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Danielle Swaney, PhD

Title(s)Assistant Professor, Cellular Molecular Pharmacology
SchoolSchool of Medicine
Address1700 4th Street
San Francisco CA 94158
Phone415-734-2767
ORCID ORCID Icon0000-0001-6119-6084 Additional info
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    Collapse Research 
    Collapse Research Activities and Funding
    Inclusion membrane protein (Inc) modulation of the innate immune response to Chlamydia trachomatis
    NIH/NIAID R56AI152526Sep 4, 2020 - Aug 31, 2021
    Role: Principal Investigator
    Childhood ?Omics? and Mycobacterium tuberculosis-derived BiOsignatures (COMBO) for TB diagnosis in high HIV prevalence settings
    NIH/NIAID 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/NIGMS 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/NCI R21CA235303Feb 15, 2019 - Jan 31, 2022
    Role: Co-Investigator

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    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.
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    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. Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms. Science. 2020 Oct 15. 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. PMID: 33060197.
      View in: PubMed   Mentions:    Fields:    
    2. An ultra-high affinity synthetic nanobody blocks SARS-CoV-2 infection by locking Spike into an inactive conformation. bioRxiv. 2020 Aug 10. Schoof M, Faust B, Saunders RA, Sangwan S, Rezelj V, Hoppe N, Boone M, Billesbølle CB, Zimanyi M, Deshpande I, Liang J, Anand AA, Dobzinski N, Zha BS, Barsi-Rhyne B, Belyy V, Barile-Hill AW, Gupta S, Simoneau CR, Leon K, White KM, Nock S, Liu Y, Krogan NJ, Ralston CY, Swaney DL, García-Sastre A, Ott M, Vignuzzi M, Walter P, Manglik A. PMID: 32817938.
      View in: PubMed   Mentions:
    3. 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.
      View in: PubMed   Mentions: 17     Fields:    Translation:HumansAnimalsCellsPHPublic Health
    4. 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.
      View in: PubMed   Mentions:    Fields:    Translation:AnimalsCells
    5. Unbiased Proteomic Profiling Uncovers a Targetable GNAS/PKA/PP2A Axis in Small Cell Lung Cancer Stem Cells. Cancer Cell. 2020 Jul 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.
      View in: PubMed   Mentions:    Fields:    
    6. 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.
      View in: PubMed   Mentions: 218     Fields:    Translation:HumansAnimalsCellsPHPublic Health
    7. A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing. bioRxiv. 2020 Mar 22. Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, O'Meara MJ, 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, Naing ZZC, Zhou Y, Peng S, Kirby IT, Melnyk JE, Chorba JS, Lou K, Dai SA, Shen W, Shi Y, Zhang Z, Barrio-Hernandez I, Memon D, Hernandez-Armenta C, Mathy CJP, Perica T, Pilla KB, Ganesan SJ, Saltzberg DJ, Ramachandran R, Liu X, Rosenthal SB, Calviello L, Venkataramanan S, Lin Y, Wankowicz SA, Bohn M, Trenker R, Young JM, Cavero D, Hiatt J, Roth T, Rathore U, Subramanian A, Noack J, Hubert M, Roesch F, Vallet T, Meyer B, White KM, Miorin L, Agard D, Emerman M, Ruggero D, García-Sastre A, Jura N, von Zastrow M, Taunton J, Schwartz O, Vignuzzi M, d'Enfert C, Mukherjee S, Jacobson M, Malik HS, Fujimori DG, Ideker T, Craik CS, Floor S, Fraser JS, Gross J, Sali A, Kortemme T, Beltrao P, Shokat K, Shoichet BK, Krogan NJ. PMID: 32511329.
      View in: PubMed   Mentions:
    8. 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.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    9. Dynamic post-translational modification profiling of Mycobacterium tuberculosis-infected primary macrophages. Elife. 2020 Jan 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.
      View in: PubMed   Mentions:    Fields:    
    10. 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.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    11. GENE-37. VESTIBULAR SCHWANNOMA IS COMPRISED OF NEURAL CREST AND IMMUNE SUBGROUPS. Neuro-Oncology. 2019 Nov 11; 21(Supplement_6):vi105-vi105. S John Liu, Harish Vasudevan, Melike Pekmezci, Abrar Choudhury, Brian Lien, Jonathan Breshears, Danielle Swaney, Stephen Magill, Ursula Lang, William Chen, Chetna Gopinath, Maria Castro, Javier Villanueva-Meyer, Steve Braunstein, Patricia Sneed, Daniel Lim, Arie Perry, Nevan Krogran, Mike McDermott, Mitchel Berger, Philip Theodosopoulos, David Raleigh. .
      View in: Publisher Site   Mentions:
    12. 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.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansAnimalsCells
    13. 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.
      View in: PubMed   Mentions: 5     Fields:    Translation:Cells
    14. Abstract 934: Physical and Genetic Interaction Analyses in Human Pluripotent Stem Cell-Derived Cardiomyocytes to Study Protein Quality Control Disease in the Heart. Circulation Research. 2019 Aug 2; 125(Suppl_1). Juan A Perez-Bermejo, Luke M Judge, Kenneth Wu, Christina L Jensen, Robyn M Kaake, Danielle Swaney, Po-Lin So, Nevan J Krogan, Bruce R Conklin. .
      View in: Publisher Site   Mentions:
    15. 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.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansAnimalsCells
    16. 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.
      View in: PubMed   Mentions: 4     Fields:    Translation:AnimalsCells
    17. 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.
      View in: PubMed   Mentions:    Fields:    Translation:AnimalsCells
    18. 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.
      View in: PubMed   Mentions: 31     Fields:    Translation:HumansAnimalsCells
    19. 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.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansCells
    20. 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.
      View in: PubMed   Mentions:
    21. 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.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansAnimalsCells
    22. 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.
      View in: PubMed   Mentions: 3     Fields:    Translation:AnimalsCells
    23. 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: 15     Fields:    Translation:AnimalsCells
    24. 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:    Fields:    Translation:Cells
    25. 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: 1     Fields:    Translation:Cells
    26. 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: 3     Fields:    Translation:Cells
    27. Phosphorylation of ubiquitin at Ser65 affects its polymerization, targets, and proteome-wide turnover. . 2015 Sep; 16(9):1131-44. Swaney DL, Rodríguez-Mias RA, Villén J. PMID: 26142280.
      View in: PubMed   Mentions:
    28. 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.
      View in: PubMed   Mentions: 31     Fields:    Translation:HumansAnimalsCells
    29. 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.
      View in: PubMed   Mentions: 155     Fields:    Translation:AnimalsCells
    30. Correction to “Affinity-Based Probes Based on Type II Kinase Inhibitors”. Journal of the American Chemical Society. 2013 Jan 16; 135(2):948-948. Pratistha Ranjitkar, B. Gayani K. Perera, Danielle L. Swaney, Sanjay B. Hari, Eric T. Larson, Ratika Krishnamurty, Ethan A. Merritt, Judit Villén, Dustin J. Maly. .
      View in: Publisher Site   Mentions:
    31. 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.
      View in: PubMed   Mentions: 12     Fields:    
    32. 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.
      View in: PubMed   Mentions: 142     Fields:    Translation:HumansAnimalsCells
    33. 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.
      View in: PubMed   Mentions: 129     Fields:    Translation:HumansCells
    34. 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.
      View in: PubMed   Mentions: 23     Fields:    Translation:AnimalsCells
    35. 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.
      View in: PubMed   Mentions: 115     Fields:    Translation:Cells
    36. 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.
      View in: PubMed   Mentions: 60     Fields:    Translation:HumansAnimalsCells
    37. 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.
      View in: PubMed   Mentions: 53     Fields:    Translation:AnimalsCells
    38. 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.
      View in: PubMed   Mentions: 66     Fields:    Translation:Animals
    39. 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.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansAnimalsCells
    40. 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.
      View in: PubMed   Mentions: 18     Fields:    Translation:Animals
    41. 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.
      View in: PubMed   Mentions: 89     Fields:    Translation:HumansCells
    42. 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.
      View in: PubMed   Mentions: 136     Fields:    Translation:Humans
    43. 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.
      View in: PubMed   Mentions: 57     Fields:    Translation:HumansCells
    44. 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: 48     Fields:    Translation:AnimalsCells
    45. 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: 133     Fields:    Translation:AnimalsCells
    46. 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.
      View in: PubMed   Mentions: 136     Fields:    Translation:Cells
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