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1.Soares-Schanoski A, Sauerwald N, Goforth C, Periasamy S, Weir D, Lizewski S, Lizewski R, Ge Y, Kuzmina N, Nair V, Vangeti S, Marjanovic N, Cappuccio A, Cheng W, Mofsowitz S, Miller C, Yu X, George M-C, Zaslavsky E, Bukreyev A, Troyanskaya O, Sealfon S, Letizia A, Ramos I. Asymptomatic SARS-CoV-2 Infection Is Associated With Higher Levels of Serum IL-17C, Matrix Metalloproteinase 10 and Fibroblast Growth Factors Than Mild Symptomatic COVID-19. Front Immunol. 2022;13:821730. PMCID: PMC9037090 Reference Link
1.Buksh B, Knutson S, Oakley J, Bissonnette N, Oblinsky D, Schwoerer M, Seath C, Geri J, Rodriguez-Rivera F, Parker D, Scholes G, Ploss A, MacMillan D. μMap-Red: Proximity Labeling by Red Light Photocatalysis. J Am Chem Soc. 2022;144(14):6154–6162. PMCID: PMC9843638 Reference Link
1.Omenn G, Lane L, Overall C, Paik Y-K, Cristea I, Corrales F, Lindskog C, Weintraub S, Roehrl M, Liu S, Bandeira N, Srivastava S, Chen Y-J, Aebersold R, Moritz R, Deutsch E. Progress Identifying and Analyzing the Human Proteome: 2021 Metrics from the HUPO Human Proteome Project. J Proteome Res. 2021;20(12):5227–5240. PMCID: PMC9340669 Reference Link
1.Shi W, Sheng X, Dorr K, Hutton J, Emerson J, Davies H, Andrade T, Wasson L, Greco T, Hashimoto Y, Federspiel J, Robbe Z, Chen X, Arnold A, Cristea I, Conlon F. Cardiac proteomics reveals sex chromosome-dependent differences between males and females that arise prior to gonad formation. Dev Cell. 2021;56(21):3019–3034.e7. PMCID: PMC9290207 Reference Link
1.Ghergurovich J, Lang J, Levin M, Briones N, Facista S, Mueller C, Cowan A, McBride M, Rodriguez E, Killian A, Dao T, Lamont J, Barron A, Su X, Hendricks W, Espina V, Von Hoff D, O’Shaughnessy J, Rabinowitz J. Local production of lactate, ribose phosphate, and amino acids within human triple-negative breast cancer. Med. 2021;2(6):736–754. PMCID: PMC8248508 Reference Link
1.Johnson A, Stadlmeier M, Wühr M. TMTpro Complementary Ion Quantification Increases Plexing and Sensitivity for Accurate Multiplexed Proteomics at the MS2 Level. J Proteome Res. 2021;20(6):3043–3052. PMCID: PMC8330405 Reference Link
1.de Boer I, Alpers C, Azeloglu E, Balis U, Barasch J, Barisoni L, Blank K, Bomback A, Brown K, Dagher P, Dighe A, Eadon M, El-Achkar T, Gaut J, Hacohen N, He Y, Hodgin J, Jain S, Kellum J, Kiryluk K, Knight R, Laszik Z, Lienczewski C, Mariani L, McClelland R, Menez S, Moledina D, Mooney S, O’Toole J, Palevsky P, Parikh C, Poggio E, Rosas S, Rosengart M, Sarwal M, Schaub J, Sedor J, Sharma K, Steck B, Toto R, Troyanskaya O, Tuttle K, Vazquez M, Waikar S, Williams K, Wilson F, Zhang K, Iyengar R, Kretzler M, Himmelfarb J, Kidney Precision Medicine Project. Rationale and design of the Kidney Precision Medicine Project. Kidney Int. 2021;99(3):498–510. PMCID: PMC8330551 Reference Link
1.Kan L, Ott S, Joseph B, Park E, Dai W, Kleiner R, Claridge-Chang A, Lai E. A neural mA/Ythdf pathway is required for learning and memory in Drosophila. Nat Commun. 2021;12(1):1458. PMCID: PMC7935873 Reference Link
1.Ringel A, Drijvers J, Baker G, Catozzi A, García-Cañaveras J, Gassaway B, Miller B, Juneja V, Nguyen T, Joshi S, Yao C-H, Yoon H, Sage P, LaFleur M, Trombley J, Jacobson C, Maliga Z, Gygi S, Sorger P, Rabinowitz J, Sharpe A, Haigis M. Obesity Shapes Metabolism in the Tumor Microenvironment to Suppress Anti-Tumor Immunity. Cell. 2020;183(7):1848–1866.e26. PMCID: PMC8064125 Reference Link
1.Omenn G, Lane L, Overall C, Cristea I, Corrales F, Lindskog C, Paik Y-K, Van Eyk J, Liu S, Pennington S, Snyder M, Baker M, Bandeira N, Aebersold R, Moritz R, Deutsch E. Research on the Human Proteome Reaches a Major Milestone: >90% of Predicted Human Proteins Now Credibly Detected, According to the HUPO Human Proteome Project. J Proteome Res. 2020;19(12):4735–4746. PMCID: PMC7718309 Reference Link
1.Adhikari S, Nice E, Deutsch E, Lane L, Omenn G, Pennington S, Paik Y-K, Overall C, Corrales F, Cristea I, Van Eyk J, Uhlén M, Lindskog C, Chan D, Bairoch A, Waddington J, Justice J, LaBaer J, Rodriguez H, He F, Kostrzewa M, Ping P, Gundry R, Stewart P, Srivastava S, Srivastava S, Nogueira F, Domont G, Vandenbrouck Y, P Y Lam M, Wennersten S, Vizcaino J, Wilkins M, Schwenk J, Lundberg E, Bandeira N, Marko-Varga G, Weintraub S, Pineau C, Kusebauch U, Moritz R, Ahn S, Palmblad M, Snyder M, Aebersold R, Baker M. A high-stringency blueprint of the human proteome. Nat Commun. 2020;11(1):5301. PMCID: PMC7568584 Reference Link
1.Hoshino A, Kim H, Bojmar L, Gyan K, Cioffi M, Hernandez J, Zambirinis C, Rodrigues G, Molina H, Heissel S, Mark M, Steiner L, Benito-Martin A, Lucotti S, Di Giannatale A, Offer K, Nakajima M, Williams C, Nogués L, Vatter F, Hashimoto A, Davies A, Freitas D, Kenific C, Ararso Y, Buehring W, Lauritzen P, Ogitani Y, Sugiura K, Takahashi N, Alečković M, Bailey K, Jolissant J, Wang H, Harris A, Schaeffer M, García-Santos G, Posner Z, Balachandran V, Khakoo Y, Raju P, Scherz A, Sagi I, Scherz-Shouval R, Yarden Y, Oren M, Malladi M, Petriccione M, De Braganca K, Donzelli M, Fischer C, Vitolano S, Wright G, Ganshaw L, Marrano M, Ahmed A, DeStefano J, Danzer E, Roehrl M, Lacayo N, Vincent T, Weiser M, Brady M, Meyers P, Wexler L, Ambati S, Chou A, Slotkin E, Modak S, Roberts S, Basu E, Diolaiti D, Krantz B, Cardoso F, Simpson A, Berger M, Rudin C, Simeone D, Jain M, Ghajar C, Batra S, Stanger B, Bui J, Brown K, Rajasekhar V, Healey J, de Sousa M, Kramer K, Sheth S, Baisch J, Pascual V, Heaton T, La Quaglia M, Pisapia D, Schwartz R, Zhang H, Liu Y, Shukla A, Blavier L, DeClerck Y, LaBarge M, Bissell M, Caffrey T, Grandgenett P, Hollingsworth M, Bromberg J, Costa-Silva B, Peinado H, Kang Y, Garcia B, O’Reilly E, Kelsen D, Trippett T, Jones D, Matei I, Jarnagin W, Lyden D. Extracellular Vesicle and Particle Biomarkers Define Multiple Human Cancers. Cell. 2020;182(4):1044–1061.e18. PMCID: PMC7522766 Reference Link
1.Kennedy M, Hofstadter W, Cristea I. TRANSPIRE: A Computational Pipeline to Elucidate Intracellular Protein Movements from Spatial Proteomics Data Sets. J Am Soc Mass Spectrom. 2020;31(7):1422–1439. PMCID: PMC7737664 Reference Link
1.Martin J, Sheehan J, Bratton B, Moore G, Mateus A, Li S, Kim H, Rabinowitz J, Typas A, Savitski M, Wilson M, Gitai Z. A Dual-Mechanism Antibiotic Kills Gram-Negative Bacteria and Avoids Drug Resistance. Cell. 2020;181(7):1518–1532.e14. PMCID: PMC7780349 Reference Link
1.Burton A, Haugbro M, Gates L, Bagert J, Allis D, Muir T. In situ chromatin interactomics using a chemical bait and trap approach. Nat Chem. 2020;12(6):520–527. PMCID: PMC7331920 Reference Link
1.Greco T, Kennedy M, Cristea I. Proteomic Technologies for Deciphering Local and Global Protein Interactions. Trends Biochem Sci. 2020;45(5):454–455. PMID: 32035732 Reference Link
1.Hashimoto Y, Sheng X, Murray-Nerger L, Cristea I. Temporal dynamics of protein complex formation and dissociation during human cytomegalovirus infection. Nat Commun. 2020;11(1):806. PMCID: PMC7010728 Reference Link
1.Winer B, Edgel K, Zou X, Sellau J, Hadiwidjojo S, Garver L, McDonough C, Kelleher N, Thomas P, Villasante E, Ploss A, Gerbasi V. Identification of Plasmodium falciparum proteoforms from liver stage models. Malar J. 2020;19(1):10. PMCID: PMC6947969 Reference Link
1.Nechay M, Kleiner R. High-throughput approaches to profile RNA-protein interactions. Curr Opin Chem Biol. 2020;54:37–44. PMCID: PMC7131871 Reference Link
1.Lum K, Howard T, Pan C, Cristea I. Charge-Mediated Pyrin Oligomerization Nucleates Antiviral IFI16 Sensing of Herpesvirus DNA. mBio. 2019;10(4). PMCID: PMC6650555 Reference Link
1.Murray L, Combs A, Rekapalli P, Cristea I. Methods for characterizing protein acetylation during viral infection. Methods Enzymol. 2019;626:587–620. PMCID: PMC6889803 Reference Link
1.Hashimoto Y, Greco T, Cristea I. Contribution of Mass Spectrometry-Based Proteomics to Discoveries in Developmental Biology. Adv Exp Med Biol. 2019;1140:143–154. PMID: 31347046 Reference Link
1.Peshkin L, Gupta M, Ryazanova L, Wühr M. Bayesian Confidence Intervals for Multiplexed Proteomics Integrate Ion-statistics with Peptide Quantification Concordance. Mol Cell Proteomics. 2019;18(10):2108–2120. PMCID: PMC6773559 Reference Link
1.Federspiel J, Cristea I. Considerations for Identifying Endogenous Protein Complexes from Tissue via Immunoaffinity Purification and Quantitative Mass Spectrometry. Methods Mol Biol. 2019;1977:115–143. PMID: 30980326 Reference Link
1.Arguello E, Srikumar T, Kleiner R. A Photocrosslinking-Based RNA Chemical Proteomics Approach to Profile m A-Regulated Protein-RNA Interactions. Curr Protoc Nucleic Acid Chem. 2018;75(1):e69. PMID: 30408339 Reference Link
1.Pappireddi N, Martin L, Wühr M. A Review on Quantitative Multiplexed Proteomics. Chembiochem. 2019;20(10):1210–1224. PMCID: PMC6520187 Reference Link
1.Nguyen T, Pappireddi N, Wühr M. Proteomics of nucleocytoplasmic partitioning. Curr Opin Chem Biol. 2019;48:55–63. PMCID: PMC6382543 Reference Link
1.Cook K, Cristea I. Location is everything: protein translocations as a viral infection strategy. Curr Opin Chem Biol. 2019;48:34–43. PMCID: PMC6382524 Reference Link
1.Gupta M, Sonnett M, Ryazanova L, Presler M, Wühr M. Quantitative Proteomics of Xenopus Embryos I, Sample Preparation. Methods Mol Biol. 2018;1865:175–194. PMCID: PMC6564683 Reference Link
1.Sonnett M, Gupta M, Nguyen T, Wühr M. Quantitative Proteomics for Xenopus Embryos II, Data Analysis. Methods Mol Biol. 2018;1865:195–215. PMCID: PMC6534117 Reference Link
1.Beltran P, Cook K, Hashimoto Y, Galitzine C, Murray L, Vitek O, Cristea I. Infection-Induced Peroxisome Biogenesis Is a Metabolic Strategy for Herpesvirus Replication. Cell Host Microbe. 2018;24(4):526–541.e7. PMCID: PMC6195127 Reference Link
1.Chou D, Adamson B, Dephoure N, Tan X, Nottke A, Hurov K, Gygi S, Colaiácovo M, Elledge S. A chromatin localization screen reveals poly (ADP ribose)-regulated recruitment of the repressive polycomb and NuRD complexes to sites of DNA damage. Proc Natl Acad Sci U S A. 2010;107(43):18475–80. PMCID: PMC2972950 Reference Link
1.Arguello E, DeLiberto A, Kleiner R. RNA Chemical Proteomics Reveals the N-Methyladenosine (mA)-Regulated Protein-RNA Interactome. J Am Chem Soc. 2017;139(48):17249–17252. PMID: 29140688 Reference Link
1.Zhang Y, Avalos J. Traditional and novel tools to probe the mitochondrial metabolism in health and disease. Wiley Interdiscip Rev Syst Biol Med. 2017;9(2). PMID: 28067471 Reference Link
1.Sauls K, Greco T, Wang L, Zou M, Villasmil M, Qian L, Cristea I, Conlon F. Initiating Events in Direct Cardiomyocyte Reprogramming. Cell Rep. 2018;22(7):1913–1922. PMCID: PMC6045814 Reference Link
1.Aebersold R, Agar J, Amster J, Baker M, Bertozzi C, Boja E, Costello C, Cravatt B, Fenselau C, Garcia B, Ge Y, Gunawardena J, Hendrickson R, Hergenrother P, Huber C, Ivanov A, Jensen O, Jewett M, Kelleher N, Kiessling L, Krogan N, Larsen M, Loo J, Loo R, Lundberg E, MacCoss M, Mallick P, Mootha V, Mrksich M, Muir T, Patrie S, Pesavento J, Pitteri S, Rodriguez H, Saghatelian A, Sandoval W, Schlüter H, Sechi S, Slavoff S, Smith L, Snyder M, Thomas P, Uhlén M, Van Eyk J, Vidal M, Walt D, White F, Williams E, Wohlschlager T, Wysocki V, Yates N, Young N, Zhang B. How many human proteoforms are there?. Nat Chem Biol. 2018;14(3):206–214. PMCID: PMC5837046 Reference Link
1.Jenness C, Giunta S, Müller M, Kimura H, Muir T, Funabiki H. HELLS and CDCA7 comprise a bipartite nucleosome remodeling complex defective in ICF syndrome. Proc Natl Acad Sci U S A. 2018;115(5):E876-E885. PMCID: PMC5798369 Reference Link
1.Rowland E, Snowden C, Cristea I. Protein lipoylation: an evolutionarily conserved metabolic regulator of health and disease. Curr Opin Chem Biol. 2018;42:76–85. PMCID: PMC5965299 Reference Link
1.Rowland E, Greco T, Snowden C, McCabe A, Silhavy T, Cristea I. Sirtuin Lipoamidase Activity Is Conserved in Bacteria as a Regulator of Metabolic Enzyme Complexes. mBio. 2017;8(5). PMCID: PMC5596343 Reference Link
1.Kennedy L, Kaltenbrun E, Greco T, Temple B, Herring L, Cristea I, Conlon F. Formation of a TBX20-CASZ1 protein complex is protective against dilated cardiomyopathy and critical for cardiac homeostasis. PLoS Genet. 2017;13(9):e1007011. PMCID: PMC5629033 Reference Link
1.Gong Y, Cao R, Ding G, Hong S, Zhou W, Lu W, Damle M, Fang B, Wang C, Qian J, Lie N, Lanzillotta C, Rabinowitz J, Sun Z. Integrated omics approaches to characterize a nuclear receptor corepressor-associated histone deacetylase in mouse skeletal muscle. Mol Cell Endocrinol. 2018;471:22–32. PMCID: PMC5702591 Reference Link
1.Cristea I. The Host-Pathogen Ecosystem Viewed Through the Prism of Proteomics. Mol Cell Proteomics. 2017;16(4 suppl 1):S1-S4. PMCID: PMC5393400 Reference Link
1.Beltran P, Federspiel J, Sheng X, Cristea I. Proteomics and integrative omic approaches for understanding host-pathogen interactions and infectious diseases. Mol Syst Biol. 2017;13(3):922. PMCID: PMC5371729 Reference Link
1.Greco T, Cristea I. Proteomics Tracing the Footsteps of Infectious Disease. Mol Cell Proteomics. 2017;16(4 suppl 1):S5-S14. PMCID: PMC5393401 Reference Link