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Ruedi Aebersold - Related publications

Systems biology Eidgenössische Technische Hochschule Zürich, Zürich, ZH, Switzerland 
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50 most relevant papers in past 60 days:
Year Citation  Score
2021 Wippel HH, Chavez JD, Tang X, Bruce JE. Quantitative interactome analysis with chemical cross-linking and mass spectrometry. Current Opinion in Chemical Biology. PMID 34393043 DOI: 10.1016/j.cbpa.2021.06.011   
2021 Rossouw SC, Bendou H, Blignaut RJ, Bell L, Rigby J, Christoffels A. Evaluation of Protein Purification Techniques and Effects of Storage Duration on LC-MS/MS Analysis of Archived FFPE Human CRC Tissues. Pathology Oncology Research : Por. 27: 622855. PMID 34257588 DOI: 10.3389/pore.2021.622855   
2021 Yin B, Caggiano LR, Li RC, McGowan E, Holmes JW, Ewald SE. Automated Spatially Targeted Optical Microproteomics Investigates Inflammatory Lesions . Journal of Proteome Research. PMID 34436902 DOI: 10.1021/acs.jproteome.1c00505   
2021 van Bergen W, Heck AJR, Baggelaar MP. Recent advancements in mass spectrometry-based tools to investigate newly synthesized proteins. Current Opinion in Chemical Biology. PMID 34364788 DOI: 10.1016/j.cbpa.2021.07.001   
2021 Frauenstein A, Ebner S, Hansen FM, Sinha A, Phulphagar K, Swatek K, Hornburg D, Mann M, Meissner F. Identification of covalent modifications regulating immune signaling complex composition and phenotype. Molecular Systems Biology. 17: e10125. PMID 34318608 DOI: 10.15252/msb.202010125   
2021 Periasamy P, Rajandran S, Ziegman R, Casey M, Nakamura K, Kore H, Datta K, Gowda H. A simple organic solvent precipitation method to improve detection of low molecular weight proteins. Proteomics. e2100152. PMID 34390184 DOI: 10.1002/pmic.202100152   
2021 Fossati A, Richards AL, Chen KH, Jaganath D, Cattamanchi A, Ernst JD, Swaney DL. Toward Comprehensive Plasma Proteomics by Orthogonal Protease Digestion. Journal of Proteome Research. PMID 34319755 DOI: 10.1021/acs.jproteome.1c00357   
2021 Tao J, Jia S, Wang M, Huang Z, Wang B, Zhang W, Wei Y, Li W, Jiang H, Du Z. Systematic Identification of Proteins Binding with Cisplatin in Blood by Affinity Chromatography and a Four-Dimensional Proteomic Method. Journal of Proteome Research. PMID 34427088 DOI: 10.1021/acs.jproteome.1c00535   
2021 Smythers AL, Iannetta AA, Hicks LM. Crosslinking mass spectrometry unveils novel interactions and structural distinctions in the model green alga . Molecular Omics. PMID 34499065 DOI: 10.1039/d1mo00197c   
2021 Liu X, Zhang Y, Ward LD, Yan Q, Bohnuud T, Hernandez R, Lao S, Yuan J, Fan F. A proteomic platform to identify off-target proteins associated with therapeutic modalities that induce protein degradation or gene silencing. Scientific Reports. 11: 15856. PMID 34349202 DOI: 10.1038/s41598-021-95354-3   
2021 Matsui Y, Abe Y, Uno K, Miyano S. RoDiCE: robust differential protein co-expression analysis for cancer complexome. Bioinformatics (Oxford, England). PMID 34529752 DOI: 10.1093/bioinformatics/btab612   
2021 Wheat A, Yu C, Wang X, Burke AM, Chemmama IE, Kaake RM, Baker P, Rychnovsky SD, Yang J, Huang L. Protein interaction landscapes revealed by advanced in vivo cross-linking-mass spectrometry. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34349018 DOI: 10.1073/pnas.2023360118   
2021 Li W, Zhang Q, Wang X, Wang H, Zuo W, Xie H, Tang J, Wang M, Zeng Z, Cai W, Tang D, Dai Y. Comparative Proteomic Analysis to Investigate the Pathogenesis of Oral Adenoid Cystic Carcinoma. Acs Omega. 6: 18623-18634. PMID 34337202 DOI: 10.1021/acsomega.1c01270   
2021 Bennett JL, Nguyen GTH, Donald WA. Protein-Small Molecule Interactions in Native Mass Spectrometry. Chemical Reviews. PMID 34449207 DOI: 10.1021/acs.chemrev.1c00293   
2021 Gray T, Storz G, Papenfort K. Small Proteins; Big Questions. Journal of Bacteriology. JB0034121. PMID 34309401 DOI: 10.1128/JB.00341-21   
2021 Gaspar VP, Ramos AC, Cloutier P, Pattaro Junior JR, Duarte Junior FF, Bouchard A, Seixas FAV, Coulombe B, Fernandez MA. Interactome Analysis of KIN (Kin17) Shows New Functions of This Protein. Current Issues in Molecular Biology. 43: 767-781. PMID 34449532 DOI: 10.3390/cimb43020056   
2021 Xu M, Zhang X, Yu J, Guo Z, Li Y, Song X, He K, Li G, Chi Y. Proteome-Wide Analysis of Lysine 2-Hydroxyisobutyrylation in in Peanuts. Frontiers in Microbiology. 12: 719337. PMID 34489910 DOI: 10.3389/fmicb.2021.719337   
2021 Li Y, Wang Z, Li LP, You ZH, Huang WZ, Zhan XK, Wang YB. Robust and accurate prediction of protein-protein interactions by exploiting evolutionary information. Scientific Reports. 11: 16910. PMID 34413375 DOI: 10.1038/s41598-021-96265-z   
2021 Li S, Zhang Z, Li X, Tan Y, Wang L, Chen Z. An iteration model for identifying essential proteins by combining comprehensive PPI network with biological information. Bmc Bioinformatics. 22: 430. PMID 34496745 DOI: 10.1186/s12859-021-04300-7   
2021 Zeng X, Xiang Y, Liu Q, Wang L, Ma Q, Ma W, Zeng D, Yin Y, Wang D. Nanopore Technology for the Application of Protein Detection. Nanomaterials (Basel, Switzerland). 11. PMID 34443773 DOI: 10.3390/nano11081942   
2021 Birukou I, Zawadzki M, Graser G, Young S. Protein Characterization by MALDI In-Source Decay Mass Spectrometry in Support of Safety Assessments of Genetically Modified Crops. Journal of Agricultural and Food Chemistry. PMID 34428040 DOI: 10.1021/acs.jafc.1c00512   
2021 Al-Jabiry A, Palmer M, Langridge J, Bellamy-Carter J, Robinson D, Oldham NJ. Combined Chemical Modification and Collision Induced Unfolding Using Native Ion Mobility-mass Spectrometry Provides Insights into Protein Gas-phase Structure. Chemistry (Weinheim An Der Bergstrasse, Germany). PMID 34289194 DOI: 10.1002/chem.202101857   
2021 Betancourt LH, Gil J, Sanchez A, Doma V, Kuras M, Murillo JR, Velasquez E, Çakır U, Kim Y, Sugihara Y, Parada IP, Szeitz B, Appelqvist R, Wieslander E, Welinder C, et al. The Human Melanoma Proteome Atlas-Complementing the melanoma transcriptome. Clinical and Translational Medicine. 11: e451. PMID 34323402 DOI: 10.1002/ctm2.451   
2021 Li W, Wang X, Zhang Q, Wang H, Zuo W, Xie H, Tang J, Wang M, Zeng Z, Cai W, Tang D, Dai Y. Quantitative ubiquitylomics reveals the ubiquitination regulation landscape in oral adenoid cystic carcinoma. Bioscience Reports. PMID 34350460 DOI: 10.1042/BSR20211532   
2021 Orsburn BC. Evaluation of the Sensitivity of Proteomics Methods Using the Absolute Copy Number of Proteins in a Single Cell as a Metric. Proteomes. 9. PMID 34287363 DOI: 10.3390/proteomes9030034   
2021 Orsburn BC. Evaluation of the Sensitivity of Proteomics Methods Using the Absolute Copy Number of Proteins in a Single Cell as a Metric. Proteomes. 9. PMID 34287363 DOI: 10.3390/proteomes9030034   
2021 Hargett AA, Marcella AM, Yu H, Li C, Orwenyo J, Battistel MD, Wang LX, Freedberg DI. Glycosylation States on Intact Proteins Determined by NMR Spectroscopy. Molecules (Basel, Switzerland). 26. PMID 34299586 DOI: 10.3390/molecules26144308   
2021 Shao D, Huang L, Wang Y, He K, Cui X, Wang Y, Ma Q, Cui J. DeepSec: a deep learning framework for secreted protein discovery in human body fluids. Bioinformatics (Oxford, England). PMID 34398224 DOI: 10.1093/bioinformatics/btab545   
2021 Gopal A, Herr AE. Segmentation-Based analysis of single-cell immunoblots. Electrophoresis. PMID 34357587 DOI: 10.1002/elps.202100144   
2021 Murali R, Zhang H, Cai Z, Lam L, Greene M. Rational Design of Constrained Peptides as Protein Interface Inhibitors. Antibodies (Basel, Switzerland). 10. PMID 34449551 DOI: 10.3390/antib10030032   
2021 Velasquez EF, Garcia YA, Ramirez I, Gholkar AA, Torres JZ. CANVS: an easy-to-use application for the analysis and visualization of mass spectrometry-based protein-protein interaction/association data. Molecular Biology of the Cell. mbcE21050257. PMID 34432510 DOI: 10.1091/mbc.E21-05-0257   
2021 Sarma A, Gunasekaran D, Rex DAB, Sikha T, Phukan H, Kiran KM, Pinto SM, Prasad TSK, Madanan MG. Extracellular Proteome Analysis Shows the Abundance of Histidine Kinase Sensor Protein, DNA Helicase, Putative Lipoprotein Containing Peptidase M75 Domain and Peptidase C39 Domain Protein in Grown in EMJH Medium. Pathogens (Basel, Switzerland). 10. PMID 34358002 DOI: 10.3390/pathogens10070852   
2021 Johnson RL, Blaber HG, Evans T, Worthy HL, Pope JR, Jones DD. Designed Artificial Protein Heterodimers With Coupled Functions Constructed Using Bio-Orthogonal Chemistry. Frontiers in Chemistry. 9: 733550. PMID 34422774 DOI: 10.3389/fchem.2021.733550   
2021 Mao Y, Zheng J, Feng S, Tian R. [Comparison of the performance of secretome analysis based on metabolic labeling by three unnatural sugars]. SE Pu = Chinese Journal of Chromatography. 39: 1086-1093. PMID 34505430 DOI: 10.3724/SP.J.1123.2021.04017   
2021 Duś-Szachniewicz K, Gdesz-Birula K, Zduniak K, Wiśniewski JR. Proteomic-Based Analysis of Hypoxia- and Physioxia-Responsive Proteins and Pathways in Diffuse Large B-Cell Lymphoma. Cells. 10. PMID 34440794 DOI: 10.3390/cells10082025   
2021 Liu Y, Chen W, He Z. Essential Protein Recognition via Community Significance. Ieee/Acm Transactions On Computational Biology and Bioinformatics. PMID 34347602 DOI: 10.1109/TCBB.2021.3102018   
2021 Rais Y, Fu Z, Drabovich AP. Mass spectrometry-based proteomics in basic and translational research of SARS-CoV-2 coronavirus and its emerging mutants. Clinical Proteomics. 18: 19. PMID 34384361 DOI: 10.1186/s12014-021-09325-x   
2021 Hong Z, Liu J, Chen Y. An interpretable machine learning method for homo-trimeric protein interface residue-residue interaction prediction. Biophysical Chemistry. 278: 106666. PMID 34418678 DOI: 10.1016/j.bpc.2021.106666   
2021 Yousefi R, Jevdokimenko K, Kluever V, Pacheu-Grau D, Fornasiero EF. Influence of Subcellular Localization and Functional State on Protein Turnover. Cells. 10. PMID 34359917 DOI: 10.3390/cells10071747   
2021 Yu ZQ, Liu XM, Zhao D, Xu DD, Du LL. Visual detection of binary, ternary, and quaternary protein interactions in fission yeast by Pil1 co-tethering assay. Journal of Cell Science. PMID 34499173 DOI: 10.1242/jcs.258774   
2021 Perszyk RE, Kristensen AS, Lyuboslavsky P, Traynelis SF. Three-dimensional missense tolerance ratio analysis. Genome Research. PMID 34301626 DOI: 10.1101/gr.275528.121   
2021 Kim SJ, Dixon AS, Owen SC. Split-enzyme Immunoassay to Monitor EGFR-HER2 Heterodimerization on Cell Surfaces. Acta Biomaterialia. PMID 34496282 DOI: 10.1016/j.actbio.2021.08.055   
2021 Soltermann F, Struwe WB, Kukura P. Label-free methods for optical characterization of protein-protein interactions. Physical Chemistry Chemical Physics : Pccp. 23: 16488-16500. PMID 34342317 DOI: 10.1039/d1cp01072g   
2021 Kobak KA, Lawrence MM, Pharaoh G, Borowik AK, Peelor FF, Shipman PD, Griffin TM, Van Remmen H, Miller BF. Determining the contributions of protein synthesis and breakdown to muscle atrophy requires non-steady-state equations. Journal of Cachexia, Sarcopenia and Muscle. PMID 34418329 DOI: 10.1002/jcsm.12772   
2021 Singhal N, Garg A, Singh N, Gulati P, Kumar M, Goel M. Efficacy of signal peptide predictors in identifying signal peptides in the experimental secretome of Picrophilous torridus, a thermoacidophilic archaeon. Plos One. 16: e0255826. PMID 34358261 DOI: 10.1371/journal.pone.0255826   
2021 Chen L, Kashina A. Post-translational Modifications of the Protein Termini. Frontiers in Cell and Developmental Biology. 9: 719590. PMID 34395449 DOI: 10.3389/fcell.2021.719590   
2021 Zhang L, Wu CL, Yang P, Wang YC, Zhang LL, Yang XY. Chilling injury mechanism of hardy kiwifruit (Actinidia arguta) was revealed by proteome of label-free techniques. Journal of Food Biochemistry. e13897. PMID 34390016 DOI: 10.1111/jfbc.13897   
2021 Erozenci LA, Piersma SR, Pham TV, Bijnsdorp IV, Jimenez CR. Longitudinal stability of urinary extracellular vesicle protein patterns within and between individuals. Scientific Reports. 11: 15629. PMID 34341426 DOI: 10.1038/s41598-021-95082-8   
2021 Park SY, Egan S, Cura AJ, Aron KL, Xu X, Zheng M, Borys M, Ghose S, Li Z, Lee K. Untargeted proteomics reveals upregulation of stress response pathways during CHO-based monoclonal antibody manufacturing process leading to disulfide bond reduction. Mabs. 13: 1963094. PMID 34424810 DOI: 10.1080/19420862.2021.1963094   
2021 Saikat ASM, Uddin ME, Ahmad T, Mahmud S, Imran MAS, Ahmed S, Alyami SA, Moni MA. Structural and Functional Elucidation of IF-3 Protein of Involved in Protein Biosynthesis: An Approach. Biomed Research International. 2021: 9050026. PMID 34307671 DOI: 10.1155/2021/9050026