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. Characterization of a lipid-based jumbo phage compartment as a hub for early phage infection. Cell Host Microbe. 2024 Jun 07. Mozumdar D, Fossati A, Stevenson E, Guan J, Nieweglowska E, Rao S, Agard D, Swaney DL, Bondy-Denomy J. PMID: 38870941.
      View in: PubMed   Mentions:    Fields:    
    2. 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:
    3. The Chlamydia trachomatis Inc Tri1 interacts with TRAF7 to displace native TRAF7 interacting partners. Microbiol Spectr. 2024 May 30; 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.
      View in: PubMed   Mentions:    Fields:    
    4. Targeting a lineage-specific PI3K?-Akt signaling module in acute myeloid leukemia using a heterobifunctional degrader molecule. Nat Cancer. 2024 May 30. 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:    Fields:    
    5. 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:
    6. 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.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    7. 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
    8. 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:
    9. 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:
    10. 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:
    11. 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: 1     Fields:    Translation:Humans
    12. 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:    Fields:    Translation:AnimalsCells
    13. 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
    14. 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:    Fields:    Translation:Cells
    15. 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:
    16. 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: 1     Fields:    Translation:HumansCells
    17. 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: 2     Fields:    Translation:Animals
    18. 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:
    19. 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: 2     Fields:    Translation:HumansCells
    20. 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: 18     Fields:    Translation:HumansCells
    21. 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: 9     Fields:    Translation:HumansCellsPHPublic Health
    22. 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: 1     Fields:    Translation:Cells
    23. 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:
    24. 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:
    25. 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:
    26. Functional analysis of a common BAG3 allele associated with protection from heart failure. Nature Cardiovascular Research. 2023 Jun 26; 2(7):615-628. Perez-Bermejo PJ, Judge JL, Jensen JC, Wu WK, Watry WH, Truong TA, Ho HJ, Carter CM, Runyon RW, Kaake KR, Pulido PE, Mandegar MM, Swaney SD, So SP, Krogan KN, Conklin CB. .
      View in: Publisher Site   Mentions:
    27. 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:
    28. 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:    Fields:    Translation:AnimalsCells
    29. 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:
    30. 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:
    31. 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: 6     Fields:    Translation:HumansCells
    32. 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:
    33. 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:
    34. 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  
    35. 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:
    36. 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:
    37. 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: 3     Fields:    Translation:HumansCells
    38. 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: 10     Fields:    Translation:AnimalsCells
    39. 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: 71     Fields:    Translation:HumansCells
    40. 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: 5     Fields:    Translation:HumansCells
    41. 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: 4     Fields:    Translation:HumansCells
    42. 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: 68     Fields:    Translation:HumansCells
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    81. 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.
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    82. 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
    83. 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
    84. 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
    85. 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: 35     Fields:    Translation:AnimalsCells
    86. 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: 41     Fields:    Translation:HumansAnimalsCells
    87. 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: 302     Fields:    Translation:AnimalsCells
    88. 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:
    89. 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:    
    90. 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: 205     Fields:    Translation:HumansAnimalsCells
    91. 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: 146     Fields:    Translation:HumansCells
    92. 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
    93. 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: 179     Fields:    Translation:Cells
    94. 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: 68     Fields:    Translation:HumansAnimalsCells
    95. 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
    96. 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: 72     Fields:    Translation:Animals
    97. 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
    98. 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
    99. 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: 96     Fields:    Translation:HumansCells
    100. 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: 147     Fields:    Translation:Humans
    101. 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
    102. 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
    103. 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: 173     Fields:    Translation:AnimalsCells
    104. 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: 152     Fields:    Translation:Cells
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