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Alan Jarmusch

Title(s)Postdoctoral Scholar, School of Pharmacy and Pharmaceutical Science
SchoolHealth Sciences
Address9500 Gilman Drive #0751
La Jolla CA 92093
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    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. Protocol for community-created public MS/MS reference spectra within the Global Natural Products Social Molecular Networking infrastructure. Rapid Commun Mass Spectrom. 2020 May 30; 34(10):e8725. Vargas F, Weldon KC, Sikora N, Wang M, Zhang Z, Gentry EC, Panitchpakdi MW, Caraballo-Rodríguez AM, Dorrestein PC, Jarmusch AK. PMID: 31930757.
      View in: PubMed   Mentions:    Fields:    
    2. Reproducible molecular networking of untargeted mass spectrometry data using GNPS. Nat Protoc. 2020 May 13. Aron AT, Gentry EC, McPhail KL, Nothias LF, Nothias-Esposito M, Bouslimani A, Petras D, Gauglitz JM, Sikora N, Vargas F, van der Hooft JJJ, Ernst M, Kang KB, Aceves CM, Caraballo-Rodríguez AM, Koester I, Weldon KC, Bertrand S, Roullier C, Sun K, Tehan RM, Boya P CA, Christian MH, Gutiérrez M, Ulloa AM, Tejeda Mora JA, Mojica-Flores R, Lakey-Beitia J, Vásquez-Chaves V, Zhang Y, Calderón AI, Tayler N, Keyzers RA, Tugizimana F, Ndlovu N, Aksenov AA, Jarmusch AK, Schmid R, Truman AW, Bandeira N, Wang M, Dorrestein PC. PMID: 32405051.
      View in: PubMed   Mentions:    Fields:    
    3. Enhanced Characterization of Drug Metabolism and the Influence of the Intestinal Microbiome: A Pharmacokinetic, Microbiome, and Untargeted Metabolomics Study. Clin Transl Sci. 2020 Mar 26. Jarmusch AK, Vrbanac A, Momper JD, Ma JD, Alhaja M, Liyanage M, Knight R, Dorrestein PC, Tsunoda SM. PMID: 32216086.
      View in: PubMed   Mentions:    Fields:    
    4. Mammalian ovarian lipid distributions by desorption electrospray ionization-mass spectrometry (DESI-MS) imaging. Anal Bioanal Chem. 2020 Feb; 412(6):1251-1262. Cordeiro FB, Jarmusch AK, León M, Ferreira CR, Pirro V, Eberlin LS, Hallett J, Miglino MA, Cooks RG. PMID: 31953714.
      View in: PubMed   Mentions:    Fields:    Translation:Animals
    5. Ambient Lipidomic Analysis of Single Mammalian Oocytes and Preimplantation Embryos Using Desorption Electrospray Ionization (DESI) Mass Spectrometry. Methods Mol Biol. 2020; 2064:159-179. Ferreira CR, Pirro V, Jarmusch AK, Alfaro CM, Cooks RG. PMID: 31565774.
      View in: PubMed   Mentions:    Fields:    
    6. Mass spectrometry searches using MASST. Nat Biotechnol. 2020 01; 38(1):23-26. Wang M, Jarmusch AK, Vargas F, Aksenov AA, Gauglitz JM, Weldon K, Petras D, da Silva R, Quinn R, Melnik AV, van der Hooft JJJ, Caraballo-Rodríguez AM, Nothias LF, Aceves CM, Panitchpakdi M, Brown E, Di Ottavio F, Sikora N, Elijah EO, Labarta-Bajo L, Gentry EC, Shalapour S, Kyle KE, Puckett SP, Watrous JD, Carpenter CS, Bouslimani A, Ernst M, Swafford AD, Zúñiga EI, Balunas MJ, Klassen JL, Loomba R, Knight R, Bandeira N, Dorrestein PC. PMID: 31894142.
      View in: PubMed   Mentions: 1     Fields:    
    7. Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol. 2019 Sep; 37(9):1091. Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, Bai Y, Bisanz JE, Bittinger K, Brejnrod A, Brislawn CJ, Brown CT, Callahan BJ, Caraballo-Rodríguez AM, Chase J, Cope EK, Da Silva R, Diener C, Dorrestein PC, Douglas GM, Durall DM, Duvallet C, Edwardson CF, Ernst M, Estaki M, Fouquier J, Gauglitz JM, Gibbons SM, Gibson DL, Gonzalez A, Gorlick K, Guo J, Hillmann B, Holmes S, Holste H, Huttenhower C, Huttley GA, Janssen S, Jarmusch AK, Jiang L, Kaehler BD, Kang KB, Keefe CR, Keim P, Kelley ST, Knights D, Koester I, Kosciolek T, Kreps J, Langille MGI, Lee J, Ley R, Liu YX, Loftfield E, Lozupone C, Maher M, Marotz C, Martin BD, McDonald D, McIver LJ, Melnik AV, Metcalf JL, Morgan SC, Morton JT, Naimey AT, Navas-Molina JA, Nothias LF, Orchanian SB, Pearson T, Peoples SL, Petras D, Preuss ML, Pruesse E, Rasmussen LB, Rivers A, Robeson MS, Rosenthal P, Segata N, Shaffer M, Shiffer A, Sinha R, Song SJ, Spear JR, Swafford AD, Thompson LR, Torres PJ, Trinh P, Tripathi A, Turnbaugh PJ, Ul-Hasan S, van der Hooft JJJ, Vargas F, Vázquez-Baeza Y, Vogtmann E, von Hippel M, Walters W, Wan Y, Wang M, Warren J, Weber KC, Williamson CHD, Willis AD, Xu ZZ, Zaneveld JR, Zhang Y, Zhu Q, Knight R, Caporaso JG. PMID: 31399723.
      View in: PubMed   Mentions: 4     Fields:    
    8. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol. 2019 08; 37(8):852-857. Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, Bai Y, Bisanz JE, Bittinger K, Brejnrod A, Brislawn CJ, Brown CT, Callahan BJ, Caraballo-Rodríguez AM, Chase J, Cope EK, Da Silva R, Diener C, Dorrestein PC, Douglas GM, Durall DM, Duvallet C, Edwardson CF, Ernst M, Estaki M, Fouquier J, Gauglitz JM, Gibbons SM, Gibson DL, Gonzalez A, Gorlick K, Guo J, Hillmann B, Holmes S, Holste H, Huttenhower C, Huttley GA, Janssen S, Jarmusch AK, Jiang L, Kaehler BD, Kang KB, Keefe CR, Keim P, Kelley ST, Knights D, Koester I, Kosciolek T, Kreps J, Langille MGI, Lee J, Ley R, Liu YX, Loftfield E, Lozupone C, Maher M, Marotz C, Martin BD, McDonald D, McIver LJ, Melnik AV, Metcalf JL, Morgan SC, Morton JT, Naimey AT, Navas-Molina JA, Nothias LF, Orchanian SB, Pearson T, Peoples SL, Petras D, Preuss ML, Pruesse E, Rasmussen LB, Rivers A, Robeson MS, Rosenthal P, Segata N, Shaffer M, Shiffer A, Sinha R, Song SJ, Spear JR, Swafford AD, Thompson LR, Torres PJ, Trinh P, Tripathi A, Turnbaugh PJ, Ul-Hasan S, van der Hooft JJJ, Vargas F, Vázquez-Baeza Y, Vogtmann E, von Hippel M, Walters W, Wan Y, Wang M, Warren J, Weber KC, Williamson CHD, Willis AD, Xu ZZ, Zaneveld JR, Zhang Y, Zhu Q, Knight R, Caporaso JG. PMID: 31341288.
      View in: PubMed   Mentions: 85     Fields:    Translation:Humans
    9. Untargeted mass spectrometry-based metabolomics approach unveils molecular changes in raw and processed foods and beverages. Food Chem. 2020 Jan 01; 302:125290. Gauglitz JM, Aceves CM, Aksenov AA, Aleti G, Almaliti J, Bouslimani A, Brown EA, Campeau A, Caraballo-Rodríguez AM, Chaar R, da Silva RR, Demko AM, Di Ottavio F, Elijah E, Ernst M, Ferguson LP, Holmes X, Jarmusch AK, Jiang L, Kang KB, Koester I, Kwan B, Li J, Li Y, Melnik AV, Molina-Santiago C, Ni B, Oom AL, Panitchpakdi MW, Petras D, Quinn R, Sikora N, Spengler K, Teke B, Tripathi A, Ul-Hasan S, van der Hooft JJJ, Vargas F, Vrbanac A, Vu AQ, Wang SC, Weldon K, Wilson K, Wozniak JM, Yoon M, Bandeira N, Dorrestein PC. PMID: 31404873.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    10. Initial Development toward Non-Invasive Drug Monitoring via Untargeted Mass Spectrometric Analysis of Human Skin. Anal Chem. 2019 07 02; 91(13):8062-8069. Jarmusch AK, Elijah EO, Vargas F, Bouslimani A, da Silva RR, Ernst M, Wang M, Del Rosario KK, Dorrestein PC, Tsunoda SM. PMID: 31074958.
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    11. Metabolites and Lipids Associated with Fetal Swine Anatomy via Desorption Electrospray Ionization - Mass Spectrometry Imaging. Sci Rep. 2019 05 10; 9(1):7247. León M, Ferreira CR, Eberlin LS, Jarmusch AK, Pirro V, Rodrigues ACB, Favaron PO, Miglino MA, Cooks RG. PMID: 31076607.
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    12. Computational Removal of Undesired Mass Spectral Features Possessing Repeat Units via a Kendrick Mass Filter. J Am Soc Mass Spectrom. 2019 Feb; 30(2):268-277. da Silva RR, Vargas F, Ernst M, Nguyen NH, Bolleddu S, Del Rosario KK, Tsunoda SM, Dorrestein PC, Jarmusch AK. PMID: 30267361.
      View in: PubMed   Mentions:    Fields:    
    13. Fatty Acid Patterns Detected By Ambient Ionization Mass Spectrometry in Canine Invasive Urothelial Carcinoma From Dogs of Different Breeds. Bladder Cancer. 2018 Jul 30; 4(3):283-291. D'Hue CA, Dhawan D, Peat T, Ramos-Vara J, Jarmusch A, Knapp DW, Cooks RG. PMID: 30112439.
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    14. Direct ion generation from swabs. Talanta. 2018 Jul 01; 184:356-363. Jarmusch AK, Pirro V, Logsdon DL, Cooks RG. PMID: 29674054.
      View in: PubMed   Mentions: 1     Fields:    
    15. Feasibility of desorption electrospray ionization mass spectrometry for diagnosis of oral tongue squamous cell carcinoma. Rapid Commun Mass Spectrom. 2018 Jan 30; 32(2):133-141. D'Hue C, Moore M, Summerlin DJ, Jarmusch A, Alfaro C, Mantravadi A, Bewley A, Gregory Farwell D, Cooks RG. PMID: 29078250.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    16. Analysis of human gliomas by swab touch spray-mass spectrometry: applications to intraoperative assessment of surgical margins and presence of oncometabolites. Analyst. 2017 Oct 23; 142(21):4058-4066. Pirro V, Llor RS, Jarmusch AK, Alfaro CM, Cohen-Gadol AA, Hattab EM, Cooks RG. PMID: 28984323.
      View in: PubMed   Mentions: 4     Fields:    Translation:Humans
    17. Multiple reaction monitoring (MRM)-profiling for biomarker discovery applied to human polycystic ovarian syndrome. Rapid Commun Mass Spectrom. 2017 Sep 15; 31(17):1462-1470. Cordeiro FB, Ferreira CR, Sobreira TJP, Yannell KE, Jarmusch AK, Cedenho AP, Lo Turco EG, Cooks RG. PMID: 28656689.
      View in: PubMed   Mentions: 4     Fields:    Translation:Humans
    18. N-Acetylaspartate and 2-Hydroxyglutarate Assessed in Human Brain Tissue by Mass Spectrometry as Neuronal Markers of Oncogenesis. Clin Chem. 2017 11; 63(11):1766-1767. Yannell KE, Smith K, Alfaro CM, Jarmusch AK, Pirro V, Cooks RG. PMID: 28877920.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    19. Coupling Targeted and Untargeted Mass Spectrometry for Metabolome-Microbiome-Wide Association Studies of Human Fecal Samples. Anal Chem. 2017 07 18; 89(14):7549-7559. Melnik AV, da Silva RR, Hyde ER, Aksenov AA, Vargas F, Bouslimani A, Protsyuk I, Jarmusch AK, Tripathi A, Alexandrov T, Knight R, Dorrestein PC. PMID: 28628333.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansCells
    20. Intraoperative assessment of tumor margins during glioma resection by desorption electrospray ionization-mass spectrometry. Proc Natl Acad Sci U S A. 2017 06 27; 114(26):6700-6705. Pirro V, Alfaro CM, Jarmusch AK, Hattab EM, Cohen-Gadol AA, Cooks RG. PMID: 28607048.
      View in: PubMed   Mentions: 13     Fields:    Translation:HumansCTClinical Trials
    21. Utility of neurological smears for intrasurgical brain cancer diagnostics and tumour cell percentage by DESI-MS. Analyst. 2017 Jan 26; 142(3):449-454. Pirro V, Jarmusch AK, Alfaro CM, Hattab EM, Cohen-Gadol AA, Cooks RG. PMID: 28112301.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    22. From single cells to our planet-recent advances in using mass spectrometry for spatially resolved metabolomics. Curr Opin Chem Biol. 2017 02; 36:24-31. Petras D, Jarmusch AK, Dorrestein PC. PMID: 28086192.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansAnimalsCells
    23. Differential Lipid Profiles of Normal Human Brain Matter and Gliomas by Positive and Negative Mode Desorption Electrospray Ionization - Mass Spectrometry Imaging. PLoS One. 2016; 11(9):e0163180. Jarmusch AK, Alfaro CM, Pirro V, Hattab EM, Cohen-Gadol AA, Cooks RG. PMID: 27658243.
      View in: PubMed   Mentions: 5     Fields:    
    24. Lipid dynamics in zebrafish embryonic development observed by DESI-MS imaging and nanoelectrospray-MS. Mol Biosyst. 2016 06; 12(7):2069-79. Pirro V, Guffey SC, Sepúlveda MS, Mahapatra CT, Ferreira CR, Jarmusch AK, Cooks RG. PMID: 27120110.
      View in: PubMed   Mentions: 4     Fields:    Translation:AnimalsCells
    25. Ambient ionization mass spectrometric analysis of human surgical specimens to distinguish renal cell carcinoma from healthy renal tissue. Anal Bioanal Chem. 2016 Aug; 408(20):5407-14. Alfaro CM, Jarmusch AK, Pirro V, Kerian KS, Masterson TA, Cheng L, Cooks RG. PMID: 27206411.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansCells
    26. Lipid and metabolite profiles of human brain tumors by desorption electrospray ionization-MS. Proc Natl Acad Sci U S A. 2016 Feb 09; 113(6):1486-91. Jarmusch AK, Pirro V, Baird Z, Hattab EM, Cohen-Gadol AA, Cooks RG. PMID: 26787885.
      View in: PubMed   Mentions: 34     Fields:    Translation:Humans
    27. Ambient Ionization Mass Spectrometry for Point-of-Care Diagnostics and Other Clinical Measurements. Clin Chem. 2016 Jan; 62(1):99-110. Ferreira CR, Yannell KE, Jarmusch AK, Pirro V, Ouyang Z, Cooks RG. PMID: 26467505.
      View in: PubMed   Mentions: 13     Fields:    Translation:Humans
    28. Characteristic lipid profiles of canine non-Hodgkin's lymphoma from surgical biopsy tissue sections and fine needle aspirate smears by desorption electrospray ionization--mass spectrometry. Analyst. 2015 Sep 21; 140(18):6321-9. Jarmusch AK, Kerian KS, Pirro V, Peat T, Thompson CA, Ramos-Vara JA, Childress MO, Cooks RG. PMID: 26236993.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansAnimals
    29. Comparison of electrospray ionization and atmospheric pressure photoionization liquid chromatography mass spectrometry methods for analysis of ergot alkaloids from endophyte-infected sleepygrass (Achnatherum robustum). J Pharm Biomed Anal. 2016 Jan 05; 117:11-7. Jarmusch AK, Musso AM, Shymanovich T, Jarmusch SA, Weavil MJ, Lovin ME, Ehrmann BM, Saari S, Nichols DE, Faeth SH, Cech NB. PMID: 26340558.
      View in: PubMed   Mentions: 2     Fields:    Translation:Animals
    30. Ambient ionisation mass spectrometry for lipid profiling and structural analysis of mammalian oocytes, preimplantation embryos and stem cells. Reprod Fertil Dev. 2015 May; 27(4):621-37. Ferreira CR, Jarmusch AK, Pirro V, Alfaro CM, González-Serrano AF, Niemann H, Wheeler MB, Rabel RA, Hallett JE, Houser R, Kaufman A, Cooks RG. PMID: 25763644.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansAnimalsCells
    31. Skin molecule maps using mass spectrometry. Proc Natl Acad Sci U S A. 2015 Apr 28; 112(17):5261-2. Cooks RG, Jarmusch AK, Ferreira CR, Pirro V. PMID: 25902544.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    32. Differentiation of prostate cancer from normal tissue in radical prostatectomy specimens by desorption electrospray ionization and touch spray ionization mass spectrometry. Analyst. 2015 Feb 21; 140(4):1090-8. Kerian KS, Jarmusch AK, Pirro V, Koch MO, Masterson TA, Cheng L, Cooks RG. PMID: 25521825.
      View in: PubMed   Mentions: 17     Fields:    Translation:Humans
    33. Direct drug analysis from oral fluid using medical swab touch spray mass spectrometry. Anal Chim Acta. 2015 Feb 25; 861:47-54. Pirro V, Jarmusch AK, Vincenti M, Cooks RG. PMID: 25702273.
      View in: PubMed   Mentions: 6     Fields:    
    34. Alkaloid variation among epichloid endophytes of sleepygrass (Achnatherum robustum) and consequences for resistance to insect herbivores. J Chem Ecol. 2015 Jan; 41(1):93-104. Shymanovich T, Saari S, Lovin ME, Jarmusch AK, Jarmusch SA, Musso AM, Charlton ND, Young CA, Cech NB, Faeth SH. PMID: 25501262.
      View in: PubMed   Mentions: 11     Fields:    Translation:Animals
    35. Detection of strep throat causing bacterium directly from medical swabs by touch spray-mass spectrometry. Analyst. 2014 Oct 07; 139(19):4785-9. Jarmusch AK, Pirro V, Kerian KS, Cooks RG. PMID: 25102079.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansCells
    36. Rapid discrimination of bacteria by paper spray mass spectrometry. Anal Chem. 2014 Aug 05; 86(15):7500-7. Hamid AM, Jarmusch AK, Pirro V, Pincus DH, Clay BG, Gervasi G, Cooks RG. PMID: 25014713.
      View in: PubMed   Mentions: 13     Fields:    Translation:Cells
    37. Polyhydroxyanthraquinones as quorum sensing inhibitors from the guttates of Penicillium restrictum and their analysis by desorption electrospray ionization mass spectrometry. J Nat Prod. 2014 Jun 27; 77(6):1351-8. Figueroa M, Jarmusch AK, Raja HA, El-Elimat T, Kavanaugh JS, Horswill AR, Cooks RG, Cech NB, Oberlies NH. PMID: 24911880.
      View in: PubMed   Mentions: 27     Fields:    Translation:AnimalsCells
    38. Touch spray mass spectrometry for in situ analysis of complex samples. Analyst. 2014 Jun 07; 139(11):2714-20. Kerian KS, Jarmusch AK, Cooks RG. PMID: 24756256.
      View in: PubMed   Mentions: 17     Fields:    Translation:HumansAnimalsCellsPHPublic Health
    39. Emerging capabilities of mass spectrometry for natural products. Nat Prod Rep. 2014 Jun; 31(6):730-8. Jarmusch AK, Cooks RG. PMID: 24700087.
      View in: PubMed   Mentions: 13     Fields:    Translation:AnimalsCells
    40. Ambient mass spectrometry for the intraoperative molecular diagnosis of human brain tumors. Proc Natl Acad Sci U S A. 2013 Jan 29; 110(5):1611-6. Eberlin LS, Norton I, Orringer D, Dunn IF, Liu X, Ide JL, Jarmusch AK, Ligon KL, Jolesz FA, Golby AJ, Santagata S, Agar NY, Cooks RG. PMID: 23300285.
      View in: PubMed   Mentions: 68     Fields:    Translation:Humans