmström J, Niméus E. A Combined Shotgun and Targeted Mass Spectrometry Strategy for Breast Cancer Biomarker Discovery. Journal of Proteome Research. PMID 25944384 DOI: 10.1021/acs.jproteome.5b00315  0.56
2015 Röst HL, Schmitt U, Aebersold R, Malmström L. Fast and Efficient XML Data Access for Next-Generation Mass Spectrometry. Plos One. 10: e0125108. PMID 25927999 DOI: 10.1371/journal.pone.0125108  0.56
2015 Oliveira AP, Ludwig C, Zampieri M, Weisser H, Aebersold R, Sauer U. Dynamic phosphoproteomics reveals TORC1-dependent regulation of yeast nucleotide and amino acid biosynthesis. Science Signaling. 8: rs4. PMID 25921291 DOI: 10.1126/scisignal.2005768  1
2015 Bausch-Fluck D, Hofmann A, Bock T, Frei AP, Cerciello F, Jacobs A, Moest H, Omasits U, Gundry RL, Yoon C, Schiess R, Schmidt A, Mirkowska P, Härtlová A, Van Eyk JE, ... ... Aebersold R, et al. A mass spectrometric-derived cell surface protein atlas. Plos One. 10: e0121314. PMID 25894527 DOI: 10.1371/journal.pone.0121314  0.44
2015 Oliveira AP, Dimopoulos S, Busetto AG, Christen S, Dechant R, Falter L, Haghir Chehreghani M, Jozefczuk S, Ludwig C, Rudroff F, Schulz JC, González A, Soulard A, Stracka D, Aebersold R, et al. Inferring causal metabolic signals that regulate the dynamic TORC1-dependent transcriptome. Molecular Systems Biology. 11: 802. PMID 25888284 DOI: 10.15252/msb.20145475  1
2015 Rispal D, Eltschinger S, Stahl M, Vaga S, Bodenmiller B, Abraham Y, Filipuzzi I, Movva NR, Aebersold R, Helliwell SB, Loewith R. Target of Rapamycin Complex 2 Regulates Actin Polarization and Endocytosis via Multiple Pathways. The Journal of Biological Chemistry. 290: 14963-78. PMID 25882841 DOI: 10.1074/jbc.M114.627794  1
2015 Greber BJ, Bieri P, Leibundgut M, Leitner A, Aebersold R, Boehringer D, Ban N. Ribosome. The complete structure of the 55S mammalian mitochondrial ribosome. Science (New York, N.Y.). 348: 303-8. PMID 25837512 DOI: 10.1126/science.aaa3872  1
2015 Röst HL, Rosenberger G, Aebersold R, Malmström L. Efficient visualization of high-throughput targeted proteomics experiments: TAPIR. Bioinformatics (Oxford, England). 31: 2415-7. PMID 25788625 DOI: 10.1093/bioinformatics/btv152  0.56
2015 Suni V, Imanishi SY, Maiolica A, Aebersold R, Corthals GL. Confident site localization using a simulated phosphopeptide spectral library. Journal of Proteome Research. 14: 2348-59. PMID 25774671 DOI: 10.1021/acs.jproteome.5b00050  1
2015 Guo T, Kouvonen P, Koh CC, Gillet LC, Wolski WE, Röst HL, Rosenberger G, Collins BC, Blum LC, Gillessen S, Joerger M, Jochum W, Aebersold R. Rapid mass spectrometric conversion of tissue biopsy samples into permanent quantitative digital proteome maps. Nature Medicine. 21: 407-13. PMID 25730263 DOI: 10.1038/nm.3807  1
2015 Schubert OT, Gillet LC, Collins BC, Navarro P, Rosenberger G, Wolski WE, Lam H, Amodei D, Mallick P, MacLean B, Aebersold R. Building high-quality assay libraries for targeted analysis of SWATH MS data. Nature Protocols. 10: 426-41. PMID 25675208 DOI: 10.1038/nprot.2015.015  1
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. Quantitative variability of 342 plasma proteins in a human twin population. Molecular Systems Biology. 11: 786. PMID 25652787 DOI: 10.15252/msb.20145728  1
2015 Gatti M, Pinato S, Maiolica A, Rocchio F, Prato MG, Aebersold R, Penengo L. RNF168 promotes noncanonical K27 ubiquitination to signal DNA damage. Cell Reports. 10: 226-38. PMID 25578731 DOI: 10.1016/j.celrep.2014.12.021  1
2015 Selevsek N, Chang CY, Gillet LC, Navarro P, Bernhardt OM, Reiter L, Cheng LY, Vitek O, Aebersold R. Reproducible and consistent quantification of the Saccharomyces cerevisiae proteome by SWATH-mass spectrometry. Molecular & Cellular Proteomics : McP. 14: 739-49. PMID 25561506 DOI: 10.1074/mcp.M113.035550  1
2015 Shao S, Guo T, Aebersold R. Mass spectrometry-based proteomic quest for diabetes biomarkers. Biochimica Et Biophysica Acta. 1854: 519-527. PMID 25556002 DOI: 10.1016/j.bbapap.2014.12.012  1
2015 Deroo S, Stengel F, Mohammadi A, Henry N, Hubin E, Krammer EM, Aebersold R, Raussens V. Chemical cross-linking/mass spectrometry maps the amyloid β peptide binding region on both apolipoprotein E domains. Acs Chemical Biology. 10: 1010-6. PMID 25546376 DOI: 10.1021/cb500994j  1
2015 Bouyssié D, Dubois M, Nasso S, Gonzalez de Peredo A, Burlet-Schiltz O, Aebersold R, Monsarrat B. mzDB: a file format using multiple indexing strategies for the efficient analysis of large LC-MS/MS and SWATH-MS data sets. Molecular & Cellular Proteomics : McP. 14: 771-81. PMID 25505153 DOI: 10.1074/mcp.O114.039115  1
2015 Sajic T, Liu Y, Aebersold R. Using data-independent, high-resolution mass spectrometry in protein biomarker research: perspectives and clinical applications. Proteomics. Clinical Applications. 9: 307-21. PMID 25504613 DOI: 10.1002/prca.201400117  1
2015 Lebert D, Louwagie M, Goetze S, Picard G, Ossola R, Duquesne C, Basler K, Ferro M, Rinner O, Aebersold R, Garin J, Mouz N, Brunner E, Brun V. DIGESTIF: a universal quality standard for the control of bottom-up proteomics experiments. Journal of Proteome Research. 14: 787-803. PMID 25495225 DOI: 10.1021/pr500834z  1
2015 Efremov RG, Leitner A, Aebersold R, Raunser S. Architecture and conformational switch mechanism of the ryanodine receptor. Nature. 517: 39-43. PMID 25470059 DOI: 10.1038/nature13916  1
2015 Kuilman T, Maiolica A, Godfrey M, Scheidel N, Aebersold R, Uhlmann F. Identification of Cdk targets that control cytokinesis. The Embo Journal. 34: 81-96. PMID 25371407 DOI: 10.15252/embj.201488958  1
2015 Heikkinen AT, Friedlein A, Matondo M, Hatley OJ, Petsalo A, Juvonen R, Galetin A, Rostami-Hodjegan A, Aebersold R, Lamerz J, Dunkley T, Cutler P, Parrott N. Quantitative ADME proteomics - CYP and UGT enzymes in the Beagle dog liver and intestine. Pharmaceutical Research. 32: 74-90. PMID 25033762 DOI: 10.1007/s11095-014-1446-8  1
2015 Caron E, Kowalewski DJ, Koh CC, Sturm T, Schuster H, Aebersold R. Analysis of major histocompatibility complex (MHC) immunopeptidomes using mass spectrometry Molecular and Cellular Proteomics. 14: 3105-3117. DOI: 10.1074/mcp.M0115.052431  1
2014 Erzberger JP, Stengel F, Pellarin R, Zhang S, Schaefer T, Aylett CHS, Cimermančič P, Boehringer D, Sali A, Aebersold R, Ban N. Molecular Architecture of the 40S⋅eIF1⋅eIF3 Translation Initiation Complex. Cell. 159: 1227-1228. PMID 28898626 DOI: 10.1016/j.cell.2014.11.001  0.36
2014 Gengenbacher M, Mouritsen J, Schubert OT, Aebersold R, Kaufmann SH. Mycobacterium tuberculosis in the Proteomics Era. Microbiology Spectrum. 2. PMID 26105825 DOI: 10.1128/microbiolspec.MGM2-0020-2013  1
2014 Rosenberger G, Koh CC, Guo T, Röst HL, Kouvonen P, Collins BC, Heusel M, Liu Y, Caron E, Vichalkovski A, Faini M, Schubert OT, Faridi P, Ebhardt HA, Matondo M, ... ... Aebersold R, et al. A repository of assays to quantify 10,000 human proteins by SWATH-MS. Scientific Data. 1: 140031. PMID 25977788 DOI: 10.1038/sdata.2014.31  1
2014 Vaga S, Bernardo-Faura M, Cokelaer T, Maiolica A, Barnes CA, Gillet LC, Hegemann B, van Drogen F, Sharifian H, Klipp E, Peter M, Saez-Rodriguez J, Aebersold R. Phosphoproteomic analyses reveal novel cross-modulation mechanisms between two signaling pathways in yeast. Molecular Systems Biology. 10: 767. PMID 25492886 DOI: 10.15252/msb.20145112  1
2014 Gubin MM, Zhang X, Schuster H, Caron E, Ward JP, Noguchi T, Ivanova Y, Hundal J, Arthur CD, Krebber WJ, Mulder GE, Toebes M, Vesely MD, Lam SS, Korman AJ, ... ... Aebersold R, et al. Checkpoint blockade cancer immunotherapy targets tumour-specific mutant antigens. Nature. 515: 577-81. PMID 25428507 DOI: 10.1038/nature13988  1
2014 Joachimiak LA, Walzthoeni T, Liu CW, Aebersold R, Frydman J. The structural basis of substrate recognition by the eukaryotic chaperonin TRiC/CCT. Cell. 159: 1042-55. PMID 25416944 DOI: 10.1016/j.cell.2014.10.042  1
2014 Huis in 't Veld PJ, Herzog F, Ladurner R, Davidson IF, Piric S, Kreidl E, Bhaskara V, Aebersold R, Peters JM. Characterization of a DNA exit gate in the human cohesin ring. Science (New York, N.Y.). 346: 968-72. PMID 25414306 DOI: 10.1126/science.1256904  1
2014 Ebhardt HA, Nan J, Chaulk SG, Fahlman RP, Aebersold R. Enzymatic generation of peptides flanked by basic amino acids to obtain MS/MS spectra with 2× sequence coverage. Rapid Communications in Mass Spectrometry : Rcm. 28: 2735-43. PMID 25380496 DOI: 10.1002/rcm.7069  1
2014 Greber BJ, Boehringer D, Leibundgut M, Bieri P, Leitner A, Schmitz N, Aebersold R, Ban N. The complete structure of the large subunit of the mammalian mitochondrial ribosome. Nature. 515: 283-6. PMID 25271403 DOI: 10.1038/nature13895  1
2014 Wu Y, Williams EG, Dubuis S, Mottis A, Jovaisaite V, Houten SM, Argmann CA, Faridi P, Wolski W, Kutalik Z, Zamboni N, Auwerx J, Aebersold R. Multilayered genetic and omics dissection of mitochondrial activity in a mouse reference population. Cell. 158: 1415-30. PMID 25215496 DOI: 10.1016/j.cell.2014.07.039  1
2014 Erzberger JP, Stengel F, Pellarin R, Zhang S, Schaefer T, Aylett CH, Cimermančič P, Boehringer D, Sali A, Aebersold R, Ban N. Molecular architecture of the 40Sâ‹…eIF1â‹…eIF3 translation initiation complex. Cell. 158: 1123-35. PMID 25171412 DOI: 10.1016/j.cell.2014.07.044  1
2014 Birol M, Enchev RI, Padilla A, Stengel F, Aebersold R, Betzi S, Yang Y, Hoh F, Peter M, Dumas C, Echalier A. Structural and biochemical characterization of the Cop9 signalosome CSN5/CSN6 heterodimer. Plos One. 9: e105688. PMID 25144743 DOI: 10.1371/journal.pone.0105688  1
2014 Greco V, Pieragostino D, Piras C, Aebersold R, Wiltfang J, Caltagirone C, Bernardini S, Urbani A. Direct analytical sample quality assessment for biomarker investigation: qualifying cerebrospinal fluid samples. Proteomics. 14: 1954-62. PMID 25044759 DOI: 10.1002/pmic.201300565  1
2014 Braun KA, Vaga S, Dombek KM, Fang F, Palmisano S, Aebersold R, Young ET. Phosphoproteomic analysis identifies proteins involved in transcription-coupled mRNA decay as targets of Snf1 signaling. Science Signaling. 7: ra64. PMID 25005228 DOI: 10.1126/scisignal.2005000  1
2014 Fengos G, Schmidt A, Martin K, Fluri E, Aebersold R, Iber D, Pertz O. Spatial proteomic and phospho-proteomic organization in three prototypical cell migration modes. Proteome Science. 12: 23. PMID 24987309 DOI: 10.1186/1477-5956-12-23  1
2014 Raijmakers R, Olsen JV, Aebersold R, Heck AJ. PRIME-XS, a European infrastructure for proteomics. Molecular & Cellular Proteomics : McP. 13: 1901-4. PMID 24958170 DOI: 10.1074/mcp.E114.040162  1
2014 Leitner A, Joachimiak LA, Unverdorben P, Walzthoeni T, Frydman J, Förster F, Aebersold R. Chemical cross-linking/mass spectrometry targeting acidic residues in proteins and protein complexes. Proceedings of the National Academy of Sciences of the United States of America. 111: 9455-60. PMID 24938783 DOI: 10.1073/pnas.1320298111  1
2014 Goldman A, Roy J, Bodenmiller B, Wanka S, Landry CR, Aebersold R, Cyert MS. The calcineurin signaling network evolves via conserved kinase-phosphatase modules that transcend substrate identity. Molecular Cell. 55: 422-35. PMID 24930733 DOI: 10.1016/j.molcel.2014.05.012  1
2014 Jünger MA, Aebersold R. Mass spectrometry-driven phosphoproteomics: patterning the systems biology mosaic. Wiley Interdisciplinary Reviews. Developmental Biology. 3: 83-112. PMID 24902836 DOI: 10.1002/wdev.121  1
2014 Walzer M, Pernas LE, Nasso S, Bittremieux W, Nahnsen S, Kelchtermans P, Pichler P, van den Toorn HW, Staes A, Vandenbussche J, Mazanek M, Taus T, Scheltema RA, Kelstrup CD, Gatto L, ... ... Aebersold R, et al. qcML: an exchange format for quality control metrics from mass spectrometry experiments. Molecular & Cellular Proteomics : McP. 13: 1905-13. PMID 24760958 DOI: 10.1074/mcp.M113.035907  1
2014 Rosenberger G, Ludwig C, Röst HL, Aebersold R, Malmström L. aLFQ: an R-package for estimating absolute protein quantities from label-free LC-MS/MS proteomics data. Bioinformatics (Oxford, England). 30: 2511-3. PMID 24753486 DOI: 10.1093/bioinformatics/btu200  1
2014 Liu Y, Chen J, Sethi A, Li QK, Chen L, Collins B, Gillet LC, Wollscheid B, Zhang H, Aebersold R. 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: 1753-68. PMID 24741114 DOI: 10.1074/mcp.M114.038273  1
2014 Röst HL, Rosenberger G, Navarro P, Gillet L, Miladinović SM, Schubert OT, Wolski W, Collins BC, Malmström J, Malmström L, Aebersold R. OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data. Nature Biotechnology. 32: 219-23. PMID 24727770 DOI: 10.1038/nbt.2841  1
2014 Toprak UH, Gillet LC, Maiolica A, Navarro P, Leitner A, Aebersold R. Conserved peptide fragmentation as a benchmarking tool for mass spectrometers and a discriminating feature for targeted proteomics. Molecular & Cellular Proteomics : McP. 13: 2056-71. PMID 24623587 DOI: 10.1074/mcp.O113.036475  1
2014 Aebersold R, Bader GD, Edwards AM, van Eyk J, Kussman M, Qin J, Omenn GS. Highlights of B/D-HPP and HPP Resource Pillar Workshops at 12th Annual HUPO World Congress of Proteomics: September 14-18, 2013, Yokohama, Japan. Proteomics. 14: 975-88. PMID 24596128 DOI: 10.1002/pmic.201400041  1
2014 Roncagalli R, Hauri S, Fiore F, Liang Y, Chen Z, Sansoni A, Kanduri K, Joly R, Malzac A, Lähdesmäki H, Lahesmaa R, Yamasaki S, Saito T, Malissen M, Aebersold R, et al. Quantitative proteomics analysis of signalosome dynamics in primary T cells identifies the surface receptor CD6 as a Lat adaptor-independent TCR signaling hub. Nature Immunology. 15: 384-92. PMID 24584089 DOI: 10.1038/ni.2843  1
2014 Politis A, Stengel F, Hall Z, Hernández H, Leitner A, Walzthoeni T, Robinson CV, Aebersold R. A mass spectrometry-based hybrid method for structural modeling of protein complexes. Nature Methods. 11: 403-6. PMID 24509631 DOI: 10.1038/nmeth.2841  1
2014 Carr SA, Abbatiello SE, Ackermann BL, Borchers C, Domon B, Deutsch EW, Grant RP, Hoofnagle AN, Hüttenhain R, Koomen JM, Liebler DC, Liu T, MacLean B, Mani DR, Mansfield E, ... ... Aebersold R, et al. Targeted peptide measurements in biology and medicine: best practices for mass spectrometry-based assay development using a fit-for-purpose approach. Molecular & Cellular Proteomics : McP. 13: 907-17. PMID 24443746 DOI: 10.1074/mcp.M113.036095  1
2014 Chang CY, Sabidó E, Aebersold R, Vitek O. Targeted protein quantification using sparse reference labeling. Nature Methods. 11: 301-4. PMID 24441934 DOI: 10.1038/nmeth.2806  1
2014 Papinski D, Schuschnig M, Reiter W, Wilhelm L, Barnes CA, Maiolica A, Hansmann I, Pfaffenwimmer T, Kijanska M, Stoffel I, Lee SS, Brezovich A, Lou JH, Turk BE, Aebersold R, et al. Early steps in autophagy depend on direct phosphorylation of Atg9 by the Atg1 kinase. Molecular Cell. 53: 471-83. PMID 24440502 DOI: 10.1016/j.molcel.2013.12.011  1
2014 Röst HL, Schmitt U, Aebersold R, Malmström L. pyOpenMS: a Python-based interface to the OpenMS mass-spectrometry algorithm library. Proteomics. 14: 74-7. PMID 24420968 DOI: 10.1002/pmic.201300246  1
2014 Greber BJ, Boehringer D, Leitner A, Bieri P, Voigts-Hoffmann F, Erzberger JP, Leibundgut M, Aebersold R, Ban N. Architecture of the large subunit of the mammalian mitochondrial ribosome. Nature. 505: 515-9. PMID 24362565 DOI: 10.1038/nature12890  1
2014 Leitner A, Walzthoeni T, Aebersold R. Lysine-specific chemical cross-linking of protein complexes and identification of cross-linking sites using LC-MS/MS and the xQuest/xProphet software pipeline. Nature Protocols. 9: 120-37. PMID 24356771 DOI: 10.1038/nprot.2013.168  1
2014 Kiel C, Ebhardt HA, Burnier J, Portugal C, Sabidó E, Zimmermann T, Aebersold R, Serrano L. Quantification of ErbB network proteins in three cell types using complementary approaches identifies cell-general and cell-type-specific signaling proteins. Journal of Proteome Research. 13: 300-13. PMID 24313378 DOI: 10.1021/pr400878x  1
2014 Gerster S, Kwon T, Ludwig C, Matondo M, Vogel C, Marcotte EM, Aebersold R, Bühlmann P. Statistical approach to protein quantification. Molecular & Cellular Proteomics : McP. 13: 666-77. PMID 24255132 DOI: 10.1074/mcp.M112.025445  1
2014 Vialas V, Sun Z, Loureiro y Penha CV, Carrascal M, Abián J, Monteoliva L, Deutsch EW, Aebersold R, Moritz RL, Gil C. A Candida albicans PeptideAtlas. Journal of Proteomics. 97: 62-8. PMID 23811049 DOI: 10.1016/j.jprot.2013.06.020  1
2014 Gaubitz C, Oliveira TM, Prouteau M, Leitner A, Karuppasamy M, Konstantinidou G, Rispal D, Eltschinger S, Robinson GC, Thore S, Aebersold R, Schaffitzel C, Loewith R. Molecular Basis of the Rapamycin Insensitivity of Target Of Rapamycin Complex 2 Molecular Cell. DOI: 10.1016/j.molcel.2015.04.031  1
2014 Quandt A, Espona L, Balasko A, Weisser H, Brusniak MY, Kunszt P, Aebersold R, Malmström L. Using synthetic peptides to benchmark peptide identification software and search parameters for MS/MS data analysis Eupa Open Proteomics. 5: 21-31. DOI: 10.1016/j.euprot.2014.10.001  1
2013 Hauri S, Wepf A, van Drogen A, Varjosalo M, Tapon N, Aebersold R, Gstaiger M. Interaction proteome of human Hippo signaling: modular control of the co-activator YAP1. Molecular Systems Biology. 9: 713. PMID 24366813 DOI: 10.1002/msb.201304750  1
2013 Hausser J, Syed AP, Selevsek N, van Nimwegen E, Jaskiewicz L, Aebersold R, Zavolan M. Timescales and bottlenecks in miRNA-dependent gene regulation. Molecular Systems Biology. 9: 711. PMID 24301800 DOI: 10.1038/msb.2013.68  1
2013 Cortes T, Schubert OT, Rose G, Arnvig KB, Comas I, Aebersold R, Young DB. Genome-wide mapping of transcriptional start sites defines an extensive leaderless transcriptome in Mycobacterium tuberculosis. Cell Reports. 5: 1121-31. PMID 24268774 DOI: 10.1016/j.celrep.2013.10.031  1
2013 Cerciello F, Choi M, Nicastri A, Bausch-Fluck D, Ziegler A, Vitek O, Felley-Bosco E, Stahel R, Aebersold R, Wollscheid B. Identification of a seven glycopeptide signature for malignant pleural mesothelioma in human serum by selected reaction monitoring. Clinical Proteomics. 10: 16. PMID 24207061 DOI: 10.1186/1559-0275-10-16  1
2013 Collins BC, Gillet LC, Rosenberger G, Röst HL, Vichalkovski A, Gstaiger M, Aebersold R. Quantifying protein interaction dynamics by SWATH mass spectrometry: application to the 14-3-3 system. Nature Methods. 10: 1246-53. PMID 24162925 DOI: 10.1038/nmeth.2703  1
2013 Lambert JP, Ivosev G, Couzens AL, Larsen B, Taipale M, Lin ZY, Zhong Q, Lindquist S, Vidal M, Aebersold R, Pawson T, Bonner R, Tate S, Gingras AC. Mapping differential interactomes by affinity purification coupled with data-independent mass spectrometry acquisition. Nature Methods. 10: 1239-45. PMID 24162924 DOI: 10.1038/nmeth.2702  1
2013 Liu Y, Hüttenhain R, Collins B, Aebersold R. Mass spectrometric protein maps for biomarker discovery and clinical research. Expert Review of Molecular Diagnostics. 13: 811-25. PMID 24138574 DOI: 10.1586/14737159.2013.845089  1
2013 Kahraman A, Herzog F, Leitner A, Rosenberger G, Aebersold R, Malmström L. Cross-link guided molecular modeling with ROSETTA. Plos One. 8: e73411. PMID 24069194 DOI: 10.1371/journal.pone.0073411  1
2013 Pfaff J, Hennig J, Herzog F, Aebersold R, Sattler M, Niessing D, Meister G. Structural features of Argonaute-GW182 protein interactions. Proceedings of the National Academy of Sciences of the United States of America. 110: E3770-9. PMID 24043833 DOI: 10.1073/pnas.1308510110  1
2013 Nguyen VQ, Ranjan A, Stengel F, Wei D, Aebersold R, Wu C, Leschziner AE. Molecular architecture of the ATP-dependent chromatin-remodeling complex SWR1. Cell. 154: 1220-31. PMID 24034246 DOI: 10.1016/j.cell.2013.08.018  1
2013 Tosi A, Haas C, Herzog F, Gilmozzi A, Berninghausen O, Ungewickell C, Gerhold CB, Lakomek K, Aebersold R, Beckmann R, Hopfner KP. Structure and subunit topology of the INO80 chromatin remodeler and its nucleosome complex. Cell. 154: 1207-19. PMID 24034245 DOI: 10.1016/j.cell.2013.08.016  1
2013 Mellacheruvu D, Wright Z, Couzens AL, Lambert JP, St-Denis NA, Li T, Miteva YV, Hauri S, Sardiu ME, Low TY, Halim VA, Bagshaw RD, Hubner NC, Al-Hakim A, Bouchard A, ... ... Aebersold R, et al. The CRAPome: a contaminant repository for affinity purification-mass spectrometry data. Nature Methods. 10: 730-6. PMID 23921808 DOI: 10.1038/nmeth.2557  1
2013 Surinova S, Hüttenhain R, Chang CY, Espona L, Vitek O, Aebersold R. Automated selected reaction monitoring data analysis workflow for large-scale targeted proteomic studies. Nature Protocols. 8: 1602-19. PMID 23887179 DOI: 10.1038/nprot.2013.091  1
2013 Sabidó E, Wu Y, Bautista L, Porstmann T, Chang CY, Vitek O, Stoffel M, Aebersold R. Targeted proteomics reveals strain-specific changes in the mouse insulin and central metabolic pathways after a sustained high-fat diet. Molecular Systems Biology. 9: 681. PMID 23860498 DOI: 10.1038/msb.2013.36  1
2013 Leitner A, Aebersold R. SnapShot: mass spectrometry for protein and proteome analyses. Cell. 154: 252-252.e1. PMID 23827686 DOI: 10.1016/j.cell.2013.06.025  1
2013 Aebersold R, Burlingame AL, Bradshaw RA. Western blots versus selected reaction monitoring assays: time to turn the tables? Molecular & Cellular Proteomics : McP. 12: 2381-2. PMID 23756428 DOI: 10.1074/mcp.E113.031658  1
2013 Schubert OT, Mouritsen J, Ludwig C, Röst HL, Rosenberger G, Arthur PK, Claassen M, Campbell DS, Sun Z, Farrah T, Gengenbacher M, Maiolica A, Kaufmann SH, Moritz RL, Aebersold R. The Mtb proteome library: a resource of assays to quantify the complete proteome of Mycobacterium tuberculosis. Cell Host & Microbe. 13: 602-12. PMID 23684311 DOI: 10.1016/j.chom.2013.04.008  1
2013 Varjosalo M, Keskitalo S, Van Drogen A, Nurkkala H, Vichalkovski A, Aebersold R, Gstaiger M. The protein interaction landscape of the human CMGC kinase group. Cell Reports. 3: 1306-20. PMID 23602568 DOI: 10.1016/j.celrep.2013.03.027  1
2013 Templeton AJ, Dutoit V, Cathomas R, Rothermundt C, Bärtschi D, Dröge C, Gautschi O, Borner M, Fechter E, Stenner F, Winterhalder R, Müller B, Schiess R, Wild PJ, Rüschoff JH, ... ... Aebersold R, et al. Phase 2 trial of single-agent everolimus in chemotherapy-naive patients with castration-resistant prostate cancer (SAKK 08/08). European Urology. 64: 150-8. PMID 23582881 DOI: 10.1016/j.eururo.2013.03.040  1
2013 Zampar GG, Kümmel A, Ewald J, Jol S, Niebel B, Picotti P, Aebersold R, Sauer U, Zamboni N, Heinemann M. Temporal system-level organization of the switch from glycolytic to gluconeogenic operation in yeast. Molecular Systems Biology. 9: 651. PMID 23549479 DOI: 10.1038/msb.2013.11  1
2013 Gstaiger M, Aebersold R. Genotype-phenotype relationships in light of a modular protein interaction landscape. Molecular Biosystems. 9: 1064-7. PMID 23529396 DOI: 10.1039/c3mb25583b  1
2013 Walzthoeni T, Leitner A, Stengel F, Aebersold R. Mass spectrometry supported determination of protein complex structure. Current Opinion in Structural Biology. 23: 252-60. PMID 23522702 DOI: 10.1016/j.sbi.2013.02.008  1
2013 Gunaratne J, Schmidt A, Quandt A, Neo SP, Saraç OS, Gracia T, Loguercio S, Ahrné E, Xia RL, Tan KH, Lössner C, Bähler J, Beyer A, Blackstock W, Aebersold R. Extensive mass spectrometry-based analysis of the fission yeast proteome: the Schizosaccharomyces pombe PeptideAtlas. Molecular & Cellular Proteomics : McP. 12: 1741-51. PMID 23462206 DOI: 10.1074/mcp.M112.023754  1
2013 Varjosalo M, Sacco R, Stukalov A, van Drogen A, Planyavsky M, Hauri S, Aebersold R, Bennett KL, Colinge J, Gstaiger M, Superti-Furga G. Interlaboratory reproducibility of large-scale human protein-complex analysis by standardized AP-MS. Nature Methods. 10: 307-14. PMID 23455922 DOI: 10.1038/nmeth.2400  1
2013 Stützer I, Selevsek N, Esterházy D, Schmidt A, Aebersold R, Stoffel M. Systematic proteomic analysis identifies β-site amyloid precursor protein cleaving enzyme 2 and 1 (BACE2 and BACE1) substrates in pancreatic β-cells. The Journal of Biological Chemistry. 288: 10536-47. PMID 23430253 DOI: 10.1074/jbc.M112.444703  1
2013 von Meyenn F, Porstmann T, Gasser E, Selevsek N, Schmidt A, Aebersold R, Stoffel M. Glucagon-induced acetylation of Foxa2 regulates hepatic lipid metabolism. Cell Metabolism. 17: 436-47. PMID 23416070 DOI: 10.1016/j.cmet.2013.01.014  1
2013 Wippich F, Bodenmiller B, Trajkovska MG, Wanka S, Aebersold R, Pelkmans L. Dual specificity kinase DYRK3 couples stress granule condensation/dissolution to mTORC1 signaling. Cell. 152: 791-805. PMID 23415227 DOI: 10.1016/j.cell.2013.01.033  1
2013 Hüttenhain R, Surinova S, Ossola R, Sun Z, Campbell D, Cerciello F, Schiess R, Bausch-Fluck D, Rosenberger G, Chen J, Rinner O, Kusebauch U, Hajdúch M, Moritz RL, Wollscheid B, ... Aebersold R, et al. N-glycoprotein SRMAtlas: a resource of mass spectrometric assays for N-glycosites enabling consistent and multiplexed protein quantification for clinical applications. Molecular & Cellular Proteomics : McP. 12: 1005-16. PMID 23408683 DOI: 10.1074/mcp.O112.026617  1
2013 Berti M, Ray Chaudhuri A, Thangavel S, Gomathinayagam S, Kenig S, Vujanovic M, Odreman F, Glatter T, Graziano S, Mendoza-Maldonado R, Marino F, Lucic B, Biasin V, Gstaiger M, Aebersold R, et al. Human RECQ1 promotes restart of replication forks reversed by DNA topoisomerase I inhibition. Nature Structural & Molecular Biology. 20: 347-54. PMID 23396353 DOI: 10.1038/nsmb.2501  1
2013 Weisser H, Nahnsen S, Grossmann J, Nilse L, Quandt A, Brauer H, Sturm M, Kenar E, Kohlbacher O, Aebersold R, Malmström L. An automated pipeline for high-throughput label-free quantitative proteomics. Journal of Proteome Research. 12: 1628-44. PMID 23391308 DOI: 10.1021/pr300992u  1
2013 Mirzaei H, Knijnenburg TA, Kim B, Robinson M, Picotti P, Carter GW, Li S, Dilworth DJ, Eng JK, Aitchison JD, Shmulevich I, Galitski T, Aebersold R, Ranish J. Systematic measurement of transcription factor-DNA interactions by targeted mass spectrometry identifies candidate gene regulatory proteins. Proceedings of the National Academy of Sciences of the United States of America. 110: 3645-50. PMID 23388641 DOI: 10.1073/pnas.1216918110  1
2013 Picotti P, Clément-Ziza M, Lam H, Campbell DS, Schmidt A, Deutsch EW, Röst H, Sun Z, Rinner O, Reiter L, Shen Q, Michaelson JJ, Frei A, Alberti S, Kusebauch U, ... ... Aebersold R, et al. A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis. Nature. 494: 266-70. PMID 23334424 DOI: 10.1038/nature11835  1
2013 Liu Y, Hüttenhain R, Surinova S, Gillet LC, Mouritsen J, Brunner R, Navarro P, Aebersold R. Quantitative measurements of N-linked glycoproteins in human plasma by SWATH-MS. Proteomics. 13: 1247-56. PMID 23322582 DOI: 10.1002/pmic.201200417  1
2013 Wong CC, Cociorva D, Miller CA, Schmidt A, Monell C, Aebersold R, Yates JR. Proteomics of Pyrococcus furiosus (Pfu): Identification of Extracted Proteins by Three Independent Methods. Journal of Proteome Research. 12: 763-70. PMID 23298259 DOI: 10.1021/pr300840j  1
2013 Bontron S, Jaquenoud M, Vaga S, Talarek N, Bodenmiller B, Aebersold R, De Virgilio C. Yeast endosulfines control entry into quiescence and chronological life span by inhibiting protein phosphatase 2A. Cell Reports. 3: 16-22. PMID 23273919 DOI: 10.1016/j.celrep.2012.11.025  1
2013 Picotti P, Bodenmiller B, Aebersold R. Proteomics meets the scientific method. Nature Methods. 10: 24-7. PMID 23269373 DOI: 10.1038/nmeth.2291  1
2012 Karlsson C, Malmström L, Aebersold R, Malmström J. Proteome-wide selected reaction monitoring assays for the human pathogen Streptococcus pyogenes. Nature Communications. 3: 1301. PMID 23250431 DOI: 10.1038/ncomms2297  1
2012 Clough T, Thaminy S, Ragg S, Aebersold R, Vitek O. Statistical protein quantification and significance analysis in label-free LC-MS experiments with complex designs. Bmc Bioinformatics. 13: S6. PMID 23176351 DOI: 10.1186/1471-2105-13-S16-S6  1
2012 Oliveira AP, Ludwig C, Picotti P, Kogadeeva M, Aebersold R, Sauer U. Regulation of yeast central metabolism by enzyme phosphorylation. Molecular Systems Biology. 8: 623. PMID 23149688 DOI: 10.1038/msb.2012.55  1
2012 Wu CC, Herzog F, Jennebach S, Lin YC, Pai CY, Aebersold R, Cramer P, Chen HT. RNA polymerase III subunit architecture and implications for open promoter complex formation. Proceedings of the National Academy of Sciences of the United States of America. 109: 19232-7. PMID 23132938 DOI: 10.1073/pnas.1211665109  1
2012 Ciferri C, Lander GC, Maiolica A, Herzog F, Aebersold R, Nogales E. Molecular architecture of human polycomb repressive complex 2. Elife. 1: e00005. PMID 23110252 DOI: 10.7554/eLife.00005  1
2012 Marguerat S, Schmidt A, Codlin S, Chen W, Aebersold R, Bähler J. Quantitative analysis of fission yeast transcriptomes and proteomes in proliferating and quiescent cells. Cell. 151: 671-83. PMID 23101633 DOI: 10.1016/j.cell.2012.09.019  1
2012 Glatter T, Ludwig C, Ahrné E, Aebersold R, Heck AJ, Schmidt A. Large-scale quantitative assessment of different in-solution protein digestion protocols reveals superior cleavage efficiency of tandem Lys-C/trypsin proteolysis over trypsin digestion. Journal of Proteome Research. 11: 5145-56. PMID 23017020 DOI: 10.1021/pr300273g  1
2012 Herzog F, Kahraman A, Boehringer D, Mak R, Bracher A, Walzthoeni T, Leitner A, Beck M, Hartl FU, Ban N, Malmström L, Aebersold R. Structural probing of a protein phosphatase 2A network by chemical cross-linking and mass spectrometry. Science (New York, N.Y.). 337: 1348-52. PMID 22984071 DOI: 10.1126/science.1221483  1
2012 Frei AP, Jeon OY, Kilcher S, Moest H, Henning LM, Jost C, Plückthun A, Mercer J, Aebersold R, Carreira EM, Wollscheid B. Direct identification of ligand-receptor interactions on living cells and tissues. Nature Biotechnology. 30: 997-1001. PMID 22983091 DOI: 10.1038/nbt.2354  1
2012 Bock T, Moest H, Omasits U, Dolski S, Lundberg E, Frei A, Hofmann A, Bausch-Fluck D, Jacobs A, Krayenbuehl N, Uhlen M, Aebersold R, Frei K, Wollscheid B. Proteomic analysis reveals drug accessible cell surface N-glycoproteins of primary and established glioblastoma cell lines. Journal of Proteome Research. 11: 4885-93. PMID 22909291 DOI: 10.1021/pr300360a  1
2012 Sato K, Sundaramoorthy E, Rajendra E, Hattori H, Jeyasekharan AD, Ayoub N, Schiess R, Aebersold R, Nishikawa H, Sedukhina AS, Wada H, Ohta T, Venkitaraman AR. A DNA-damage selective role for BRCA1 E3 ligase in claspin ubiquitylation, CHK1 activation, and DNA repair. Current Biology : Cb. 22: 1659-66. PMID 22863316 DOI: 10.1016/j.cub.2012.07.034  1
2012 Bislev SL, Deutsch EW, Sun Z, Farrah T, Aebersold R, Moritz RL, Bendixen E, Codrea MC. A Bovine PeptideAtlas of milk and mammary gland proteomes. Proteomics. 12: 2895-9. PMID 22837157 DOI: 10.1002/pmic.201200057  1
2012 Hood LE, Omenn GS, Moritz RL, Aebersold R, Yamamoto KR, Amos M, Hunter-Cevera J, Locascio L. New and improved proteomics technologies for understanding complex biological systems: addressing a grand challenge in the life sciences. Proteomics. 12: 2773-83. PMID 22807061 DOI: 10.1002/pmic.201270086  1
2012 Hüttenhain R, Soste M, Selevsek N, Röst H, Sethi A, Carapito C, Farrah T, Deutsch EW, Kusebauch U, Moritz RL, Niméus-Malmström E, Rinner O, Aebersold R. Reproducible quantification of cancer-associated proteins in body fluids using targeted proteomics. Science Translational Medicine. 4: 142ra94. PMID 22786679 DOI: 10.1126/scitranslmed.3003989  1
2012 Walzthoeni T, Claassen M, Leitner A, Herzog F, Bohn S, Förster F, Beck M, Aebersold R. False discovery rate estimation for cross-linked peptides identified by mass spectrometry. Nature Methods. 9: 901-3. PMID 22772729 DOI: 10.1038/nmeth.2103  1
2012 Kohli BM, Pflieger D, Mueller LN, Carbonetti G, Aebersold R, Nitsch RM, Konietzko U. Interactome of the amyloid precursor protein APP in brain reveals a protein network involved in synaptic vesicle turnover and a close association with Synaptotagmin-1. Journal of Proteome Research. 11: 4075-90. PMID 22731840 DOI: 10.1021/pr300123g  1
2012 Picotti P, Aebersold R. Selected reaction monitoring-based proteomics: workflows, potential, pitfalls and future directions. Nature Methods. 9: 555-66. PMID 22669653 DOI: 10.1038/nmeth.2015  1
2012 Pulliainen AT, Pieles K, Brand CS, Hauert B, Böhm A, Quebatte M, Wepf A, Gstaiger M, Aebersold R, Dessauer CW, Dehio C. Bacterial effector binds host cell adenylyl cyclase to potentiate Gαs-dependent cAMP production. Proceedings of the National Academy of Sciences of the United States of America. 109: 9581-6. PMID 22635269 DOI: 10.1073/pnas.1117651109  1
2012 Maiolica A, Jünger MA, Ezkurdia I, Aebersold R. Targeted proteome investigation via selected reaction monitoring mass spectrometry. Journal of Proteomics. 75: 3495-513. PMID 22579752 DOI: 10.1016/j.jprot.2012.04.048  1
2012 Ebhardt HA, Sabidó E, Hüttenhain R, Collins B, Aebersold R. Range of protein detection by selected/multiple reaction monitoring mass spectrometry in an unfractionated human cell culture lysate. Proteomics. 12: 1185-93. PMID 22577020 DOI: 10.1002/pmic.201100543  1
2012 Carapito C, Aebersold R. Targeted proteomics. Proteomics. 12: 1073. PMID 22577009 DOI: 10.1002/pmic.201270035  1
2012 Röst H, Malmström L, Aebersold R. A computational tool to detect and avoid redundancy in selected reaction monitoring. Molecular & Cellular Proteomics : McP. 11: 540-9. PMID 22535207 DOI: 10.1074/mcp.M111.013045  1
2012 Leitner A, Joachimiak LA, Bracher A, Mönkemeyer L, Walzthoeni T, Chen B, Pechmann S, Holmes S, Cong Y, Ma B, Ludtke S, Chiu W, Hartl FU, Aebersold R, Frydman J. The molecular architecture of the eukaryotic chaperonin TRiC/CCT. Structure (London, England : 1993). 20: 814-25. PMID 22503819 DOI: 10.1016/j.str.2012.03.007  1
2012 Waldemarson S, Krogh M, Alaiya A, Kirik U, Schedvins K, Auer G, Hansson KM, Ossola R, Aebersold R, Lee H, Malmström J, James P. Protein expression changes in ovarian cancer during the transition from benign to malignant. Journal of Proteome Research. 11: 2876-89. PMID 22471520 DOI: 10.1021/pr201258q  1
2012 Jovanovic M, Reiter L, Clark A, Weiss M, Picotti P, Rehrauer H, Frei A, Neukomm LJ, Kaufman E, Wollscheid B, Simard MJ, Miska EA, Aebersold R, Gerber AP, Hengartner MO. RIP-chip-SRM--a new combinatorial large-scale approach identifies a set of translationally regulated bantam/miR-58 targets in C. elegans. Genome Research. 22: 1360-71. PMID 22454234 DOI: 10.1101/gr.133330.111  1
2012 Paik YK, Omenn GS, Uhlen M, Hanash S, Marko-Varga G, Aebersold R, Bairoch A, Yamamoto T, Legrain P, Lee HJ, Na K, Jeong SK, He F, Binz PA, Nishimura T, et al. Standard guidelines for the chromosome-centric human proteome project. Journal of Proteome Research. 11: 2005-13. PMID 22443261 DOI: 10.1021/pr200824a  1
2012 Bensimon A, Heck AJ, Aebersold R. Mass spectrometry-based proteomics and network biology. Annual Review of Biochemistry. 81: 379-405. PMID 22439968 DOI: 10.1146/annurev-biochem-072909-100424  1
2012 Paik YK, Jeong SK, Omenn GS, Uhlen M, Hanash S, Cho SY, Lee HJ, Na K, Choi EY, Yan F, Zhang F, Zhang Y, Snyder M, Cheng Y, Chen R, ... ... Aebersold R, et al. The Chromosome-Centric Human Proteome Project for cataloging proteins encoded in the genome. Nature Biotechnology. 30: 221-3. PMID 22398612 DOI: 10.1038/nbt.2152  1
2012 Jennebach S, Herzog F, Aebersold R, Cramer P. Crosslinking-MS analysis reveals RNA polymerase I domain architecture and basis of rRNA cleavage. Nucleic Acids Research. 40: 5591-601. PMID 22396529 DOI: 10.1093/nar/gks220  1
2012 Sabidó E, Quehenberger O, Shen Q, Chang CY, Shah I, Armando AM, Andreyev A, Vitek O, Dennis EA, Aebersold R. Targeted proteomics of the eicosanoid biosynthetic pathway completes an integrated genomics-proteomics-metabolomics picture of cellular metabolism. Molecular & Cellular Proteomics : McP. 11: M111.014746. PMID 22361236 DOI: 10.1074/mcp.M111.014746  1
2012 Farrah T, Deutsch EW, Kreisberg R, Sun Z, Campbell DS, Mendoza L, Kusebauch U, Brusniak MY, Hüttenhain R, Schiess R, Selevsek N, Aebersold R, Moritz RL. PASSEL: the PeptideAtlas SRMexperiment library. Proteomics. 12: 1170-5. PMID 22318887 DOI: 10.1002/pmic.201100515  1
2012 Lamond AI, Uhlen M, Horning S, Makarov A, Robinson CV, Serrano L, Hartl FU, Baumeister W, Werenskiold AK, Andersen JS, Vorm O, Linial M, Aebersold R, Mann M. Advancing cell biology through proteomics in space and time (PROSPECTS). Molecular & Cellular Proteomics : McP. 11: O112.017731. PMID 22311636 DOI: 10.1074/mcp.O112.017731  1
2012 Lasker K, Förster F, Bohn S, Walzthoeni T, Villa E, Unverdorben P, Beck F, Aebersold R, Sali A, Baumeister W. Molecular architecture of the 26S proteasome holocomplex determined by an integrative approach. Proceedings of the National Academy of Sciences of the United States of America. 109: 1380-7. PMID 22307589 DOI: 10.1073/pnas.1120559109  1
2012 Jones AM, Aebersold R, Ahrens CH, Apweiler R, Baerenfaller K, Baker M, Bendixen E, Briggs S, Brownridge P, Brunner E, Daube M, Deutsch EW, Grossniklaus U, Heazlewood J, Hengartner MO, et al. The HUPO initiative on Model Organism Proteomes, iMOP. Proteomics. 12: 340-5. PMID 22290800 DOI: 10.1002/pmic.201290014  1
2012 Leitner A, Reischl R, Walzthoeni T, Herzog F, Bohn S, Förster F, Aebersold R. Expanding the chemical cross-linking toolbox by the use of multiple proteases and enrichment by size exclusion chromatography. Molecular & Cellular Proteomics : McP. 11: M111.014126. PMID 22286754 DOI: 10.1074/mcp.M111.014126  1
2012 Malmström L, Malmström J, Selevsek N, Rosenberger G, Aebersold R. Automated workflow for large-scale selected reaction monitoring experiments. Journal of Proteome Research. 11: 1644-53. PMID 22283722 DOI: 10.1021/pr200844d  1
2012 Gillet LC, Navarro P, Tate S, Röst H, Selevsek N, Reiter L, Bonner R, Aebersold R. Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis. Molecular & Cellular Proteomics : McP. 11: O111.016717. PMID 22261725 DOI: 10.1074/mcp.O111.016717  1
2012 Bislev SL, Kusebauch U, Codrea MC, Beynon RJ, Harman VM, Røntved CM, Aebersold R, Moritz RL, Bendixen E. Quantotypic properties of QconCAT peptides targeting bovine host response to Streptococcus uberis. Journal of Proteome Research. 11: 1832-43. PMID 22256911 DOI: 10.1021/pr201064g  1
2012 Chang CY, Picotti P, Hüttenhain R, Heinzelmann-Schwarz V, Jovanovic M, Aebersold R, Vitek O. Protein significance analysis in selected reaction monitoring (SRM) measurements. Molecular & Cellular Proteomics : McP. 11: M111.014662. PMID 22190732 DOI: 10.1074/mcp.M111.014662  1
2012 Stengel F, Aebersold R, Robinson CV. Joining forces: integrating proteomics and cross-linking with the mass spectrometry of intact complexes. Molecular & Cellular Proteomics : McP. 11: R111.014027. PMID 22180098 DOI: 10.1074/mcp.R111.014027  1
2012 Sabidó E, Selevsek N, Aebersold R. Mass spectrometry-based proteomics for systems biology. Current Opinion in Biotechnology. 23: 591-7. PMID 22169889 DOI: 10.1016/j.copbio.2011.11.014  1
2012 Deutsch EW, Chambers M, Neumann S, Levander F, Binz PA, Shofstahl J, Campbell DS, Mendoza L, Ovelleiro D, Helsens K, Martens L, Aebersold R, Moritz RL, Brusniak MY. TraML--a standard format for exchange of selected reaction monitoring transition lists. Molecular & Cellular Proteomics : McP. 11: R111.015040. PMID 22159873 DOI: 10.1074/mcp.R111.015040  1
2012 Danzer C, Eckhardt K, Schmidt A, Fankhauser N, Ribrioux S, Wollscheid B, Müller L, Schiess R, Züllig R, Lehmann R, Spinas G, Aebersold R, Krek W. Comprehensive description of the N-glycoproteome of mouse pancreatic β-cells and human islets. Journal of Proteome Research. 11: 1598-608. PMID 22148984 DOI: 10.1021/pr2007895  0.44
2012 Malmström J, Karlsson C, Nordenfelt P, Ossola R, Weisser H, Quandt A, Hansson K, Aebersold R, Malmström L, Björck L. Streptococcus pyogenes in human plasma: adaptive mechanisms analyzed by mass spectrometry-based proteomics. The Journal of Biological Chemistry. 287: 1415-25. PMID 22117078 DOI: 10.1074/jbc.M111.267674  1
2012 Ludwig C, Claassen M, Schmidt A, Aebersold R. Estimation of absolute protein quantities of unlabeled samples by selected reaction monitoring mass spectrometry. Molecular & Cellular Proteomics : McP. 11: M111.013987. PMID 22101334 DOI: 10.1074/mcp.M111.013987  1
2012 Claassen M, Reiter L, Hengartner MO, Buhmann JM, Aebersold R. Generic comparison of protein inference engines. Molecular & Cellular Proteomics : McP. 11: O110.007088. PMID 22057310 DOI: 10.1074/mcp.O110.007088  1
2011 Bauch A, Adamczyk I, Buczek P, Elmer FJ, Enimanev K, Glyzewski P, Kohler M, Pylak T, Quandt A, Ramakrishnan C, Beisel C, Malmström L, Aebersold R, Rinn B. openBIS: a flexible framework for managing and analyzing complex data in biology research. Bmc Bioinformatics. 12: 468. PMID 22151573 DOI: 10.1186/1471-2105-12-468  1
2011 Beck M, Schmidt A, Malmstroem J, Claassen M, Ori A, Szymborska A, Herzog F, Rinner O, Ellenberg J, Aebersold R. The quantitative proteome of a human cell line. Molecular Systems Biology. 7: 549. PMID 22068332 DOI: 10.1038/msb.2011.82  1
2011 Glatter T, Schittenhelm RB, Rinner O, Roguska K, Wepf A, Jünger MA, Köhler K, Jevtov I, Choi H, Schmidt A, Nesvizhskii AI, Stocker H, Hafen E, Aebersold R, Gstaiger M. Modularity and hormone sensitivity of the Drosophila melanogaster insulin receptor/target of rapamycin interaction proteome. Molecular Systems Biology. 7: 547. PMID 22068330 DOI: 10.1038/msb.2011.79  1
2011 Zhang J, Vaga S, Chumnanpuen P, Kumar R, Vemuri GN, Aebersold R, Nielsen J. Mapping the interaction of Snf1 with TORC1 in Saccharomyces cerevisiae. Molecular Systems Biology. 7: 545. PMID 22068328 DOI: 10.1038/msb.2011.80  1
2011 Aebersold R. Editorial: from data to results. Molecular & Cellular Proteomics : McP. 10: E111.014787. PMID 21969611 DOI: 10.1074/mcp.E111.014787  1
2011 Blattner C, Jennebach S, Herzog F, Mayer A, Cheung AC, Witte G, Lorenzen K, Hopfner KP, Heck AJ, Aebersold R, Cramer P. Molecular basis of Rrn3-regulated RNA polymerase I initiation and cell growth. Genes & Development. 25: 2093-105. PMID 21940764 DOI: 10.1101/gad.17363311  1
2011 Esterházy D, Stützer I, Wang H, Rechsteiner MP, Beauchamp J, Döbeli H, Hilpert H, Matile H, Prummer M, Schmidt A, Lieske N, Boehm B, Marselli L, Bosco D, Kerr-Conte J, ... Aebersold R, et al. Bace2 is a β cell-enriched protease that regulates pancreatic β cell function and mass. Cell Metabolism. 14: 365-77. PMID 21907142 DOI: 10.1016/j.cmet.2011.06.018  1
2011 Shteynberg D, Deutsch EW, Lam H, Eng JK, Sun Z, Tasman N, Mendoza L, Moritz RL, Aebersold R, Nesvizhskii AI. iProphet: multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates. Molecular & Cellular Proteomics : McP. 10: M111.007690. PMID 21876204 DOI: 10.1074/mcp.M111.007690  1
2011 Omenn GS, Baker MS, Aebersold R. Recent Workshops of the HUPO Human Plasma Proteome Project (HPPP): a bridge with the HUPO CardioVascular Initiative and the emergence of SRM targeted proteomics. Proteomics. 11: 3439-43. PMID 21850651 DOI: 10.1002/pmic.201100382  1
2011 Ritz D, Vuk M, Kirchner P, Bug M, Schütz S, Hayer A, Bremer S, Lusk C, Baloh RH, Lee H, Glatter T, Gstaiger M, Aebersold R, Weihl CC, Meyer H. Endolysosomal sorting of ubiquitylated caveolin-1 is regulated by VCP and UBXD1 and impaired by VCP disease mutations. Nature Cell Biology. 13: 1116-23. PMID 21822278 DOI: 10.1038/ncb2301  1
2011 Hyung SW, Lee MY, Yu JH, Shin B, Jung HJ, Park JM, Han W, Lee KM, Moon HG, Zhang H, Aebersold R, Hwang D, Lee SW, Yu MH, Noh DY. A serum protein profile predictive of the resistance to neoadjuvant chemotherapy in advanced breast cancers. Molecular & Cellular Proteomics : McP. 10: M111.011023. PMID 21799047 DOI: 10.1074/mcp.M111.011023  1
2011 Maier T, Schmidt A, Güell M, Kühner S, Gavin AC, Aebersold R, Serrano L. Quantification of mRNA and protein and integration with protein turnover in a bacterium. Molecular Systems Biology. 7: 511. PMID 21772259 DOI: 10.1038/msb.2011.38  0.44
2011 Schmidt A, Beck M, Malmström J, Lam H, Claassen M, Campbell D, Aebersold R. Absolute quantification of microbial proteomes at different states by directed mass spectrometry. Molecular Systems Biology. 7: 510. PMID 21772258 DOI: 10.1038/msb.2011.37  0.56
2011 Legrain P, Aebersold R, Archakov A, Bairoch A, Bala K, Beretta L, Bergeron J, Borchers CH, Corthals GL, Costello CE, Deutsch EW, Domon B, Hancock W, He F, Hochstrasser D, et al. The human proteome project: current state and future direction. Molecular & Cellular Proteomics : McP. 10: M111.009993. PMID 21742803 DOI: 10.1074/mcp.M111.009993  1
2011 Kälin M, Cima I, Schiess R, Fankhauser N, Powles T, Wild P, Templeton A, Cerny T, Aebersold R, Krek W, Gillessen S. Novel prognostic markers in the serum of patients with castration-resistant prostate cancer derived from quantitative analysis of the pten conditional knockout mouse proteome. European Urology. 60: 1235-43. PMID 21741162 DOI: 10.1016/j.eururo.2011.06.038  1
2011 Higdon R, Reiter L, Hather G, Haynes W, Kolker N, Stewart E, Bauman AT, Picotti P, Schmidt A, van Belle G, Aebersold R, Kolker E. IPM: An integrated protein model for false discovery rate estimation and identification in high-throughput proteomics. Journal of Proteomics. 75: 116-21. PMID 21718813 DOI: 10.1016/j.jprot.2011.06.003  1
2011 Kahraman A, Malmström L, Aebersold R. Xwalk: computing and visualizing distances in cross-linking experiments. Bioinformatics (Oxford, England). 27: 2163-4. PMID 21666267 DOI: 10.1093/bioinformatics/btr348  1
2011 Farrah T, Deutsch EW, Omenn GS, Campbell DS, Sun Z, Bletz JA, Mallick P, Katz JE, Malmström J, Ossola R, Watts JD, Lin B, Zhang H, Moritz RL, Aebersold R. A high-confidence human plasma proteome reference set with estimated concentrations in PeptideAtlas. Molecular & Cellular Proteomics : McP. 10: M110.006353. PMID 21632744 DOI: 10.1074/mcp.M110.006353  1
2011 Kisko K, Brozzo MS, Missimer J, Schleier T, Menzel A, Leppänen VM, Alitalo K, Walzthoeni T, Aebersold R, Ballmer-Hofer K. Structural analysis of vascular endothelial growth factor receptor-2/ligand complexes by small-angle X-ray solution scattering. Faseb Journal : Official Publication of the Federation of American Societies For Experimental Biology. 25: 2980-6. PMID 21613573 DOI: 10.1096/fj.11-185397  1
2011 Wiedl T, Arni S, Roschitzki B, Grossmann J, Collaud S, Soltermann A, Hillinger S, Aebersold R, Weder W. Activity-based proteomics: identification of ABHD11 and ESD activities as potential biomarkers for human lung adenocarcinoma. Journal of Proteomics. 74: 1884-94. PMID 21596165 DOI: 10.1016/j.jprot.2011.04.030  1
2011 Hoofnagle AN, Aebersold R, Anderson NL, Felsenfeld A, Liebler DC. Painting a moving picture: large-scale proteomics efforts and their potential for changing patient care. Clinical Chemistry. 57: 1357-60. PMID 21540400 DOI: 10.1373/clinchem.2010.158311  1
2011 Legrain P, Aebersold R, Archakov A, Bairoch A, Bala K, Beretta L, Bergeron J, Borchers C, Corthals GL, Costello CE, Deutsch EW, Domon B, Hancock W, He F, Hochstrasser D, et al. The human proteome project: Current state and future direction. Molecular & Cellular Proteomics : McP. PMID 21531903 DOI: 10.1074/mcp.O111.009993  1
2011 Farrah T, Deutsch EW, Aebersold R. Using the Human Plasma PeptideAtlas to study human plasma proteins. Methods in Molecular Biology (Clifton, N.J.). 728: 349-74. PMID 21468960 DOI: 10.1007/978-1-61779-068-3_23  1
2011 Ossola R, Schiess R, Picotti P, Rinner O, Reiter L, Aebersold R. Biomarker validation in blood specimens by selected reaction monitoring mass spectrometry of N-glycosites. Methods in Molecular Biology (Clifton, N.J.). 728: 179-94. PMID 21468948 DOI: 10.1007/978-1-61779-068-3_11  1
2011 Reiter L, Rinner O, Picotti P, Hüttenhain R, Beck M, Brusniak MY, Hengartner MO, Aebersold R. mProphet: automated data processing and statistical validation for large-scale SRM experiments. Nature Methods. 8: 430-5. PMID 21423193 DOI: 10.1038/nmeth.1584  0.56
2011 Brusniak MY, Kwok ST, Christiansen M, Campbell D, Reiter L, Picotti P, Kusebauch U, Ramos H, Deutsch EW, Chen J, Moritz RL, Aebersold R. ATAQS: A computational software tool for high throughput transition optimization and validation for selected reaction monitoring mass spectrometry. Bmc Bioinformatics. 12: 78. PMID 21414234 DOI: 10.1186/1471-2105-12-78  0.48
2011 Claassen M, Aebersold R, Buhmann JM. Proteome coverage prediction for integrated proteomics datasets. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 18: 283-93. PMID 21385034 DOI: 10.1089/cmb.2010.0261  0.56
2011 Selevsek N, Matondo M, Sanchez Carbayo M, Aebersold R, Domon B. Systematic quantification of peptides/proteins in urine using selected reaction monitoring. Proteomics. 11: 1135-47. PMID 21360671 DOI: 10.1002/pmic.201000599  0.32
2011 Laurell E, Beck K, Krupina K, Theerthagiri G, Bodenmiller B, Horvath P, Aebersold R, Antonin W, Kutay U. Phosphorylation of Nup98 by multiple kinases is crucial for NPC disassembly during mitotic entry. Cell. 144: 539-50. PMID 21335236 DOI: 10.1016/j.cell.2011.01.012  1
2011 Cima I, Schiess R, Wild P, Kaelin M, Schüffler P, Lange V, Picotti P, Ossola R, Templeton A, Schubert O, Fuchs T, Leippold T, Wyler S, Zehetner J, Jochum W, ... ... Aebersold R, et al. Cancer genetics-guided discovery of serum biomarker signatures for diagnosis and prognosis of prostate cancer. Proceedings of the National Academy of Sciences of the United States of America. 108: 3342-7. PMID 21300890 DOI: 10.1073/pnas.1013699108  1
2011 Costenoble R, Picotti P, Reiter L, Stallmach R, Heinemann M, Sauer U, Aebersold R. Comprehensive quantitative analysis of central carbon and amino-acid metabolism in Saccharomyces cerevisiae under multiple conditions by targeted proteomics. Molecular Systems Biology. 7: 464. PMID 21283140 DOI: 10.1038/msb.2010.122  0.36
2011 Scherrer T, Femmer C, Schiess R, Aebersold R, Gerber AP. Defining potentially conserved RNA regulons of homologous zinc-finger RNA-binding proteins. Genome Biology. 12: R3. PMID 21232131 DOI: 10.1186/gb-2011-12-1-r3  1
2011 Ramos H, Shannon P, Brusniak MY, Kusebauch U, Moritz RL, Aebersold R. The Protein Information and Property Explorer 2: gaggle-like exploration of biological proteomic data within one webpage. Proteomics. 11: 154-8. PMID 21182202 DOI: 10.1002/pmic.201000459  1
2011 Yan W, Luo J, Robinson M, Eng J, Aebersold R, Ranish J. Index-ion triggered MS2 ion quantification: a novel proteomics approach for reproducible detection and quantification of targeted proteins in complex mixtures. Molecular & Cellular Proteomics : McP. 10: M110.005611. PMID 21169564 DOI: 10.1074/mcp.M110.005611  1
2011 Surinova S, Schiess R, Hüttenhain R, Cerciello F, Wollscheid B, Aebersold R. On the development of plasma protein biomarkers. Journal of Proteome Research. 10: 5-16. PMID 21142170 DOI: 10.1021/pr1008515  1
2011 Bodenmiller B, Aebersold R. Phosphoproteome resource for systems biology research. Methods in Molecular Biology (Clifton, N.J.). 694: 307-22. PMID 21082442 DOI: 10.1007/978-1-60761-977-2_19  0.36
2011 Beck M, Claassen M, Aebersold R. Comprehensive proteomics. Current Opinion in Biotechnology. 22: 3-8. PMID 20888217 DOI: 10.1016/j.copbio.2010.09.002  0.56
2011 Pan S, Chen R, Aebersold R, Brentnall TA. Mass spectrometry based glycoproteomics--from a proteomics perspective. Molecular & Cellular Proteomics : McP. 10: R110.003251. PMID 20736408 DOI: 10.1074/mcp.R110.003251  1
2011 Kiyonami R, Schoen A, Prakash A, Peterman S, Zabrouskov V, Picotti P, Aebersold R, Huhmer A, Domon B. Increased selectivity, analytical precision, and throughput in targeted proteomics. Molecular & Cellular Proteomics : McP. 10: M110.002931. PMID 20664071 DOI: 10.1074/mcp.M110.002931  1
2010 Bülow MH, Aebersold R, Pankratz MJ, Jünger MA. The Drosophila FoxA ortholog Fork head regulates growth and gene expression downstream of Target of rapamycin. Plos One. 5: e15171. PMID 21217822 DOI: 10.1371/journal.pone.0015171  1
2010 Bodenmiller B, Wanka S, Kraft C, Urban J, Campbell D, Pedrioli PG, Gerrits B, Picotti P, Lam H, Vitek O, Brusniak MY, Roschitzki B, Zhang C, Shokat KM, Schlapbach R, ... ... Aebersold R, et al. Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast. Science Signaling. 3: rs4. PMID 21177495 DOI: 10.1126/scisignal.2001182  0.36
2010 Bensimon A, Schmidt A, Ziv Y, Elkon R, Wang SY, Chen DJ, Aebersold R, Shiloh Y. ATM-dependent and -independent dynamics of the nuclear phosphoproteome after DNA damage. Science Signaling. 3: rs3. PMID 21139141 DOI: 10.1126/scisignal.2001034  0.44
2010 Bandyopadhyay S, Mehta M, Kuo D, Sung MK, Chuang R, Jaehnig EJ, Bodenmiller B, Licon K, Copeland W, Shales M, Fiedler D, Dutkowski J, Guénolé A, van Attikum H, Shokat KM, ... ... Aebersold R, et al. Rewiring of genetic networks in response to DNA damage. Science (New York, N.Y.). 330: 1385-9. PMID 21127252 DOI: 10.1126/science.1195618  1
2010 Bohn S, Beck F, Sakata E, Walzthoeni T, Beck M, Aebersold R, Förster F, Baumeister W, Nickell S. Structure of the 26S proteasome from Schizosaccharomyces pombe at subnanometer resolution. Proceedings of the National Academy of Sciences of the United States of America. 107: 20992-7. PMID 21098295 DOI: 10.1073/pnas.1015530107  1
2010 Bodenmiller B, Aebersold R. Quantitative analysis of protein phosphorylation on a system-wide scale by mass spectrometry-based proteomics. Methods in Enzymology. 470: 317-34. PMID 20946816 DOI: 10.1016/S0076-6879(10)70013-6  0.36
2010 Ahrens CH, Brunner E, Qeli E, Basler K, Aebersold R. Generating and navigating proteome maps using mass spectrometry. Nature Reviews. Molecular Cell Biology. 11: 789-801. PMID 20944666 DOI: 10.1038/nrm2973  1
2010 Jovanovic M, Reiter L, Picotti P, Lange V, Bogan E, Hurschler BA, Blenkiron C, Lehrbach NJ, Ding XC, Weiss M, Schrimpf SP, Miska EA, Grosshans H, Aebersold R, Hengartner MO. A quantitative targeted proteomics approach to validate predicted microRNA targets in C. elegans. Nature Methods. 7: 837-42. PMID 20835247 DOI: 10.1038/nmeth.1504  1
2010 Nilsson T, Mann M, Aebersold R, Yates JR, Bairoch A, Bergeron JJ. Mass spectrometry in high-throughput proteomics: ready for the big time. Nature Methods. 7: 681-5. PMID 20805795 DOI: 10.1038/nmeth0910-681  1
2010 Mirzaei H, Rogers RS, Grimes B, Eng J, Aderem A, Aebersold R. Characterizing the connectivity of poly-ubiquitin chains by selected reaction monitoring mass spectrometry. Molecular Biosystems. 6: 2004-14. PMID 20694217 DOI: 10.1039/c005242f  1
2010 Duncan MW, Aebersold R, Caprioli RM. The pros and cons of peptide-centric proteomics. Nature Biotechnology. 28: 659-64. PMID 20622832 DOI: 10.1038/nbt0710-659  1
2010 Hofmann A, Gerrits B, Schmidt A, Bock T, Bausch-Fluck D, Aebersold R, Wollscheid B. Proteomic cell surface phenotyping of differentiating acute myeloid leukemia cells. Blood. 116: e26-34. PMID 20570859 DOI: 10.1182/blood-2010-02-271270  0.44
2010 Lam H, Aebersold R. Using spectral libraries for peptide identification from tandem mass spectrometry (MS/MS) data. Current Protocols in Protein Science / Editorial Board, John E. Coligan ... [Et Al.]. Unit 25.5. PMID 20393975 DOI: 10.1002/0471140864.ps2505s60  1
2010 Leitner A, Walzthoeni T, Kahraman A, Herzog F, Rinner O, Beck M, Aebersold R. Probing native protein structures by chemical cross-linking, mass spectrometry, and bioinformatics. Molecular & Cellular Proteomics : McP. 9: 1634-49. PMID 20360032 DOI: 10.1074/mcp.R000001-MCP201  0.56
2010 Kümmel A, Ewald JC, Fendt SM, Jol SJ, Picotti P, Aebersold R, Sauer U, Zamboni N, Heinemann M. Differential glucose repression in common yeast strains in response to HXK2 deletion. Fems Yeast Research. 10: 322-32. PMID 20199578 DOI: 10.1111/j.1567-1364.2010.00609.x  1
2010 Breslow DK, Collins SR, Bodenmiller B, Aebersold R, Simons K, Shevchenko A, Ejsing CS, Weissman JS. Orm family proteins mediate sphingolipid homeostasis. Nature. 463: 1048-53. PMID 20182505 DOI: 10.1038/nature08787  0.36
2010 Deutsch EW, Mendoza L, Shteynberg D, Farrah T, Lam H, Tasman N, Sun Z, Nilsson E, Pratt B, Prazen B, Eng JK, Martin DB, Nesvizhskii AI, Aebersold R. A guided tour of the Trans-Proteomic Pipeline. Proteomics. 10: 1150-9. PMID 20101611 DOI: 10.1002/pmic.200900375  1
2010 Deutsch EW, Shteynberg D, Lam H, Sun Z, Eng JK, Carapito C, von Haller PD, Tasman N, Mendoza L, Farrah T, Aebersold R. Trans-Proteomic Pipeline supports and improves analysis of electron transfer dissociation data sets. Proteomics. 10: 1190-5. PMID 20082347 DOI: 10.1002/pmic.200900567  1
2010 Lam H, Aebersold R. Spectral library searching for peptide identification via tandem MS. Methods in Molecular Biology (Clifton, N.J.). 604: 95-103. PMID 20013366 DOI: 10.1007/978-1-60761-444-9_7  1
2010 Picotti P, Rinner O, Stallmach R, Dautel F, Farrah T, Domon B, Wenschuh H, Aebersold R. High-throughput generation of selected reaction-monitoring assays for proteins and proteomes. Nature Methods. 7: 43-6. PMID 19966807 DOI: 10.1038/nmeth.1408  0.36
2010 Lam H, Deutsch EW, Aebersold R. Artificial decoy spectral libraries for false discovery rate estimation in spectral library searching in proteomics. Journal of Proteome Research. 9: 605-10. PMID 19916561 DOI: 10.1021/pr900947u  0.48
2009 Brentnall TA, Pan S, Bronner MP, Crispin DA, Mirzaei H, Cooke K, Tamura Y, Nikolskaya T, Jebailey L, Goodlett DR, McIntosh M, Aebersold R, Rabinovitch PS, Chen R. Proteins That Underlie Neoplastic Progression of Ulcerative Colitis. Proteomics. Clinical Applications. 3: 1326. PMID 20098637  1
2009 Kühner S, van Noort V, Betts MJ, Leo-Macias A, Batisse C, Rode M, Yamada T, Maier T, Bader S, Beltran-Alvarez P, Castaño-Diez D, Chen WH, Devos D, Güell M, Norambuena T, ... ... Aebersold R, et al. Proteome organization in a genome-reduced bacterium. Science (New York, N.Y.). 326: 1235-40. PMID 19965468 DOI: 10.1126/science.1176343  1
2009 Goetze S, Qeli E, Mosimann C, Staes A, Gerrits B, Roschitzki B, Mohanty S, Niederer EM, Laczko E, Timmerman E, Lange V, Hafen E, Aebersold R, Vandekerckhove J, Basler K, et al. Identification and functional characterization of N-terminally acetylated proteins in Drosophila melanogaster. Plos Biology. 7: e1000236. PMID 19885390 DOI: 10.1371/journal.pbio.1000236  1
2009 Beck M, Malmström JA, Lange V, Schmidt A, Deutsch EW, Aebersold R. Visual proteomics of the human pathogen Leptospira interrogans. Nature Methods. 6: 817-23. PMID 19838170 DOI: 10.1038/nmeth.1390  1
2009 Hüttenhain R, Malmström J, Picotti P, Aebersold R. Perspectives of targeted mass spectrometry for protein biomarker verification. Current Opinion in Chemical Biology. 13: 518-25. PMID 19818677 DOI: 10.1016/j.cbpa.2009.09.014  0.36
2009 Schmidt A, Claassen M, Aebersold R. Directed mass spectrometry: towards hypothesis-driven proteomics. Current Opinion in Chemical Biology. 13: 510-7. PMID 19775930 DOI: 10.1016/j.cbpa.2009.08.016  0.56
2009 Gstaiger M, Aebersold R. Applying mass spectrometry-based proteomics to genetics, genomics and network biology. Nature Reviews. Genetics. 10: 617-27. PMID 19687803 DOI: 10.1038/nrg2633  0.32
2009 Huber A, Bodenmiller B, Uotila A, Stahl M, Wanka S, Gerrits B, Aebersold R, Loewith R. Characterization of the rapamycin-sensitive phosphoproteome reveals that Sch9 is a central coordinator of protein synthesis. Genes & Development. 23: 1929-43. PMID 19684113 DOI: 10.1101/gad.532109  0.36
2009 Picotti P, Bodenmiller B, Mueller LN, Domon B, Aebersold R. Full dynamic range proteome analysis of S. cerevisiae by targeted proteomics. Cell. 138: 795-806. PMID 19664813 DOI: 10.1016/j.cell.2009.05.051  0.36
2009 Tan CS, Bodenmiller B, Pasculescu A, Jovanovic M, Hengartner MO, Jørgensen C, Bader GD, Aebersold R, Pawson T, Linding R. Comparative analysis reveals conserved protein phosphorylation networks implicated in multiple diseases. Science Signaling. 2: ra39. PMID 19638616 DOI: 10.1126/scisignal.2000316  1
2009 Eisenacher M, Martens L, Hardt T, Kohl M, Barsnes H, Helsens K, Häkkinen J, Levander F, Aebersold R, Vandekerckhove J, Dunn MJ, Lisacek F, Siepen JA, Hubbard SJ, Binz PA, et al. Getting a grip on proteomics data - Proteomics Data Collection (ProDaC). Proteomics. 9: 3928-33. PMID 19637238 DOI: 10.1002/pmic.200900247  1
2009 Reiter L, Claassen M, Schrimpf SP, Jovanovic M, Schmidt A, Buhmann JM, Hengartner MO, Aebersold R. Protein identification false discovery rates for very large proteomics data sets generated by tandem mass spectrometry. Molecular & Cellular Proteomics : McP. 8: 2405-17. PMID 19608599 DOI: 10.1074/mcp.M900317-MCP200  0.56
2009 Malmström J, Beck M, Schmidt A, Lange V, Deutsch EW, Aebersold R. Proteome-wide cellular protein concentrations of the human pathogen Leptospira interrogans. Nature. 460: 762-5. PMID 19606093 DOI: 10.1038/nature08184  1
2009 Sherwood CA, Eastham A, Lee LW, Peterson A, Eng JK, Shteynberg D, Mendoza L, Deutsch EW, Risler J, Tasman N, Aebersold R, Lam H, Martin DB. MaRiMba: a software application for spectral library-based MRM transition list assembly. Journal of Proteome Research. 8: 4396-405. PMID 19603829 DOI: 10.1021/pr900010h  1
2009 Claassen M, Aebersold R, Buhmann JM. Proteome coverage prediction with infinite Markov models. Bioinformatics (Oxford, England). 25: i154-60. PMID 19477982 DOI: 10.1093/bioinformatics/btp233  0.56
2009 Domon B, Bodenmiller B, Carapito C, Hao Z, Huehmer A, Aebersold R. Electron transfer dissociation in conjunction with collision activation to investigate the Drosophila melanogaster phosphoproteome. Journal of Proteome Research. 8: 2633-9. PMID 19435317 DOI: 10.1021/pr800834e  0.36
2009 Mirzaei H, Brusniak MY, Mueller LN, Letarte S, Watts JD, Aebersold R. Halogenated peptides as internal standards (H-PINS): introduction of an MS-based internal standard set for liquid chromatography-mass spectrometry. Molecular & Cellular Proteomics : McP. 8: 1934-46. PMID 19411281 DOI: 10.1074/mcp.M800569-MCP200  1
2009 Theis M, Slabicki M, Junqueira M, Paszkowski-Rogacz M, Sontheimer J, Kittler R, Heninger AK, Glatter T, Kruusmaa K, Poser I, Hyman AA, Pisabarro MT, Gstaiger M, Aebersold R, Shevchenko A, et al. Comparative profiling identifies C13orf3 as a component of the Ska complex required for mammalian cell division. The Embo Journal. 28: 1453-65. PMID 19387489 DOI: 10.1038/emboj.2009.114  0.32
2009 Schiess R, Wollscheid B, Aebersold R. Targeted proteomic strategy for clinical biomarker discovery. Molecular Oncology. 3: 33-44. PMID 19383365 DOI: 10.1016/j.molonc.2008.12.001  1
2009 Aebersold R, Auffray C, Baney E, Barillot E, Brazma A, Brett C, Brunak S, Butte A, Califano A, Celis J, Cufer T, Ferrell J, Galas D, Gallahan D, Gatenby R, et al. Report on EU-USA workshop: how systems biology can advance cancer research (27 October 2008). Molecular Oncology. 3: 9-17. PMID 19383362 DOI: 10.1016/j.molonc.2008.11.003  1
2009 Pan S, Chen R, Reimel BA, Crispin DA, Mirzaei H, Cooke K, Coleman JF, Lane Z, Bronner MP, Goodlett DR, McIntosh MW, Traverso W, Aebersold R, Brentnall TA. Quantitative proteomics investigation of pancreatic intraepithelial neoplasia. Electrophoresis. 30: 1132-44. PMID 19373808 DOI: 10.1002/elps.200800752  1
2009 Wollscheid B, Bausch-Fluck D, Henderson C, O'Brien R, Bibel M, Schiess R, Aebersold R, Watts JD. Mass-spectrometric identification and relative quantification of N-linked cell surface glycoproteins. Nature Biotechnology. 27: 378-86. PMID 19349973 DOI: 10.1038/nbt.1532  1
2009 Schrimpf SP, Weiss M, Reiter L, Ahrens CH, Jovanovic M, Malmström J, Brunner E, Mohanty S, Lercher MJ, Hunziker PE, Aebersold R, von Mering C, Hengartner MO. Comparative functional analysis of the Caenorhabditis elegans and Drosophila melanogaster proteomes. Plos Biology. 7: e48. PMID 19260763 DOI: 10.1371/journal.pbio.1000048  1
2009 Loevenich SN, Brunner E, King NL, Deutsch EW, Stein SE, Aebersold R, Hafen E. The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation. Bmc Bioinformatics. 10: 59. PMID 19210778 DOI: 10.1186/1471-2105-10-59  1
2009 Wepf A, Glatter T, Schmidt A, Aebersold R, Gstaiger M. Quantitative interaction proteomics using mass spectrometry. Nature Methods. 6: 203-5. PMID 19198594 DOI: 10.1038/nmeth.1302  0.44
2009 Glatter T, Wepf A, Aebersold R, Gstaiger M. An integrated workflow for charting the human interaction proteome: insights into the PP2A system. Molecular Systems Biology. 5: 237. PMID 19156129 DOI: 10.1038/msb.2008.75  0.32
2009 Leidel S, Pedrioli PG, Bucher T, Brost R, Costanzo M, Schmidt A, Aebersold R, Boone C, Hofmann K, Peter M. Ubiquitin-related modifier Urm1 acts as a sulphur carrier in thiolation of eukaryotic transfer RNA. Nature. 458: 228-32. PMID 19145231 DOI: 10.1038/nature07643  0.44
2009 Sumara G, Formentini I, Collins S, Sumara I, Windak R, Bodenmiller B, Ramracheya R, Caille D, Jiang H, Platt KA, Meda P, Aebersold R, Rorsman P, Ricci R. Regulation of PKD by the MAPK p38delta in insulin secretion and glucose homeostasis. Cell. 136: 235-48. PMID 19135240 DOI: 10.1016/j.cell.2008.11.018  0.36
2009 Anderson NL, Anderson NG, Pearson TW, Borchers CH, Paulovich AG, Patterson SD, Gillette M, Aebersold R, Carr SA. A human proteome detection and quantitation project. Molecular & Cellular Proteomics : McP. 8: 883-6. PMID 19131327 DOI: 10.1074/mcp.R800015-MCP200  1
2009 Gehlenborg N, Yan W, Lee IY, Yoo H, Nieselt K, Hwang D, Aebersold R, Hood L. Prequips--an extensible software platform for integration, visualization and analysis of LC-MS/MS proteomics data. Bioinformatics (Oxford, England). 25: 682-3. PMID 19129212 DOI: 10.1093/bioinformatics/btp005  1
2009 Yan W, Aebersold R, Raines EW. Evolution of organelle-associated protein profiling. Journal of Proteomics. 72: 4-11. PMID 19110081 DOI: 10.1016/j.jprot.2008.11.017  0.56
2009 Pan S, Aebersold R, Chen R, Rush J, Goodlett DR, McIntosh MW, Zhang J, Brentnall TA. Mass spectrometry based targeted protein quantification: methods and applications. Journal of Proteome Research. 8: 787-97. PMID 19105742 DOI: 10.1021/pr800538n  1
2009 Ulintz PJ, Yocum AK, Bodenmiller B, Aebersold R, Andrews PC, Nesvizhskii AI. Comparison of MS(2)-only, MSA, and MS(2)/MS(3) methodologies for phosphopeptide identification. Journal of Proteome Research. 8: 887-99. PMID 19072539 DOI: 10.1021/pr800535h  1
2009 Schiess R, Mueller LN, Schmidt A, Mueller M, Wollscheid B, Aebersold R. Analysis of cell surface proteome changes via label-free, quantitative mass spectrometry. Molecular & Cellular Proteomics : McP. 8: 624-38. PMID 19036722 DOI: 10.1074/mcp.M800172-MCP200  1
2009 Urwyler S, Nyfeler Y, Ragaz C, Lee H, Mueller LN, Aebersold R, Hilbi H. Proteome analysis of Legionella vacuoles purified by magnetic immunoseparation reveals secretory and endosomal GTPases. Traffic (Copenhagen, Denmark). 10: 76-87. PMID 18980612 DOI: 10.1111/j.1600-0854.2008.00851.x  1
2009 Goudreault M, D'Ambrosio LM, Kean MJ, Mullin MJ, Larsen BG, Sanchez A, Chaudhry S, Chen GI, Sicheri F, Nesvizhskii AI, Aebersold R, Raught B, Gingras AC. A PP2A phosphatase high density interaction network identifies a novel striatin-interacting phosphatase and kinase complex linked to the cerebral cavernous malformation 3 (CCM3) protein. Molecular & Cellular Proteomics : McP. 8: 157-71. PMID 18782753 DOI: 10.1074/mcp.M800266-MCP200  1
2008 Letarte S, Brusniak MY, Campbell D, Eddes J, Kemp CJ, Lau H, Mueller L, Schmidt A, Shannon P, Kelly-Spratt KS, Vitek O, Zhang H, Aebersold R, Watts JD. Differential Plasma Glycoproteome of p19 Skin Cancer Mouse Model Using the Corra Label-Free LC-MS Proteomics Platform. Clinical Proteomics. 4: 105. PMID 20157627 DOI: 10.1007/s12014-008-9018-8  1
2008 Brusniak MY, Bodenmiller B, Campbell D, Cooke K, Eddes J, Garbutt A, Lau H, Letarte S, Mueller LN, Sharma V, Vitek O, Zhang N, Aebersold R, Watts JD. Corra: Computational framework and tools for LC-MS discovery and targeted mass spectrometry-based proteomics. Bmc Bioinformatics. 9: 542. PMID 19087345 DOI: 10.1186/1471-2105-9-542  1
2008 Bodenmiller B, Campbell D, Gerrits B, Lam H, Jovanovic M, Picotti P, Schlapbach R, Aebersold R. PhosphoPep--a database of protein phosphorylation sites in model organisms. Nature Biotechnology. 26: 1339-40. PMID 19060867 DOI: 10.1038/nbt1208-1339  0.36
2008 Tress ML, Bodenmiller B, Aebersold R, Valencia A. Proteomics studies confirm the presence of alternative protein isoforms on a large scale. Genome Biology. 9: R162. PMID 19017398 DOI: 10.1186/gb-2008-9-11-r162  1
2008 Picotti P, Lam H, Campbell D, Deutsch EW, Mirzaei H, Ranish J, Domon B, Aebersold R. A database of mass spectrometric assays for the yeast proteome. Nature Methods. 5: 913-4. PMID 18974732 DOI: 10.1038/nmeth1108-913  1
2008 Lange V, Picotti P, Domon B, Aebersold R. Selected reaction monitoring for quantitative proteomics: a tutorial. Molecular Systems Biology. 4: 222. PMID 18854821 DOI: 10.1038/msb.2008.61  1
2008 Chi Y, Welcker M, Hizli AA, Posakony JJ, Aebersold R, Clurman BE. Identification of CDK2 substrates in human cell lysates. Genome Biology. 9: R149. PMID 18847512 DOI: 10.1186/gb-2008-9-10-r149  1
2008 Lam H, Deutsch EW, Eddes JS, Eng JK, Stein SE, Aebersold R. Building consensus spectral libraries for peptide identification in proteomics. Nature Methods. 5: 873-5. PMID 18806791 DOI: 10.1038/nmeth.1254  1
2008 Hwang D, Zhang N, Lee H, Yi E, Zhang H, Lee IY, Hood L, Aebersold R. MS-BID: a Java package for label-free LC-MS-based comparative proteomic analysis. Bioinformatics (Oxford, England). 24: 2641-2. PMID 18805798 DOI: 10.1093/bioinformatics/btn491  1
2008 Taylor CF, Binz PA, Aebersold R, Affolter M, Barkovich R, Deutsch EW, Horn DM, Hühmer A, Kussmann M, Lilley K, Macht M, Mann M, Müller D, Neubert TA, Nickson J, et al. Guidelines for reporting the use of mass spectrometry in proteomics. Nature Biotechnology. 26: 860-1. PMID 18688232 DOI: 10.1038/nbt0808-860  1
2008 Ramos H, Shannon P, Aebersold R. The protein information and property explorer: an easy-to-use, rich-client web application for the management and functional analysis of proteomic data. Bioinformatics (Oxford, England). 24: 2110-1. PMID 18635572 DOI: 10.1093/bioinformatics/btn363  1
2008 Rubio ED, Reiss DJ, Welcsh PL, Disteche CM, Filippova GN, Baliga NS, Aebersold R, Ranish JA, Krumm A. CTCF physically links cohesin to chromatin. Proceedings of the National Academy of Sciences of the United States of America. 105: 8309-14. PMID 18550811 DOI: 10.1073/pnas.0801273105  1
2008 Zhang Q, Menon R, Deutsch EW, Pitteri SJ, Faca VM, Wang H, Newcomb LF, Depinho RA, Bardeesy N, Dinulescu D, Hung KE, Kucherlapati R, Jacks T, Politi K, Aebersold R, et al. A mouse plasma peptide atlas as a resource for disease proteomics. Genome Biology. 9: R93. PMID 18522751 DOI: 10.1186/gb-2008-9-6-r93  1
2008 Schmidt A, Gehlenborg N, Bodenmiller B, Mueller LN, Campbell D, Mueller M, Aebersold R, Domon B. An integrated, directed mass spectrometric approach for in-depth characterization of complex peptide mixtures. Molecular & Cellular Proteomics : McP. 7: 2138-50. PMID 18511481 DOI: 10.1074/mcp.M700498-MCP200  0.44
2008 Deutsch EW, Lam H, Aebersold R. PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows. Embo Reports. 9: 429-34. PMID 18451766 DOI: 10.1038/embor.2008.56  0.48
2008 Lange V, Malmström JA, Didion J, King NL, Johansson BP, Schäfer J, Rameseder J, Wong CH, Deutsch EW, Brusniak MY, Bühlmann P, Björck L, Domon B, Aebersold R. Targeted quantitative analysis of Streptococcus pyogenes virulence factors by multiple reaction monitoring. Molecular & Cellular Proteomics : McP. 7: 1489-500. PMID 18408245 DOI: 10.1074/mcp.M800032-MCP200  1
2008 Yan W, Hwang D, Aebersold R. Quantitative proteomic analysis to profile dynamic changes in the spatial distribution of cellular proteins. Methods in Molecular Biology (Clifton, N.J.). 432: 389-401. PMID 18370032 DOI: 10.1007/978-1-59745-028-7_26  0.56
2008 Rinner O, Seebacher J, Walzthoeni T, Mueller LN, Beck M, Schmidt A, Mueller M, Aebersold R. Identification of cross-linked peptides from large sequence databases. Nature Methods. 5: 315-8. PMID 18327264 DOI: 10.1038/nmeth.1192  0.56
2008 Qi Y, Ranish JA, Zhu X, Krones A, Zhang J, Aebersold R, Rose DW, Rosenfeld MG, Carrière C. Atbf1 is required for the Pit1 gene early activation. Proceedings of the National Academy of Sciences of the United States of America. 105: 2481-6. PMID 18272476 DOI: 10.1073/pnas.0712196105  1
2008 Deutsch EW, Lam H, Aebersold R. Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics. Physiological Genomics. 33: 18-25. PMID 18212004 DOI: 10.1152/physiolgenomics.00298.2007  0.48
2008 Zou Z, Ibisate M, Zhou Y, Aebersold R, Xia Y, Zhang H. Synthesis and evaluation of superparamagnetic silica particles for extraction of glycopeptides in the microtiter plate format. Analytical Chemistry. 80: 1228-34. PMID 18197692 DOI: 10.1021/ac701950h  1
2008 Mueller LN, Brusniak MY, Mani DR, Aebersold R. An assessment of software solutions for the analysis of mass spectrometry based quantitative proteomics data. Journal of Proteome Research. 7: 51-61. PMID 18173218 DOI: 10.1021/pr700758r  1
2008 Mirzaei H, McBee JK, Watts J, Aebersold R. Comparative evaluation of current peptide production platforms used in absolute quantification in proteomics. Molecular & Cellular Proteomics : McP. 7: 813-23. PMID 18089551 DOI: 10.1074/mcp.M700495-MCP200  1
2008 Pflieger D, Jünger MA, Müller M, Rinner O, Lee H, Gehrig PM, Gstaiger M, Aebersold R. Quantitative proteomic analysis of protein complexes: concurrent identification of interactors and their state of phosphorylation. Molecular & Cellular Proteomics : McP. 7: 326-46. PMID 17956857 DOI: 10.1074/mcp.M700282-MCP200  1
2008 Ulintz PJ, Bodenmiller B, Andrews PC, Aebersold R, Nesvizhskii AI. Investigating MS2/MS3 matching statistics: a model for coupling consecutive stage mass spectrometry data for increased peptide identification confidence. Molecular & Cellular Proteomics : McP. 7: 71-87. PMID 17872894 DOI: 10.1074/mcp.M700128-MCP200  1
2008 Klimek J, Eddes JS, Hohmann L, Jackson J, Peterson A, Letarte S, Gafken PR, Katz JE, Mallick P, Lee H, Schmidt A, Ossola R, Eng JK, Aebersold R, Martin DB. The standard protein mix database: a diverse data set to assist in the production of improved Peptide and protein identification software tools. Journal of Proteome Research. 7: 96-103. PMID 17711323 DOI: 10.1021/pr070244j  1
2007 Aebersold R, Griffin TJ, Donohoe S. Isotope-coded affinity tagging of proteins. Csh Protocols. 2007: pdb.prot4728. PMID 21357116  1
2007 Ahrens CH, Brunner E, Hafen E, Aebersold R, Basler K. A proteome catalog of Drosophila melanogaster: an essential resource for targeted quantitative proteomics. Fly. 1: 182-6. PMID 18820430  0.36
2007 Chen R, Pan S, Aebersold R, Brentnall TA. Proteomics studies of pancreatic cancer. Proteomics. Clinical Applications. 1: 1582-1591. PMID 18633454 DOI: 10.1002/prca.200700414  1
2007 Bodenmiller B, Malmstrom J, Gerrits B, Campbell D, Lam H, Schmidt A, Rinner O, Mueller LN, Shannon PT, Pedrioli PG, Panse C, Lee HK, Schlapbach R, Aebersold R. PhosphoPep--a phosphoproteome resource for systems biology research in Drosophila Kc167 cells. Molecular Systems Biology. 3: 139. PMID 17940529 DOI: 10.1038/msb4100182  0.44
2007 Djouder N, Metzler SC, Schmidt A, Wirbelauer C, Gstaiger M, Aebersold R, Hess D, Krek W. S6K1-mediated disassembly of mitochondrial URI/PP1gamma complexes activates a negative feedback program that counters S6K1 survival signaling. Molecular Cell. 28: 28-40. PMID 17936702 DOI: 10.1016/j.molcel.2007.08.010  0.44
2007 Jones AR, Miller M, Aebersold R, Apweiler R, Ball CA, Brazma A, Degreef J, Hardy N, Hermjakob H, Hubbard SJ, Hussey P, Igra M, Jenkins H, Julian RK, Laursen K, et al. The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics. Nature Biotechnology. 25: 1127-33. PMID 17921998 DOI: 10.1038/nbt1347  1
2007 Kim B, Nesvizhskii AI, Rani PG, Hahn S, Aebersold R, Ranish JA. The transcription elongation factor TFIIS is a component of RNA polymerase II preinitiation complexes. Proceedings of the National Academy of Sciences of the United States of America. 104: 16068-73. PMID 17913884 DOI: 10.1073/pnas.0704573104  1
2007 Nesvizhskii AI, Vitek O, Aebersold R. Analysis and validation of proteomic data generated by tandem mass spectrometry. Nature Methods. 4: 787-97. PMID 17901868 DOI: 10.1038/nmeth1088  1
2007 Mueller LN, Rinner O, Schmidt A, Letarte S, Bodenmiller B, Brusniak MY, Vitek O, Aebersold R, Müller M. SuperHirn - a novel tool for high resolution LC-MS-based peptide/protein profiling. Proteomics. 7: 3470-80. PMID 17726677 DOI: 10.1002/pmic.200700057  1
2007 Noll H, Alcedo J, Daube M, Frei E, Schiltz E, Hunt J, Humphries T, Matranga V, Hochstrasser M, Aebersold R, Lee H, Noll M. The toposome, essential for sea urchin cell adhesion and development, is a modified iron-less calcium-binding transferrin. Developmental Biology. 310: 54-70. PMID 17707791 DOI: 10.1016/j.ydbio.2007.07.016  1
2007 Demers C, Chaturvedi CP, Ranish JA, Juban G, Lai P, Morle F, Aebersold R, Dilworth FJ, Groudine M, Brand M. Activator-mediated recruitment of the MLL2 methyltransferase complex to the beta-globin locus. Molecular Cell. 27: 573-84. PMID 17707229 DOI: 10.1016/j.molcel.2007.06.022  1
2007 Malmström J, Lee H, Aebersold R. Advances in proteomic workflows for systems biology. Current Opinion in Biotechnology. 18: 378-84. PMID 17698335 DOI: 10.1016/j.copbio.2007.07.005  1
2007 Taylor CF, Paton NW, Lilley KS, Binz PA, Julian RK, Jones AR, Zhu W, Apweiler R, Aebersold R, Deutsch EW, Dunn MJ, Heck AJ, Leitner A, Macht M, Mann M, et al. The minimum information about a proteomics experiment (MIAPE). Nature Biotechnology. 25: 887-93. PMID 17687369 DOI: 10.1038/nbt1329  1
2007 Stahl-Zeng J, Lange V, Ossola R, Eckhardt K, Krek W, Aebersold R, Domon B. High sensitivity detection of plasma proteins by multiple reaction monitoring of N-glycosites. Molecular & Cellular Proteomics : McP. 6: 1809-17. PMID 17644760 DOI: 10.1074/mcp.M700132-MCP200  1
2007 Lessard J, Wu JI, Ranish JA, Wan M, Winslow MM, Staahl BT, Wu H, Aebersold R, Graef IA, Crabtree GR. An essential switch in subunit composition of a chromatin remodeling complex during neural development. Neuron. 55: 201-15. PMID 17640523 DOI: 10.1016/j.neuron.2007.06.019  1
2007 Prakash A, Piening B, Whiteaker J, Zhang H, Shaffer SA, Martin D, Hohmann L, Cooke K, Olson JM, Hansen S, Flory MR, Lee H, Watts J, Goodlett DR, Aebersold R, et al. Assessing bias in experiment design for large scale mass spectrometry-based quantitative proteomics. Molecular & Cellular Proteomics : McP. 6: 1741-8. PMID 17617667 DOI: 10.1074/mcp.M600470-MCP200  1
2007 Au E, Richter MW, Vincent AJ, Tetzlaff W, Aebersold R, Sage EH, Roskams AJ. SPARC from olfactory ensheathing cells stimulates Schwann cells to promote neurite outgrowth and enhances spinal cord repair. The Journal of Neuroscience : the Official Journal of the Society For Neuroscience. 27: 7208-21. PMID 17611274 DOI: 10.1523/JNEUROSCI.0509-07.2007  1
2007 Gingras AC, Gstaiger M, Raught B, Aebersold R. Analysis of protein complexes using mass spectrometry. Nature Reviews. Molecular Cell Biology. 8: 645-54. PMID 17593931 DOI: 10.1038/nrm2208  1
2007 Zhou Y, Aebersold R, Zhang H. Isolation of N-linked glycopeptides from plasma. Analytical Chemistry. 79: 5826-37. PMID 17591751 DOI: 10.1021/ac0623181  1
2007 Picotti P, Aebersold R, Domon B. The implications of proteolytic background for shotgun proteomics. Molecular & Cellular Proteomics : McP. 6: 1589-98. PMID 17533221 DOI: 10.1074/mcp.M700029-MCP200  0.36
2007 Chen R, Brentnall TA, Pan S, Cooke K, Moyes KW, Lane Z, Crispin DA, Goodlett DR, Aebersold R, Bronner MP. Quantitative proteomics analysis reveals that proteins differentially expressed in chronic pancreatitis are also frequently involved in pancreatic cancer. Molecular & Cellular Proteomics : McP. 6: 1331-42. PMID 17496331 DOI: 10.1074/mcp.M700072-MCP200  1
2007 Lu Y, Bottari P, Aebersold R, Turecek F, Gelb MH. Absolute quantification of specific proteins in complex mixtures using visible isotope-coded affinity tags. Methods in Molecular Biology (Clifton, N.J.). 359: 159-76. PMID 17484117 DOI: 10.1007/978-1-59745-255-7_11  1
2007 Ranish JA, Brand M, Aebersold R. Using stable isotope tagging and mass spectrometry to characterize protein complexes and to detect changes in their composition. Methods in Molecular Biology (Clifton, N.J.). 359: 17-35. PMID 17484108 DOI: 10.1007/978-1-59745-255-7_2  1
2007 Brunner E, Ahrens CH, Mohanty S, Baetschmann H, Loevenich S, Potthast F, Deutsch EW, Panse C, de Lichtenberg U, Rinner O, Lee H, Pedrioli PG, Malmstrom J, Koehler K, Schrimpf S, ... ... Aebersold R, et al. A high-quality catalog of the Drosophila melanogaster proteome. Nature Biotechnology. 25: 576-83. PMID 17450130 DOI: 10.1038/nbt1300  1
2007 Tian Y, Zhou Y, Elliott S, Aebersold R, Zhang H. Solid-phase extraction of N-linked glycopeptides. Nature Protocols. 2: 334-9. PMID 17406594 DOI: 10.1038/nprot.2007.42  1
2007 Bodenmiller B, Mueller LN, Pedrioli PG, Pflieger D, Jünger MA, Eng JK, Aebersold R, Tao WA. An integrated chemical, mass spectrometric and computational strategy for (quantitative) phosphoproteomics: application to Drosophila melanogaster Kc167 cells. Molecular Biosystems. 3: 275-86. PMID 17372656 DOI: 10.1039/b617545g  1
2007 Chen R, Pan S, Cooke K, Moyes KW, Bronner MP, Goodlett DR, Aebersold R, Brentnall TA. Comparison of pancreas juice proteins from cancer versus pancreatitis using quantitative proteomic analysis. Pancreas. 34: 70-9. PMID 17198186 DOI: 10.1097/01.mpa.0000240615.20474.fd  1
2007 Mallick P, Schirle M, Chen SS, Flory MR, Lee H, Martin D, Ranish J, Raught B, Schmitt R, Werner T, Kuster B, Aebersold R. Computational prediction of proteotypic peptides for quantitative proteomics. Nature Biotechnology. 25: 125-31. PMID 17195840 DOI: 10.1038/nbt1275  1
2007 Jasavala R, Martinez H, Thumar J, Andaya A, Gingras AC, Eng JK, Aebersold R, Han DK, Wright ME. Identification of putative androgen receptor interaction protein modules: cytoskeleton and endosomes modulate androgen receptor signaling in prostate cancer cells. Molecular & Cellular Proteomics : McP. 6: 252-71. PMID 17052974 DOI: 10.1074/mcp.M600169-MCP200  1
2006 Shiio Y, Aebersold R. Quantitative proteome analysis using isotope-coded affinity tags and mass spectrometry. Nature Protocols. 1: 139-45. PMID 17406225 DOI: 10.1038/nprot.2006.22  1
2006 Chen R, Pan S, Yi EC, Donohoe S, Bronner MP, Potter JD, Goodlett DR, Aebersold R, Brentnall TA. Quantitative proteomic profiling of pancreatic cancer juice. Proteomics. 6: 3871-9. PMID 16739137 DOI: 10.1002/pmic.200500702  1
2006 Gan RR, Yi EC, Chiu Y, Lee H, Kao YC, Wu TH, Aebersold R, Goodlett DR, Ng WV. Proteome analysis of Halobacterium sp. NRC-1 facilitated by the biomodule analysis tool BMSorter. Molecular & Cellular Proteomics : McP. 5: 987-97. PMID 16497792 DOI: 10.1074/mcp.M500367-MCP200  1
2005 Corthals GL, Aebersold R, Goodlett DR. Identification of phosphorylation sites using microimmobilized metal affinity chromatography. Methods in Enzymology. 405: 66-81. PMID 16413311 DOI: 10.1016/S0076-6879(05)05004-4  1
2005 Chen SS, Deutsch EW, Yi EC, Li XJ, Goodlett DR, Aebersold R. Improving mass and liquid chromatography based identification of proteins using bayesian scoring. Journal of Proteome Research. 4: 2174-84. PMID 16335964 DOI: 10.1021/pr050251c  1
2005 Chen SS, Aebersold R. LC-MS solvent composition monitoring and chromatography alignment using mobile phase tracer molecules. Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences. 829: 107-14. PMID 16242386 DOI: 10.1016/j.jchromb.2005.09.039  1
2005 Chen R, Yi EC, Donohoe S, Pan S, Eng J, Cooke K, Crispin DA, Lane Z, Goodlett DR, Bronner MP, Aebersold R, Brentnall TA. Pancreatic cancer proteome: the proteins that underlie invasion, metastasis, and immunologic escape. Gastroenterology. 129: 1187-97. PMID 16230073 DOI: 10.1053/j.gastro.2005.08.001  1
2005 Tao WA, Wollscheid B, O'Brien R, Eng JK, Li XJ, Bodenmiller B, Watts JD, Hood L, Aebersold R. Quantitative phosphoproteome analysis using a dendrimer conjugation chemistry and tandem mass spectrometry. Nature Methods. 2: 591-8. PMID 16094384 DOI: 10.1038/nmeth776  1
2005 Gingras AC, Caballero M, Zarske M, Sanchez A, Hazbun TR, Fields S, Sonenberg N, Hafen E, Raught B, Aebersold R. A novel, evolutionarily conserved protein phosphatase complex involved in cisplatin sensitivity. Molecular & Cellular Proteomics : McP. 4: 1725-40. PMID 16085932 DOI: 10.1074/mcp.M500231-MCP200  1
2005 Zhang J, Goodlett DR, Quinn JF, Peskind E, Kaye JA, Zhou Y, Pan C, Yi E, Eng J, Wang Q, Aebersold RH, Montine TJ. Quantitative proteomics of cerebrospinal fluid from patients with Alzheimer disease. Journal of Alzheimer's Disease : Jad. 7: 125-33; discussion 1. PMID 15851850  1
2005 Yi EC, Li XJ, Cooke K, Lee H, Raught B, Page A, Aneliunas V, Hieter P, Goodlett DR, Aebersold R. Increased quantitative proteome coverage with (13)C/(12)C-based, acid-cleavable isotope-coded affinity tag reagent and modified data acquisition scheme. Proteomics. 5: 380-7. PMID 15648049 DOI: 10.1002/pmic.200400970  1
2005 Gingras AC, Aebersold R, Raught B. Advances in protein complex analysis using mass spectrometry. The Journal of Physiology. 563: 11-21. PMID 15611014 DOI: 10.1113/jphysiol.2004.080440  1
2005 Zhang J, Goodlett DR, Peskind ER, Quinn JF, Zhou Y, Wang Q, Pan C, Yi E, Eng J, Aebersold RH, Montine TJ. Quantitative proteomic analysis of age-related changes in human cerebrospinal fluid. Neurobiology of Aging. 26: 207-27. PMID 15582749 DOI: 10.1016/j.neurobiolaging.2004.03.012  1
2004 Marelli M, Smith JJ, Jung S, Yi E, Nesvizhskii AI, Christmas RH, Saleem RA, Tam YY, Fagarasanu A, Goodlett DR, Aebersold R, Rachubinski RA, Aitchison JD. Quantitative mass spectrometry reveals a role for the GTPase Rho1p in actin organization on the peroxisome membrane. The Journal of Cell Biology. 167: 1099-112. PMID 15596542 DOI: 10.1083/jcb.200404119  1
2004 Tian Q, Feetham MC, Tao WA, He XC, Li L, Aebersold R, Hood L. Proteomic analysis identifies that 14-3-3zeta interacts with beta-catenin and facilitates its activation by Akt. Proceedings of the National Academy of Sciences of the United States of America. 101: 15370-5. PMID 15492215 DOI: 10.1073/pnas.0406499101  1
2004 Wollscheid B, von Haller PD, Yi E, Donohoe S, Vaughn K, Keller A, Nesvizhskii AI, Eng J, Li XJ, Goodlett DR, Aebersold R, Watts JD. Lipid raft proteins and their identification in T lymphocytes. Sub-Cellular Biochemistry. 37: 121-52. PMID 15376619  1
2004 Yan W, Lee H, Yi EC, Reiss D, Shannon P, Kwieciszewski BK, Coito C, Li XJ, Keller A, Eng J, Galitski T, Goodlett DR, Aebersold R, Katze MG. System-based proteomic analysis of the interferon response in human liver cells. Genome Biology. 5: R54. PMID 15287976 DOI: 10.1186/gb-2004-5-8-r54  1
2004 Zhou Y, Gu G, Goodlett DR, Zhang T, Pan C, Montine TJ, Montine KS, Aebersold RH, Zhang J. Analysis of alpha-synuclein-associated proteins by quantitative proteomics. The Journal of Biological Chemistry. 279: 39155-64. PMID 15234983 DOI: 10.1074/jbc.M405456200  1
2004 Lee H, Yi EC, Wen B, Reily TP, Pohl L, Nelson S, Aebersold R, Goodlett DR. Optimization of reversed-phase microcapillary liquid chromatography for quantitative proteomics. Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences. 803: 101-10. PMID 15026003 DOI: 10.1016/j.jchromb.2003.09.005  1
2004 Hardwidge PR, Rodriguez-Escudero I, Goode D, Donohoe S, Eng J, Goodlett DR, Aebersold R, Finlay BB. Proteomic analysis of the intestinal epithelial cell response to enteropathogenic Escherichia coli. The Journal of Biological Chemistry. 279: 20127-36. PMID 14988394 DOI: 10.1074/jbc.M401228200  1
2004 MacKay VL, Li X, Flory MR, Turcott E, Law GL, Serikawa KA, Xu XL, Lee H, Goodlett DR, Aebersold R, Zhao LP, Morris DR. Gene expression analyzed by high-resolution state array analysis and quantitative proteomics: response of yeast to mating pheromone. Molecular & Cellular Proteomics : McP. 3: 478-89. PMID 14766929 DOI: 10.1074/mcp.M300129-MCP200  1
2004 Martin DB, Gifford DR, Wright ME, Keller A, Yi E, Goodlett DR, Aebersold R, Nelson PS. Quantitative proteomic analysis of proteins released by neoplastic prostate epithelium. Cancer Research. 64: 347-55. PMID 14729644 DOI: 10.1158/0008-5472.CAN-03-2062  1
2003 Yi EC, Lee H, Aebersold R, Goodlett DR. A microcapillary trap cartridge-microcapillary high-performance liquid chromatography electrospray ionization emitter device capable of peptide tandem mass spectrometry at the attomole level on an ion trap mass spectrometer with automated routine operation. Rapid Communications in Mass Spectrometry : Rcm. 17: 2093-8. PMID 12955739 DOI: 10.1002/rcm.1150  1
2003 Goo YA, Yi EC, Baliga NS, Tao WA, Pan M, Aebersold R, Goodlett DR, Hood L, Ng WV. Proteomic analysis of an extreme halophilic archaeon, Halobacterium sp. NRC-1. Molecular & Cellular Proteomics : McP. 2: 506-24. PMID 12872007 DOI: 10.1074/mcp.M300044-MCP200  1
2003 Guina T, Wu M, Miller SI, Purvine SO, Yi EC, Eng J, Goodlett DR, Aebersold R, Ernst RK, Lee KA. Proteomic analysis of Pseudomonas aeruginosa grown under magnesium limitation. Journal of the American Society For Mass Spectrometry. 14: 742-51. PMID 12837596 DOI: 10.1016/S1044-0305(03)00133-8  1
2003 Shiio Y, Eisenman RN, Yi EC, Donohoe S, Goodlett DR, Aebersold R. Quantitative proteomic analysis of chromatin-associated factors. Journal of the American Society For Mass Spectrometry. 14: 696-703. PMID 12837591 DOI: 10.1016/S1044-0305(03)00204-6  1
2003 von Haller PD, Yi E, Donohoe S, Vaughn K, Keller A, Nesvizhskii AI, Eng J, Li XJ, Goodlett DR, Aebersold R, Watts JD. The application of new software tools to quantitative protein profiling via isotope-coded affinity tag (ICAT) and tandem mass spectrometry: II. Evaluation of tandem mass spectrometry methodologies for large-scale protein analysis, and the application of statistical tools for data analysis and interpretation. Molecular & Cellular Proteomics : McP. 2: 428-42. PMID 12832459 DOI: 10.1074/mcp.M300041-MCP200  1
2003 von Haller PD, Yi E, Donohoe S, Vaughn K, Keller A, Nesvizhskii AI, Eng J, Li XJ, Goodlett DR, Aebersold R, Watts JD. The application of new software tools to quantitative protein profiling via isotope-coded affinity tag (ICAT) and tandem mass spectrometry: I. Statistically annotated datasets for peptide sequences and proteins identified via the application of ICAT and tandem mass spectrometry to proteins copurifying with T cell lipid rafts. Molecular & Cellular Proteomics : McP. 2: 426-7. PMID 12832456 DOI: 10.1074/mcp.D300002-MCP200  1
2003 Griffin TJ, Lock CM, Li XJ, Patel A, Chervetsova I, Lee H, Wright ME, Ranish JA, Chen SS, Aebersold R. Abundance ratio-dependent proteomic analysis by mass spectrometry. Analytical Chemistry. 75: 867-74. PMID 12622378 DOI: 10.1021/ac026127j  1
2003 Patterson SD, Aebersold RH. Proteomics: The first decade and beyond Nature Genetics. 33: 311-323. PMID 12610541 DOI: 10.1038/ng1106  1
2003 Guina T, Purvine SO, Yi EC, Eng J, Goodlett DR, Aebersold R, Miller SI. Quantitative proteomic analysis indicates increased synthesis of a quinolone by Pseudomonas aeruginosa isolates from cystic fibrosis airways. Proceedings of the National Academy of Sciences of the United States of America. 100: 2771-6. PMID 12601166 DOI: 10.1073/pnas.0435846100  1
2003 Ranish JA, Yi EC, Leslie DM, Purvine SO, Goodlett DR, Eng J, Aebersold R. The study of macromolecular complexes by quantitative proteomics. Nature Genetics. 33: 349-55. PMID 12590263 DOI: 10.1038/ng1101  1
2003 Chikamori K, Grabowski DR, Kinter M, Willard BB, Yadav S, Aebersold RH, Bukowski RM, Hickson ID, Andersen AH, Ganapathi R, Ganapathi MK. Phosphorylation of serine 1106 in the catalytic domain of topoisomerase II alpha regulates enzymatic activity and drug sensitivity. The Journal of Biological Chemistry. 278: 12696-702. PMID 12569090 DOI: 10.1074/jbc.M300837200  1
2003 Tao WA, Aebersold R. Advances in quantitative proteomics via stable isotope tagging and mass spectrometry. Current Opinion in Biotechnology. 14: 110-8. PMID 12566010 DOI: 10.1016/S0958-1669(02)00018-6  1
2002 Gygi SP, Rist B, Griffin TJ, Eng J, Aebersold R. Proteome analysis of low-abundance proteins using multidimensional chromatography and isotope-coded affinity tags. Journal of Proteome Research. 1: 47-54. PMID 12643526 DOI: 10.1021/pr015509n  1
2002 Flory MR, Griffin TJ, Martin D, Aebersold R. Advances in quantitative proteomics using stable isotope tags. Trends in Biotechnology. 20: S23-9. PMID 12570156  1
2002 Baliga NS, Pan M, Goo YA, Yi EC, Goodlett DR, Dimitrov K, Shannon P, Aebersold R, Ng WV, Hood L. Coordinate regulation of energy transduction modules in Halobacterium sp. analyzed by a global systems approach. Proceedings of the National Academy of Sciences of the United States of America. 99: 14913-8. PMID 12403819 DOI: 10.1073/pnas.192558999  1
2002 Shiio Y, Donohoe S, Yi EC, Goodlett DR, Aebersold R, Eisenman RN. Quantitative proteomic analysis of Myc oncoprotein function. The Embo Journal. 21: 5088-96. PMID 12356725  1
2002 Yi EC, Marelli M, Lee H, Purvine SO, Aebersold R, Aitchison JD, Goodlett DR. Approaching complete peroxisome characterization by gas-phase fractionation. Electrophoresis. 23: 3205-16. PMID 12298092 DOI: 10.1002/1522-2683(200209)23:18<3205::AID-ELPS3205>3.0.CO;2-Y  1
2002 Lee H, Griffin TJ, Gygi SP, Rist B, Aebersold R. Development of a multiplexed microcapillary liquid chromatography system for high-throughput proteome analysis. Analytical Chemistry. 74: 4353-60. PMID 12236342 DOI: 10.1021/ac025757i  1
2002 Griffin TJ, Gygi SP, Ideker T, Rist B, Eng J, Hood L, Aebersold R. Complementary profiling of gene expression at the transcriptome and proteome levels in Saccharomyces cerevisiae. Molecular & Cellular Proteomics : McP. 1: 323-33. PMID 12096114  1
2002 James EA, Gygi SP, Adams ML, Pierce RH, Fausto N, Aebersold RH, Nelson SD, Bruschi SA. Mitochondrial aconitase modification, functional inhibition, and evidence for a supramolecular complex of the TCA cycle by the renal toxicant S-(1,1,2,2-tetrafluoroethyl)-L-cysteine. Biochemistry. 41: 6789-97. PMID 12022883 DOI: 10.1021/bi020038j  1
2002 Hamerman JA, Hayashi F, Schroeder LA, Gygi SP, Haas AL, Hampson L, Coughlin P, Aebersold R, Aderem A. Serpin 2a is induced in activated macrophages and conjugates to a ubiquitin homolog. Journal of Immunology (Baltimore, Md. : 1950). 168: 2415-23. PMID 11859133  1
2002 Dramsi S, Scheid MP, Maiti A, Hojabrpour P, Chen X, Schubert K, Goodlett DR, Aebersold R, Duronio V. Identification of a novel phosphorylation site, Ser-170, as a regulator of bad pro-apoptotic activity. The Journal of Biological Chemistry. 277: 6399-405. PMID 11717309 DOI: 10.1074/jbc.M109990200  1
2001 Griffin TJ, Goodlett DR, Aebersold R. Advances in proteome analysis by mass spectrometry. Current Opinion in Biotechnology. 12: 607-12. PMID 11849943 DOI: 10.1016/S0958-1669(01)00268-3  1
2001 Griffin TJ, Han DK, Gygi SP, Rist B, Lee H, Aebersold R, Parker KC. Toward a high-throughput approach to quantitative proteomic analysis: expression-dependent protein identification by mass spectrometry. Journal of the American Society For Mass Spectrometry. 12: 1238-46. PMID 11766750 DOI: 10.1016/S1044-0305(01)00316-6  1
2001 Aebersold R, Goodlett DR. Mass spectrometry in proteomics. Chemical Reviews. 101: 269-95. PMID 11712248  1
2001 von Haller PD, Donohoe S, Goodlett DR, Aebersold R, Watts JD. Mass spectrometric characterization of proteins extracted from Jurkat T cell detergent-resistant membrane domains. Proteomics. 1: 1010-21. PMID 11683502 DOI: 10.1002/1615-9861(200108)1:8<1010::AID-PROT1010>3.0.CO;2-L  1
2001 Griffin TJ, Aebersold R. Advances in proteome analysis by mass spectrometry. The Journal of Biological Chemistry. 276: 45497-500. PMID 11585843 DOI: 10.1074/jbc.R100014200  1
2001 Smolka MB, Zhou H, Purkayastha S, Aebersold R. Optimization of the isotope-coded affinity tag-labeling procedure for quantitative proteome analysis. Analytical Biochemistry. 297: 25-31. PMID 11567524 DOI: 10.1006/abio.2001.5318  1
2001 Goodlett DR, Keller A, Watts JD, Newitt R, Yi EC, Purvine S, Eng JK, von Haller P, Aebersold R, Kolker E. Differential stable isotope labeling of peptides for quantitation and de novo sequence derivation. Rapid Communications in Mass Spectrometry : Rcm. 15: 1214-21. PMID 11445905 DOI: 10.1002/rcm.362  1
2001 Ideker T, Thorsson V, Ranish JA, Christmas R, Buhler J, Eng JK, Bumgarner R, Goodlett DR, Aebersold R, Hood L. Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science (New York, N.Y.). 292: 929-34. PMID 11340206 DOI: 10.1126/science.292.5518.929  1
2001 Griffin TJ, Gygi SP, Rist B, Aebersold R, Loboda A, Jilkine A, Ens W, Standing KG. Quantitative proteomic analysis using a MALDI quadrupole time-of-flight mass spectrometer. Analytical Chemistry. 73: 978-86. PMID 11289445 DOI: 10.1021/ac001169y  1
2000 Katze MG, Kwieciszewski B, Goodlett DR, Blakely CM, Neddermann P, Tan SL, Aebersold R. Ser2194 is a highly conserved major phosphorylation site of the hepatitis c virus nonstructural protein NS5A Virology. 278: 501-513. PMID 11118372 DOI: 10.1006/viro.2000.0662  1
2000 Heller M, Goodlett DR, Watts JD, Aebersold R. A comprehensive characterization of the T-cell antigen receptor complex composition by microcapillary liquid chromatography-tandem mass spectrometry. Electrophoresis. 21: 2180-95. PMID 10892729 DOI: 10.1002/1522-2683(20000601)21:11<2180::AID-ELPS2180>3.0.CO;2-#  1
2000 Goodlett DR, Bruce JE, Anderson GA, Rist B, Pasa-Tolic L, Fiehn O, Smith RD, Aebersold R. Protein identification with a single accurate mass of a cysteine- containing peptide and constrained database searching Analytical Chemistry. 72: 1112-1118. PMID 10740847 DOI: 10.1021/ac9913210  1
2000 Goodlett DR, Aebersold R, Watts JD. Quantitative in vitro kinase reaction as a guide for phosphoprotein analysis by mass spectrometry. Rapid Communications in Mass Spectrometry : Rcm. 14: 344-8. PMID 10700036 DOI: 10.1002/(SICI)1097-0231(20000315)14:5<344::AID-RCM866>3.0.CO;2-W  1
1999 Gallis B, Corthals GL, Goodlett DR, Ueba H, Kim F, Presnell SR, Figeys D, Harrison DG, Berk BC, Aebersold R, Corson MA. Identification of flow-dependent endothelial nitric-oxide synthase phosphorylation sites by mass spectrometry and regulation of phosphorylation and nitric oxide production by the phosphatidylinositol 3-kinase inhibitor LY294002 Journal of Biological Chemistry. 274: 30101-30108. PMID 10514497 DOI: 10.1074/jbc.274.42.30101  1
1999 Figeys D. Data-dependent modulation of solid-phase extraction capillary electrophoresis for the analysis of complex peptide and phosphopeptide mixtures by tandem mass spectrometry: Application to endothelial nitric oxide synthase Analytical Chemistry. 71: 2279-2287. PMID 10405598  1
1999 Watts JD, Aebersold R, Polverino AJ, Patterson SD, Gu M. Ceramide second messengers and ceramide assays Trends in Biochemical Sciences. 24: 228. PMID 10366850  1
1999 Watts JD, Ming G, Patterson SD, Aebersold R, Polverino AJ. On the complexities of ceramide changes in cells undergoing apoptosis: Lack of evidence for a second messenger function in apoptotic induction Cell Death and Differentiation. 6: 105-114. PMID 10200556  1
1999 Figeys D, Aebersold R. Microfabricated modules for sample handling, sample concentration and flow mixing: Application to protein analysis by tandem mass spectrometry Journal of Biomechanical Engineering. 121: 7-12. PMID 10080083  1
1999 Susin SA, Lorenzo HK, Zamzami N, Marzo I, Snow BE, Brothers GM, Mangion J, Jacotot E, Costantini P, Loeffler M, Larochette N, Goodlett DR, Aebersold R, Siderovski DP, Penninger JM, et al. Molecular characterization of mitochondrial apoptosis-inducing factor. Nature. 397: 441-6. PMID 9989411 DOI: 10.1038/17135  1
1998 Figeys D, Lock C, Taylor L, Aebersold R. Microfabricated device coupled with an electrospray ionization quadrupole time-of-flight mass spectrometer: Protein identifications based on enhanced-resolution mass spectrometry and tandem mass spectrometry data Rapid Communications in Mass Spectrometry. 12: 1435-1444. PMID 9796531  1
1998 Figeys D, Zhang Y, Aebersold R. Optimization of solid phase microextraction - Capillary zone electrophoresis - Mass spectrometry for high sensitivity protein identification Electrophoresis. 19: 2338-2347. PMID 9788318 DOI: 10.1002/elps.1150191314  1
1998 Figeys D, Gygi SP, McKinnon G, Aebersold R. An Integrated Microfluidics-Tandem Mass Spectrometry System for Automated Protein Analysis Analytical Chemistry. 70: 3728-3734. PMID 9751017  1
1998 Figeys D, Aebersold R. Nanoflow Solvent Gradient Delivery from a Microfabricated Device for Protein Identifications by Electrospray Ionization Mass Spectrometry Analytical Chemistry. 70: 3721-3727. PMID 9751016  1
1998 Haynes PA, Gygi SP, Figeys D, Aebersold R. Proteome analysis: biological assay or data archive? Electrophoresis. 19: 1862-71. PMID 9740046 DOI: 10.1002/elps.1150191104  1
1998 Aebersold R, Figeys D, Gygi S, Corthals G, Haynes P, Rist B, Sherman J, Zhang Y, Goodlett D. Towards an integrated analytical technology for the generation of multidimensional protein expression maps. Journal of Protein Chemistry. 17: 533-5. PMID 9723742  1
1998 Figeys D, Gygi SP, Zhang Y, Watts J, Gu M, Aebersold R. Electrophoresis combined with novel mass spectrometry techniques: Powerful tools for the analysis of proteins and proteomes Electrophoresis. 19: 1811-1818. PMID 9719564  1
1998 Zhang Y, Figeys D, Aebersold R. Purification of trypsin for mass spectrometric identification of proteins at high sensitivity Analytical Biochemistry. 261: 124-127. PMID 9683523 DOI: 10.1006/abio.1998.2666  1
1998 Figeys D, Aebersold R. High sensitivity analysis of proteins and peptides by capillary electrophoresis-tandem mass spectrometry: Recent developments in technology and applications Electrophoresis. 19: 885-892. PMID 9638934 DOI: 10.1002/elps.1150190603  1
1997 Raval-Fernandes S, Sawant LA, Aebersold RH, Ducret A, Rome LH. Axonal proteins involved in myelination: characterization of a collagen-like protein. Developmental Neuroscience. 19: 421-9. PMID 9323462 DOI: 10.1159/000111239  1
1997 Figeys D, Aebersold R. Capillary electrophoresis of peptides and proteins at neutral pH in capillaries covalently coated with polyethyleneimine Journal of Chromatography B: Biomedical Applications. 695: 163-168. PMID 9271140 DOI: 10.1016/S0378-4347(97)00022-4  1
1997 Figeys D, Ning Y, Aebersold R. A Microfabricated Device for Rapid Protein Identification by Microelectrospray Ion Trap Mass Spectrometry Analytical Chemistry. 69: 3153-3160. PMID 9271059  1
1997 Watts JD, Gu M, Polverino AJ, Patterson SD, Aebersold R. Fas-induced apoptosis of T cells occurs independently of ceramide generation. Proceedings of the National Academy of Sciences of the United States of America. 94: 7292-6. PMID 9207084  1
1997 Figeys D, Aebersold R. High sensitivity identification of proteins by electrospray ionization tandem mass spectrometry: Initial comparison between, an ion trap mass spectrometer and a triple quadrupole mass spectrometer Electrophoresis. 18: 360-368. PMID 9150914 DOI: 10.1002/elps.1150180310  1
1997 Figeys D, Ducret A, Aebersold R. Identification of proteins by capillary electrophoresis-tandem mass spectrometry. Evaluation of an on-line solid-phase extraction device Journal of Chromatography A. 763: 295-306. PMID 9129327 DOI: 10.1016/S0021-9673(96)00847-3  1
1996 Figeys D, Ducret A, Yates JR, Aebersold R. Protein Identification by Solid Phase Microextraction–Capillary Zone Electrophoresis–Microelectrospray–Tandem Mass Spectrometry Nature Biotechnology. 14: 1579-1583. PMID 9634825 DOI: 10.1038/nbt1196-1579  1
1996 Figeys D, Van Oostveen I, Ducret A, Aebersold R. Protein identification by capillary zone electrophoresis/microelectrospray ionization-tandem mass spectrometry at the subfemtomole level Analytical Chemistry. 68: 1822-1828. PMID 8686909 DOI: 10.1021/ac960191h  1
1995 Patterson SD, Aebersold R. Mass spectrometric approaches for the identification of gel-separated proteins Electrophoresis. 16: 1791-1814. PMID 8586048  1
1992 Patterson SD, Hess D, Yungwirth T, Aebersold R. High-yield recovery of electroblotted proteins and cleavage fragments from a cationic polyvinylidene fluoride-based membrane Analytical Biochemistry. 202: 193-203. PMID 1377888 DOI: 10.1016/0003-2697(92)90227-X  1
1991 Wettenhall RE, Aebersold RH, Hood LE. Solid-phase sequencing of 32P-labeled phosphopeptides at picomole and subpicomole levels. Methods in Enzymology. 201: 186-99. PMID 1943764  1
1990 Lin CS, Aebersold RH, Leavitt J. Correction of the N-terminal sequences of the human plastin isoforms by using anchored polymerase chain reaction: Identification of a potential calcium-binding domain Molecular and Cellular Biology. 10: 1818-1821. PMID 2378651  1
1990 Aebersold R, Pipes GD, Wettenhall RE, Nika H, Hood LE. Covalent attachment of peptides for high sensitivity solid-phase sequence analysis. Analytical Biochemistry. 187: 56-65. PMID 2372121 DOI: 10.1016/0003-2697(90)90417-8  1
1990 Aebersold R, Leavitt J. Sequence analysis of proteins separated by polyacrylamide gel electrophoresis: Towards an integrated protein database Electrophoresis. 11: 517-527. PMID 2226408 DOI: 10.1002/elps.1150110702  1
1989 Saavedra RA, Fors L, Aebersold RH, Arden B, Horvath S, Sanders J, Hood L. The myelin proteins of the shark brain are similar to the myelin proteins of the mammalian peripheral nervous system. Journal of Molecular Evolution. 29: 149-56. PMID 2478717  1
1988 Aebersold RH, Pipes G, Hood LE, Kent SB. N-terminal and internal sequence determination of microgram amounts of proteins separated by isoelectric focusing in immobilized pH gradients. Electrophoresis. 9: 520-30. PMID 3243248 DOI: 10.1002/elps.1150090912  1
1988 Lin CS, Aebersold RH, Kent SB, Varma M, Leavitt J. Molecular cloning and characterization of plastin, a human leukocyte protein expressed in transformed human fibroblasts. Molecular and Cellular Biology. 8: 4659-68. PMID 3211125  1
1988 Aebersold RH, Pipes GD, Nika H, Hood LE, Kent SB. Covalent immobilization of proteins for high-sensitivity sequence analysis: electroblotting onto chemically activated glass from sodium dodecyl sulfate-polyacrylamide gels. Biochemistry. 27: 6860-7. PMID 3196688  1
1987 Aebersold RH, Leavitt J, Saavedra RA, Hood LE, Kent SB. Internal amino acid sequence analysis of proteins separated by one- or two-dimensional gel electrophoresis after in situ protease digestion on nitrocellulose. Proceedings of the National Academy of Sciences of the United States of America. 84: 6970-4. PMID 3313383  1
1986 Aebersold RH, Teplow DB, Hood LE, Kent SB. Electroblotting onto activated glass. High efficiency preparation of proteins from analytical sodium dodecyl sulfate-polyacrylamide gels for direct sequence analysis. The Journal of Biological Chemistry. 261: 4229-38. PMID 3949810  1
1986 Tempst P, Woo DD, Teplow DB, Aebersold R, Hood LE, Kent SB. Microscale structure analysis of a high-molecular-weight, hydrophobic membrane glycoprotein fraction with platelet-derived growth factor-dependent kinase activity. Journal of Chromatography. 359: 403-12. PMID 3733938 DOI: 10.1016/0021-9673(86)80094-2  1
1986 Herbst H, Grütter T, Aebersold R, Braun DG. Combinatorial diversity in the generation of antibody molecules. The complete amino-acid sequence of the variable domain of a monoclonal anti-streptococcal group A polysaccharide antibody. Biological Chemistry Hoppe-Seyler. 367: 843-51. PMID 3539142  1
1986 Clark-Lewis I, Aebersold R, Ziltener H, Schrader JW, Hood LE, Kent SB. Automated chemical synthesis of a protein growth factor for hemopoietic cells, interleukin-3. Science (New York, N.Y.). 231: 134-9. PMID 3079915  1
1986 Rice CM, Aebersold R, Teplow DB, Pata J, Bell JR, Vorndam AV, Trent DW, Brandriss MW, Schlesinger JJ, Strauss JH. Partial N-terminal amino acid sequences of three nonstructural proteins of two flaviviruses. Virology. 151: 1-9. PMID 3008425 DOI: 10.1016/0042-6822(86)90098-X  1
1985 Oesch B, Westaway D, Wälchli M, McKinley MP, Kent SB, Aebersold R, Barry RA, Tempst P, Teplow DB, Hood LE. A cellular gene encodes scrapie PrP 27-30 protein. Cell. 40: 735-46. PMID 2859120 DOI: 10.1016/0092-8674(85)90333-2  1
1984 Aebersold R, Herbst H, Chang JY, Braun DG. Murine V kappa 21A isotype sequence: monoclonal antibody 50S10.1 specific for the group A streptococcal polysaccharide. Hoppe-Seyler's Zeitschrift FüR Physiologische Chemie. 365: 1385-91. PMID 6441769 DOI: 10.1515/bchm2.1984.365.2.1385  1
1984 Aebersold R, Herbst H, Grütter T, Chang JY, Braun DG. Murine V kappa 25 and V kappa 27 amino-acid sequences of C57B1/6 origin: monoclonal antibodies 17S29.1 and 22S25.1 specific for the group A-streptococcal polysaccharide. Hoppe-Seyler's Zeitschrift FüR Physiologische Chemie. 365: 1375-83. PMID 6441768  0.56
1984 Aebersold R, Ledermann F, Braun DG, Chang JY. Microisolation of DABITC-derivatized protein by gel electrophoresis: application to the purification of antibody heavy and light chains. Analytical Biochemistry. 136: 465-9. PMID 6426344 DOI: 10.1016/0003-2697(84)90245-8  1
1984 Todd I, Chang SP, Perlmutter RM, Aebersold R, Heusser CH, Hood L, Rittenberg MB. Immunologic memory to phosphocholine. V. Hybridomas representative of group II antibodies utilize V kappa 1-3 gene(s). Journal of Immunology (Baltimore, Md. : 1950). 132: 1556-60. PMID 6420467  1
1983 Chang JY, Herbst H, Aebersold R, Braun DG. A new isotype sequence (V kappa 27) of the variable region of kappa-light chains from a mouse hybridoma-derived anti-(streptococcal group A polysaccharide) antibody containing an additional cysteine residue. Application of the dimethylaminoazobenzene isothiocyanate technique for the isolation of peptides. The Biochemical Journal. 211: 173-80. PMID 6409088  1
1982 Herbst H, Chang JY, Aebersold R, Braun DG. Murine VK25 isotype sequence: monoclonal antibody 2S1.3 specific for the group A streptococcal polysaccharide. Hoppe-Seyler's Zeitschrift FüR Physiologische Chemie. 363: 1069-76. PMID 7141411 DOI: 10.1515/bchm2.1982.363.2.1069  1
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