Omenn G, Lane L, Overall C, Pineau C, Packer N, Cristea I, Lindskog C, Weintraub S, Orchard S, Roehrl M, Nice E, Liu S, Bandeira N, Chen Y-J, Guo T, Aebersold R, Moritz R, Deutsch E. The 2022 Report on the Human Proteome from the HUPO Human Proteome Project. J Proteome Res. 2023;22(4):1024–1042. PMCID: PMC10081950

Nguyen T, Costa E, Deibert T, Reyes J, Keber F, Tomschik M, Stadlmeier M, Gupta M, Kumar C, Cruz E, Amodeo A, Gatlin J, Wühr M. Differential nuclear import sets the timing of protein access to the embryonic genome. Nat Commun. 2022;13(1):5887. PMCID: PMC9537182

Kennedy M, Greco T, Song B, Cristea I. HTT-OMNI: A Web-based Platform for Huntingtin Interaction Exploration and Multi-omics Data Integration. Mol Cell Proteomics. 2022;21(10):100275. PMCID: PMC9540350

Miller C, Henderson M, Mantopoulos D, Leskov I, Greco T, Schwarzbauer J, Prenner J. The Proteome of Preretinal Tissue in Proliferative Vitreoretinopathy. Ophthalmic Surg Lasers Imaging Retina. 2021;52(S1):S5-S12. PMID: 34310239

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

Lindström N, Sealfon R, Chen X, Parvez R, Ransick A, Brandine G, Guo J, Hill B, Tran T, Kim A, Zhou J, Tadych A, Watters A, Wong A, Lovero E, Grubbs B, Thornton M, McMahon J, Smith A, Ruffins S, Armit C, Troyanskaya O, McMahon A. Spatial transcriptional mapping of the human nephrogenic program. Dev Cell. 2021;56(16):2381–2398.e6. PMCID: PMC8396064

Sheng X, Cristea I. The antiviral sirtuin 3 bridges protein acetylation to mitochondrial integrity and metabolism during human cytomegalovirus infection. PLoS Pathog. 2021;17(4):e1009506. PMCID: PMC8078788

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

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

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

Cao W, Kabelitz S, Gupta M, Yeung E, Lin S, Rammelt C, Ihling C, Pekovic F, Low T, Siddiqui N, Cheng M, Angers S, Smibert C, Wühr M, Wahle E, Lipshitz H. Precise Temporal Regulation of Post-transcriptional Repressors Is Required for an Orderly Drosophila Maternal-to-Zygotic Transition. Cell Rep. 2020;31(12):107783. PMCID: PMC7372737

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

Federspiel J, Tandon P, Wilczewski C, Wasson L, Herring L, Venkatesh S, Cristea I, Conlon F. Conservation and divergence of protein pathways in the vertebrate heart. PLoS Biol. 2019;17(9):e3000437. PMCID: PMC6750614

Murray L, Combs A, Rekapalli P, Cristea I. Methods for characterizing protein acetylation during viral infection. Methods Enzymol. 2019;626:587–620. PMCID: PMC6889803

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

Federspiel J, Greco T, Lum K, Cristea I. Hdac4 Interactions in Huntington’s Disease Viewed Through the Prism of Multiomics. Mol Cell Proteomics. 2019;18(8 suppl 1):S92-S113. PMCID: PMC6692770

Hashimoto Y, Kinoshita N, Greco T, Federspiel J, Beltran P, Ueno N, Cristea I. Mechanical Force Induces Phosphorylation-Mediated Signaling that Underlies Tissue Response and Robustness in Xenopus Embryos. Cell Syst. 2019;8(3):226–241.e7. PMCID: PMC6453581

Cristea I, Lilley K. Editorial overview: Untangling proteome organization in space and time. Curr Opin Chem Biol. 2019;48:A1-A4. PMID: 30782346

Pappireddi N, Martin L, Wühr M. A Review on Quantitative Multiplexed Proteomics. Chembiochem. 2019;20(10):1210–1224. PMCID: PMC6520187

Nguyen T, Pappireddi N, Wühr M. Proteomics of nucleocytoplasmic partitioning. Curr Opin Chem Biol. 2019;48:55–63. PMCID: PMC6382543

Lum K, Song B, Federspiel J, Diner B, Howard T, Cristea I. Interactome and Proteome Dynamics Uncover Immune Modulatory Associations of the Pathogen Sensing Factor cGAS. Cell Syst. 2018;7(6):627–642.e6. PMCID: PMC6310102

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

Presler M, Van Itallie E, Klein A, Kunz R, Coughlin M, Peshkin L, Gygi S, Wühr M, Kirschner M. Proteomics of phosphorylation and protein dynamics during fertilization and meiotic exit in the egg. Proc Natl Acad Sci U S A. 2017;114(50):E10838-E10847. PMCID: PMC5740657

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

Mirzaei M, Gupta V, Chick J, Greco T, Wu Y, Chitranshi N, Wall R, Hone E, Deng L, Dheer Y, Abbasi M, Rezaeian M, Braidy N, You Y, Salekdeh G, Haynes P, Molloy M, Martins R, Cristea I, Gygi S, Graham S, Gupta V. Age-related neurodegenerative disease associated pathways identified in retinal and vitreous proteome from human glaucoma eyes. Sci Rep. 2017;7(1):12685. PMCID: PMC5627288

Beltran P, Cook K, Cristea I. Exploring and Exploiting Proteome Organization during Viral Infection. J Virol. 2017;91(18). PMCID: PMC5571249

Carabetta V, Cristea I. Regulation, Function, and Detection of Protein Acetylation in Bacteria. J Bacteriol. 2017;199(16). PMCID: PMC5527388

Ron-Harel N, Santos D, Ghergurovich J, Sage P, Reddy A, Lovitch S, Dephoure N, Satterstrom K, Sheffer M, Spinelli J, Gygi S, Rabinowitz J, Sharpe A, Haigis M. Mitochondrial Biogenesis and Proteome Remodeling Promote One-Carbon Metabolism for T Cell Activation. Cell Metab. 2016;24(1):104–17. PMCID: PMC5330619

Rowles D, Tsai Y-C, Greco T, Lin A, Li M, Yeh J, Cristea I. DNA methyltransferase DNMT3A associates with viral proteins and impacts HSV-1 infection. Proteomics. 2015;15(12):1968–82. PMCID: PMC4550099

Giguère S, Guise A, Beltran P, Joshi P, Greco T, Quach O, Kong J, Cristea I. The Proteomic Profile of Deleted in Breast Cancer 1 (DBC1) Interactions Points to a Multifaceted Regulation of Gene Expression. Mol Cell Proteomics. 2016;15(3):791–809. PMCID: PMC4813701

Beltran P, Mathias R, Cristea I. A Portrait of the Human Organelle Proteome In Space and Time during Cytomegalovirus Infection. Cell Syst. 2016;3(4):361–373.e6. PMCID: PMC5083158

Lum K, Cristea I. Proteomic approaches to uncovering virus-host protein interactions during the progression of viral infection. Expert Rev Proteomics. 2016;13(3):325–40. PMCID: PMC4919574

Li X, Zhang R, Patena W, Gang S, Blum S, Ivanova N, Yue R, Robertson J, Lefebvre P, Fitz-Gibbon S, Grossman A, Jonikas M. An Indexed, Mapped Mutant Library Enables Reverse Genetics Studies of Biological Processes in Chlamydomonas reinhardtii. Plant Cell. 2016;28(2):367–87. PMCID: PMC4790863

Pritykin Y, Ghersi D, Singh M. Genome-Wide Detection and Analysis of Multifunctional Genes. PLoS Comput Biol. 2015;11(10):e1004467. PMCID: PMC4593560

Henry T, Brynildsen M. Quantifying Current Events Identifies a Novel Endurance Regulator. Trends Microbiol. 2016;24(5):324–326. PMCID: PMC4841710

Oberstein A, Perlman D, Shenk T, Terry L. Human cytomegalovirus pUL97 kinase induces global changes in the infected cell phosphoproteome. Proteomics. 2015;15(12):2006–22. PMCID: PMC4522931

Wühr M, Güttler T, Peshkin L, McAlister G, Sonnett M, Ishihara K, Groen A, Presler M, Erickson B, Mitchison T, Kirschner M, Gygi S. The Nuclear Proteome of a Vertebrate. Curr Biol. 2015;25(20):2663–71. PMCID: PMC4618192

Peshkin L, Wühr M, Pearl E, Haas W, Freeman R, Gerhart J, Klein A, Horb M, Gygi S, Kirschner M. On the Relationship of Protein and mRNA Dynamics in Vertebrate Embryonic Development. Dev Cell. 2015;35(3):383–94. PMCID: PMC4776761