Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips

Large-scale phosphorylation analysis of mouse liver

Villén, J., Beausoleil, S. A., Gerber, S. A., & Gygi, S. P. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0609836104 · Cited by 730 · see citing works

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

Cox, J., & Mann, M. (2008) · Nature Biotechnology · doi:10.1038/nbt.1511 · Cited by 14,855 · see citing works

Lysine acetylation targets protein complexes and co-regulates major cellular functions

Choudhary, C., Kumar, C., Gnad, F., Nielsen, M. L., Rehman, M., Walther, T. C., Olsen, J. V., & Mann, M. (2009) · Science · doi:10.1126/science.1175371 · Cited by 4,040 · see citing works

Insights into RNA Biology from an Atlas of Mammalian mRNA-Binding Proteins

Castello, A., Fischer, B., Eichelbaum, K., Horos, R., Beckmann, B. M., Strein, C., Davey, N. E., Humphreys, D. T., Preiss, T., Steinmetz, L. M., et al. (2012) · Cell · doi:10.1016/j.cell.2012.04.031 · Cited by 2,132 · see citing works

Lenalidomide Causes Selective Degradation of IKZF1 and IKZF3 in Multiple Myeloma Cells

Krönke, J., Udeshi, N. D., Narla, A., Grauman, P., Hurst, S. N., McConkey, M., Svinkina, T., Heckl, D., Comer, E., Li, X., et al. (2014) · Science · doi:10.1126/science.1244851 · Cited by 1,879 · see citing works

L-Arginine Modulates T Cell Metabolism and Enhances Survival and Anti-tumor Activity

Geiger, R., Rieckmann, J. C., Wolf, T., Basso, C., Feng, Y., Fuhrer, T., Kogadeeva, M., Picotti, P., Meissner, F., Mann, M., et al. (2016) · Cell · doi:10.1016/j.cell.2016.09.031 · Cited by 1,775 · see citing works

Translation of CircRNAs

Pamudurti, N. R., Bartok, O., Jens, M., Ashwal-Fluss, R., Stottmeister, C., Ruhe, L., Hanan, M., Wyler, E., Perez-Hernandez, D., Ramberger, E., et al. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.02.021 · Cited by 1,810 · see citing works

Minimal, encapsulated proteomic-sample processing applied to copy-number estimation in eukaryotic cells

Kulak, N. A., Pichler, G., Paron, I., Nagaraj, N., & Mann, M. (2014) · Nature Methods · doi:10.1038/nmeth.2834 · Cited by 1,719 · see citing works

Senescence-associated reprogramming promotes cancer stemness

Milanovic, M., Fan, D. N. Y., Belenki, D., Däbritz, J. H. M., Zhao, Z., Yu, Y., Dörr, J. R., Dimitrova, L., Lenze, D., Monteiro Barbosa, I. A., et al. (2018) · Nature · doi:10.1038/nature25167 · Cited by 1,131 · see citing works

Cardioprotection and lifespan extension by the natural polyamine spermidine

Eisenberg, T., Abdellatif, M., Schroeder, S., Primessnig, U., Stekovic, S., Pendl, T., Harger, A., Schipke, J., Zimmermann, A., Schmidt, A., et al. (2016) · Nature Medicine · doi:10.1038/nm.4222 · Cited by 1,168 · see citing works

Deep proteome and transcriptome mapping of a human cancer cell line

Nagaraj, N., Wisniewski, J. R., Geiger, T., Cox, J., Kircher, M., Kelso, J., Pääbo, S., & Mann, M. (2011) · Molecular Systems Biology · doi:10.1038/msb.2011.81 · Cited by 979 · see citing works

Dual proteome-scale networks reveal cell-specific remodeling of the human interactome

Huttlin, E. L., Bruckner, R. J., Navarrete-Perea, J., Cannon, J. R., Baltier, K., Gebreab, F., Gygi, M. P., Thornock, A., Zarraga, G., Tam, S., et al. (2020) · doi:10.1101/2020.01.19.905109 · Cited by 960 · see citing works

The target landscape of clinical kinase drugs

Klaeger, S., Heinzlmeir, S., Wilhelm, M., Polzer, H., Vick, B., Koenig, P.-A., Reinecke, M., Ruprecht, B., Petzoldt, S., Meng, C., et al. (2017) · Science · doi:10.1126/science.aan4368 · Cited by 854 · see citing works

Cell type- and brain region-resolved mouse brain proteome

Sharma, K., Schmitt, S., Bergner, C. G., Tyanova, S., Kannaiyan, N., Manrique-Hoyos, N., Kongi, K., Cantuti, L., Hanisch, U.-K., Philips, M.-A., et al. (2015) · Nature Neuroscience · doi:10.1038/nn.4160 · Cited by 871 · see citing works

Comparative Proteomic Analysis of Eleven Common Cell Lines Reveals Ubiquitous but Varying Expression of Most Proteins

Geiger, T., Wehner, A., Schaab, C., Cox, J., & Mann, M. (2012) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m111.014050 · Cited by 797 · see citing works

Targeted delivery of a PD-1-blocking scFv by CAR-T cells enhances anti-tumor efficacy in vivo

Rafiq, S., Yeku, O. O., Jackson, H. J., Purdon, T. J., van Leeuwen, D. G., Drakes, D. J., Song, M., Miele, M. M., Li, Z., Wang, P., et al. (2018) · Nature Biotechnology · doi:10.1038/nbt.4195 · Cited by 833 · see citing works

Bifidobacteria or Fiber Protects against Diet-Induced Microbiota-Mediated Colonic Mucus Deterioration

Schroeder, B. O., Birchenough, G. M. H., Ståhlman, M., Arike, L., Johansson, M. E. V., Hansson, G. C., & Bäckhed, F. (2018) · Cell Host & Microbe · doi:10.1016/j.chom.2017.11.004 · Cited by 713 · see citing works

Potential roles of gut microbiome and metabolites in modulating ALS in mice

Blacher, E., Bashiardes, S., Shapiro, H., Rothschild, D., Mor, U., Dori-Bachash, M., Kleimeyer, C., Moresi, C., Harnik, Y., Zur, M., et al. (2019) · Nature · doi:10.1038/s41586-019-1443-5 · Cited by 700 · see citing works

Electrophilic properties of itaconate and derivatives regulate the IκBζ–ATF3 inflammatory axis

Bambouskova, M., Gorvel, L., Lampropoulou, V., Sergushichev, A., Loginicheva, E., Johnson, K., Korenfeld, D., Mathyer, M. E., Kim, H., Huang, L.-H., et al. (2018) · Nature · doi:10.1038/s41586-018-0052-z · Cited by 713 · see citing works

Initiation of myoblast to brown fat switch by a PRDM16–C/EBP-β transcriptional complex

Kajimura, S., Seale, P., Kubota, K., Lunsford, E., Frangioni, J. V., Gygi, S. P., & Spiegelman, B. M. (2009) · Nature · doi:10.1038/nature08262 · Cited by 703 · see citing works

Irisin Mediates Effects on Bone and Fat via αV Integrin Receptors

Kim, H., Wrann, C. D., Jedrychowski, M., Vidoni, S., Kitase, Y., Nagano, K., Zhou, C., Chou, J., Parkman, V.-J. A., Novick, S. J., et al. (2018) · Cell · doi:10.1016/j.cell.2018.10.025 · Cited by 638 · see citing works

Metabolic modulation of tumours with engineered bacteria for immunotherapy

Canale, F. P., Basso, C., Antonini, G., Perotti, M., Li, N., Sokolovska, A., Neumann, J., James, M. J., Geiger, S., Jin, W., et al. (2021) · Nature · doi:10.1038/s41586-021-04003-2 · Cited by 619 · see citing works

Widespread Proteome Remodeling and Aggregation in Aging C. elegans

Walther, D. M., Kasturi, P., Zheng, M., Pinkert, S., Vecchi, G., Ciryam, P., Morimoto, R. I., Dobson, C. M., Vendruscolo, M., Mann, M., et al. (2015) · Cell · doi:10.1016/j.cell.2015.03.032 · Cited by 569 · see citing works

Loss of TREM2 function increases amyloid seeding but reduces plaque-associated ApoE

Parhizkar, S., Arzberger, T., Brendel, M., Kleinberger, G., Deussing, M., Focke, C., Nuscher, B., Xiong, M., Ghasemigharagoz, A., Katzmarski, N., et al. (2019) · Nature Neuroscience · doi:10.1038/s41593-018-0296-9 · Cited by 555 · see citing works

The cGAS–STING pathway drives type I IFN immunopathology in COVID-19

Domizio, J. D., Gulen, M. F., Saidoune, F., Thacker, V. V., Yatim, A., Sharma, K., Nass, T., Guenova, E., Schaller, M., Conrad, C., et al. (2022) · Nature · doi:10.1038/s41586-022-04421-w · Cited by 538 · see citing works

SARS-CoV-2 infection triggers profibrotic macrophage responses and lung fibrosis

Wendisch, D., Dietrich, O., Mari, T., von Stillfried, S., Ibarra, I. L., Mittermaier, M., Mache, C., Chua, R. L., Knoll, R., Timm, S., et al. (2021) · Cell · doi:10.1016/j.cell.2021.11.033 · Cited by 528 · see citing works

Ultra‐high sensitivity mass spectrometry quantifies single‐cell proteome changes upon perturbation

Brunner, A., Thielert, M., Vasilopoulou, C., Ammar, C., Coscia, F., Mund, A., Hoerning, O. B., Bache, N., Apalategui, A., Lubeck, M., et al. (2022) · Molecular Systems Biology · doi:10.15252/msb.202110798 · Cited by 544 · see citing works

Gene‐specific correlation of RNA and protein levels in human cells and tissues

Edfors, F., Danielsson, F., Hallström, B. M., Käll, L., Lundberg, E., Pontén, F., Forsström, B., & Uhlén, M. (2016) · Molecular Systems Biology · doi:10.15252/msb.20167144 · Cited by 493 · see citing works

Transcriptional and Translational Differences of Microglia from Male and Female Brains

Guneykaya, D., Ivanov, A., Hernandez, D. P., Haage, V., Wojtas, B., Meyer, N., Maricos, M., Jordan, P., Buonfiglioli, A., Gielniewski, B., et al. (2018) · Cell Reports · doi:10.1016/j.celrep.2018.08.001 · Cited by 477 · see citing works

A Genome-wide CRISPR Screen in Primary Immune Cells to Dissect Regulatory Networks

Parnas, O., Jovanovic, M., Eisenhaure, T. M., Herbst, R. H., Dixit, A., Ye, C. J., Przybylski, D., Platt, R. J., Tirosh, I., Sanjana, N. E., et al. (2015) · Cell · doi:10.1016/j.cell.2015.06.059 · Cited by 440 · see citing works

Dynamic profiling of the protein life cycle in response to pathogens

Jovanovic, M., Rooney, M. S., Mertins, P., Przybylski, D., Chevrier, N., Satija, R., Rodriguez, E. H., Fields, A. P., Schwartz, S., Raychowdhury, R., et al. (2015) · Science · doi:10.1126/science.1259038 · Cited by 460 · see citing works

Quantitative proteomics combined with BAC TransgeneOmics reveals in vivo protein interactions

Hubner, N. C., Bird, A. W., Cox, J., Splettstoesser, B., Bandilla, P., Poser, I., Hyman, A., & Mann, M. (2010) · Journal of Cell Biology · doi:10.1083/jcb.200911091 · Cited by 440 · see citing works

η-Secretase processing of APP inhibits neuronal activity in the hippocampus

Willem, M., Tahirovic, S., Busche, M. A., Ovsepian, S. V., Chafai, M., Kootar, S., Hornburg, D., Evans, L. D. B., Moore, S., Daria, A., et al. (2015) · Nature · doi:10.1038/nature14864 · Cited by 398 · see citing works

Plasma Proteomics Identify Biomarkers and Pathogenesis of COVID-19

Shu, T., Ning, W., Wu, D., Xu, J., Han, Q., Huang, M., Zou, X., Yang, Q., Yuan, Y., Bie, Y., et al. (2020) · Immunity · doi:10.1016/j.immuni.2020.10.008 · Cited by 337 · see citing works

Defining the transcriptome and proteome in three functionally different human cell lines

Lundberg, E., Fagerberg, L., Klevebring, D., Matic, I., Geiger, T., Cox, J., Älgenäs, C., Lundeberg, J., Mann, M., & Uhlen, M. (2010) · Molecular Systems Biology · doi:10.1038/msb.2010.106 · Cited by 373 · see citing works

Cooperative and independent roles of the Drp1 adaptors Mff, MiD49 and MiD51 in mitochondrial fission

Osellame, L. D., Singh, A. P., Stroud, D. A., Palmer, C. S., Stojanovski, D., Ramachandran, R., & Ryan, M. T. (2016) · Journal of Cell Science · doi:10.1242/jcs.185165 · Cited by 336 · see citing works

The gut microbiota promotes hepatic fatty acid desaturation and elongation in mice

Kindt, A., Liebisch, G., Clavel, T., Haller, D., Hörmannsperger, G., Yoon, H., Kolmeder, D., Sigruener, A., Krautbauer, S., Seeliger, C., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-05767-4 · Cited by 311 · see citing works

Dynamics of the skeletal muscle secretome during myoblast differentiation

Henningsen, J., Rigbolt, K. T. G., Blagoev, B., Pedersen, B. K., & Kratchmarova, I. (2010) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m110.002113 · Cited by 303 · see citing works

Slow TCA flux and ATP production in primary solid tumours but not metastases

Bartman, C. R., Weilandt, D. R., Shen, Y., Lee, W. D., Han, Y., TeSlaa, T., Jankowski, C. S. R., Samarah, L., Park, N. R., da Silva-Diz, V., et al. (2023) · Nature · doi:10.1038/s41586-022-05661-6 · Cited by 299 · see citing works

Integrated Omics of Metastatic Colorectal Cancer

Li, C., Sun, Y.-D., Yu, G.-Y., Cui, J.-R., Lou, Z., Zhang, H., Huang, Y., Bai, C.-G., Deng, L.-L., Liu, P., et al. (2020) · Cancer Cell · doi:10.1016/j.ccell.2020.08.002 · Cited by 297 · see citing works

The EGFR-specific antibody cetuximab combined with chemotherapy triggers immunogenic cell death

Pozzi, C., Cuomo, A., Spadoni, I., Magni, E., Silvola, A., Conte, A., Sigismund, S., Ravenda, P. S., Bonaldi, T., Zampino, M. G., et al. (2016) · Nature Medicine · doi:10.1038/nm.4078 · Cited by 292 · see citing works

The functional interactome landscape of the human histone deacetylase family

Joshi, P., Greco, T. M., Guise, A. J., Luo, Y., Yu, F., Nesvizhskii, A. I., & Cristea, I. M. (2013) · Molecular Systems Biology · doi:10.1038/msb.2013.26 · Cited by 289 · see citing works

Variant ribosomal RNA alleles are conserved and exhibit tissue-specific expression

Parks, M. M., Kurylo, C. M., Dass, R. A., Bojmar, L., Lyden, D., Vincent, C. T., & Blanchard, S. C. (2018) · Science Advances · doi:10.1126/sciadv.aao0665 · Cited by 260 · see citing works

Ulk1-mediated phosphorylation of AMPK constitutes a negative regulatory feedback loop

Löffler, A. S., Alers, S., Dieterle, A. M., Keppeler, H., Franz-Wachtel, M., Kundu, M., Campbell, D. G., Wesselborg, S., Alessi, D. R., & Stork, B. (2011) · Autophagy · doi:10.4161/auto.7.7.15451 · Cited by 258 · see citing works

Stoichiometry of chromatin-associated protein complexes revealed by label-free quantitative mass spectrometry-based proteomics

Smits, A. H., Jansen, P. W. T. C., Poser, I., Hyman, A. A., & Vermeulen, M. (2013) · Nucleic Acids Research · doi:10.1093/nar/gks941 · Cited by 258 · see citing works

Unbiased spatial proteomics with single-cell resolution in tissues

Mund, A., Brunner, A.-D., & Mann, M. (2022) · Molecular Cell · doi:10.1016/j.molcel.2022.05.022 · Cited by 259 · see citing works

Proteome-wide Analysis of Lysine Acetylation Suggests its Broad Regulatory Scope in Saccharomyces cerevisiae

Henriksen, P., Wagner, S. A., Weinert, B. T., Sharma, S., Bačinskaja, G., Rehman, M., Juffer, A. H., Walther, T. C., Lisby, M., & Choudhary, C. (2012) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m112.017251 · Cited by 246 · see citing works

Sample Preparation by Easy Extraction and Digestion (SPEED) - A Universal, Rapid, and Detergent-free Protocol for Proteomics Based on Acid Extraction

Doellinger, J., Schneider, A., Hoeller, M., & Lasch, P. (2020) · Molecular & Cellular Proteomics · doi:10.1074/mcp.tir119.001616 · Cited by 246 · see citing works

Protein synthesis rate is the predominant regulator of protein expression during differentiation

Kristensen, A. R., Gsponer, J., & Foster, L. J. (2013) · Molecular Systems Biology · doi:10.1038/msb.2013.47 · Cited by 217 · see citing works

A molecular switch from STAT2-IRF9 to ISGF3 underlies interferon-induced gene transcription

Platanitis, E., Demiroz, D., Schneller, A., Fischer, K., Capelle, C., Hartl, M., Gossenreiter, T., Müller, M., Novatchkova, M., & Decker, T. (2019) · Nature Communications · doi:10.1038/s41467-019-10970-y · Cited by 233 · see citing works

Probing the Tumor Suppressor Function of BAP1 in CRISPR-Engineered Human Liver Organoids

Artegiani, B., van Voorthuijsen, L., Lindeboom, R. G. H., Seinstra, D., Heo, I., Tapia, P., López-Iglesias, C., Postrach, D., Dayton, T., Oka, R., et al. (2019) · Cell Stem Cell · doi:10.1016/j.stem.2019.04.017 · Cited by 218 · see citing works

Energy Homeostasis Control in <i>Drosophila</i> Adipokinetic Hormone Mutants

Gáliková, M., Diesner, M., Klepsatel, P., Hehlert, P., Xu, Y., Bickmeyer, I., Predel, R., & Kühnlein, R. P. (2015) · Genetics · doi:10.1534/genetics.115.178897 · Cited by 206 · see citing works

A streamlined mass spectrometry–based proteomics workflow for large-scale FFPE tissue analysis

Coscia, F., Doll, S., Bech, J. M., Schweizer, L., Mund, A., Lengyel, E., Lindebjerg, J., Madsen, G. I., Moreira, J. M., & Mann, M. (2020) · The Journal of Pathology · doi:10.1002/path.5420 · Cited by 200 · see citing works

Proline biosynthesis is a vent for TGFβ‐induced mitochondrial redox stress

Schwörer, S., Berisa, M., Violante, S., Qin, W., Zhu, J., Hendrickson, R. C., Cross, J. R., & Thompson, C. B. (2020) · The EMBO Journal · doi:10.15252/embj.2019103334 · Cited by 193 · see citing works

Systematic Discovery of TLR Signaling Components Delineates Viral-Sensing Circuits

Chevrier, N., Mertins, P., Artyomov, M. N., Shalek, A. K., Iannacone, M., Ciaccio, M. F., Gat-Viks, I., Tonti, E., DeGrace, M. M., Clauser, K. R., et al. (2011) · Cell · doi:10.1016/j.cell.2011.10.022 · Cited by 179 · see citing works

Clearance of senescent cells during cardiac ischemia–reperfusion injury improves recovery

Dookun, E., Walaszczyk, A., Redgrave, R., Palmowski, P., Tual‐Chalot, S., Suwana, A., Chapman, J., Jirkovsky, E., Donastorg Sosa, L., Gill, E., et al. (2020) · Aging Cell · doi:10.1111/acel.13249 · Cited by 173 · see citing works

The neuropeptide complement of the marine annelid Platynereis dumerilii

Conzelmann, M., Williams, E. A., Krug, K., Franz-Wachtel, M., Macek, B., & Jékely, G. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-906 · Cited by 165 · see citing works

Type 2 Diabetes Variants Disrupt Function of SLC16A11 through Two Distinct Mechanisms

Rusu, V., Hoch, E., Mercader, J. M., Tenen, D. E., Gymrek, M., Hartigan, C. R., DeRan, M., von Grotthuss, M., Fontanillas, P., Spooner, A., et al. (2017) · Cell · doi:10.1016/j.cell.2017.06.011 · Cited by 152 · see citing works

The ciliary membrane‐associated proteome reveals actin‐binding proteins as key components of cilia

Kohli, P., Höhne, M., Jüngst, C., Bertsch, S., Ebert, L. K., Schauss, A. C., Benzing, T., Rinschen, M. M., & Schermer, B. (2017) · The EMBO Reports · doi:10.15252/embr.201643846 · Cited by 145 · see citing works

Neuronal ribosomes exhibit dynamic and context-dependent exchange of ribosomal proteins

Fusco, C. M., Desch, K., Dörrbaum, A. R., Wang, M., Staab, A., Chan, I. C. W., Vail, E., Villeri, V., Langer, J. D., & Schuman, E. M. (2021) · Nature Communications · doi:10.1038/s41467-021-26365-x · Cited by 157 · see citing works

Characterization of the E. coli proteome and its modifications during growth and ethanol stress

Soufi, B., Krug, K., Harst, A., & Macek, B. (2015) · Frontiers in Microbiology · doi:10.3389/fmicb.2015.00103 · Cited by 142 · see citing works

Proteomic analysis of human vitreous humor

Murthy, K. R., Goel, R., Subbannayya, Y., Jacob, H. K., Murthy, P. R., Manda, S. S., Patil, A. H., Sharma, R., Sahasrabuddhe, N. A., Parashar, A., et al. (2014) · Clinical Proteomics · doi:10.1186/1559-0275-11-29 · Cited by 145 · see citing works

Molecular fingerprinting of the podocyte reveals novel gene and protein regulatory networks

Boerries, M., Grahammer, F., Eiselein, S., Buck, M., Meyer, C., Goedel, M., Bechtel, W., Zschiedrich, S., Pfeifer, D., Laloë, D., et al. (2013) · Kidney International · doi:10.1038/ki.2012.487 · Cited by 141 · see citing works

Conformational Switching of the Molecular Chaperone Hsp90 via Regulated Phosphorylation

Soroka, J., Wandinger, S. K., Mäusbacher, N., Schreiber, T., Richter, K., Daub, H., & Buchner, J. (2012) · Molecular Cell · doi:10.1016/j.molcel.2011.12.031 · Cited by 139 · see citing works

The impact of exercise on mitochondrial dynamics and the role of Drp1 in exercise performance and training adaptations in skeletal muscle

Moore, T. M., Zhou, Z., Cohn, W., Norheim, F., Lin, A. J., Kalajian, N., Strumwasser, A. R., Cory, K., Whitney, K., Ho, T., et al. (2019) · Molecular Metabolism · doi:10.1016/j.molmet.2018.11.012 · Cited by 131 · see citing works

Nuclear and cytoplasmic huntingtin inclusions exhibit distinct biochemical composition, interactome and ultrastructural properties

Riguet, N., Mahul-Mellier, A.-L., Maharjan, N., Burtscher, J., Croisier, M., Knott, G., Hastings, J., Patin, A., Reiterer, V., Farhan, H., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-26684-z · Cited by 118 · see citing works

7q11.23 dosage-dependent dysregulation in human pluripotent stem cells affects transcriptional programs in disease-relevant lineages

Adamo, A., Atashpaz, S., Germain, P.-L., Zanella, M., D'Agostino, G., Albertin, V., Chenoweth, J., Micale, L., Fusco, C., Unger, C., et al. (2015) · Nature Genetics · doi:10.1038/ng.3169 · Cited by 129 · see citing works

Endogenous rRNA Sequence Variation Can Regulate Stress Response Gene Expression and Phenotype

Kurylo, C. M., Parks, M. M., Juette, M. F., Zinshteyn, B., Altman, R. B., Thibado, J. K., Vincent, C. T., & Blanchard, S. C. (2018) · Cell Reports · doi:10.1016/j.celrep.2018.08.093 · Cited by 117 · see citing works

Systems‐wide analysis of BCR signalosomes and downstream phosphorylation and ubiquitylation

Satpathy, S., Wagner, S. A., Beli, P., Gupta, R., Kristiansen, T. A., Malinova, D., Francavilla, C., Tolar, P., Bishop, G. A., Hostager, B. S., et al. (2015) · Molecular Systems Biology · doi:10.15252/msb.20145880 · Cited by 124 · see citing works

Atg38 is required for autophagy-specific phosphatidylinositol 3-kinase complex integrity

Araki, Y., Ku, W.-C., Akioka, M., May, A. I., Hayashi, Y., Arisaka, F., Ishihama, Y., & Ohsumi, Y. (2013) · Journal of Cell Biology · doi:10.1083/jcb.201304123 · Cited by 119 · see citing works

Decoding the Transcriptional Response to Ischemic Stroke in Young and Aged Mouse Brain

Androvic, P., Kirdajova, D., Tureckova, J., Zucha, D., Rohlova, E., Abaffy, P., Kriska, J., Valny, M., Anderova, M., Kubista, M., et al. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.107777 · Cited by 118 · see citing works

ELOF1 is a transcription-coupled DNA repair factor that directs RNA polymerase II ubiquitylation

van der Weegen, Y., de Lint, K., van den Heuvel, D., Nakazawa, Y., Mevissen, T. E. T., van Schie, J. J. M., San Martin Alonso, M., Boer, D. E. C., González-Prieto, R., Narayanan, I. V., et al. (2021) · Nature Cell Biology · doi:10.1038/s41556-021-00688-9 · Cited by 114 · see citing works

Proteomic analysis of decellularized pancreatic matrix identifies collagen V as a critical regulator for islet organogenesis from human pluripotent stem cells

Bi, H., Ye, K., & Jin, S. (2020) · Biomaterials · doi:10.1016/j.biomaterials.2019.119673 · Cited by 105 · see citing works

Control of human hemoglobin switching by LIN28B-mediated regulation of BCL11A translation

Basak, A., Munschauer, M., Lareau, C. A., Montbleau, K. E., Ulirsch, J. C., Hartigan, C. R., Schenone, M., Lian, J., Wang, Y., Huang, Y., et al. (2020) · Nature Genetics · doi:10.1038/s41588-019-0568-7 · Cited by 105 · see citing works

Cell cycle-resolved chromatin proteomics reveals the extent of mitotic preservation of the genomic regulatory landscape

Ginno, P. A., Burger, L., Seebacher, J., Iesmantavicius, V., & Schübeler, D. (2018) · Nature Communications · doi:10.1038/s41467-018-06007-5 · Cited by 91 · see citing works

Dysregulation of a long noncoding RNA reduces leptin leading to a leptin-responsive form of obesity

Dallner, O. S., Marinis, J. M., Lu, Y.-H., Birsoy, K., Werner, E., Fayzikhodjaeva, G., Dill, B. D., Molina, H., Moscati, A., Kutalik, Z., et al. (2019) · Nature Medicine · doi:10.1038/s41591-019-0370-1 · Cited by 106 · see citing works

Combined quantification of intracellular (phospho-)proteins and transcriptomics from fixed single cells

Gerlach, J. P., van Buggenum, J. A. G., Tanis, S. E. J., Hogeweg, M., Heuts, B. M. H., Muraro, M. J., Elze, L., Rivello, F., Rakszewska, A., van Oudenaarden, A., et al. (2019) · Scientific Reports · doi:10.1038/s41598-018-37977-7 · Cited by 104 · see citing works

A covalent and cleavable antibody-DNA conjugation strategy for sensitive protein detection via immuno-PCR

van Buggenum, J. A. G. L., Gerlach, J. P., Eising, S., Schoonen, L., van Eijl, R. A. P. M., Tanis, S. E. J., Hogeweg, M., Hubner, N. C., van Hest, J. C., Bonger, K. M., et al. (2016) · Scientific Reports · doi:10.1038/srep22675 · Cited by 93 · see citing works

Identification of cancer-cytotoxic modulators of PDE3A by predictive chemogenomics

de Waal, L., Lewis, T. A., Rees, M. G., Tsherniak, A., Wu, X., Choi, P. S., Gechijian, L., Hartigan, C., Faloon, P. W., Hickey, M. J., et al. (2016) · Nature Chemical Biology · doi:10.1038/nchembio.1984 · Cited by 96 · see citing works

Delicate metabolic control and coordinated stress response critically determine antifungal tolerance of Candida albicans biofilm persisters

Li, P., Seneviratne, C. J., Alpi, E., Vizcaino, J. A., & Jin, L. (2015) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.00543-15 · Cited by 95 · see citing works

Interactions of the Antiviral Factor Interferon Gamma-Inducible Protein 16 (IFI16) Mediate Immune Signaling and Herpes Simplex Virus-1 Immunosuppression

Diner, B. A., Lum, K. K., Javitt, A., & Cristea, I. M. (2015) · Molecular &amp; Cellular Proteomics · doi:10.1074/mcp.m114.047068 · Cited by 93 · see citing works

Degradation of CCNK/CDK12 is a druggable vulnerability of colorectal cancer

Dieter, S. M., Siegl, C., Codó, P. L., Huerta, M., Ostermann-Parucha, A. L., Schulz, E., Zowada, M. K., Martin, S., Laaber, K., Nowrouzi, A., et al. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.109394 · Cited by 95 · see citing works

Novel insights from a multiomics dissection of the Hayflick limit

Chan, M., Yuan, H., Soifer, I., Maile, T. M., Wang, R. Y., Ireland, A., O'Brien, J. J., Goudeau, J., Chan, L. J., Vijay, T., et al. (2022) · eLife · doi:10.7554/elife.70283 · Cited by 99 · see citing works

Structural and mechanistic basis of the EMC-dependent biogenesis of distinct transmembrane clients

Miller-Vedam, L. E., Bräuning, B., Popova, K. D., Schirle Oakdale, N. T., Bonnar, J. L., Prabu, J. R., Boydston, E. A., Sevillano, N., Shurtleff, M. J., Stroud, R. M., et al. (2020) · eLife · doi:10.7554/elife.62611 · Cited by 87 · see citing works

SUGAR-seq enables simultaneous detection of glycans, epitopes, and the transcriptome in single cells

Kearney, C. J., Vervoort, S. J., Ramsbottom, K. M., Todorovski, I., Lelliott, E. J., Zethoven, M., Pijpers, L., Martin, B. P., Semple, T., Martelotto, L., et al. (2021) · Science Advances · doi:10.1126/sciadv.abe3610 · Cited by 87 · see citing works

Multiomic analysis of cervical squamous cell carcinoma identifies cellular ecosystems with biological and clinical relevance

Fan, J., Lu, F., Qin, T., Peng, W., Zhuang, X., Li, Y., Hou, X., Fang, Z., Yang, Y., Guo, E., et al. (2023) · Nature Genetics · doi:10.1038/s41588-023-01570-0 · Cited by 93 · see citing works

Endonuclease G mediates α‐synuclein cytotoxicity during Parkinson's disease

Büttner, S., Habernig, L., Broeskamp, F., Ruli, D., Vögtle, F. N., Vlachos, M., Macchi, F., Küttner, V., Carmona‐Gutierrez, D., Eisenberg, T., et al. (2013) · The EMBO Journal · doi:10.1038/emboj.2013.228 · Cited by 87 · see citing works

Mapping Proteoforms and Protein Complexes From King Cobra Venom Using Both Denaturing and Native Top-down Proteomics

Melani, R. D., Skinner, O. S., Fornelli, L., Domont, G. B., Compton, P. D., & Kelleher, N. L. (2016) · Molecular &amp; Cellular Proteomics · doi:10.1074/mcp.m115.056523 · Cited by 85 · see citing works

Profiling the Escherichia coli membrane protein interactome captured in Peptidisc libraries

Carlson, M. L., Stacey, R. G., Young, J. W., Wason, I. S., Zhao, Z., Rattray, D. G., Scott, N., Kerr, C. H., Babu, M., Foster, L. J., et al. (2019) · eLife · doi:10.7554/elife.46615 · Cited by 74 · see citing works

Complementary RNA and Protein Profiling Identifies Iron as a Key Regulator of Mitochondrial Biogenesis

Rensvold, J. W., Ong, S.-E., Jeevananthan, A., Carr, S. A., Mootha, V. K., & Pagliarini, D. J. (2013) · Cell Reports · doi:10.1016/j.celrep.2012.11.029 · Cited by 82 · see citing works

Genome-wide identification and quantification of protein synthesis in cultured cells and whole tissues by puromycin-associated nascent chain proteomics (PUNCH-P)

Aviner, R., Geiger, T., & Elroy-Stein, O. (2014) · Nature Protocols · doi:10.1038/nprot.2014.051 · Cited by 76 · see citing works

Lysosomal dysfunction in Down syndrome and Alzheimer mouse models is caused by v-ATPase inhibition by Tyr ⁶⁸² -phosphorylated APP βCTF

Im, E., Jiang, Y., Stavrides, P. H., Darji, S., Erdjument-Bromage, H., Neubert, T. A., Choi, J. Y., Wegiel, J., Lee, J.-H., & Nixon, R. A. (2023) · Science Advances · doi:10.1126/sciadv.adg1925 · Cited by 80 · see citing works

Annotation of loci from genome-wide association studies using tissue-specific quantitative interaction proteomics

The QT Interval International GWAS Consortium (QT-IGC), Lundby, A., Rossin, E. J., Steffensen, A. B., Acha, M. R., Newton-Cheh, C., Pfeufer, A., Lynch, S. N., Olesen, S.-P., Brunak, S., et al. (2014) · Nature Methods · doi:10.1038/nmeth.2997 · Cited by 71 · see citing works

A CSB-PAF1C axis restores processive transcription elongation after DNA damage repair

van den Heuvel, D., Spruijt, C. G., González-Prieto, R., Kragten, A., Paulsen, M. T., Zhou, D., Wu, H., Apelt, K., van der Weegen, Y., Yang, K., et al. (2020) · doi:10.1101/2020.01.04.894808 · Cited by 69 · see citing works

Human METTL18 is a histidine-specific methyltransferase that targets RPL3 and affects ribosome biogenesis and function

Małecki, J. M., Odonohue, M.-F., Kim, Y., Jakobsson, M. E., Gessa, L., Pinto, R., Wu, J., Davydova, E., Moen, A., Olsen, J. V., et al. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab088 · Cited by 59 · see citing works

Statins affect cancer cell plasticity with distinct consequences for tumor progression and metastasis

Dorsch, M., Kowalczyk, M., Planque, M., Heilmann, G., Urban, S., Dujardin, P., Forster, J., Ueffing, K., Nothdurft, S., Oeck, S., et al. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.110056 · Cited by 55 · see citing works

’Ropy’ Phenotype, Exopolysaccharides and Metabolism: Study on Food Isolated Potential Probiotics LAB

Cirrincione, S., Breuer, Y., Mangiapane, E., Mazzoli, R., & Pessione, E. (2018) · Microbiological Research · doi:10.1016/j.micres.2018.07.004 · Cited by 53 · see citing works

Mesenchymal stromal cell activation by breast cancer secretomes in bioengineered 3D microenvironments

Blache, U., Horton, E. R., Xia, T., Schoof, E. M., Blicher, L. H., Schönenberger, A., Snedeker, J. G., Martin, I., Erler, J. T., & Ehrbar, M. (2019) · Life Science Alliance · doi:10.26508/lsa.201900304 · Cited by 49 · see citing works

Polyubiquitinylation Profile in Down Syndrome Brain Before and After the Development of Alzheimer Neuropathology

Tramutola, A., Di Domenico, F., Barone, E., Arena, A., Giorgi, A., di Francesco, L., Schininà, M. E., Coccia, R., Head, E., Butterfield, D. A., et al. (2017) · Antioxidants &amp; Redox Signaling · doi:10.1089/ars.2016.6686 · Cited by 49 · see citing works

Lysozyme-Induced Transcriptional Regulation of TNF-α Pathway Genes in Cells of the Monocyte Lineage

Bergamo, A., Gerdol, M., Pallavicini, A., Greco, S., Schepens, I., Hamelin, R., Armand, F., Dyson, P. J., & Sava, G. (2019) · International Journal of Molecular Sciences · doi:10.3390/ijms20215502 · Cited by 42 · see citing works

PRISMA: Protein Interaction Screen on Peptide Matrix Reveals Interaction Footprints and Modifications- Dependent Interactome of Intrinsically Disordered C/EBPβ

Dittmar, G., Hernandez, D. P., Kowenz-Leutz, E., Kirchner, M., Kahlert, G., Wesolowski, R., Baum, K., Knoblich, M., Hofstätter, M., Muller, A., et al. (2019) · iScience · doi:10.1016/j.isci.2019.02.026 · Cited by 41 · see citing works