Danielle Swaney, PhD

Title(s)Associate Professor, Cellular Molecular Pharmacology
SchoolSchool of Medicine
Address1700 4th Street, #001
San Francisco CA 94158
Phone415-734-2767
ORCID ORCID Icon0000-0001-6119-6084 Additional info
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    Collapse Biography 
    Collapse Education and Training
    University of Washington, Seattle, WAPostdoctoral Scholar10/2014Proteomics
    University of Wisconsin, Madison, WIPhD08/2009Analytical Chemistry
    Winona State University, Winona, MNBS05/2005Chemistry

    Collapse Overview 
    Collapse Overview
    My interest is in using proteomics approaches to advance our understanding of both basic and disease biology. Of particular interest to me is the study of protein-protein interactions/complexes and post-translational modification signaling in the context of infection and neurodegeneration.

    My lab at UCSF is encompassed within the larger lab of Nevan Krogan. This provides scientists the best of both worlds - access to big-lab support and resources, but with strong small-lab mentorship. Additionally, I manage the proteomics facility at both the UCSF Weill Institute for Neurosciences, and at the Gladstone Institutes, where I am a visiting scientist.

    Collapse Research 
    Collapse Research Activities and Funding
    THE HARC CENTER: HIV ACCESSORY AND REGULATORY COMPLEXES: PROTEOMICS CORE
    NIH/NIAID U54AI170792Jul 15, 2022 - Apr 30, 2027
    Role: PI
    Genetic and Proteomic Approaches to Reveal Bacterial Vulnerabilities to Phage Predation
    NIH/NIAID R01AI167412May 20, 2022 - Apr 30, 2027
    Role: Co-Investigator
    QCRG Pandemic Response Program: Proteomics Core
    NIH/NIAID U19AI171110May 16, 2022 - Apr 30, 2025
    Role: PI
    Uncovering the genetic mechanisms of the Chromosome 17q21.31 Tau haplotype on neurodegeneration risk in FTD and PSP
    NIH U54NS123746Sep 1, 2021 - Aug 31, 2026
    Role: Co-Investigator
    Inclusion membrane protein (Inc) modulation of the innate immune response to Chlamydia trachomatis
    NIH R56AI152526Sep 4, 2020 - Aug 31, 2021
    Role: Co-Principal Investigator
    Childhood ?Omics? and Mycobacterium tuberculosis-derived BiOsignatures (COMBO) for TB diagnosis in high HIV prevalence settings
    NIH R01AI152161Apr 22, 2020 - Mar 31, 2025
    Role: Co-Investigator
    Proteomic and Genetic Approaches Defining Apolipoprotein E4 Neuropathologic Mechanisms
    NIH/NIA R01AG059751Sep 15, 2019 - May 31, 2024
    Role: Co-Investigator
    A universal multiplexing approach to unlock the hidden proteome
    NIH R01GM133981Sep 15, 2019 - Aug 31, 2023
    Role: Principal Investigator
    CasCUT&RUN: An in vivo method to analyze locus-specific protein complexes driving transcription of target genes in cancer
    NIH R21CA235303Feb 15, 2019 - Jan 31, 2022
    Role: Co-Investigator

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    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
    Newest   |   Oldest   |   Most Cited   |   Most Discussed   |   Timeline   |   Field Summary   |   Plain Text
    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Protocol for mapping differential protein-protein interaction networks using affinity purification-mass spectrometry. STAR Protoc. 2024 Nov 02; 5(4):103286. Kaushal P, Ummadi MR, Jang GM, Delgado Y, Makanani SK, Alba K, Winters DM, Blanc SF, Xu J, Polacco B, Zhou Y, Stevenson E, Eckhardt M, Zuliani-Alvarez L, Kaake R, Swaney DL, Krogan NJ, Bouhaddou M. PMID: 39488835.
      View in: PubMed   Mentions:    Fields:    
    2. MerlinS13 phosphorylation regulates meningioma Wnt signaling and magnetic resonance imaging features. Nat Commun. 2024 Sep 09; 15(1):7873. Eaton CD, Avalos L, Liu SJ, Chen Z, Zakimi N, Casey-Clyde T, Bisignano P, Lucas CG, Stevenson E, Choudhury A, Vasudevan HN, Magill ST, Young JS, Krogan NJ, Villanueva-Meyer JE, Swaney DL, Raleigh DR. PMID: 39251601; PMCID: PMC11383945.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimalsCells
    3. EGFR and EGFRvIII coopt host defense pathways, promoting progression in glioblastoma. Neuro Oncol. 2024 Sep 09. An Z, Fan QW, Wang L, Yoda H, Barata MJ, Jimenez-Morales D, Phillips JJ, Swaney DL, Stevenson E, Lee E, Krogan N, Weiss WA. PMID: 39248287.
      View in: PubMed   Mentions: 2     Fields:    
    4. The Mac1 ADP-ribosylhydrolase is a Therapeutic Target for SARS-CoV-2. bioRxiv. 2024 Aug 29. Suryawanshi RK, Jaishankar P, Correy GJ, Rachman MM, O'Leary PC, Taha TY, Zapatero-Belinchón FJ, McCavittMalvido M, Doruk YU, Stevens MGV, Diolaiti ME, Jogalekar MP, Richards AL, Montano M, Rosecrans J, Matthay M, Togo T, Gonciarz RL, Gopalkrishnan S, Neitz RJ, Krogan NJ, Swaney DL, Shoichet BK, Ott M, Renslo AR, Ashworth A, Fraser JS. PMID: 39149230; PMCID: PMC11326214.
      View in: PubMed   Mentions:
    5. Multiscale photocatalytic proximity labeling reveals cell surface neighbors on and between cells. Science. 2024 Jul 19; 385(6706):eadl5763. Lin Z, Schaefer K, Lui I, Yao Z, Fossati A, Swaney DL, Palar A, Sali A, Wells JA. PMID: 39024454.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansCells
    6. Characterization of a lipid-based jumbo phage compartment as a hub for early phage infection. Cell Host Microbe. 2024 Jul 10; 32(7):1050-1058.e7. Mozumdar D, Fossati A, Stevenson E, Guan J, Nieweglowska E, Rao S, Agard D, Swaney DL, Bondy-Denomy J. PMID: 38870941; PMCID: PMC11239273.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    7. The disease-causing tau V337M mutation induces tau hypophosphorylation and perturbs axon morphology pathways. bioRxiv. 2024 Jun 06. Mohl GA, Dixon G, Marzette E, McKetney J, Samelson AJ, Serras CP, Jin J, Li A, Boggess SC, Swaney DL, Kampmann M. PMID: 38895329; PMCID: PMC11185762.
      View in: PubMed   Mentions:
    8. Targeting a lineage-specific PI3Kɣ-Akt signaling module in acute myeloid leukemia using a heterobifunctional degrader molecule. Nat Cancer. 2024 Jul; 5(7):1082-1101. Kelly LM, Rutter JC, Lin KH, Ling F, Duchmann M, Latour E, Arang N, Pasquer H, Ho Nhat D, Charles J, Killarney ST, Ang HX, Namor F, Culeux C, Lombard B, Loew D, Swaney DL, Krogan NJ, Brunel L, Carretero É, Verdié P, Amblard M, Fodil S, Huynh T, Sebert M, Adès L, Raffoux E, Fenouille N, Itzykson R, Lobry C, Benajiba L, Forget A, Martin AR, Wood KC, Puissant A. PMID: 38816660.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimalsCells
    9. The Chlamydia trachomatis Inc Tri1 interacts with TRAF7 to displace native TRAF7 interacting partners. Microbiol Spectr. 2024 Jul 02; 12(7):e0045324. Herrera CM, McMahon E, Swaney DL, Sherry J, Pha K, Adams-Boone K, Johnson JR, Krogan NJ, Stevers M, Solomon D, Elwell C, Engel J. PMID: 38814079; PMCID: PMC11218536.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    10. Mapping Differential Protein-Protein Interaction Networks using Affinity Purification Mass Spectrometry. ArXiv. 2024 May 15. Kaushal P, Ummadi MR, Jang GM, Delgado Y, Makanani SK, Blanc SF, Winters DM, Xu J, Polacco B, Zhou Y, Stevenson E, Eckhardt M, Zuliani-Alvarez L, Kaake R, Swaney DL, Krogan N, Bouhaddou M. PMID: 38800652; PMCID: PMC11118664.
      View in: PubMed   Mentions:
    11. ATG7(2) Interacts With Metabolic Proteins and Regulates Central Energy Metabolism. Traffic. 2024 Apr; 25(4):e12933. Ostacolo K, López García de Lomana A, Larat C, Hjaltalin V, Holm KY, Hlynsdóttir SS, Soucheray M, Sooman L, Rolfsson O, Krogan NJ, Steingrimsson E, Swaney DL, Ogmundsdottir MH. PMID: 38600522; PMCID: PMC11480896.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    12. Spatial control of sensory adaptation modulates mechanosensing in Pseudomonas aeruginosa. bioRxiv. 2024 Feb 27. Patino R, Kühn MJ, Macmillan H, Inclan YF, Chavez I, Von Dollen J, Johnson JR, Swaney DL, Krogan NJ, Persat A, Engel JN. PMID: 38464290; PMCID: PMC10925122.
      View in: PubMed   Mentions:
    13. CRISPR-Cas9 screen of E3 ubiquitin ligases identifies TRAF2 and UHRF1 as regulators of HIV latency in primary human T cells. mBio. 2024 Apr 10; 15(4):e0222223. Rathore U, Haas P, Easwar Kumar V, Hiatt J, Haas KM, Bouhaddou M, Swaney DL, Stevenson E, Zuliani-Alvarez L, McGregor MJ, Turner-Groth A, Ochieng' Olwal C, Bediako Y, Braberg H, Soucheray M, Ott M, Eckhardt M, Hultquist JF, Marson A, Kaake RM, Krogan NJ. PMID: 38411080; PMCID: PMC11005436.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    14. The Chlamydia trachomatis Inc Tri1 interacts with TRAF7 to displace native TRAF7 interacting partners. bioRxiv. 2024 Feb 26. Herrera CM, McMahon E, Swaney DL, Sherry J, Pha K, Adams-Boone K, Johnson JR, Krogan NJ, Stevers M, Solomon D, Elwell C, Engel J. PMID: 38464023; PMCID: PMC10925117.
      View in: PubMed   Mentions:
    15. A foundational atlas of autism protein interactions reveals molecular convergence. bioRxiv. 2024 Feb 08. Wang B, Vartak R, Zaltsman Y, Naing ZZC, Hennick KM, Polacco BJ, Bashir A, Eckhardt M, Bouhaddou M, Xu J, Sun N, Lasser MC, Zhou Y, McKetney J, Guiley KZ, Chan U, Kaye JA, Chadha N, Cakir M, Gordon M, Khare P, Drake S, Drury V, Burke DF, Gonzalez S, Alkhairy S, Thomas R, Lam S, Morris M, Bader E, Seyler M, Baum T, Krasnoff R, Wang S, Pham P, Arbalaez J, Pratt D, Chag S, Mahmood N, Rolland T, Bourgeron T, Finkbeiner S, Swaney DL, Bandyopadhay S, Ideker T, Beltrao P, Willsey HR, Obernier K, Nowakowski TJ, Hüttenhain R, State MW, Willsey AJ, Krogan NJ. PMID: 38076945; PMCID: PMC10705567.
      View in: PubMed   Mentions:
    16. Epigenetic reprogramming shapes the cellular landscape of schwannoma. Nat Commun. 2024 Jan 12; 15(1):476. Liu SJ, Casey-Clyde T, Cho NW, Swinderman J, Pekmezci M, Dougherty MC, Foster K, Chen WC, Villanueva-Meyer JE, Swaney DL, Vasudevan HN, Choudhury A, Pak J, Breshears JD, Lang UE, Eaton CD, Hiam-Galvez KJ, Stevenson E, Chen KH, Lien BV, Wu D, Braunstein SE, Sneed PK, Magill ST, Lim D, McDermott MW, Berger MS, Perry A, Krogan NJ, Hansen MR, Spitzer MH, Gilbert L, Theodosopoulos PV, Raleigh DR. PMID: 38216587; PMCID: PMC10786948.
      View in: PubMed   Mentions: 3     Fields:    Translation:Humans
    17. Cross-family small GTPase ubiquitination by the intracellular pathogen Legionella pneumophila. Mol Biol Cell. 2024 Mar 01; 35(3):ar27. Steinbach A, Bhadkamkar V, Jimenez-Morales D, Stevenson E, Jang GM, Krogan NJ, Swaney DL, Mukherjee S. PMID: 38117589; PMCID: PMC10916871.
      View in: PubMed   Mentions: 1     Fields:    Translation:AnimalsCells
    18. In vivo protein turnover rates in varying oxygen tensions nominate MYBBP1A as a mediator of the hyperoxia response. Sci Adv. 2023 Dec 08; 9(49):eadj4884. Chen X, Haribowo AG, Baik AH, Fossati A, Stevenson E, Chen YR, Reyes NS, Peng T, Matthay MA, Traglia M, Pico AR, Jarosz DF, Buchwalter A, Ghaemmaghami S, Swaney DL, Jain IH. PMID: 38064566; PMCID: PMC10708181.
      View in: PubMed   Mentions:    Fields:    Translation:Animals
    19. Molecular determinants of the crosstalk between endosomal microautophagy and chaperone-mediated autophagy. Cell Rep. 2023 12 26; 42(12):113529. Krause GJ, Kirchner P, Stiller B, Morozova K, Diaz A, Chen KH, Krogan NJ, Agullo-Pascual E, Clement CC, Lindenau K, Swaney DL, Dilipkumar S, Bravo-Cordero JJ, Santambrogio L, Cuervo AM. PMID: 38060380; PMCID: PMC10807933.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    20. Multi-scale photocatalytic proximity labeling reveals cell surface neighbors on and between cells. bioRxiv. 2023 Oct 29. Lin Z, Schaefer K, Lui I, Yao Z, Fossati A, Swaney DL, Palar A, Sali A, Wells JA. PMID: 37961561; PMCID: PMC10634877.
      View in: PubMed   Mentions: 1  
    21. A Legionella toxin exhibits tRNA mimicry and glycosyl transferase activity to target the translation machinery and trigger a ribotoxic stress response. Nat Cell Biol. 2023 Nov; 25(11):1600-1615. Subramanian A, Wang L, Moss T, Voorhies M, Sangwan S, Stevenson E, Pulido EH, Kwok S, Chalkley RJ, Li KH, Krogan NJ, Swaney DL, Burlingame AL, Floor SN, Sil A, Walter P, Mukherjee S. PMID: 37857833; PMCID: PMC11005034.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    22. High-throughput chemogenetic drug screening reveals PKC-RhoA/PKN as a targetable signaling vulnerability in GNAQ-driven uveal melanoma. Cell Rep Med. 2023 11 21; 4(11):101244. Arang N, Lubrano S, Ceribelli M, Rigiracciolo DC, Saddawi-Konefka R, Faraji F, Ramirez SI, Kim D, Tosto FA, Stevenson E, Zhou Y, Wang Z, Bogomolovas J, Molinolo AA, Swaney DL, Krogan NJ, Yang J, Coma S, Pachter JA, Aplin AE, Alessi DR, Thomas CJ, Gutkind JS. PMID: 37858338; PMCID: PMC10694608.
      View in: PubMed   Mentions: 4     Fields:    Translation:Animals
    23. Lysosomal proteomics reveals mechanisms of neuronal apoE4associated lysosomal dysfunction. bioRxiv. 2023 Oct 02. Krogsaeter EK, McKetney J, Marquez A, Cakir Z, Stevenson E, Jang GM, Rao A, Zhou A, Huang Y, Krogan NJ, Swaney DL. PMID: 37873080; PMCID: PMC10592882.
      View in: PubMed   Mentions:
    24. Proteomic and genetic analyses of influenza A viruses identify pan-viral host targets. Nat Commun. 2023 09 27; 14(1):6030. Haas KM, McGregor MJ, Bouhaddou M, Polacco BJ, Kim EY, Nguyen TT, Newton BW, Urbanowski M, Kim H, Williams MAP, Rezelj VV, Hardy A, Fossati A, Stevenson EJ, Sukerman E, Kim T, Penugonda S, Moreno E, Braberg H, Zhou Y, Metreveli G, Harjai B, Tummino TA, Melnyk JE, Soucheray M, Batra J, Pache L, Martin-Sancho L, Carlson-Stevermer J, Jureka AS, Basler CF, Shokat KM, Shoichet BK, Shriver LP, Johnson JR, Shaw ML, Chanda SK, Roden DM, Carter TC, Kottyan LC, Chisholm RL, Pacheco JA, Smith ME, Schrodi SJ, Albrecht RA, Vignuzzi M, Zuliani-Alvarez L, Swaney DL, Eckhardt M, Wolinsky SM, White KM, Hultquist JF, Kaake RM, García-Sastre A, Krogan NJ. PMID: 37758692; PMCID: PMC10533562.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansCells
    25. Impact of SARS-CoV-2 ORF6 and its variant polymorphisms on host responses and viral pathogenesis. Cell Host Microbe. 2023 10 11; 31(10):1668-1684.e12. Kehrer T, Cupic A, Ye C, Yildiz S, Bouhaddou M, Crossland NA, Barrall EA, Cohen P, Tseng A, Çagatay T, Rathnasinghe R, Flores D, Jangra S, Alam F, Mena I, Aslam S, Saqi A, Rutkowska M, Ummadi MR, Pisanelli G, Richardson RB, Veit EC, Fabius JM, Soucheray M, Polacco BJ, Ak B, Marin A, Evans MJ, Swaney DL, Gonzalez-Reiche AS, Sordillo EM, van Bakel H, Simon V, Zuliani-Alvarez L, Fontoura BMA, Rosenberg BR, Krogan NJ, Martinez-Sobrido L, García-Sastre A, Miorin L. PMID: 37738983; PMCID: PMC10750313.
      View in: PubMed   Mentions: 26     Fields:    Translation:HumansCells
    26. SARS-CoV-2 variants evolve convergent strategies to remodel the host response. Cell. 2023 10 12; 186(21):4597-4614.e26. Bouhaddou M, Reuschl AK, Polacco BJ, Thorne LG, Ummadi MR, Ye C, Rosales R, Pelin A, Batra J, Jang GM, Xu J, Moen JM, Richards AL, Zhou Y, Harjai B, Stevenson E, Rojc A, Ragazzini R, Whelan MVX, Furnon W, De Lorenzo G, Cowton V, Syed AM, Ciling A, Deutsch N, Pirak D, Dowgier G, Mesner D, Turner JL, McGovern BL, Rodriguez ML, Leiva-Rebollo R, Dunham AS, Zhong X, Eckhardt M, Fossati A, Liotta NF, Kehrer T, Cupic A, Rutkowska M, Mena I, Aslam S, Hoffert A, Foussard H, Olwal CO, Huang W, Zwaka T, Pham J, Lyons M, Donohue L, Griffin A, Nugent R, Holden K, Deans R, Aviles P, Lopez-Martin JA, Jimeno JM, Obernier K, Fabius JM, Soucheray M, Hüttenhain R, Jungreis I, Kellis M, Echeverria I, Verba K, Bonfanti P, Beltrao P, Sharan R, Doudna JA, Martinez-Sobrido L, Patel AH, Palmarini M, Miorin L, White K, Swaney DL, Garcia-Sastre A, Jolly C, Zuliani-Alvarez L, Towers GJ, Krogan NJ. PMID: 37738970; PMCID: PMC10604369.
      View in: PubMed   Mentions: 19     Fields:    Translation:HumansCellsPHPublic Health
    27. Next-generation proteomics for quantitative Jumbophage-bacteria interaction mapping. Nat Commun. 2023 08 24; 14(1):5156. Fossati A, Mozumdar D, Kokontis C, Mèndez-Moran M, Nieweglowska E, Pelin A, Li Y, Guo B, Krogan NJ, Agard DA, Bondy-Denomy J, Swaney DL. PMID: 37620325; PMCID: PMC10449902.
      View in: PubMed   Mentions: 8     Fields:    Translation:Cells
    28. The microenvironment dictates glycocalyx construction and immune surveillance. Res Sq. 2023 Aug 16. Tharp KM, Park S, Timblin GA, Richards AL, Berg JA, Twells NM, Riley NM, Peltan EL, Shon DJ, Stevenson E, Tsui K, Palomba F, Lefebvre AEYT, Soens RW, Ayad NME, Hoeve-Scott JT, Healy K, Digman M, Dillin A, Bertozzi CR, Swaney DL, Mahal LK, Cantor JR, Paszek MJ, Weaver VM. PMID: 37645943; PMCID: PMC10462183.
      View in: PubMed   Mentions:
    29. Cross-family small GTPase ubiquitination by the intracellular pathogen Legionella pneumophila. bioRxiv. 2023 Aug 03. Steinbach AM, Bhadkamkar VL, Jimenez-Morales D, Stevenson E, Jang GM, Krogan NJ, Swaney DL, Mukherjee S. PMID: 37577546; PMCID: PMC10418220.
      View in: PubMed   Mentions:
    30. CRISPR screens in iPSC-derived neurons reveal principles of tau proteostasis. bioRxiv. 2023 Jun 26. Samelson AJ, Ariqat N, McKetney J, Rohanitazangi G, Bravo CP, Goodness D, Tian R, Grosjean P, Abskharon R, Eisenberg D, Kanaan NM, Gan L, Condello C, Swaney DL, Kampmann M. PMID: 37398204; PMCID: PMC10312804.
      View in: PubMed   Mentions: 1  
    31. Functional analysis of a common BAG3 allele associated with protection from heart failure. Nat Cardiovasc Res. 2023 Jul; 2(7):615-628. Perez-Bermejo JA, Judge LM, Jensen CL, Wu K, Watry HL, Truong A, Ho JJ, Carter M, Runyon WV, Kaake RM, Pulido EH, Mandegar MA, Swaney DL, So PL, Krogan NJ, Conklin BR. PMID: 39195919.
      View in: PubMed   Mentions: 4  Translation:HumansCells
    32. Deep learning from harmonized peptide libraries enables retention time prediction of diverse post translational modifications. bioRxiv. 2023 Jun 02. Wilburn DB, Shannon AE, Spicer V, Richards AL, Yeung D, Swaney DL, Krokhin OV, Searle BC. PMID: 37398395; PMCID: PMC10312522.
      View in: PubMed   Mentions:
    33. Quantitative Proteomic Analysis Reveals apoE4-Dependent Phosphorylation of the Actin-Regulating Protein VASP. Mol Cell Proteomics. 2023 05; 22(5):100541. Cakir Z, Lord SJ, Zhou Y, Jang GM, Polacco BJ, Eckhardt M, Jimenez-Morales D, Newton BW, Orr AL, Johnson JR, da Cruz A, Mullins RD, Krogan NJ, Mahley RW, Swaney DL. PMID: 37019383; PMCID: PMC10196575.
      View in: PubMed   Mentions: 1     Fields:    Translation:AnimalsCells
    34. MerlinS13 phosphorylation controls meningioma Wnt signaling and magnetic resonance imaging features. Res Sq. 2023 Mar 14. Eaton C, Avalos L, Liu SJ, Casey-Clyde T, Bisignano P, Lucas CH, Stevenson E, Choudhury A, Vasudevan H, Magill S, Krogan N, Villanueva-Meyer J, Swaney D, Raleigh D. PMID: 36993679; PMCID: PMC10055685.
      View in: PubMed   Mentions:
    35. Next-generation interaction proteomics for quantitative Jumbophage-bacteria interaction mapping. bioRxiv. 2023 Feb 23. Fossati A, Mozumdar D, Kokontis C, Mèndez-Moran M, Nieweglowska E, Pelin A, Li Y, Guo B, Krogan NJ, Agard DA, Bondy-Denomy J, Swaney DL. PMID: 36711836; PMCID: PMC9882154.
      View in: PubMed   Mentions:
    36. Oncogenic PKA signaling increases c-MYC protein expression through multiple targetable mechanisms. Elife. 2023 01 24; 12. Chan GKL, Maisel S, Hwang YC, Pascual BC, Wolber RRB, Vu P, Patra KC, Bouhaddou M, Kenerson HL, Lim HC, Long D, Yeung RS, Sethupathy P, Swaney DL, Krogan NJ, Turnham RE, Riehle KJ, Scott JD, Bardeesy N, Gordan JD. PMID: 36692000; PMCID: PMC9925115.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansCells
    37. Quantitative proteomic analysis reveals apoE4-dependent phosphorylation of the actin regulating protein VASP. Alzheimer's & Dementia. 2022 Dec 20; 18(S3). Cakir CZ, Polacco PB, Krogan KN, Mahley MR, Swaney SD. .
      View in: Publisher Site   Mentions:
    38. Abstract B016: Inhibition of KRASG12C in colon cancer illustrates a link between beta-catenin, WNK, and the GID complex. Cancer Research. 2022 Dec 1; 82(23_Supplement_1):b016-b016. Nayak NK, Hwang HY, Wang WL, Swaney SD, Krogan KN, Gordan GJ. .
      View in: Publisher Site   Mentions:
    39. Impact of SARS-CoV-2 ORF6 and its variant polymorphisms on host responses and viral pathogenesis. bioRxiv. 2022 Nov 30. Kehrer T, Cupic A, Ye C, Yildiz S, Bouhhadou M, Crossland NA, Barrall E, Cohen P, Tseng A, Çagatay T, Rathnasinghe R, Flores D, Jangra S, Alam F, Mena N, Aslam S, Saqi A, Marin A, Rutkowska M, Ummadi MR, Pisanelli G, Richardson RB, Veit EC, Fabius JM, Soucheray M, Polacco BJ, Evans MJ, Swaney DL, Gonzalez-Reiche AS, Sordillo EM, van Bakel H, Simon V, Zuliani-Alvarez L, Fontoura BMA, Rosenberg BR, Krogan NJ, Martinez-Sobrido L, García-Sastre A, Miorin L. PMID: 36299428; PMCID: PMC9603824.
      View in: PubMed   Mentions: 1  
    40. CSIG-37. MERLIN S13 DEPHOSPHORYLATION DRIVES MENINGIOMA WNT SIGNALLING AND CELL PROLIFERATION. Neuro-Oncology. 2022 Nov 14; 24(Supplement_7):vii47-vii47. Eaton EC, John Liu JS, Lucas LC, Casey-Clyde CT, Choudhury CA, Daggubati DV, Vasudevan VH, Swaney SD, Raleigh RD. .
      View in: Publisher Site   Mentions:
    41. EPCO-01. EPIGENETIC REPROGRAMMING SHAPES THE MOLECULAR AND CELLULAR LANDSCAPE OF SCHWANNOMA. Neuro-Oncology. 2022 Nov 14; 24(Supplement_7):vii115-vii115. Liu LS, Casey-Clyde CT, Swinderman SJ, Cho CN, Vasudevan VH, Foster FK, Pekmezci PM, Chen CW, Villanueva-Meyer VJ, Hiam-Galvez HK, Swaney SD, Choudhury CA, Breshears BJ, Stevenson SE, Chen CK, Lien LB, Wu WD, Lang LU, Magill MS, Lim LD, McDermott MM, Berger BM, Perry PA, Krogan KN, Spitzer SM, Gilbert GL, Theodospoulos TP, Raleigh RD. .
      View in: Publisher Site   Mentions:
    42. Resistance to ATR Inhibitors Is Mediated by Loss of the Nonsense-Mediated Decay Factor UPF2. Cancer Res. 2022 11 02; 82(21):3950-3961. O'Leary PC, Chen H, Doruk YU, Williamson T, Polacco B, McNeal AS, Shenoy T, Kale N, Carnevale J, Stevenson E, Quigley DA, Chou J, Feng FY, Swaney DL, Krogan NJ, Kim M, Diolaiti ME, Ashworth A. PMID: 36273492; PMCID: PMC9633439.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansCells
    43. Reduced endosomal microautophagy activity in aging associates with enhanced exocyst-mediated protein secretion. Aging Cell. 2022 10; 21(10):e13713. Krause GJ, Diaz A, Jafari M, Khawaja RR, Agullo-Pascual E, Santiago-Fernández O, Richards AL, Chen KH, Dmitriev P, Sun Y, See SK, Abdelmohsen K, Mazan-Mamczarz K, Krogan NJ, Gorospe M, Swaney DL, Sidoli S, Bravo-Cordero JJ, Kampmann M, Cuervo AM. PMID: 36116133; PMCID: PMC9577956.
      View in: PubMed   Mentions: 12     Fields:    Translation:AnimalsCells
    44. Meningioma DNA methylation groups identify biological drivers and therapeutic vulnerabilities. Nat Genet. 2022 05; 54(5):649-659. Choudhury A, Magill ST, Eaton CD, Prager BC, Chen WC, Cady MA, Seo K, Lucas CG, Casey-Clyde TJ, Vasudevan HN, Liu SJ, Villanueva-Meyer JE, Lam TC, Pu JK, Li LF, Leung GK, Swaney DL, Zhang MY, Chan JW, Qiu Z, Martin MV, Susko MS, Braunstein SE, Bush NAO, Schulte JD, Butowski N, Sneed PK, Berger MS, Krogan NJ, Perry A, Phillips JJ, Solomon DA, Costello JF, McDermott MW, Rich JN, Raleigh DR. PMID: 35534562; PMCID: PMC9374001.
      View in: PubMed   Mentions: 92     Fields:    Translation:HumansCells
    45. The E3 ligase TRIM1 ubiquitinates LRRK2 and controls its localization, degradation, and toxicity. J Cell Biol. 2022 04 04; 221(4). Stormo AED, Shavarebi F, FitzGibbon M, Earley EM, Ahrendt H, Lum LS, Verschueren E, Swaney DL, Skibinski G, Ravisankar A, van Haren J, Davis EJ, Johnson JR, Von Dollen J, Balen C, Porath J, Crosio C, Mirescu C, Iaccarino C, Dauer WT, Nichols RJ, Wittmann T, Cox TC, Finkbeiner S, Krogan NJ, Oakes SA, Hiniker A. PMID: 35266954; PMCID: PMC8919618.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansCells
    46. Data-Independent Acquisition Protease-Multiplexing Enables Increased Proteome Sequence Coverage Across Multiple Fragmentation Modes. J Proteome Res. 2022 04 01; 21(4):1124-1136. Richards AL, Chen KH, Wilburn DB, Stevenson E, Polacco BJ, Searle BC, Swaney DL. PMID: 35234472; PMCID: PMC9035370.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansCells
    47. Tau interactome maps synaptic and mitochondrial processes associated with neurodegeneration. Cell. 2022 02 17; 185(4):712-728.e14. Tracy TE, Madero-Pérez J, Swaney DL, Chang TS, Moritz M, Konrad C, Ward ME, Stevenson E, Hüttenhain R, Kauwe G, Mercedes M, Sweetland-Martin L, Chen X, Mok SA, Wong MY, Telpoukhovskaia M, Min SW, Wang C, Sohn PD, Martin J, Zhou Y, Luo W, Trojanowski JQ, Lee VMY, Gong S, Manfredi G, Coppola G, Krogan NJ, Geschwind DH, Gan L. PMID: 35063084; PMCID: PMC8857049.
      View in: PubMed   Mentions: 88     Fields:    Translation:HumansCells
    48. Evolution of enhanced innate immune evasion by SARS-CoV-2. Nature. 2022 02; 602(7897):487-495. Thorne LG, Bouhaddou M, Reuschl AK, Zuliani-Alvarez L, Polacco B, Pelin A, Batra J, Whelan MVX, Hosmillo M, Fossati A, Ragazzini R, Jungreis I, Ummadi M, Rojc A, Turner J, Bischof ML, Obernier K, Braberg H, Soucheray M, Richards A, Chen KH, Harjai B, Memon D, Hiatt J, Rosales R, McGovern BL, Jahun A, Fabius JM, White K, Goodfellow IG, Takeuchi Y, Bonfanti P, Shokat K, Jura N, Verba K, Noursadeghi M, Beltrao P, Kellis M, Swaney DL, García-Sastre A, Jolly C, Towers GJ, Krogan NJ. PMID: 34942634; PMCID: PMC8850198.
      View in: PubMed   Mentions: 184     Fields:    Translation:HumansCells
    49. Therapeutic implications of activating noncanonical PIK3CA mutations in head and neck squamous cell carcinoma. J Clin Invest. 2021 11 15; 131(22). Jin N, Keam B, Cho J, Lee MJ, Kim HR, Torosyan H, Jura N, Ng PK, Mills GB, Li H, Zeng Y, Barbash Z, Tarcic G, Kang H, Bauman JE, Kim MO, VanLandingham NK, Swaney DL, Krogan NJ, Johnson DE, Grandis JR. PMID: 34779417; PMCID: PMC8592538.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansAnimalsCells
    50. Caveolin-1 and Sox-2 are predictive biomarkers of cetuximab response in head and neck cancer. JCI Insight. 2021 10 22; 6(20). Bouhaddou M, Lee RH, Li H, Bhola NE, O'Keefe RA, Naser M, Zhu TR, Nwachuku K, Duvvuri U, Olshen AB, Roy R, Hechmer A, Bolen J, Keysar SB, Jimeno A, Mills GB, Vandenberg S, Swaney DL, Johnson DE, Krogan NJ, Grandis JR. PMID: 34546978; PMCID: PMC8564908.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansAnimals
    51. Systems-level effects of allosteric perturbations to a model molecular switch. Nature. 2021 11; 599(7883):152-157. Perica T, Mathy CJP, Xu J, Jang G?, Zhang Y, Kaake R, Ollikainen N, Braberg H, Swaney DL, Lambright DG, Kelly MJS, Krogan NJ, Kortemme T. PMID: 34646016; PMCID: PMC8571063.
      View in: PubMed   Mentions: 6     Fields:    Translation:AnimalsCells
    52. A protein interaction landscape of breast cancer. Science. 2021 Oct; 374(6563):eabf3066. Kim M, Park J, Bouhaddou M, Kim K, Rojc A, Modak M, Soucheray M, McGregor MJ, O'Leary P, Wolf D, Stevenson E, Foo TK, Mitchell D, Herrington KA, Muñoz DP, Tutuncuoglu B, Chen KH, Zheng F, Kreisberg JF, Diolaiti ME, Gordan JD, Coppé JP, Swaney DL, Xia B, van 't Veer L, Ashworth A, Ideker T, Krogan NJ. PMID: 34591612; PMCID: PMC9040556.
      View in: PubMed   Mentions: 50     Fields:    Translation:HumansCells
    53. Interpretation of cancer mutations using a multiscale map of protein systems. Science. 2021 Oct; 374(6563):eabf3067. Zheng F, Kelly MR, Ramms DJ, Heintschel ML, Tao K, Tutuncuoglu B, Lee JJ, Ono K, Foussard H, Chen M, Herrington KA, Silva E, Liu SN, Chen J, Churas C, Wilson N, Kratz A, Pillich RT, Patel DN, Park J, Kuenzi B, Yu MK, Licon K, Pratt D, Kreisberg JF, Kim M, Swaney DL, Nan X, Fraley SI, Gutkind JS, Krogan NJ, Ideker T. PMID: 34591613; PMCID: PMC9126298.
      View in: PubMed   Mentions: 20     Fields:    Translation:Humans
    54. A protein network map of head and neck cancer reveals PIK3CA mutant drug sensitivity. Science. 2021 Oct; 374(6563):eabf2911. Swaney DL, Ramms DJ, Wang Z, Park J, Goto Y, Soucheray M, Bhola N, Kim K, Zheng F, Zeng Y, McGregor M, Herrington KA, O'Keefe R, Jin N, VanLandingham NK, Foussard H, Von Dollen J, Bouhaddou M, Jimenez-Morales D, Obernier K, Kreisberg JF, Kim M, Johnson DE, Jura N, Grandis JR, Gutkind JS, Ideker T, Krogan NJ. PMID: 34591642; PMCID: PMC9005332.
      View in: PubMed   Mentions: 25     Fields:    Translation:HumansAnimalsCells
    55. Restriction factor compendium for influenza A virus reveals a mechanism for evasion of autophagy. Nat Microbiol. 2021 10; 6(10):1319-1333. Martin-Sancho L, Tripathi S, Rodriguez-Frandsen A, Pache L, Sanchez-Aparicio M, McGregor MJ, Haas KM, Swaney DL, Nguyen TT, Mamede JI, Churas C, Pratt D, Rosenthal SB, Riva L, Nguyen C, Beltran-Raygoza N, Soonthornvacharin S, Wang G, Jimenez-Morales D, De Jesus PD, Moulton HM, Stein DA, Chang MW, Benner C, Ideker T, Albrecht RA, Hultquist JF, Krogan NJ, García-Sastre A, Chanda SK. PMID: 34556855; PMCID: PMC9683089.
      View in: PubMed   Mentions: 19     Fields:    Translation:HumansCells
    56. Brown adipocyte ATF4 activation improves thermoregulation and systemic metabolism. Cell Rep. 2021 09 21; 36(12):109742. Paulo E, Zhang Y, Masand R, Huynh TL, Seo Y, Swaney DL, Soucheray M, Stevenson E, Jimenez-Morales D, Krogan NJ, Wang B. PMID: 34551310; PMCID: PMC9202523.
      View in: PubMed   Mentions: 9     Fields:    Translation:AnimalsCells
    57. Toward Comprehensive Plasma Proteomics by Orthogonal Protease Digestion. J Proteome Res. 2021 08 06; 20(8):4031-4040. Fossati A, Richards AL, Chen KH, Jaganath D, Cattamanchi A, Ernst JD, Swaney DL. PMID: 34319755; PMCID: PMC8442619.
      View in: PubMed   Mentions: 7     Fields:    Translation:Humans
    58. A ciliopathy complex builds distal appendages to initiate ciliogenesis. J Cell Biol. 2021 09 06; 220(9). Kumar D, Rains A, Herranz-Pérez V, Lu Q, Shi X, Swaney DL, Stevenson E, Krogan NJ, Huang B, Westlake C, Garcia-Verdugo JM, Yoder BK, Reiter JF. PMID: 34241634; PMCID: PMC8276316.
      View in: PubMed   Mentions: 18     Fields:    Translation:HumansAnimalsCells
    59. Adhesion-mediated mechanosignaling forces mitohormesis. Cell Metab. 2021 07 06; 33(7):1322-1341.e13. Tharp KM, Higuchi-Sanabria R, Timblin GA, Ford B, Garzon-Coral C, Schneider C, Muncie JM, Stashko C, Daniele JR, Moore AS, Frankino PA, Homentcovschi S, Manoli SS, Shao H, Richards AL, Chen KH, Hoeve JT, Ku GM, Hellerstein M, Nomura DK, Saijo K, Gestwicki J, Dunn AR, Krogan NJ, Swaney DL, Dillin A, Weaver VM. PMID: 34019840; PMCID: PMC8266765.
      View in: PubMed   Mentions: 53     Fields:    Translation:HumansAnimalsCells
    60. Chaperone-mediated autophagy prevents collapse of the neuronal metastable proteome. Cell. 2021 05 13; 184(10):2696-2714.e25. Bourdenx M, Martín-Segura A, Scrivo A, Rodriguez-Navarro JA, Kaushik S, Tasset I, Diaz A, Storm NJ, Xin Q, Juste YR, Stevenson E, Luengo E, Clement CC, Choi SJ, Krogan NJ, Mosharov EV, Santambrogio L, Grueninger F, Collin L, Swaney DL, Sulzer D, Gavathiotis E, Cuervo AM. PMID: 33891876; PMCID: PMC8152331.
      View in: PubMed   Mentions: 113     Fields:    Translation:AnimalsCells
    61. The AMBRA1 E3 ligase adaptor regulates the stability of cyclin D. Nature. 2021 04; 592(7856):794-798. Chaikovsky AC, Li C, Jeng EE, Loebell S, Lee MC, Murray CW, Cheng R, Demeter J, Swaney DL, Chen SH, Newton BW, Johnson JR, Drainas AP, Shue YT, Seoane JA, Srinivasan P, He A, Yoshida A, Hipkins SQ, McCrea E, Poltorack CD, Krogan NJ, Diehl JA, Kong C, Jackson PK, Curtis C, Petrov DA, Bassik MC, Winslow MM, Sage J. PMID: 33854239; PMCID: PMC8246597.
      View in: PubMed   Mentions: 63     Fields:    Translation:HumansAnimalsCells
    62. CIDer: A Statistical Framework for Interpreting Differences in CID and HCD Fragmentation. J Proteome Res. 2021 04 02; 20(4):1951-1965. Wilburn DB, Richards AL, Swaney DL, Searle BC. PMID: 33729787; PMCID: PMC8256874.
      View in: PubMed   Mentions: 7     Fields:    
    63. An ultrapotent synthetic nanobody neutralizes SARS-CoV-2 by stabilizing inactive Spike. Science. 2020 12 18; 370(6523):1473-1479. Schoof M, Faust B, Saunders RA, Sangwan S, Rezelj V, Hoppe N, Boone M, Billesbølle CB, Puchades C, Azumaya CM, Kratochvil HT, Zimanyi M, Deshpande I, Liang J, Dickinson S, Nguyen HC, Chio CM, Merz GE, Thompson MC, Diwanji D, Schaefer K, Anand AA, Dobzinski N, Zha BS, Simoneau CR, Leon K, White KM, Chio US, Gupta M, Jin M, Li F, Liu Y, Zhang K, Bulkley D, Sun M, Smith AM, Rizo AN, Moss F, Brilot AF, Pourmal S, Trenker R, Pospiech T, Gupta S, Barsi-Rhyne B, Belyy V, Barile-Hill AW, Nock S, Liu Y, Krogan NJ, Ralston CY, Swaney DL, García-Sastre A, Ott M, Vignuzzi M, QCRG Structural Biology Consortium, Walter P, Manglik A. PMID: 33154106; PMCID: PMC7857409.
      View in: PubMed   Mentions: 223     Fields:    Translation:HumansAnimalsCells
    64. Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms. Science. 2020 12 04; 370(6521). Gordon DE, Hiatt J, Bouhaddou M, Rezelj VV, Ulferts S, Braberg H, Jureka AS, Obernier K, Guo JZ, Batra J, Kaake RM, Weckstein AR, Owens TW, Gupta M, Pourmal S, Titus EW, Cakir M, Soucheray M, McGregor M, Cakir Z, Jang G, O'Meara MJ, Tummino TA, Zhang Z, Foussard H, Rojc A, Zhou Y, Kuchenov D, Hüttenhain R, Xu J, Eckhardt M, Swaney DL, Fabius JM, Ummadi M, Tutuncuoglu B, Rathore U, Modak M, Haas P, Haas KM, Naing ZZC, Pulido EH, Shi Y, Barrio-Hernandez I, Memon D, Petsalaki E, Dunham A, Marrero MC, Burke D, Koh C, Vallet T, Silvas JA, Azumaya CM, Billesbølle C, Brilot AF, Campbell MG, Diallo A, Dickinson MS, Diwanji D, Herrera N, Hoppe N, Kratochvil HT, Liu Y, Merz GE, Moritz M, Nguyen HC, Nowotny C, Puchades C, Rizo AN, Schulze-Gahmen U, Smith AM, Sun M, Young ID, Zhao J, Asarnow D, Biel J, Bowen A, Braxton JR, Chen J, Chio CM, Chio US, Deshpande I, Doan L, Faust B, Flores S, Jin M, Kim K, Lam VL, Li F, Li J, Li YL, Li Y, Liu X, Lo M, Lopez KE, Melo AA, Moss FR, Nguyen P, Paulino J, Pawar KI, Peters JK, Pospiech TH, Safari M, Sangwan S, Schaefer K, Thomas PV, Thwin AC, Trenker R, Tse E, Tsui TKM, Wang F, Whitis N, Yu Z, Zhang K, Zhang Y, Zhou F, Saltzberg D, QCRG Structural Biology Consortium, Hodder AJ, Shun-Shion AS, Williams DM, White KM, Rosales R, Kehrer T, Miorin L, Moreno E, Patel AH, Rihn S, Khalid MM, Vallejo-Gracia A, Fozouni P, Simoneau CR, Roth TL, Wu D, Karim MA, Ghoussaini M, Dunham I, Berardi F, Weigang S, Chazal M, Park J, Logue J, McGrath M, Weston S, Haupt R, Hastie CJ, Elliott M, Brown F, Burness KA, Reid E, Dorward M, Johnson C, Wilkinson SG, Geyer A, Giesel DM, Baillie C, Raggett S, Leech H, Toth R, Goodman N, Keough KC, Lind AL, Zoonomia Consortium, Klesh RJ, Hemphill KR, Carlson-Stevermer J, Oki J, Holden K, Maures T, Pollard KS, Sali A, Agard DA, Cheng Y, Fraser JS, Frost A, Jura N, Kortemme T, Manglik A, Southworth DR, Stroud RM, Alessi DR, Davies P, Frieman MB, Ideker T, Abate C, Jouvenet N, Kochs G, Shoichet B, Ott M, Palmarini M, et al. PMID: 33060197; PMCID: PMC7808408.
      View in: PubMed   Mentions: 382     Fields:    Translation:HumansCells
    65. The Global Phosphorylation Landscape of SARS-CoV-2 Infection. Cell. 2020 08 06; 182(3):685-712.e19. Bouhaddou M, Memon D, Meyer B, White KM, Rezelj VV, Correa Marrero M, Polacco BJ, Melnyk JE, Ulferts S, Kaake RM, Batra J, Richards AL, Stevenson E, Gordon DE, Rojc A, Obernier K, Fabius JM, Soucheray M, Miorin L, Moreno E, Koh C, Tran QD, Hardy A, Robinot R, Vallet T, Nilsson-Payant BE, Hernandez-Armenta C, Dunham A, Weigang S, Knerr J, Modak M, Quintero D, Zhou Y, Dugourd A, Valdeolivas A, Patil T, Li Q, Hüttenhain R, Cakir M, Muralidharan M, Kim M, Jang G, Tutuncuoglu B, Hiatt J, Guo JZ, Xu J, Bouhaddou S, Mathy CJP, Gaulton A, Manners EJ, Félix E, Shi Y, Goff M, Lim JK, McBride T, O'Neal MC, Cai Y, Chang JCJ, Broadhurst DJ, Klippsten S, De Wit E, Leach AR, Kortemme T, Shoichet B, Ott M, Saez-Rodriguez J, tenOever BR, Mullins RD, Fischer ER, Kochs G, Grosse R, García-Sastre A, Vignuzzi M, Johnson JR, Shokat KM, Swaney DL, Beltrao P, Krogan NJ. PMID: 32645325; PMCID: PMC7321036.
      View in: PubMed   Mentions: 551     Fields:    Translation:HumansAnimalsCellsPHPublic Health
    66. The kinase Isr1 negatively regulates hexosamine biosynthesis in S. cerevisiae. PLoS Genet. 2020 06; 16(6):e1008840. Alme EB, Stevenson E, Krogan NJ, Swaney DL, Toczyski DP. PMID: 32579556; PMCID: PMC7340321.
      View in: PubMed   Mentions: 3     Fields:    Translation:AnimalsCells
    67. Unbiased Proteomic Profiling Uncovers a Targetable GNAS/PKA/PP2A Axis in Small Cell Lung Cancer Stem Cells. Cancer Cell. 2020 07 13; 38(1):129-143.e7. Coles GL, Cristea S, Webber JT, Levin RS, Moss SM, He A, Sangodkar J, Hwang YC, Arand J, Drainas AP, Mooney NA, Demeter J, Spradlin JN, Mauch B, Le V, Shue YT, Ko JH, Lee MC, Kong C, Nomura DK, Ohlmeyer M, Swaney DL, Krogan NJ, Jackson PK, Narla G, Gordan JD, Shokat KM, Sage J. PMID: 32531271; PMCID: PMC7363571.
      View in: PubMed   Mentions: 44     Fields:    Translation:HumansAnimalsCells
    68. A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature. 2020 07; 583(7816):459-468. Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, White KM, O'Meara MJ, Rezelj VV, Guo JZ, Swaney DL, Tummino TA, Hüttenhain R, Kaake RM, Richards AL, Tutuncuoglu B, Foussard H, Batra J, Haas K, Modak M, Kim M, Haas P, Polacco BJ, Braberg H, Fabius JM, Eckhardt M, Soucheray M, Bennett MJ, Cakir M, McGregor MJ, Li Q, Meyer B, Roesch F, Vallet T, Mac Kain A, Miorin L, Moreno E, Naing ZZC, Zhou Y, Peng S, Shi Y, Zhang Z, Shen W, Kirby IT, Melnyk JE, Chorba JS, Lou K, Dai SA, Barrio-Hernandez I, Memon D, Hernandez-Armenta C, Lyu J, Mathy CJP, Perica T, Pilla KB, Ganesan SJ, Saltzberg DJ, Rakesh R, Liu X, Rosenthal SB, Calviello L, Venkataramanan S, Liboy-Lugo J, Lin Y, Huang XP, Liu Y, Wankowicz SA, Bohn M, Safari M, Ugur FS, Koh C, Savar NS, Tran QD, Shengjuler D, Fletcher SJ, O'Neal MC, Cai Y, Chang JCJ, Broadhurst DJ, Klippsten S, Sharp PP, Wenzell NA, Kuzuoglu-Ozturk D, Wang HY, Trenker R, Young JM, Cavero DA, Hiatt J, Roth TL, Rathore U, Subramanian A, Noack J, Hubert M, Stroud RM, Frankel AD, Rosenberg OS, Verba KA, Agard DA, Ott M, Emerman M, Jura N, von Zastrow M, Verdin E, Ashworth A, Schwartz O, d'Enfert C, Mukherjee S, Jacobson M, Malik HS, Fujimori DG, Ideker T, Craik CS, Floor SN, Fraser JS, Gross JD, Sali A, Roth BL, Ruggero D, Taunton J, Kortemme T, Beltrao P, Vignuzzi M, García-Sastre A, Shokat KM, Shoichet BK, Krogan NJ. PMID: 32353859; PMCID: PMC7431030.
      View in: PubMed   Mentions: 2478     Fields:    Translation:HumansAnimalsCellsPHPublic Health
    69. A Quantitative Genetic Interaction Map of HIV Infection. Mol Cell. 2020 04 16; 78(2):197-209.e7. Gordon DE, Watson A, Roguev A, Zheng S, Jang GM, Kane J, Xu J, Guo JZ, Stevenson E, Swaney DL, Franks-Skiba K, Verschueren E, Shales M, Crosby DC, Frankel AD, Marson A, Marazzi I, Cagney G, Krogan NJ. PMID: 32084337; PMCID: PMC7462049.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansCells
    70. Dynamic post-translational modification profiling of Mycobacterium tuberculosis-infected primary macrophages. Elife. 2020 01 17; 9. Budzik JM, Swaney DL, Jimenez-Morales D, Johnson JR, Garelis NE, Repasy T, Roberts AW, Popov LM, Parry TJ, Pratt D, Ideker T, Krogan NJ, Cox JS. PMID: 31951200; PMCID: PMC7030789.
      View in: PubMed   Mentions: 23     Fields:    Translation:HumansAnimalsCells
    71. The functional landscape of the human phosphoproteome. Nat Biotechnol. 2020 03; 38(3):365-373. Ochoa D, Jarnuczak AF, Viéitez C, Gehre M, Soucheray M, Mateus A, Kleefeldt AA, Hill A, Garcia-Alonso L, Stein F, Krogan NJ, Savitski MM, Swaney DL, Vizcaíno JA, Noh KM, Beltrao P. PMID: 31819260; PMCID: PMC7100915.
      View in: PubMed   Mentions: 158     Fields:    Translation:HumansCells
    72. Systematic Identification of Host Cell Regulators of Legionella pneumophila Pathogenesis Using a Genome-wide CRISPR Screen. Cell Host Microbe. 2019 10 09; 26(4):551-563.e6. Jeng EE, Bhadkamkar V, Ibe NU, Gause H, Jiang L, Chan J, Jian R, Jimenez-Morales D, Stevenson E, Krogan NJ, Swaney DL, Snyder MP, Mukherjee S, Bassik MC. PMID: 31540829; PMCID: PMC6800164.
      View in: PubMed   Mentions: 49     Fields:    Translation:HumansAnimalsCells
    73. Anti-CRISPR-Associated Proteins Are Crucial Repressors of Anti-CRISPR Transcription. Cell. 2019 09 05; 178(6):1452-1464.e13. Stanley SY, Borges AL, Chen KH, Swaney DL, Krogan NJ, Bondy-Denomy J, Davidson AR. PMID: 31474367; PMCID: PMC6754177.
      View in: PubMed   Mentions: 57     Fields:    Translation:Cells
    74. KRASG12C inhibition produces a driver-limited state revealing collateral dependencies. Sci Signal. 2019 05 28; 12(583). Lou K, Steri V, Ge AY, Hwang YC, Yogodzinski CH, Shkedi AR, Choi ALM, Mitchell DC, Swaney DL, Hann B, Gordan JD, Shokat KM, Gilbert LA. PMID: 31138768; PMCID: PMC6871662.
      View in: PubMed   Mentions: 77     Fields:    Translation:HumansAnimalsCells
    75. Abstract P6-06-01: Analyzing the physical and functional protein interaction landscape of breast cancer. Poster Session Abstracts. 2019 Feb 15; p6-06-01-p6-06-01. Kim KM, Kim KK, Tutuncuoglu TB, Soucheray SM, Swaney SD, Zheng ZF, Park PJ, O'Leary OP, Coppé CJ, van 't Veer vL, Ashworth AA, Ideker IT, Krogan KN. .
      View in: Publisher Site   Mentions:
    76. Neuronal Apolipoprotein E4 Expression Results in Proteome-Wide Alterations and Compromises Bioenergetic Capacity by Disrupting Mitochondrial Function. J Alzheimers Dis. 2019; 68(3):991-1011. Orr AL, Kim C, Jimenez-Morales D, Newton BW, Johnson JR, Krogan NJ, Swaney DL, Mahley RW. PMID: 30883359; PMCID: PMC6481541.
      View in: PubMed   Mentions: 40     Fields:    Translation:AnimalsCells
    77. TCO, a Putative Transcriptional Regulator in Arabidopsis, Is a Target of the Protein Kinase CK2. Int J Mol Sci. 2018 Dec 28; 20(1). Weinman LM, Running KLD, Carey NS, Stevenson EJ, Swaney DL, Chow BY, Krogan NJ, Krogan NT. PMID: 30597831; PMCID: PMC6337506.
      View in: PubMed   Mentions:    Fields:    Translation:AnimalsCells
    78. Comparative Flavivirus-Host Protein Interaction Mapping Reveals Mechanisms of Dengue and Zika Virus Pathogenesis. Cell. 2018 12 13; 175(7):1931-1945.e18. Shah PS, Link N, Jang GM, Sharp PP, Zhu T, Swaney DL, Johnson JR, Von Dollen J, Ramage HR, Satkamp L, Newton B, Hüttenhain R, Petit MJ, Baum T, Everitt A, Laufman O, Tassetto M, Shales M, Stevenson E, Iglesias GN, Shokat L, Tripathi S, Balasubramaniam V, Webb LG, Aguirre S, Willsey AJ, Garcia-Sastre A, Pollard KS, Cherry S, Gamarnik AV, Marazzi I, Taunton J, Fernandez-Sesma A, Bellen HJ, Andino R, Krogan NJ. PMID: 30550790; PMCID: PMC6474419.
      View in: PubMed   Mentions: 172     Fields:    Translation:HumansAnimalsCells
    79. Multiple Routes to Oncogenesis Are Promoted by the Human Papillomavirus-Host Protein Network. Cancer Discov. 2018 11; 8(11):1474-1489. Eckhardt M, Zhang W, Gross AM, Von Dollen J, Johnson JR, Franks-Skiba KE, Swaney DL, Johnson TL, Jang GM, Shah PS, Brand TM, Archambault J, Kreisberg JF, Grandis JR, Ideker T, Krogan NJ. PMID: 30209081; PMCID: PMC6375299.
      View in: PubMed   Mentions: 48     Fields:    Translation:HumansCells
    80. Abstract B45: Studying the interactome of breast cancer: The cancer cell map initiative. Validation of Driver Mutations. 2018 Aug 1; b45-b45. Kim KM, Kim KK, Soucheray SM, Swaney SD, Krogan KN. .
      View in: Publisher Site   Mentions:
    81. Extending chemical perturbations of the ubiquitin fitness landscape in a classroom setting reveals new constraints on sequence tolerance. Biol Open. 2018 Jul 23; 7(7). Mavor D, Barlow KA, Asarnow D, Birman Y, Britain D, Chen W, Green EM, Kenner LR, Mensa B, Morinishi LS, Nelson CA, Poss EM, Suresh P, Tian R, Arhar T, Ary BE, Bauer DP, Bergman ID, Brunetti RM, Chio CM, Dai SA, Dickinson MS, Elledge SK, Helsell CVM, Hendel NL, Kang E, Kern N, Khoroshkin MS, Kirkemo LL, Lewis GR, Lou K, Marin WM, Maxwell AM, McTigue PF, Myers-Turnbull D, Nagy TL, Natale AM, Oltion K, Pourmal S, Reder GK, Rettko NJ, Rohweder PJ, Schwarz DMC, Tan SK, Thomas PV, Tibble RW, Town JP, Tsai MK, Ugur FS, Wassarman DR, Wolff AM, Wu TS, Bogdanoff D, Li J, Thorn KS, O'Conchúir S, Swaney DL, Chow ED, Madhani HD, Redding S, Bolon DN, Kortemme T, DeRisi JL, Kampmann M, Fraser JS. PMID: 30037883; PMCID: PMC6078352.
      View in: PubMed   Mentions: 13     Fields:    
    82. Sympathetic inputs regulate adaptive thermogenesis in brown adipose tissue through cAMP-Salt inducible kinase axis. Sci Rep. 2018 Jul 20; 8(1):11001. Paulo E, Wu D, Wang Y, Zhang Y, Wu Y, Swaney DL, Soucheray M, Jimenez-Morales D, Chawla A, Krogan NJ, Wang B. PMID: 30030465; PMCID: PMC6054673.
      View in: PubMed   Mentions: 25     Fields:    Translation:HumansAnimalsCells
    83. Proteome Imbalance of Mitochondrial Electron Transport Chain in Brown Adipocytes Leads to Metabolic Benefits. Cell Metab. 2018 03 06; 27(3):616-629.e4. Masand R, Paulo E, Wu D, Wang Y, Swaney DL, Jimenez-Morales D, Krogan NJ, Wang B. PMID: 29514069; PMCID: PMC6020063.
      View in: PubMed   Mentions: 19     Fields:    Translation:AnimalsCells
    84. Abstract PR04: HER3 crosstalk with HPV16-E6E7 is a feedback resistance mechanism to PI3K-targeted therapies in head and neck cancer. Viral Cancers HPV/EBV. 2017 Dec 1; pr04-pr04. Brand BT, Hartmann HS, Bhola BN, Li LH, Zeng ZY, O'Keefe OR, Ranall RM, Bandyopadhyay BS, Soucheray SM, Swaney SD, Krogan KN, Kemp KC, Duvvuri DU, Johnson JD, Ozbun OM, Bauman BJ, Grandis GJ. .
      View in: Publisher Site   Mentions:
    85. Abstract P1-05-31: Studying the interactome of breast cancer: The cancer cell map initiative. Poster Session Abstracts. 2017 Feb 15; p1-05-31-p1-05-31. Kim KM, Kim KK, Soucheray SM, Swaney SD, Krogan KN. .
      View in: Publisher Site   Mentions:
    86. Evolution of protein phosphorylation across 18 fungal species. Science. 2016 10 14; 354(6309):229-232. Studer RA, Rodriguez-Mias RA, Haas KM, Hsu JI, Viéitez C, Solé C, Swaney DL, Stanford LB, Liachko I, Böttcher R, Dunham MJ, de Nadal E, Posas F, Beltrao P, Villén J. PMID: 27738172.
      View in: PubMed   Mentions: 41     Fields:    Translation:AnimalsCells
    87. Enrichment of Modified Peptides via Immunoaffinity Precipitation with Modification-Specific Antibodies. Cold Spring Harb Protoc. 2016 Mar 01; 2016(3):pdb.prot088013. Swaney DL, Villén J. PMID: 26933248.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    88. Enrichment of Phosphopeptides via Immobilized Metal Affinity Chromatography. Cold Spring Harb Protoc. 2016 Mar 01; 2016(3):pdb.prot088005. Swaney DL, Villén J. PMID: 26933247.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    89. Proteomic Analysis of Protein Posttranslational Modifications by Mass Spectrometry. Cold Spring Harb Protoc. 2016 Mar 01; 2016(3):pdb.top077743. Swaney DL, Villén J. PMID: 26933252.
      View in: PubMed   Mentions: 5     Fields:    Translation:Cells
    90. Phosphorylation of ubiquitin at Ser65 affects its polymerization, targets, and proteome-wide turnover. EMBO Rep. 2015 Sep; 16(9):1131-44. Swaney DL, Rodríguez-Mias RA, Villén J. PMID: 26142280; PMCID: PMC4576982.
      View in: PubMed   Mentions: 38     Fields:    Translation:AnimalsCells
    91. E2~Ub conjugates regulate the kinase activity of Shigella effector OspG during pathogenesis. EMBO J. 2014 Mar 03; 33(5):437-49. Pruneda JN, Smith FD, Daurie A, Swaney DL, Villén J, Scott JD, Stadnyk AW, Le Trong I, Stenkamp RE, Klevit RE, Rohde JR, Brzovic PS. PMID: 24446487; PMCID: PMC3989626.
      View in: PubMed   Mentions: 45     Fields:    Translation:HumansAnimalsCells
    92. Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation. Nat Methods. 2013 Jul; 10(7):676-82. Swaney DL, Beltrao P, Starita L, Guo A, Rush J, Fields S, Krogan NJ, Villén J. PMID: 23749301; PMCID: PMC3868471.
      View in: PubMed   Mentions: 320     Fields:    Translation:AnimalsCells
    93. Correction to “Affinity-Based Probes Based on Type II Kinase Inhibitors”. Journal of the American Chemical Society. 2013 Jan 16; 135(2):948-948. Ranjitkar RP, Perera PB, Swaney SD, Hari HS, Larson LE, Krishnamurty KR, Merritt ME, Villén VJ, Maly MD. .
      View in: Publisher Site   Mentions:
    94. Affinity-based probes based on type II kinase inhibitors. J Am Chem Soc. 2012 Nov 21; 134(46):19017-25. Ranjitkar P, Perera BG, Swaney DL, Swaney DL, Hari SB, Larson ET, Krishnamurty R, Merritt EA, Villén J, Maly DJ. PMID: 23088519; PMCID: PMC3523701.
      View in: PubMed   Mentions: 16     Fields:    
    95. Systematic functional prioritization of protein posttranslational modifications. Cell. 2012 Jul 20; 150(2):413-25. Beltrao P, Albanèse V, Kenner LR, Swaney DL, Burlingame A, Villén J, Lim WA, Fraser JS, Frydman J, Krogan NJ. PMID: 22817900; PMCID: PMC3404735.
      View in: PubMed   Mentions: 215     Fields:    Translation:HumansAnimalsCells
    96. Proteomic and phosphoproteomic comparison of human ES and iPS cells. Nat Methods. 2011 Sep 11; 8(10):821-7. Phanstiel DH, Brumbaugh J, Wenger CD, Tian S, Probasco MD, Bailey DJ, Swaney DL, Tervo MA, Bolin JM, Ruotti V, Stewart R, Thomson JA, Coon JJ. PMID: 21983960; PMCID: PMC3432645.
      View in: PubMed   Mentions: 147     Fields:    Translation:HumansCells
    97. Tra1 has specific regulatory roles, rather than global functions, within the SAGA co-activator complex. EMBO J. 2011 Jun 03; 30(14):2843-52. Helmlinger D, Marguerat S, Villén J, Swaney DL, Gygi SP, Bähler J, Winston F. PMID: 21642955; PMCID: PMC3160243.
      View in: PubMed   Mentions: 40     Fields:    Translation:AnimalsCells
    98. Value of using multiple proteases for large-scale mass spectrometry-based proteomics. J Proteome Res. 2010 Mar 05; 9(3):1323-9. Swaney DL, Wenger CD, Coon JJ. PMID: 20113005; PMCID: PMC2833215.
      View in: PubMed   Mentions: 183     Fields:    Translation:Cells
    99. Phosphoproteomics for the masses. ACS Chem Biol. 2010 Jan 15; 5(1):105-19. Grimsrud PA, Swaney DL, Wenger CD, Beauchene NA, Coon JJ. PMID: 20047291; PMCID: PMC2810156.
      View in: PubMed   Mentions: 69     Fields:    Translation:HumansAnimalsCells
    100. Large-scale phosphoprotein analysis in Medicago truncatula roots provides insight into in vivo kinase activity in legumes. Plant Physiol. 2010 Jan; 152(1):19-28. Grimsrud PA, den Os D, Wenger CD, Swaney DL, Schwartz D, Sussman MR, Ané JM, Coon JJ. PMID: 19923235; PMCID: PMC2799343.
      View in: PubMed   Mentions: 61     Fields:    Translation:AnimalsCells
    101. Dual-pressure linear ion trap mass spectrometer improving the analysis of complex protein mixtures. Anal Chem. 2009 Sep 15; 81(18):7757-65. Second TP, Blethrow JD, Schwartz JC, Merrihew GE, MacCoss MJ, Swaney DL, Russell JD, Coon JJ, Zabrouskov V. PMID: 19689114; PMCID: PMC2810160.
      View in: PubMed   Mentions: 74     Fields:    Translation:Animals
    102. A new probabilistic database search algorithm for ETD spectra. J Proteome Res. 2009 Jun; 8(6):3198-205. Sadygov RG, Good DM, Swaney DL, Coon JJ. PMID: 19354237; PMCID: PMC2730765.
      View in: PubMed   Mentions: 19     Fields:    Translation:Animals
    103. Toward defining the phosphoproteome of Xenopus laevis embryos. Dev Dyn. 2009 Jun; 238(6):1433-43. McGivern JV, Swaney DL, Coon JJ, Sheets MD. PMID: 19384857; PMCID: PMC2865133.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansAnimalsCells
    104. Human embryonic stem cell phosphoproteome revealed by electron transfer dissociation tandem mass spectrometry. Proc Natl Acad Sci U S A. 2009 Jan 27; 106(4):995-1000. Swaney DL, Wenger CD, Thomson JA, Coon JJ. PMID: 19144917; PMCID: PMC2633571.
      View in: PubMed   Mentions: 98     Fields:    Translation:HumansCells
    105. Decision tree-driven tandem mass spectrometry for shotgun proteomics. Nat Methods. 2008 Nov; 5(11):959-64. Swaney DL, McAlister GC, Coon JJ. PMID: 18931669; PMCID: PMC2597439.
      View in: PubMed   Mentions: 149     Fields:    Translation:Humans
    106. A proteomics grade electron transfer dissociation-enabled hybrid linear ion trap-orbitrap mass spectrometer. J Proteome Res. 2008 Aug; 7(8):3127-36. McAlister GC, Berggren WT, Griep-Raming J, Horning S, Makarov A, Phanstiel D, Stafford G, Swaney DL, Syka JE, Zabrouskov V, Coon JJ. PMID: 18613715; PMCID: PMC2601597.
      View in: PubMed   Mentions: 61     Fields:    Translation:HumansCells
    107. Tandem phosphorylation of Ser-911 and Thr-912 at the C terminus of yeast plasma membrane H+-ATPase leads to glucose-dependent activation. J Biol Chem. 2007 Dec 07; 282(49):35471-81. Lecchi S, Nelson CJ, Allen KE, Swaney DL, Thompson KL, Coon JJ, Sussman MR, Slayman CW. PMID: 17932035.
      View in: PubMed   Mentions: 59     Fields:    Translation:AnimalsCells
    108. Probing the dynamics of O-GlcNAc glycosylation in the brain using quantitative proteomics. Nat Chem Biol. 2007 Jun; 3(6):339-48. Khidekel N, Ficarro SB, Clark PM, Bryan MC, Swaney DL, Rexach JE, Sun YE, Coon JJ, Peters EC, Hsieh-Wilson LC. PMID: 17496889.
      View in: PubMed   Mentions: 179     Fields:    Translation:AnimalsCells
    109. Supplemental activation method for high-efficiency electron-transfer dissociation of doubly protonated peptide precursors. Anal Chem. 2007 Jan 15; 79(2):477-85. Swaney DL, McAlister GC, Wirtala M, Schwartz JC, Syka JE, Coon JJ. PMID: 17222010; PMCID: PMC2522365.
      View in: PubMed   Mentions: 154     Fields:    Translation:Cells
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