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A
Ali MZulfikar, Wingreen NS, Mukhopadhyay R. Hidden long evolutionary memory in a model biochemical network. Phys Rev E. 2018 ;97(4-1):040401.
Ashford P, Hernandez A, Greco TMichael, Buch A, Sodeik B, Cristea IMihaela, et al. HVint: A Strategy for Identifying Novel Protein-Protein Interactions in Herpes Simplex Virus Type 1. Mol Cell Proteomics. 2016 ;15(9):2939-53.
B
Bitbol A-F, Dwyer RS, Colwell LJ, Wingreen NS. Inferring interaction partners from protein sequences. Proc Natl Acad Sci U S A. 2016 ;113(43):12180-12185.
Budayeva HG, Cristea IM. Human Sirtuin 2 Localization, Transient Interactions, and Impact on the Proteome Point to Its Role in Intracellular Trafficking. Mol Cell Proteomics. 2016 ;15(10):3107-3125.
C
Cook KC, Cristea IM. Location is everything: protein translocations as a viral infection strategy. Curr Opin Chem Biol. 2019 ;48:34-43.
Cristea IM, Lilley KS. Editorial overview: Untangling proteome organization in space and time. Curr Opin Chem Biol. 2019 ;48:A1-A4.
Crow MS, Cristea IM. Human Antiviral Protein IFIX Suppresses Viral Gene Expression during Herpes Simplex Virus 1 (HSV-1) Infection and Is Counteracted by Virus-induced Proteasomal Degradation. Mol Cell Proteomics. 2017 ;16(4 suppl 1):S200-S214.
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Durán AHernández, Greco TM, Vollmer B, Cristea IM, Grünewald K, Topf M. Protein interactions and consensus clustering analysis uncover insights into herpesvirus virion structure and function relationships. PLoS Biol. 2019 ;17(6):e3000316.
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Federspiel JD, Cook KC, Kennedy MA, Venkatesh SS, Otter CJ, Hofstadter WA, et al. Mitochondria and Peroxisome Remodeling across Cytomegalovirus Infection Time Viewed through the Lens of Inter-ViSTA. Cell Rep. 2020 ;32(4):107943.
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Goglia AG, Toettcher JE. A bright future: optogenetics to dissect the spatiotemporal control of cell behavior. Curr Opin Chem Biol. 2019 ;48:106-113.
Gong X, Qian H, Cao P, Zhao X, Zhou Q, Lei J, et al. Structural basis for the recognition of Sonic Hedgehog by human Patched1. Science. 2018 ;361(6402).
Gorenshteyn D, Zaslavsky E, Fribourg M, Park CY, Wong AK, Tadych A, et al. Interactive Big Data Resource to Elucidate Human Immune Pathways and Diseases. Immunity. 2015 ;43(3):605-14.
Greco TM, Cristea IM. The Biochemical Evolution of Protein Complexes. Trends Biochem Sci. 2016 ;41(1):4-6.
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Hashimoto Y, Sheng X, Murray-Nerger LA, Cristea IM. Temporal dynamics of protein complex formation and dissociation during human cytomegalovirus infection. Nat Commun. 2020 ;11(1):806.
Hristov BH, Chazelle B, Singh M. uKIN Combines New and Prior Information with Guided Network Propagation to Accurately Identify Disease Genes. Cell Syst. 2020 ;10(6):470-479.e3.
Hristov BH, Singh M. Network-Based Coverage of Mutational Profiles Reveals Cancer Genes. Cell Syst. 2017 ;5(3):221-229.e4.
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Lum KK, Song B, Federspiel JD, Diner BA, Howard T, Cristea IM. Interactome and Proteome Dynamics Uncover Immune Modulatory Associations of the Pathogen Sensing Factor cGAS. Cell Syst. 2018 ;7(6):627-642.e6.
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Mirzaei M, Gupta VB, Chick JM, Greco TM, Wu Y, Chitranshi N, et al. Age-related neurodegenerative disease associated pathways identified in retinal and vitreous proteome from human glaucoma eyes. Sci Rep. 2017 ;7(1):12685.
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Nguyen T, Pappireddi N, Wühr M. Proteomics of nucleocytoplasmic partitioning. Curr Opin Chem Biol. 2019 ;48:55-63.
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Pareek V, Sha Z, He J, Wingreen NS, Benkovic SJ. Metabolic channeling: predictions, deductions, and evidence. Mol Cell. 2021 ;81(18):3775-3785.
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Sanders DW, Kedersha N, Lee DSW, Strom AR, Drake V, Riback JA, et al. Competing Protein-RNA Interaction Networks Control Multiphase Intracellular Organization. Cell. 2020 ;181(2):306-324.e28.
Seath CP, Trowbridge AD, Muir TW, MacMillan DWC. Reactive intermediates for interactome mapping. Chem Soc Rev. 2021 ;50(5):2911-2926.
Shin Y, Berry J, Pannucci N, Haataja MP, Toettcher JE, Brangwynne CP. Spatiotemporal Control of Intracellular Phase Transitions Using Light-Activated optoDroplets. Cell. 2017 ;168(1-2):159-171.e14.
T
Tareen A, Wingreen NS, Mukhopadhyay R. Asymmetry between Activators and Deactivators in Functional Protein Networks. Sci Rep. 2020 ;10(1):10131.