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A SARS-CoV-2 protein interaction map reveals targets for drug repurposing

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  1. Jiakai Hou & Yanjun Wei & Jing Zou & Roshni Jaffery & Long Sun & Shaoheng Liang & Ningbo Zheng & Ashley M. Guerrero & Nicholas A. Egan & Ritu Bohat & Si Chen & Caishang Zheng & Xiaobo Mao & S. Stephen, 2024. "Integrated multi-omics analyses identify anti-viral host factors and pathways controlling SARS-CoV-2 infection," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
  2. Pisanu Buphamalai & Tomislav Kokotovic & Vanja Nagy & Jörg Menche, 2021. "Network analysis reveals rare disease signatures across multiple levels of biological organization," Nature Communications, Nature, vol. 12(1), pages 1-15, December.
  3. Taha Y. Taha & Irene P. Chen & Jennifer M. Hayashi & Takako Tabata & Keith Walcott & Gabriella R. Kimmerly & Abdullah M. Syed & Alison Ciling & Rahul K. Suryawanshi & Hannah S. Martin & Bryan H. Bach , 2023. "Rapid assembly of SARS-CoV-2 genomes reveals attenuation of the Omicron BA.1 variant through NSP6," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
  4. Sara Sunshine & Andreas S. Puschnik & Joseph M. Replogle & Matthew T. Laurie & Jamin Liu & Beth Shoshana Zha & James K. Nuñez & Janie R. Byrum & Aidan H. McMorrow & Matthew B. Frieman & Juliane Winkle, 2023. "Systematic functional interrogation of SARS-CoV-2 host factors using Perturb-seq," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
  5. Hanbaek Lyu & Yacoub H. Kureh & Joshua Vendrow & Mason A. Porter, 2024. "Learning low-rank latent mesoscale structures in networks," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
  6. Andrea Fossati & Deepto Mozumdar & Claire Kokontis & Melissa Mèndez-Moran & Eliza Nieweglowska & Adrian Pelin & Yuping Li & Baron Guo & Nevan J. Krogan & David A. Agard & Joseph Bondy-Denomy & Daniell, 2023. "Next-generation proteomics for quantitative Jumbophage-bacteria interaction mapping," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
  7. Chachrit Khunsriraksakul & Daniel McGuire & Renan Sauteraud & Fang Chen & Lina Yang & Lida Wang & Jordan Hughey & Scott Eckert & J. Dylan Weissenkampen & Ganesh Shenoy & Olivia Marx & Laura Carrel & B, 2022. "Integrating 3D genomic and epigenomic data to enhance target gene discovery and drug repurposing in transcriptome-wide association studies," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
  8. Ramiz Salama & Fadi Al-Turjman, 2023. "Sustainable Energy Production in Smart Cities," Sustainability, MDPI, vol. 15(22), pages 1-25, November.
  9. Xiaopan Gao & Huabin Tian & Kaixiang Zhu & Qing Li & Wei Hao & Linyue Wang & Bo Qin & Hongyu Deng & Sheng Cui, 2022. "Structural basis for Sarbecovirus ORF6 mediated blockage of nucleocytoplasmic transport," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
  10. Daniel Strebinger & Chris J. Frangieh & Mirco J. Friedrich & Guilhem Faure & Rhiannon K. Macrae & Feng Zhang, 2023. "Cell type-specific delivery by modular envelope design," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
  11. David Gomez-Zepeda & Danielle Arnold-Schild & Julian Beyrle & Arthur Declercq & Ralf Gabriels & Elena Kumm & Annica Preikschat & Mateusz Krzysztof Łącki & Aurélie Hirschler & Jeewan Babu Rijal & Chris, 2024. "Thunder-DDA-PASEF enables high-coverage immunopeptidomics and is boosted by MS2Rescore with MS2PIP timsTOF fragmentation prediction model," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
  12. Maria I. Freiberger & Victoria Ruiz-Serra & Camila Pontes & Miguel Romero-Durana & Pablo Galaz-Davison & Cesar A. Ramírez-Sarmiento & Claudio D. Schuster & Marcelo A. Marti & Peter G. Wolynes & Diego , 2023. "Local energetic frustration conservation in protein families and superfamilies," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
  13. Christine E. Peters & Ursula Schulze-Gahmen & Manon Eckhardt & Gwendolyn M. Jang & Jiewei Xu & Ernst H. Pulido & Conner Bardine & Charles S. Craik & Melanie Ott & Or Gozani & Kliment A. Verba & Ruth H, 2022. "Structure-function analysis of enterovirus protease 2A in complex with its essential host factor SETD3," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
  14. Haofeng Wang & Qi Yang & Xiaoce Liu & Zili Xu & Maolin Shao & Dongxu Li & Yinkai Duan & Jielin Tang & Xianqiang Yu & Yumin Zhang & Aihua Hao & Yajie Wang & Jie Chen & Chenghao Zhu & Luke Guddat & Hong, 2023. "Structure-based discovery of dual pathway inhibitors for SARS-CoV-2 entry," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
  15. Thomas Kruse & Caroline Benz & Dimitriya H. Garvanska & Richard Lindqvist & Filip Mihalic & Fabian Coscia & Raviteja Inturi & Ahmed Sayadi & Leandro Simonetti & Emma Nilsson & Muhammad Ali & Johanna K, 2021. "Large scale discovery of coronavirus-host factor protein interaction motifs reveals SARS-CoV-2 specific mechanisms and vulnerabilities," Nature Communications, Nature, vol. 12(1), pages 1-13, December.
  16. Filip Mihalič & Caroline Benz & Eszter Kassa & Richard Lindqvist & Leandro Simonetti & Raviteja Inturi & Hanna Aronsson & Eva Andersson & Celestine N. Chi & Norman E. Davey & Anna K. Överby & Per Jemt, 2023. "Identification of motif-based interactions between SARS-CoV-2 protein domains and human peptide ligands pinpoint antiviral targets," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
  17. Nell Saunders & Blandine Monel & Nadège Cayet & Lorenzo Archetti & Hugo Moreno & Alexandre Jeanne & Agathe Marguier & Julian Buchrieser & Timothy Wai & Olivier Schwartz & Mathieu Fréchin, 2024. "Dynamic label-free analysis of SARS-CoV-2 infection reveals virus-induced subcellular remodeling," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
  18. Wen Juan Tu & Michelle Melino & Jenny Dunn & Robert D. McCuaig & Helle Bielefeldt-Ohmann & Sofiya Tsimbalyuk & Jade K. Forwood & Taniya Ahuja & John Vandermeide & Xiao Tan & Minh Tran & Quan Nguyen & , 2023. "In vivo inhibition of nuclear ACE2 translocation protects against SARS-CoV-2 replication and lung damage through epigenetic imprinting," Nature Communications, Nature, vol. 14(1), pages 1-21, December.
  19. Filip Mihalič & Leandro Simonetti & Girolamo Giudice & Marie Rubin Sander & Richard Lindqvist & Marie Berit Akpiroro Peters & Caroline Benz & Eszter Kassa & Dilip Badgujar & Raviteja Inturi & Muhammad, 2023. "Large-scale phage-based screening reveals extensive pan-viral mimicry of host short linear motifs," Nature Communications, Nature, vol. 14(1), pages 1-20, December.
  20. Ayan Chatterjee & Robin Walters & Zohair Shafi & Omair Shafi Ahmed & Michael Sebek & Deisy Gysi & Rose Yu & Tina Eliassi-Rad & Albert-László Barabási & Giulia Menichetti, 2023. "Improving the generalizability of protein-ligand binding predictions with AI-Bind," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
  21. Scotland E. Farley & Jennifer E. Kyle & Hans C. Leier & Lisa M. Bramer & Jules B. Weinstein & Timothy A. Bates & Joon-Yong Lee & Thomas O. Metz & Carsten Schultz & Fikadu G. Tafesse, 2022. "A global lipid map reveals host dependency factors conserved across SARS-CoV-2 variants," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
  22. Joseph Hiatt & Judd F. Hultquist & Michael J. McGregor & Mehdi Bouhaddou & Ryan T. Leenay & Lacy M. Simons & Janet M. Young & Paige Haas & Theodore L. Roth & Victoria Tobin & Jason A. Wojcechowskyj & , 2022. "A functional map of HIV-host interactions in primary human T cells," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
  23. Andrea M. Chiariello & Alex Abraham & Simona Bianco & Andrea Esposito & Andrea Fontana & Francesca Vercellone & Mattia Conte & Mario Nicodemi, 2024. "Multiscale modelling of chromatin 4D organization in SARS-CoV-2 infected cells," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
  24. Gabriela Dias Noske & Yun Song & Rafaela Sachetto Fernandes & Rod Chalk & Haitem Elmassoudi & Lizbé Koekemoer & C. David Owen & Tarick J. El-Baba & Carol V. Robinson & Glaucius Oliva & Andre Schutzer , 2023. "An in-solution snapshot of SARS-COV-2 main protease maturation process and inhibition," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
  25. Meghana Venkata Palukuri & Edward M Marcotte, 2021. "Super.Complex: A supervised machine learning pipeline for molecular complex detection in protein-interaction networks," PLOS ONE, Public Library of Science, vol. 16(12), pages 1-23, December.
  26. Seongryong Kim & Ji Hyang Jeon & Myeonghwan Kim & Yeji Lee & Yun-Ho Hwang & Myungsun Park & C. Han Li & Taeyoung Lee & Jung-Ah Lee & You-Me Kim & Dokeun Kim & Hyukjin Lee & You-Jin Kim & V. Narry Kim , 2024. "Innate immune responses against mRNA vaccine promote cellular immunity through IFN-β at the injection site," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
  27. Ma’ayan Israeli & Yaara Finkel & Yfat Yahalom-Ronen & Nir Paran & Theodor Chitlaru & Ofir Israeli & Inbar Cohen-Gihon & Moshe Aftalion & Reut Falach & Shahar Rotem & Uri Elia & Ital Nemet & Limor Klik, 2022. "Genome-wide CRISPR screens identify GATA6 as a proviral host factor for SARS-CoV-2 via modulation of ACE2," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
  28. Kelsey M. Haas & Michael J. McGregor & Mehdi Bouhaddou & Benjamin J. Polacco & Eun-Young Kim & Thong T. Nguyen & Billy W. Newton & Matthew Urbanowski & Heejin Kim & Michael A. P. Williams & Veronica V, 2023. "Proteomic and genetic analyses of influenza A viruses identify pan-viral host targets," Nature Communications, Nature, vol. 14(1), pages 1-27, December.
  29. Matthias M. Zimmer & Anuja Kibe & Ulfert Rand & Lukas Pekarek & Liqing Ye & Stefan Buck & Redmond P. Smyth & Luka Cicin-Sain & Neva Caliskan, 2021. "The short isoform of the host antiviral protein ZAP acts as an inhibitor of SARS-CoV-2 programmed ribosomal frameshifting," Nature Communications, Nature, vol. 12(1), pages 1-15, December.
  30. Charulata Jindal & Sandeep Kumar & Sunil Sharma & Yuk Ming Choi & Jimmy T. Efird, 2020. "The Prevention and Management of COVID-19: Seeking a Practical and Timely Solution," IJERPH, MDPI, vol. 17(11), pages 1-11, June.
  31. Asolina Braun & Louise C. Rowntree & Ziyi Huang & Kirti Pandey & Nikolas Thuesen & Chen Li & Jan Petersen & Dene R. Littler & Shabana Raji & Thi H. O. Nguyen & Emma Jappe Lange & Gry Persson & Michael, 2024. "Mapping the immunopeptidome of seven SARS-CoV-2 antigens across common HLA haplotypes," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
  32. Kshitiz Walia & Abhishek Sharma & Sankalita Paul & Priya Chouhan & Gaurav Kumar & Rajesh Ringe & Mahak Sharma & Amit Tuli, 2024. "SARS-CoV-2 virulence factor ORF3a blocks lysosome function by modulating TBC1D5-dependent Rab7 GTPase cycle," Nature Communications, Nature, vol. 15(1), pages 1-24, December.
  33. Emilie Murigneux & Laurent Softic & Corentin Aubé & Carmen Grandi & Delphine Judith & Johanna Bruce & Morgane Le Gall & François Guillonneau & Alain Schmitt & Vincent Parissi & Clarisse Berlioz-Torren, 2024. "Proteomic analysis of SARS-CoV-2 particles unveils a key role of G3BP proteins in viral assembly," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
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