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Pieter Dorrestein

Title(s)Professor, School of Pharmacy and Pharmaceutical Science
SchoolVc-health Sciences-schools
Address9500 Gilman Drive #
La Jolla CA 92093
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    Collapse Biography 
    Collapse Education and Training
    Ph.D.Cornell University

    Collapse Overview 

    Collapse Research 
    Collapse Research Activities and Funding
    Reuse of Public Metabolomics Data
    NIH R03CA211211Sep 15, 2016 - Aug 31, 2018
    Role: Principal Investigator
    Tools for rapid and accurate structure elucidation of natural products
    NIH R01GM107550Sep 5, 2013 - Jun 30, 2017
    Role: Principal Investigator
    Experiment based genome mining of ribosomal natural products
    NIH R01GM097509Apr 1, 2012 - Feb 29, 2016
    Role: Principal Investigator
    Synapt ion mobility mass spectrometer
    NIH S10RR029121Jun 15, 2011 - Jun 14, 2012
    Role: Principal Investigator
    The chemical and genetic basis of interspecies interactions
    NIH R01AI095125Mar 7, 2011 - Feb 29, 2016
    Role: Principal Investigator
    Real-Time Imaging of metabolic Communication
    NIH R01GM094802Sep 1, 2010 - Aug 31, 2015
    Role: Principal Investigator
    New approaches to sequencing of complex peptides.
    NIH R01GM086283Sep 25, 2008 - Aug 31, 2012
    Role: Principal Investigator
    Enzymology of NRPS and PKS proteins by mass spectrometry
    NIH F32GM073323Mar 16, 2005 - Aug 31, 2006
    Role: Principal 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.
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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. Open Science Resources for the Mass Spectrometry-Based Analysis of SARS-CoV-2. J Proteome Res. 2021 Feb 19. PMID: 33605735.
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    2. Tiny Earth: A Big Idea for STEM Education and Antibiotic Discovery. mBio. 2021 Feb 16; 12(1). PMID: 33593964.
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    3. A community resource for paired genomic and metabolomic data mining. Nat Chem Biol. 2021 Feb 15. PMID: 33589842.
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    4. Convergent evolution of pain-inducing defensive venom components in spitting cobras. Science. 2021 01 22; 371(6527):386-390. Kazandjian TD, Petras D, Robinson SD, van Thiel J, Greene HW, Arbuckle K, Barlow A, Carter DA, Wouters RM, Whiteley G, Wagstaff SC, Arias AS, Albulescu LO, Plettenberg Laing A, Hall C, Heap A, Penrhyn-Lowe S, McCabe CV, Ainsworth S, da Silva RR, Dorrestein PC, Richardson MK, Gutiérrez JM, Calvete JJ, Harrison RA, Vetter I, Undheim EAB, Wüster W, Casewell NR. PMID: 33479150.
      View in: PubMed   Mentions:    Fields:    Translation:AnimalsCells
    5. Identifying the effect of vancomycin on health care-associated methicillin-resistant Staphylococcus aureus strains using bacteriological and physiological media. Gigascience. 2021 Jan 09; 10(1). Rajput A, Poudel S, Tsunemoto H, Meehan M, Szubin R, Olson CA, Seif Y, Lamsa A, Dillon N, Vrbanac A, Sugie J, Dahesh S, Monk JM, Dorrestein PC, Knight R, Pogliano J, Nizet V, Feist AM, Palsson BO. PMID: 33420779.
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    6. A Multi-Omics Characterization of the Natural Product Potential of Tropical Filamentous Marine Cyanobacteria. Mar Drugs. 2021 Jan 06; 19(1). Leão T, Wang M, Moss N, da Silva R, Sanders J, Nurk S, Gurevich A, Humphrey G, Reher R, Zhu Q, Belda-Ferre P, Glukhov E, Whitner S, Alexander KL, Rex R, Pevzner P, Dorrestein PC, Knight R, Bandeira N, Gerwick WH, Gerwick L. PMID: 33418911.
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    7. Effects of Immunization With the Soil-Derived Bacterium Mycobacterium vaccae on Stress Coping Behaviors and Cognitive Performance in a "Two Hit" Stressor Model. Front Physiol. 2020; 11:524833. Foxx CL, Heinze JD, González A, Vargas F, Baratta MV, Elsayed AI, Stewart JR, Loupy KM, Arnold MR, Flux MC, Sago SA, Siebler PH, Milton LN, Lieb MW, Hassell JE, Smith DG, Lee KAK, Appiah SA, Schaefer EJ, Panitchpakdi M, Sikora NC, Weldon KC, Stamper CE, Schmidt D, Duggan DA, Mengesha YM, Ogbaselassie M, Nguyen KT, Gates CA, Schnabel K, Tran L, Jones JD, Vitaterna MH, Turek FW, Fleshner M, Dorrestein PC, Knight R, Wright KP, Lowry CA. PMID: 33469429.
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    8. Reply to: Examining microbe-metabolite correlations by linear methods. Nat Methods. 2021 Jan; 18(1):40-41. Morton JT, McDonald D, Aksenov AA, Nothias LF, Foulds JR, Quinn RA, Badri MH, Swenson TL, Van Goethem MW, Northen TR, Vazquez-Baeza Y, Wang M, Bokulich NA, Watters A, Song SJ, Bonneau R, Dorrestein PC, Knight R. PMID: 33398188.
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    9. Non-targeted tandem mass spectrometry enables the visualization of organic matter chemotype shifts in coastal seawater. Chemosphere. 2021 Jan 02; 271:129450. Petras D, Minich JJ, Cancelada LB, Torres RR, Kunselman E, Wang M, White ME, Allen EE, Prather KA, Aluwihare LI, Dorrestein PC. PMID: 33460888.
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    10. Molecular Networking: A Useful Tool for the Identification of New Psychoactive Substances in Seizures by LC-HRMS. Front Chem. 2020; 8:572952. Vincenti F, Montesano C, Di Ottavio F, Gregori A, Compagnone D, Sergi M, Dorrestein P. PMID: 33324608.
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    11. Systematic classification of unknown metabolites using high-resolution fragmentation mass spectra. Nat Biotechnol. 2020 Nov 23. PMID: 33230292.
      View in: PubMed   Mentions: 1     Fields:    
    12. Multiomics Analysis Provides Insight into the Laboratory Evolution of Escherichia coli toward the Metabolic Usage of Fluorinated Indoles. ACS Cent Sci. 2021 Jan 27; 7(1):81-92. Agostini F, Sinn L, Petras D, Schipp CJ, Kubyshkin V, Berger AA, Dorrestein PC, Rappsilber J, Budisa N, Koksch B. PMID: 33532571.
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    13. A Cutibacterium acnes antibiotic modulates human skin microbiota composition in hair follicles. Sci Transl Med. 2020 Nov 18; 12(570). Claesen J, Spagnolo JB, Ramos SF, Kurita KL, Byrd AL, Aksenov AA, Melnik AV, Wong WR, Wang S, Hernandez RD, Donia MS, Dorrestein PC, Kong HH, Segre JA, Linington RG, Fischbach MA, Lemon KP. PMID: 33208503.
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    14. Can Statistical Evaluation Tools for Chromatographic Method Development Assist in the Natural Products Workflow? A Case Study on Selected Species of the Plant Family Malpighiaceae. J Nat Prod. 2020 11 25; 83(11):3239-3249. Mannochio-Russo H, Bueno PCP, Bauermeister A, de Almeida RF, Dorrestein PC, Cavalheiro AJ, Bolzani VS. PMID: 33196207.
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    15. Chemically informed analyses of metabolomics mass spectrometry data with Qemistree. Nat Chem Biol. 2020 Nov 16. Tripathi A, Vázquez-Baeza Y, Gauglitz JM, Wang M, Dührkop K, Nothias-Esposito M, Acharya DD, Ernst M, van der Hooft JJJ, Zhu Q, McDonald D, Brejnrod AD, Gonzalez A, Handelsman J, Fleischauer M, Ludwig M, Böcker S, Nothias LF, Knight R, Dorrestein PC. PMID: 33199911.
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    16. Studying Charge Migration Fragmentation of Sodiated Precursor Ions in Collision-Induced Dissociation at the Library Scale. J Am Soc Mass Spectrom. 2020 Nov 13. Ludwig M, Broeckling CD, Dorrestein PC, Dührkop K, Schymanski EL, Böcker S, Nothias LF. PMID: 33186010.
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    17. Heterologous Expression of Cryptomaldamide in a Cyanobacterial Host. ACS Synth Biol. 2020 Nov 12. Taton A, Ecker A, Diaz B, Moss NA, Anderson B, Reher R, Leão TF, Simkovsky R, Dorrestein PC, Gerwick L, Gerwick WH, Golden JW. PMID: 33180461.
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    18. Fungal-bacterial interaction selects for quorum sensing mutants with increased production of natural antifungal compounds. Commun Biol. 2020 Nov 12; 3(1):670. Albarracín Orio AG, Petras D, Tobares RA, Aksenov AA, Wang M, Juncosa F, Sayago P, Moyano AJ, Dorrestein PC, Smania AM. PMID: 33184402.
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    19. Auto-deconvolution and molecular networking of gas chromatography-mass spectrometry data. Nat Biotechnol. 2020 Nov 09. Aksenov AA, Laponogov I, Zhang Z, Doran SLF, Belluomo I, Veselkov D, Bittremieux W, Nothias LF, Nothias-Esposito M, Maloney KN, Misra BB, Melnik AV, Smirnov A, Du X, Jones KL, Dorrestein K, Panitchpakdi M, Ernst M, van der Hooft JJJ, Gonzalez M, Carazzone C, Amézquita A, Callewaert C, Morton JT, Quinn RA, Bouslimani A, Orio AA, Petras D, Smania AM, Couvillion SP, Burnet MC, Nicora CD, Zink E, Metz TO, Artaev V, Humston-Fulmer E, Gregor R, Meijler MM, Mizrahi I, Eyal S, Anderson B, Dutton R, Lugan R, Boulch PL, Guitton Y, Prevost S, Poirier A, Dervilly G, Le Bizec B, Fait A, Persi NS, Song C, Gashu K, Coras R, Guma M, Manasson J, Scher JU, Barupal DK, Alseekh S, Fernie AR, Mirnezami R, Vasiliou V, Schmid R, Borisov RS, Kulikova LN, Knight R, Wang M, Hanna GB, Dorrestein PC, Veselkov K. PMID: 33169034.
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    20. Reduced Independence in Daily Living Is Associated with the Gut Microbiome in People with HIV and HCV. mSystems. 2020 Oct 13; 5(5). Taylor BC, Weldon KC, Ellis RJ, Franklin D, McDonald D, Humphrey G, Bryant M, Toronczak J, Schwartz T, Iudicello J, Heaton R, Grant I, Gianella S, Letendre S, Swafford A, Dorrestein PC, Knight R. PMID: 33051377.
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    21. Metabolites from Microbes Isolated from the Skin of the Panamanian Rocket Frog Colostethus panamansis (Anura: Dendrobatidae). Metabolites. 2020 Oct 13; 10(10). Martin H C, Ibáñez R, Nothias LF, Caraballo-Rodríguez AM, Dorrestein PC, Gutiérrez M. PMID: 33065987.
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    22. Gastrointestinal Surgery for Inflammatory Bowel Disease Persistently Lowers Microbiome and Metabolome Diversity. Inflamm Bowel Dis. 2020 Oct 07. PMID: 33026068.
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    23. Evaluating Organism-Wide Changes in the Metabolome and Microbiome following a Single Dose of Antibiotic. mSystems. 2020 Oct 06; 5(5). PMID: 33024048.
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    24. Depression in Individuals Coinfected with HIV and HCV Is Associated with Systematic Differences in the Gut Microbiome and Metabolome. mSystems. 2020 Sep 29; 5(5). Taylor BC, Weldon KC, Ellis RJ, Franklin D, Groth T, Gentry EC, Tripathi A, McDonald D, Humphrey G, Bryant M, Toronczak J, Schwartz T, Oliveira MF, Heaton R, Grant I, Gianella S, Letendre S, Swafford A, Dorrestein PC, Knight R. PMID: 32994287.
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    25. Mortality Risk Profiling of Staphylococcus aureus Bacteremia by Multi-omic Serum Analysis Reveals Early Predictive and Pathogenic Signatures. Cell. 2020 Sep 03; 182(5):1311-1327.e14. Wozniak JM, Mills RH, Olson J, Caldera JR, Sepich-Poore GD, Carrillo-Terrazas M, Tsai CM, Vargas F, Knight R, Dorrestein PC, Liu GY, Nizet V, Sakoulas G, Rose W, Gonzalez DJ. PMID: 32888495.
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    26. Genome Mining, Microbial Interactions, and Molecular Networking Reveals New Dibromoalterochromides from Strains of Pseudoalteromonas of Coiba National Park-Panama. Mar Drugs. 2020 Sep 03; 18(9). Atencio LA, Boya P CA, Martin H C, Mejía LC, Dorrestein PC, Gutiérrez M. PMID: 32899199.
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    27. Feature-based molecular networking in the GNPS analysis environment. Nat Methods. 2020 09; 17(9):905-908. Nothias LF, Petras D, Schmid R, Dührkop K, Rainer J, Sarvepalli A, Protsyuk I, Ernst M, Tsugawa H, Fleischauer M, Aicheler F, Aksenov AA, Alka O, Allard PM, Barsch A, Cachet X, Caraballo-Rodriguez AM, Da Silva RR, Dang T, Garg N, Gauglitz JM, Gurevich A, Isaac G, Jarmusch AK, Kameník Z, Kang KB, Kessler N, Koester I, Korf A, Le Gouellec A, Ludwig M, Martin H C, McCall LI, McSayles J, Meyer SW, Mohimani H, Morsy M, Moyne O, Neumann S, Neuweger H, Nguyen NH, Nothias-Esposito M, Paolini J, Phelan VV, Pluskal T, Quinn RA, Rogers S, Shrestha B, Tripathi A, van der Hooft JJJ, Vargas F, Weldon KC, Witting M, Yang H, Zhang Z, Zubeil F, Kohlbacher O, Böcker S, Alexandrov T, Bandeira N, Wang M, Dorrestein PC. PMID: 32839597.
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    28. ReDU: a framework to find and reanalyze public mass spectrometry data. Nat Methods. 2020 09; 17(9):901-904. Jarmusch AK, Wang M, Aceves CM, Advani RS, Aguirre S, Aksenov AA, Aleti G, Aron AT, Bauermeister A, Bolleddu S, Bouslimani A, Caraballo Rodriguez AM, Chaar R, Coras R, Elijah EO, Ernst M, Gauglitz JM, Gentry EC, Husband M, Jarmusch SA, Jones KL, Kamenik Z, Le Gouellec A, Lu A, McCall LI, McPhail KL, Meehan MJ, Melnik AV, Menezes RC, Montoya Giraldo YA, Nguyen NH, Nothias LF, Nothias-Esposito M, Panitchpakdi M, Petras D, Quinn RA, Sikora N, van der Hooft JJJ, Vargas F, Vrbanac A, Weldon KC, Knight R, Bandeira N, Dorrestein PC. PMID: 32807955.
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    29. Virulence as a Side Effect of Interspecies Interaction in Vibrio Coral Pathogens. mBio. 2020 07 21; 11(4). Rubio-Portillo E, Martin-Cuadrado AB, Caraballo-Rodríguez AM, Rohwer F, Dorrestein PC, Antón J. PMID: 32694137.
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    30. High-Resolution Longitudinal Dynamics of the Cystic Fibrosis Sputum Microbiome and Metabolome through Antibiotic Therapy. mSystems. 2020 Jun 23; 5(3). Raghuvanshi R, Vasco K, Vázquez-Baeza Y, Jiang L, Morton JT, Li D, Gonzalez A, DeRight Goldasich L, Humphrey G, Ackermann G, Swafford AD, Conrad D, Knight R, Dorrestein PC, Quinn RA. PMID: 32576651.
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    31. Paroxetine Administration Affects Microbiota and Bile Acid Levels in Mice. Front Psychiatry. 2020; 11:518. Dethloff F, Vargas F, Elijah E, Quinn R, Park DI, Herzog DP, Müller MB, Gentry EC, Knight R, Gonzalez A, Dorrestein PC, Turck CW. PMID: 32581888.
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    32. A multiomic analysis of in situ coral-turf algal interactions. Proc Natl Acad Sci U S A. 2020 06 16; 117(24):13588-13595. Roach TNF, Little M, Arts MGI, Huckeba J, Haas AF, George EE, Quinn RA, Cobián-Güemes AG, Naliboff DS, Silveira CB, Vermeij MJA, Kelly LW, Dorrestein PC, Rohwer F. PMID: 32482859.
      View in: PubMed   Mentions:    Fields:    Translation:AnimalsCells
    33. 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.
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    34. Reproducible molecular networking of untargeted mass spectrometry data using GNPS. Nat Protoc. 2020 06; 15(6):1954-1991. 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: 5     Fields:    Translation:HumansAnimals
    35. Linking genomics and metabolomics to chart specialized metabolic diversity. Chem Soc Rev. 2020 Jun 07; 49(11):3297-3314. van der Hooft JJJ, Mohimani H, Bauermeister A, Dorrestein PC, Duncan KR, Medema MH. PMID: 32393943.
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    36. A Genomic Toolkit for the Mechanistic Dissection of Intractable Human Gut Bacteria. Cell Host Microbe. 2020 06 10; 27(6):1001-1013.e9. Bisanz JE, Soto-Perez P, Noecker C, Aksenov AA, Lam KN, Kenney GE, Bess EN, Haiser HJ, Kyaw TS, Yu FB, Rekdal VM, Ha CWY, Devkota S, Balskus EP, Dorrestein PC, Allen-Vercoe E, Turnbaugh PJ. PMID: 32348781.
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    37. Enhanced Characterization of Drug Metabolism and the Influence of the Intestinal Microbiome: A Pharmacokinetic, Microbiome, and Untargeted Metabolomics Study. Clin Transl Sci. 2020 09; 13(5):972-984. Jarmusch AK, Vrbanac A, Momper JD, Ma JD, Alhaja M, Liyanage M, Knight R, Dorrestein PC, Tsunoda SM. PMID: 32216086.
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    38. Consumption of Fermented Foods Is Associated with Systematic Differences in the Gut Microbiome and Metabolome. mSystems. 2020 Mar 17; 5(2). Taylor BC, Lejzerowicz F, Poirel M, Shaffer JP, Jiang L, Aksenov A, Litwin N, Humphrey G, Martino C, Miller-Montgomery S, Dorrestein PC, Veiga P, Song SJ, McDonald D, Derrien M, Knight R. PMID: 32184365.
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    39. Interleukin-17 Inhibition in Spondyloarthritis Is Associated With Subclinical Gut Microbiome Perturbations and a Distinctive Interleukin-25-Driven Intestinal Inflammation. Arthritis Rheumatol. 2020 04; 72(4):645-657. Manasson J, Wallach DS, Guggino G, Stapylton M, Badri MH, Solomon G, Reddy SM, Coras R, Aksenov AA, Jones DR, Girija PV, Neimann AL, Heguy A, Segal LN, Dorrestein PC, Bonneau R, Guma M, Ciccia F, Ubeda C, Clemente JC, Scher JU. PMID: 31729183.
      View in: PubMed   Mentions: 4     Fields:    Translation:Humans
    40. Metabolome-Informed Microbiome Analysis Refines Metadata Classifications and Reveals Unexpected Medication Transfer in Captive Cheetahs. mSystems. 2020 Mar 10; 5(2). Gauglitz JM, Morton JT, Tripathi A, Hansen S, Gaffney M, Carpenter C, Weldon KC, Shah R, Parampil A, Fidgett AL, Swafford AD, Knight R, Dorrestein PC. PMID: 32156796.
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    41. Dietary prebiotics alter novel microbial dependent fecal metabolites that improve sleep. Sci Rep. 2020 03 02; 10(1):3848. Thompson RS, Vargas F, Dorrestein PC, Chichlowski M, Berg BM, Fleshner M. PMID: 32123201.
      View in: PubMed   Mentions: 2     Fields:    Translation:Animals
    42. Perspective: Dietary Biomarkers of Intake and Exposure-Exploration with Omics Approaches. Adv Nutr. 2020 03 01; 11(2):200-215. Maruvada P, Lampe JW, Wishart DS, Barupal D, Chester DN, Dodd D, Djoumbou-Feunang Y, Dorrestein PC, Dragsted LO, Draper J, Duffy LC, Dwyer JT, Emenaker NJ, Fiehn O, Gerszten RE, B Hu F, Karp RW, Klurfeld DM, Laughlin MR, Little AR, Lynch CJ, Moore SC, Nicastro HL, O'Brien DM, Ordovás JM, Osganian SK, Playdon M, Prentice R, Raftery D, Reisdorph N, Roche HM, Ross SA, Sang S, Scalbert A, Srinivas PR, Zeisel SH. PMID: 31386148.
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    43. Global chemical effects of the microbiome include new bile-acid conjugations. Nature. 2020 03; 579(7797):123-129. Quinn RA, Melnik AV, Vrbanac A, Fu T, Patras KA, Christy MP, Bodai Z, Belda-Ferre P, Tripathi A, Chung LK, Downes M, Welch RD, Quinn M, Humphrey G, Panitchpakdi M, Weldon KC, Aksenov A, da Silva R, Avila-Pacheco J, Clish C, Bae S, Mallick H, Franzosa EA, Lloyd-Price J, Bussell R, Thron T, Nelson AT, Wang M, Leszczynski E, Vargas F, Gauglitz JM, Meehan MJ, Gentry E, Arthur TD, Komor AC, Poulsen O, Boland BS, Chang JT, Sandborn WJ, Lim M, Garg N, Lumeng JC, Xavier RJ, Kazmierczak BI, Jain R, Egan M, Rhee KE, Ferguson D, Raffatellu M, Vlamakis H, Haddad GG, Siegel D, Huttenhower C, Mazmanian SK, Evans RM, Nizet V, Knight R, Dorrestein PC. PMID: 32103176.
      View in: PubMed   Mentions: 22     Fields:    Translation:HumansAnimals
    44. A Convolutional Neural Network-Based Approach for the Rapid Annotation of Molecularly Diverse Natural Products. J Am Chem Soc. 2020 03 04; 142(9):4114-4120. Reher R, Kim HW, Zhang C, Mao HH, Wang M, Nothias LF, Caraballo-Rodriguez AM, Glukhov E, Teke B, Leao T, Alexander KL, Duggan BM, Van Everbroeck EL, Dorrestein PC, Cottrell GW, Gerwick WH. PMID: 32045230.
      View in: PubMed   Mentions: 7     Fields:    
    45. Repeated sleep disruption in mice leads to persistent shifts in the fecal microbiome and metabolome. PLoS One. 2020; 15(2):e0229001. Bowers SJ, Vargas F, González A, He S, Jiang P, Dorrestein PC, Knight R, Wright KP, Lowry CA, Fleshner M, Vitaterna MH, Turek FW. PMID: 32078624.
      View in: PubMed   Mentions: 4     Fields:    Translation:AnimalsCells
    46. Emerging Priorities for Microbiome Research. Front Microbiol. 2020; 11:136. Cullen CM, Aneja KK, Beyhan S, Cho CE, Woloszynek S, Convertino M, McCoy SJ, Zhang Y, Anderson MZ, Alvarez-Ponce D, Smirnova E, Karstens L, Dorrestein PC, Li H, Sen Gupta A, Cheung K, Powers JG, Zhao Z, Rosen GL. PMID: 32140140.
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    47. Assessing specialized metabolite diversity of Alnus species by a digitized LC-MS/MS data analysis workflow. Phytochemistry. 2020 May; 173:112292. Kang KB, Woo S, Ernst M, van der Hooft JJJ, Nothias LF, da Silva RR, Dorrestein PC, Sung SH, Lee M. PMID: 32062198.
      View in: PubMed   Mentions:    Fields:    Translation:Animals
    48. Cryptic Species Account for the Seemingly Idiosyncratic Secondary Metabolism of Sarcophyton glaucum Specimens Collected in Palau. J Nat Prod. 2020 03 27; 83(3):693-705. Maloney KN, Botts RT, Davis TS, Okada BK, Maloney EM, Leber CA, Alvarado O, Brayton C, Caraballo-Rodríguez AM, Chari JV, Chicoine B, Crompton JC, Davis SR, Gromek SM, Kurnianda V, Quach K, Samples RM, Shieh V, Sultana CM, Tanaka J, Dorrestein PC, Balunas MJ, McFadden CS. PMID: 31971803.
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    49. The emergence of microbiome centres. Nat Microbiol. 2020 01; 5(1):2-3. Martiny JBH, Whiteson KL, Bohannan BJM, David LA, Hynson NA, McFall-Ngai M, Rawls JF, Schmidt TM, Abdo Z, Blaser MJ, Bordenstein S, Bréchot C, Bull CT, Dorrestein P, Eisen JA, Garcia-Pichel F, Gilbert J, Hofmockel KS, Holtz ML, Knight R, Mark Welch DB, McDonald D, Methé B, Mouncey NJ, Mueller NT, Pfister CA, Proctor L, Sachs JL. PMID: 31857734.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimals
    50. 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: 11     Fields:    
    51. A UHPLC-HRMS based metabolomics and chemoinformatics approach to chemically distinguish 'super foods' from a variety of plant-based foods. Food Chem. 2020 May 30; 313:126071. Di Ottavio F, Gauglitz JM, Ernst M, Panitchpakdi MW, Fanti F, Compagnone D, Dorrestein PC, Sergi M. PMID: 31927204.
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    52. De Novo Peptide Sequencing Reveals Many Cyclopeptides in the Human Gut and Other Environments. Cell Syst. 2020 01 22; 10(1):99-108.e5. Behsaz B, Mohimani H, Gurevich A, Prjibelski A, Fisher M, Vargas F, Smarr L, Dorrestein PC, Mylne JS, Pevzner PA. PMID: 31864964.
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    53. Profiling the effect of nafcillin on HA-MRSA D712 using bacteriological and physiological media. Sci Data. 2019 12 17; 6(1):322. Rajput A, Poudel S, Tsunemoto H, Meehan M, Szubin R, Olson CA, Lamsa A, Seif Y, Dillon N, Vrbanac A, Sugie J, Dahesh S, Monk JM, Dorrestein PC, Knight R, Nizet V, Palsson BO, Feist AM, Pogliano J. PMID: 31848353.
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    54. The Natural Products Atlas: An Open Access Knowledge Base for Microbial Natural Products Discovery. ACS Cent Sci. 2019 Nov 27; 5(11):1824-1833. van Santen JA, Jacob G, Singh AL, Aniebok V, Balunas MJ, Bunsko D, Neto FC, Castaño-Espriu L, Chang C, Clark TN, Cleary Little JL, Delgadillo DA, Dorrestein PC, Duncan KR, Egan JM, Galey MM, Haeckl FPJ, Hua A, Hughes AH, Iskakova D, Khadilkar A, Lee JH, Lee S, LeGrow N, Liu DY, Macho JM, McCaughey CS, Medema MH, Neupane RP, O'Donnell TJ, Paula JS, Sanchez LM, Shaikh AF, Soldatou S, Terlouw BR, Tran TA, Valentine M, van der Hooft JJJ, Vo DA, Wang M, Wilson D, Zink KE, Linington RG. PMID: 31807684.
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    55. Comparative Genomics and Metabolomics Analyses of Clavulanic Acid-Producing Streptomyces Species Provides Insight Into Specialized Metabolism. Front Microbiol. 2019; 10:2550. AbuSara NF, Piercey BM, Moore MA, Shaikh AA, Nothias LF, Srivastava SK, Cruz-Morales P, Dorrestein PC, Barona-Gómez F, Tahlan K. PMID: 31787949.
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    56. Learning representations of microbe-metabolite interactions. Nat Methods. 2019 12; 16(12):1306-1314. Morton JT, Aksenov AA, Nothias LF, Foulds JR, Quinn RA, Badri MH, Swenson TL, Van Goethem MW, Northen TR, Vazquez-Baeza Y, Wang M, Bokulich NA, Watters A, Song SJ, Bonneau R, Dorrestein PC, Knight R. PMID: 31686038.
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    57. Home chemical and microbial transitions across urbanization. Nat Microbiol. 2020 01; 5(1):108-115. McCall LI, Callewaert C, Zhu Q, Song SJ, Bouslimani A, Minich JJ, Ernst M, Ruiz-Calderon JF, Cavallin H, Pereira HS, Novoselac A, Hernandez J, Rios R, Branch OH, Blaser MJ, Paulino LC, Dorrestein PC, Knight R, Dominguez-Bello MG. PMID: 31686026.
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    58. Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads. Genome Biol. 2019 10 31; 20(1):226. Sanders JG, Nurk S, Salido RA, Minich J, Xu ZZ, Zhu Q, Martino C, Fedarko M, Arthur TD, Chen F, Boland BS, Humphrey GC, Brennan C, Sanders K, Gaffney J, Jepsen K, Khosroheidari M, Green C, Liyanage M, Dang JW, Phelan VV, Quinn RA, Bankevich A, Chang JT, Rana TM, Conrad DJ, Sandborn WJ, Smarr L, Dorrestein PC, Pevzner PA, Knight R. PMID: 31672156.
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    59. MetaMiner: A Scalable Peptidogenomics Approach for Discovery of Ribosomal Peptide Natural Products with Blind Modifications from Microbial Communities. Cell Syst. 2019 12 18; 9(6):600-608.e4. Cao L, Gurevich A, Alexander KL, Naman CB, Leão T, Glukhov E, Luzzatto-Knaan T, Vargas F, Quinn R, Bouslimani A, Nothias LF, Singh NK, Sanders JG, Benitez RAS, Thompson LR, Hamid MN, Morton JT, Mikheenko A, Shlemov A, Korobeynikov A, Friedberg I, Knight R, Venkateswaran K, Gerwick WH, Gerwick L, Dorrestein PC, Pevzner PA, Mohimani H. PMID: 31629686.
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    60. Molecular and Microbial Microenvironments in Chronically Diseased Lungs Associated with Cystic Fibrosis. mSystems. 2019 Sep 24; 4(5). Melnik AV, Vázquez-Baeza Y, Aksenov AA, Hyde E, McAvoy AC, Wang M, da Silva RR, Protsyuk I, Wu JV, Bouslimani A, Lim YW, Luzzatto-Knaan T, Comstock W, Quinn RA, Wong R, Humphrey G, Ackermann G, Spivey T, Brouha SS, Bandeira N, Lin GY, Rohwer F, Conrad DJ, Alexandrov T, Knight R, Dorrestein PC, Garg N. PMID: 31551401.
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    61. 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.
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    62. Cytotoxic Microcolin Lipopeptides from the Marine Cyanobacterium Moorea producens. J Nat Prod. 2019 09 27; 82(9):2608-2619. Yu HB, Glukhov E, Li Y, Iwasaki A, Gerwick L, Dorrestein PC, Jiao BH, Gerwick WH. PMID: 31468974.
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    63. 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.
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    64. Trait-like vulnerability of higher-order cognition and ability to maintain wakefulness during combined sleep restriction and circadian misalignment. Sleep. 2019 08 01; 42(8). Sprecher KE, Ritchie HK, Burke TM, Depner CM, Smits AN, Dorrestein PC, Fleshner M, Knight R, Lowry CA, Turek FW, Vitaterna MH, Wright KP. PMID: 31070769.
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    65. 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.
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    66. MolNetEnhancer: Enhanced Molecular Networks by Integrating Metabolome Mining and Annotation Tools. Metabolites. 2019 Jul 16; 9(7). Ernst M, Kang KB, Caraballo-Rodríguez AM, Nothias LF, Wandy J, Chen C, Wang M, Rogers S, Medema MH, Dorrestein PC, van der Hooft JJJ. PMID: 31315242.
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    67. Assessing Specialized Metabolite Diversity in the Cosmopolitan Plant Genus Euphorbia L. Front Plant Sci. 2019; 10:846. Ernst M, Nothias LF, van der Hooft JJJ, Silva RR, Saslis-Lagoudakis CH, Grace OM, Martinez-Swatson K, Hassemer G, Funez LA, Simonsen HT, Medema MH, Staerk D, Nilsson N, Lovato P, Dorrestein PC, Rønsted N. PMID: 31333695.
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    68. The impact of skin care products on skin chemistry and microbiome dynamics. BMC Biol. 2019 06 12; 17(1):47. Bouslimani A, da Silva R, Kosciolek T, Janssen S, Callewaert C, Amir A, Dorrestein K, Melnik AV, Zaramela LS, Kim JN, Humphrey G, Schwartz T, Sanders K, Brennan C, Luzzatto-Knaan T, Ackermann G, McDonald D, Zengler K, Knight R, Dorrestein PC. PMID: 31189482.
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    69. 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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    70. Investigation of Premyrsinane and Myrsinane Esters in Euphorbia cupanii and Euphobia pithyusa with MS2LDA and Combinatorial Molecular Network Annotation Propagation. J Nat Prod. 2019 06 28; 82(6):1459-1470. Nothias-Esposito M, Nothias LF, Da Silva RR, Retailleau P, Zhang Z, Leyssen P, Roussi F, Touboul D, Paolini J, Dorrestein PC, Litaudon M. PMID: 31181921.
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    71. Early-Career Scientists Shaping the World. mSystems. 2019 May 07; 4(3). Cristea IM, Dorrestein PC, Eisen JA, Gilbert JA, Huber JA, Jansson JK, Knight R, Pollard KS, Raes J, Silver PA, Webster NS, Xu J. PMID: 31219787.
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    72. Consent insufficient for data release-Response. Science. 2019 05 03; 364(6439):446. Amann RI, Baichoo S, Blencowe BJ, Bork P, Borodovsky M, Brooksbank C, Chain PSG, Colwell RR, Daffonchio DG, Danchin A, de Lorenzo V, Dorrestein PC, Finn RD, Fraser CM, Gilbert JA, Hallam SJ, Hugenholtz P, Ioannidis JPA, Jansson JK, Kim JF, Klenk HP, Klotz MG, Knight R, Konstantinidis KT, Kyrpides NC, Mason CE, McHardy AC, Meyer F, Ouzounis CA, Patrinos AAN, Podar M, Pollard KS, Ravel J, Muñoz AR, Roberts RJ, Rosselló-Móra R, Sansone SA, Schloss PD, Schriml LM, Setubal JC, Sorek R, Stevens RL, Tiedje JM, Turjanski A, Tyson GW, Ussery DW, Weinstock GM, White O, Whitman WB, Xenarios I. PMID: 31048484.
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    73. Intermittent Hypoxia and Hypercapnia Reproducibly Change the Gut Microbiome and Metabolome across Rodent Model Systems. mSystems. 2019 Mar-Apr; 4(2). Tripathi A, Xu ZZ, Xue J, Poulsen O, Gonzalez A, Humphrey G, Meehan MJ, Melnik AV, Ackermann G, Zhou D, Malhotra A, Haddad GG, Dorrestein PC, Knight R. PMID: 31058230.
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    74. Characterization of CA-MRSA TCH1516 exposed to nafcillin in bacteriological and physiological media. Sci Data. 2019 04 26; 6(1):43. Poudel S, Tsunemoto H, Meehan M, Szubin R, Olson CA, Lamsa A, Seif Y, Dillon N, Vrbanac A, Sugie J, Dahesh S, Monk JM, Dorrestein PC, Pogliano J, Knight R, Nizet V, Palsson BO, Feist AM. PMID: 31028276.
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    75. The extracellular matrix protects Bacillus subtilis colonies from Pseudomonas invasion and modulates plant co-colonization. Nat Commun. 2019 04 23; 10(1):1919. Molina-Santiago C, Pearson JR, Navarro Y, Berlanga-Clavero MV, Caraballo-Rodriguez AM, Petras D, García-Martín ML, Lamon G, Haberstein B, Cazorla FM, de Vicente A, Loquet A, Dorrestein PC, Romero D. PMID: 31015472.
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    76. Identification of the Bacterial Biosynthetic Gene Clusters of the Oral Microbiome Illuminates the Unexplored Social Language of Bacteria during Health and Disease. mBio. 2019 04 16; 10(2). Aleti G, Baker JL, Tang X, Alvarez R, Dinis M, Tran NC, Melnik AV, Zhong C, Ernst M, Dorrestein PC, Edlund A. PMID: 30992349.
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    77. Cystic Fibrosis Rapid Response: Translating Multi-omics Data into Clinically Relevant Information. mBio. 2019 04 16; 10(2). Cobián Güemes AG, Lim YW, Quinn RA, Conrad DJ, Benler S, Maughan H, Edwards R, Brettin T, Cantú VA, Cuevas D, Hamidi R, Dorrestein P, Rohwer F. PMID: 30992350.
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    78. Detection of Natural Products and Their Producers in Ocean Sediments. Appl Environ Microbiol. 2019 04 15; 85(8). Tuttle RN, Demko AM, Patin NV, Kapono CA, Donia MS, Dorrestein P, Jensen PR. PMID: 30737349.
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    79. Comprehensive mass spectrometry-guided phenotyping of plant specialized metabolites reveals metabolic diversity in the cosmopolitan plant family Rhamnaceae. Plant J. 2019 06; 98(6):1134-1144. Kang KB, Ernst M, van der Hooft JJJ, da Silva RR, Park J, Medema MH, Sung SH, Dorrestein PC. PMID: 30786088.
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    80. SIRIUS 4: a rapid tool for turning tandem mass spectra into metabolite structure information. Nat Methods. 2019 04; 16(4):299-302. Dührkop K, Fleischauer M, Ludwig M, Aksenov AA, Melnik AV, Meusel M, Dorrestein PC, Rousu J, Böcker S. PMID: 30886413.
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    81. Predicting proteome allocation, overflow metabolism, and metal requirements in a model acetogen. PLoS Comput Biol. 2019 03; 15(3):e1006848. Liu JK, Lloyd C, Al-Bassam MM, Ebrahim A, Kim JN, Olson C, Aksenov A, Dorrestein P, Zengler K. PMID: 30845144.
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    82. Heavy metal exposure causes changes in the metabolic health-associated gut microbiome and metabolites. Environ Int. 2019 05; 126:454-467. Li X, Brejnrod AD, Ernst M, Rykær M, Herschend J, Olsen NMC, Dorrestein PC, Rensing C, Sørensen SJ. PMID: 30844581.
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    83. Viscosin-like lipopeptides from frog skin bacteria inhibit Aspergillus fumigatus and Batrachochytrium dendrobatidis detected by imaging mass spectrometry and molecular networking. Sci Rep. 2019 02 28; 9(1):3019. Martin H C, Ibáñez R, Nothias LF, Boya P CA, Reinert LK, Rollins-Smith LA, Dorrestein PC, Gutiérrez M. PMID: 30816229.
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    84. Mass Spectrometry Uncovers the Role of Surfactin as an Interspecies Recruitment Factor. ACS Chem Biol. 2019 03 15; 14(3):459-467. Luzzatto-Knaan T, Melnik AV, Dorrestein PC. PMID: 30763059.
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    85. Neutrophilic proteolysis in the cystic fibrosis lung correlates with a pathogenic microbiome. Microbiome. 2019 02 13; 7(1):23. Quinn RA, Adem S, Mills RH, Comstock W, DeRight Goldasich L, Humphrey G, Aksenov AA, Melnik AV, da Silva R, Ackermann G, Bandeira N, Gonzalez DJ, Conrad D, O'Donoghue AJ, Knight R, Dorrestein PC. PMID: 30760325.
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    86. Lugdunomycin, an Angucycline-Derived Molecule with Unprecedented Chemical Architecture. Angew Chem Int Ed Engl. 2019 02 25; 58(9):2809-2814. Wu C, van der Heul HU, Melnik AV, Lübben J, Dorrestein PC, Minnaard AJ, Choi YH, van Wezel GP. PMID: 30656821.
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    87. Toward unrestricted use of public genomic data. Science. 2019 01 25; 363(6425):350-352. Amann RI, Baichoo S, Blencowe BJ, Bork P, Borodovsky M, Brooksbank C, Chain PSG, Colwell RR, Daffonchio DG, Danchin A, de Lorenzo V, Dorrestein PC, Finn RD, Fraser CM, Gilbert JA, Hallam SJ, Hugenholtz P, Ioannidis JPA, Jansson JK, Kim JF, Klenk HP, Klotz MG, Knight R, Konstantinidis KT, Kyrpides NC, Mason CE, McHardy AC, Meyer F, Ouzounis CA, Patrinos AAN, Podar M, Pollard KS, Ravel J, Muñoz AR, Roberts RJ, Rosselló-Móra R, Sansone SA, Schloss PD, Schriml LM, Setubal JC, Sorek R, Stevens RL, Tiedje JM, Turjanski A, Tyson GW, Ussery DW, Weinstock GM, White O, Whitman WB, Xenarios I. PMID: 30679363.
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    88. The Microbiome and Its Potential for Pharmacology. Handb Exp Pharmacol. 2019; 260:301-326. Chavira A, Belda-Ferre P, Kosciolek T, Ali F, Dorrestein PC, Knight R. PMID: 31820171.
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    89. Dereplication of microbial metabolites through database search of mass spectra. Nat Commun. 2018 10 02; 9(1):4035. Mohimani H, Gurevich A, Shlemov A, Mikheenko A, Korobeynikov A, Cao L, Shcherbin E, Nothias LF, Dorrestein PC, Pevzner PA. PMID: 30279420.
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    90. Qiita: rapid, web-enabled microbiome meta-analysis. Nat Methods. 2018 10; 15(10):796-798. Gonzalez A, Navas-Molina JA, Kosciolek T, McDonald D, Vázquez-Baeza Y, Ackermann G, DeReus J, Janssen S, Swafford AD, Orchanian SB, Sanders JG, Shorenstein J, Holste H, Petrus S, Robbins-Pianka A, Brislawn CJ, Wang M, Rideout JR, Bolyen E, Dillon M, Caporaso JG, Dorrestein PC, Knight R. PMID: 30275573.
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    91. 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.
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    92. Niche partitioning of a pathogenic microbiome driven by chemical gradients. Sci Adv. 2018 09; 4(9):eaau1908. Quinn RA, Comstock W, Zhang T, Morton JT, da Silva R, Tran A, Aksenov A, Nothias LF, Wangpraseurt D, Melnik AV, Ackermann G, Conrad D, Klapper I, Knight R, Dorrestein PC. PMID: 30263961.
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    93. Microbiome 101: Studying, Analyzing, and Interpreting Gut Microbiome Data for Clinicians. Clin Gastroenterol Hepatol. 2019 01; 17(2):218-230. Allaband C, McDonald D, Vázquez-Baeza Y, Minich JJ, Tripathi A, Brenner DA, Loomba R, Smarr L, Sandborn WJ, Schnabl B, Dorrestein P, Zarrinpar A, Knight R. PMID: 30240894.
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    94. Author Correction: Inflammation-induced IgA+ cells dismantle anti-liver cancer immunity. Nature. 2018 09; 561(7721):E1. Shalapour S, Lin XJ, Bastian IN, Brain J, Burt AD, Aksenov AA, Vrbanac AF, Li W, Perkins A, Matsutani T, Zhong Z, Dhar D, Navas-Molina JA, Xu J, Loomba R, Downes M, Yu RT, Evans RM, Dorrestein PC, Knight R, Benner C, Anstee QM, Karin M. PMID: 29973714.
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    95. Pumilacidins from the Octocoral-Associated Bacillus sp. DT001 Display Anti-Proliferative Effects in Plasmodium falciparum. Molecules. 2018 Aug 29; 23(9). Torres-Mendoza D, Coronado LM, Pineda LM, Guzmán HM, Dorrestein PC, Spadafora C, Gutiérrez M. PMID: 30158478.
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    96. Before platelets: the production of platelet-activating factor during growth and stress in a basal marine organism. Proc Biol Sci. 2018 08 15; 285(1884). Galtier d'Auriac I, Quinn RA, Maughan H, Nothias LF, Little M, Kapono CA, Cobian A, Reyes BT, Green K, Quistad SD, Leray M, Smith JE, Dorrestein PC, Rohwer F, Deheyn DD, Hartmann AC. PMID: 30111600.
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    97. Targeted Isolation of Neuroprotective Dicoumaroyl Neolignans and Lignans from Sageretia theezans Using in Silico Molecular Network Annotation Propagation-Based Dereplication. J Nat Prod. 2018 08 24; 81(8):1819-1828. Kang KB, Park EJ, da Silva RR, Kim HW, Dorrestein PC, Sung SH. PMID: 30106290.
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    98. Are microbiome studies ready for hypothesis-driven research? Curr Opin Microbiol. 2018 08; 44:61-69. Tripathi A, Marotz C, Gonzalez A, Vázquez-Baeza Y, Song SJ, Bouslimani A, McDonald D, Zhu Q, Sanders JG, Smarr L, Dorrestein PC, Knight R. PMID: 30059804.
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    294. A novel Entamoeba histolytica cysteine proteinase, EhCP4, is key for invasive amebiasis and a therapeutic target. J Biol Chem. 2010 Jun 11; 285(24):18516-27. He C, Nora GP, Schneider EL, Kerr ID, Hansell E, Hirata K, Gonzalez D, Sajid M, Boyd SE, Hruz P, Cobo ER, Le C, Liu WT, Eckmann L, Dorrestein PC, Houpt ER, Brinen LS, Craik CS, Roush WR, McKerrow J, Reed SL. PMID: 20378535.
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    295. Enzymatic synthesis of resorcylic acid lactones by cooperation of fungal iterative polyketide synthases involved in hypothemycin biosynthesis. J Am Chem Soc. 2010 Apr 07; 132(13):4530-1. Zhou H, Qiao K, Gao Z, Meehan MJ, Li JW, Zhao X, Dorrestein PC, Vederas JC, Tang Y. PMID: 20222707.
      View in: PubMed   Mentions: 32     Fields:    Translation:AnimalsCells
    296. Palmyramide A, a cyclic depsipeptide from a Palmyra Atoll collection of the marine cyanobacterium Lyngbya majuscula. J Nat Prod. 2010 Mar 26; 73(3):393-8. Taniguchi M, Nunnery JK, Engene N, Esquenazi E, Byrum T, Dorrestein PC, Gerwick WH. PMID: 19839606.
      View in: PubMed   Mentions: 25     Fields:    Translation:HumansCells
    297. Capturing bacterial metabolic exchange using thin film desorption electrospray ionization-imaging mass spectrometry. Anal Chem. 2010 Mar 01; 82(5):1598-600. Watrous J, Hendricks N, Meehan M, Dorrestein PC. PMID: 20121185.
      View in: PubMed   Mentions: 26     Fields:    Translation:Cells
    298. Transcriptional analysis of the jamaicamide gene cluster from the marine cyanobacterium Lyngbya majuscula and identification of possible regulatory proteins. BMC Microbiol. 2009 Dec 01; 9:247. Jones AC, Gerwick L, Gonzalez D, Dorrestein PC, Gerwick WH. PMID: 19951434.
      View in: PubMed   Mentions: 7     Fields:    Translation:Cells
    299. Expansion of the mycobacterial "PUPylome". Mol Biosyst. 2010 Feb; 6(2):376-85. Watrous J, Burns K, Liu WT, Patel A, Hook V, Bafna V, Barry CE, Bark S, Dorrestein PC. PMID: 20094657.
      View in: PubMed   Mentions: 34     Fields:    Translation:Cells
    300. Imaging mass spectrometry of natural products. Nat Prod Rep. 2009 Dec; 26(12):1521-34. Esquenazi E, Yang YL, Watrous J, Gerwick WH, Dorrestein PC. PMID: 19936384.
      View in: PubMed   Mentions: 34     Fields:    
    301. Translating metabolic exchange with imaging mass spectrometry. Nat Chem Biol. 2009 Dec; 5(12):885-7. Yang YL, Xu Y, Straight P, Dorrestein PC. PMID: 19915536.
      View in: PubMed   Mentions: 91     Fields:    Translation:Cells
    302. Marinopyrrole A target elucidation by acyl dye transfer. J Am Chem Soc. 2009 Sep 02; 131(34):12094-6. Hughes CC, Yang YL, Liu WT, Dorrestein PC, La Clair JJ, Fenical W. PMID: 19673475.
      View in: PubMed   Mentions: 24     Fields:    Translation:HumansCells
    303. Secondary metabolomics: natural products mass spectrometry goes global. ACS Chem Biol. 2009 Aug 21; 4(8):599-601. Kersten RD, Dorrestein PC. PMID: 19817465.
      View in: PubMed   Mentions: 6     Fields:    Translation:AnimalsCells
    304. Dereplication and de novo sequencing of nonribosomal peptides. Nat Methods. 2009 Aug; 6(8):596-9. Ng J, Bandeira N, Liu WT, Ghassemian M, Simmons TL, Gerwick WH, Linington R, Dorrestein PC, Pevzner PA. PMID: 19597502.
      View in: PubMed   Mentions: 36     Fields:    Translation:Cells
    305. Acyltransferase mediated polyketide release from a fungal megasynthase. J Am Chem Soc. 2009 Jun 24; 131(24):8388-9. Xie X, Meehan MJ, Xu W, Dorrestein PC, Tang Y. PMID: 19530726.
      View in: PubMed   Mentions: 28     Fields:    Translation:Animals
    306. Interpretation of tandem mass spectra obtained from cyclic nonribosomal peptides. Anal Chem. 2009 Jun 01; 81(11):4200-9. Liu WT, Ng J, Meluzzi D, Bandeira N, Gutierrez M, Simmons TL, Schultz AW, Linington RG, Moore BS, Gerwick WH, Pevzner PA, Dorrestein PC. PMID: 19413302.
      View in: PubMed   Mentions: 31     Fields:    Translation:Cells
    307. Probing marine natural product defenses with DESI-imaging mass spectrometry. Proc Natl Acad Sci U S A. 2009 May 05; 106(18):7269-70. Esquenazi E, Dorrestein PC, Gerwick WH. PMID: 19416917.
      View in: PubMed   Mentions: 17     Fields:    Translation:Animals
    308. Phosphoproteomic analysis of chemokine signaling networks. Methods Enzymol. 2009; 460:331-46. O'Hayre M, Salanga CL, Dorrestein PC, Handel TM. PMID: 19446733.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansCells
    309. Proteasomal protein degradation in Mycobacteria is dependent upon a prokaryotic ubiquitin-like protein. J Biol Chem. 2009 Jan 30; 284(5):3069-75. Burns KE, Liu WT, Boshoff HI, Dorrestein PC, Barry CE. PMID: 19028679.
      View in: PubMed   Mentions: 63     Fields:    Translation:Cells
    310. Kinetic isotope effect studies on the de novo rate of chromophore formation in fast- and slow-maturing GFP variants. Biochemistry. 2008 Sep 23; 47(38):10111-22. Pouwels LJ, Zhang L, Chan NH, Dorrestein PC, Wachter RM. PMID: 18759496.
      View in: PubMed   Mentions: 16     Fields:    Translation:Cells
    311. Discovery of a widely distributed toxin biosynthetic gene cluster. Proc Natl Acad Sci U S A. 2008 Apr 15; 105(15):5879-84. Lee SW, Mitchell DA, Markley AL, Hensler ME, Gonzalez D, Wohlrab A, Dorrestein PC, Nizet V, Dixon JE. PMID: 18375757.
      View in: PubMed   Mentions: 102     Fields:    Translation:HumansCells
    312. A sliding docking interaction is essential for sequential and processive phosphorylation of an SR protein by SRPK1. Mol Cell. 2008 Mar 14; 29(5):563-76. Ngo JC, Giang K, Chakrabarti S, Ma CT, Huynh N, Hagopian JC, Dorrestein PC, Fu XD, Adams JA, Ghosh G. PMID: 18342604.
      View in: PubMed   Mentions: 50     Fields:    Translation:HumansAnimalsCells
    313. Visualizing the spatial distribution of secondary metabolites produced by marine cyanobacteria and sponges via MALDI-TOF imaging. Mol Biosyst. 2008 Jun; 4(6):562-70. Esquenazi E, Coates C, Simmons L, Gonzalez D, Gerwick WH, Dorrestein PC. PMID: 18493654.
      View in: PubMed   Mentions: 37     Fields:    Translation:AnimalsCells
    314. Mechanistic studies on pyridoxal phosphate synthase: the reaction pathway leading to a chromophoric intermediate. J Am Chem Soc. 2008 Mar 12; 130(10):3043-52. Hanes JW, Burns KE, Hilmey DG, Chatterjee A, Dorrestein PC, Begley TP. PMID: 18271580.
      View in: PubMed   Mentions: 9     Fields:    Translation:Cells
    315. Biosynthetic origin of natural products isolated from marine microorganism-invertebrate assemblages. Proc Natl Acad Sci U S A. 2008 Mar 25; 105(12):4587-94. Simmons TL, Coates RC, Clark BR, Engene N, Gonzalez D, Esquenazi E, Dorrestein PC, Gerwick WH. PMID: 18250337.
      View in: PubMed   Mentions: 62     Fields:    Translation:AnimalsCellsPHPublic Health
    316. A phosphopantetheinylating polyketide synthase producing a linear polyene to initiate enediyne antitumor antibiotic biosynthesis. Proc Natl Acad Sci U S A. 2008 Feb 05; 105(5):1460-5. Zhang J, Van Lanen SG, Ju J, Liu W, Dorrestein PC, Li W, Kelleher NL, Shen B. PMID: 18223152.
      View in: PubMed   Mentions: 36     Fields:    Translation:Cells
    317. Top-down mass spectrometry on low-resolution instruments: characterization of phosphopantetheinylated carrier domains in polyketide and non-ribosomal biosynthetic pathways. Bioorg Med Chem Lett. 2008 May 15; 18(10):3107-11. Meluzzi D, Zheng WH, Hensler M, Nizet V, Dorrestein PC. PMID: 18006314.
      View in: PubMed   Mentions: 33     Fields:    Translation:Cells
    318. Incorporation of nonmethyl branches by isoprenoid-like logic: multiple beta-alkylation events in the biosynthesis of myxovirescin A1. Chem Biol. 2007 Jul; 14(7):835-46. Calderone CT, Iwig DF, Dorrestein PC, Kelleher NL, Walsh CT. PMID: 17656320.
      View in: PubMed   Mentions: 21     Fields:    Translation:Cells
    319. Molecular basis for chloronium-mediated meroterpene cyclization: cloning, sequencing, and heterologous expression of the napyradiomycin biosynthetic gene cluster. J Biol Chem. 2007 Jun 01; 282(22):16362-8. Winter JM, Moffitt MC, Zazopoulos E, McAlpine JB, Dorrestein PC, Moore BS. PMID: 17392281.
      View in: PubMed   Mentions: 50     Fields:    Translation:Cells
    320. Genome-wide high-throughput mining of natural-product biosynthetic gene clusters by phage display. Chem Biol. 2007 Mar; 14(3):303-12. Yin J, Straight PD, Hrvatin S, Dorrestein PC, Bumpus SB, Jao C, Kelleher NL, Kolter R, Walsh CT. PMID: 17379145.
      View in: PubMed   Mentions: 11     Fields:    Translation:Cells
    321. Facile detection of acyl and peptidyl intermediates on thiotemplate carrier domains via phosphopantetheinyl elimination reactions during tandem mass spectrometry. Biochemistry. 2006 Oct 24; 45(42):12756-66. Dorrestein PC, Bumpus SB, Calderone CT, Garneau-Tsodikova S, Aron ZD, Straight PD, Kolter R, Walsh CT, Kelleher NL. PMID: 17042494.
      View in: PubMed   Mentions: 61     Fields:    Translation:Cells
    322. Protein assembly line components in prodigiosin biosynthesis: characterization of PigA,G,H,I,J. J Am Chem Soc. 2006 Oct 04; 128(39):12600-1. Garneau-Tsodikova S, Dorrestein PC, Kelleher NL, Walsh CT. PMID: 17002325.
      View in: PubMed   Mentions: 17     Fields:    Translation:Cells
    323. Dissecting non-ribosomal and polyketide biosynthetic machineries using electrospray ionization Fourier-Transform mass spectrometry. Nat Prod Rep. 2006 Dec; 23(6):893-918. Dorrestein PC, Kelleher NL. PMID: 17119639.
      View in: PubMed   Mentions: 22     Fields:    Translation:Cells
    324. The bifunctional glyceryl transferase/phosphatase OzmB belonging to the HAD superfamily that diverts 1,3-bisphosphoglycerate into polyketide biosynthesis. J Am Chem Soc. 2006 Aug 16; 128(32):10386-7. Dorrestein PC, Van Lanen SG, Li W, Zhao C, Deng Z, Shen B, Kelleher NL. PMID: 16895402.
      View in: PubMed   Mentions: 18     Fields:    Translation:Cells
    325. Substrate specificity of the adenylation enzyme SgcC1 involved in the biosynthesis of the enediyne antitumor antibiotic C-1027. J Biol Chem. 2006 Oct 06; 281(40):29633-40. Van Lanen SG, Lin S, Dorrestein PC, Kelleher NL, Shen B. PMID: 16887797.
      View in: PubMed   Mentions: 15     Fields:    Translation:Cells
    326. Convergence of isoprene and polyketide biosynthetic machinery: isoprenyl-S-carrier proteins in the pksX pathway of Bacillus subtilis. Proc Natl Acad Sci U S A. 2006 Jun 13; 103(24):8977-82. Calderone CT, Kowtoniuk WE, Kelleher NL, Walsh CT, Dorrestein PC. PMID: 16757561.
      View in: PubMed   Mentions: 41     Fields:    Translation:Cells
    327. Investigating nonribosomal peptide and polyketide biosynthesis by direct detection of intermediates on >70 kDa polypeptides by using Fourier-transform mass spectrometry. Chembiochem. 2006 Jun; 7(6):904-7. Hicks LM, Mazur MT, Miller LM, Dorrestein PC, Schnarr NA, Khosla C, Kelleher NL. PMID: 16642537.
      View in: PubMed   Mentions: 6     Fields:    Translation:Cells
    328. A monovalent streptavidin with a single femtomolar biotin binding site. Nat Methods. 2006 Apr; 3(4):267-73. Howarth M, Chinnapen DJ, Gerrow K, Dorrestein PC, Grandy MR, Kelleher NL, El-Husseini A, Ting AY. PMID: 16554831.
      View in: PubMed   Mentions: 116     Fields:    Translation:AnimalsCells
    329. Activity screening of carrier domains within nonribosomal peptide synthetases using complex substrate mixtures and large molecule mass spectrometry. Biochemistry. 2006 Feb 14; 45(6):1537-46. Dorrestein PC, Blackhall J, Straight PD, Fischbach MA, Garneau-Tsodikova S, Edwards DJ, McLaughlin S, Lin M, Gerwick WH, Kolter R, Walsh CT, Kelleher NL. PMID: 16460000.
      View in: PubMed   Mentions: 22     Fields:    Translation:Cells
    330. Characterization of a new tailoring domain in polyketide biogenesis: the amine transferase domain of MycA in the mycosubtilin gene cluster. J Am Chem Soc. 2005 Nov 02; 127(43):14986-7. Aron ZD, Dorrestein PC, Blackhall JR, Kelleher NL, Walsh CT. PMID: 16248612.
      View in: PubMed   Mentions: 11     Fields:    Translation:Cells
    331. Dichlorination of a pyrrolyl-S-carrier protein by FADH2-dependent halogenase PltA during pyoluteorin biosynthesis. Proc Natl Acad Sci U S A. 2005 Sep 27; 102(39):13843-8. Dorrestein PC, Yeh E, Garneau-Tsodikova S, Kelleher NL, Walsh CT. PMID: 16162666.
      View in: PubMed   Mentions: 54     Fields:    Translation:Cells
    332. Biosynthesis of the beta-amino acid moiety of the enediyne antitumor antibiotic C-1027 featuring beta-amino acyl-S-carrier protein intermediates. J Am Chem Soc. 2005 Aug 24; 127(33):11594-5. Van Lanen SG, Dorrestein PC, Christenson SD, Liu W, Ju J, Kelleher NL, Shen B. PMID: 16104723.
      View in: PubMed   Mentions: 20     Fields:    Translation:Cells
    333. Reconstitution of a new cysteine biosynthetic pathway in Mycobacterium tuberculosis. J Am Chem Soc. 2005 Aug 24; 127(33):11602-3. Burns KE, Baumgart S, Dorrestein PC, Zhai H, McLafferty FW, Begley TP. PMID: 16104727.
      View in: PubMed   Mentions: 38     Fields:    Translation:Cells
    334. Simultaneous kinetic characterization of multiple protein forms by top down mass spectrometry. J Am Soc Mass Spectrom. 2005 Jul; 16(7):1052-9. Zhai H, Dorrestein PC, Chatterjee A, Begley TP, McLafferty FW. PMID: 15914018.
      View in: PubMed   Mentions: 6     Fields:    Translation:Cells
    335. Oxidative cascades: a facile biosynthetic strategy for the assembly of complex molecules. Bioorg Chem. 2005 Jun; 33(3):136-48. Dorrestein P, Begley TP. PMID: 15888307.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    336. Characterization of the formation of the pyrrole moiety during clorobiocin and coumermycin A1 biosynthesis. Biochemistry. 2005 Mar 01; 44(8):2770-80. Garneau S, Dorrestein PC, Kelleher NL, Walsh CT. PMID: 15723521.
      View in: PubMed   Mentions: 16     Fields:    Translation:Cells
    337. The biosynthesis of the thiazole phosphate moiety of thiamin: the sulfur transfer mediated by the sulfur carrier protein ThiS. Chem Biol. 2004 Oct; 11(10):1373-81. Dorrestein PC, Zhai H, McLafferty FW, Begley TP. PMID: 15489164.
      View in: PubMed   Mentions: 19     Fields:    Translation:Cells
    338. Thiamin biosynthesis in Bacillus subtilis: structure of the thiazole synthase/sulfur carrier protein complex. Biochemistry. 2004 Sep 21; 43(37):11647-57. Settembre EC, Dorrestein PC, Zhai H, Chatterjee A, McLafferty FW, Begley TP, Ealick SE. PMID: 15362849.
      View in: PubMed   Mentions: 16     Fields:    Translation:Cells
    339. The biosynthesis of the thiazole phosphate moiety of thiamin (vitamin B1): the early steps catalyzed by thiazole synthase. J Am Chem Soc. 2004 Mar 17; 126(10):3091-6. Dorrestein PC, Zhai H, Taylor SV, McLafferty FW, Begley TP. PMID: 15012138.
      View in: PubMed   Mentions: 14     Fields:    Translation:Cells
    340. Biosynthesis of the thiazole moiety of thiamin pyrophosphate (vitamin B1). Biochemistry. 2003 Oct 28; 42(42):12430-8. Park JH, Dorrestein PC, Zhai H, Kinsland C, McLafferty FW, Begley TP. PMID: 14567704.
      View in: PubMed   Mentions: 36     Fields:    Translation:Cells
    341. Aerobic tryptophan degradation pathway in bacteria: novel kynurenine formamidase. FEMS Microbiol Lett. 2003 Oct 24; 227(2):219-27. Kurnasov O, Jablonski L, Polanuyer B, Dorrestein P, Begley T, Osterman A. PMID: 14592712.
      View in: PubMed   Mentions: 31     Fields:    Translation:Cells
    342. Formation of the dimethylbenzimidazole ligand of coenzyme B(12) under physiological conditions by a facile oxidative cascade. Org Lett. 2003 Jun 26; 5(13):2211-3. Maggio-Hall LA, Dorrestein PC, Escalante-Semerena JC, Begley TP. PMID: 12816411.
      View in: PubMed   Mentions: 13     Fields:    Translation:Cells
    343. Formation of the chromophore of the pyoverdine siderophores by an oxidative cascade. Org Lett. 2003 Jun 26; 5(13):2215-7. Dorrestein PC, Poole K, Begley TP. PMID: 12816412.
      View in: PubMed   Mentions: 9     Fields:    Translation:Cells
    344. Structural and mechanistic studies on ThiO, a glycine oxidase essential for thiamin biosynthesis in Bacillus subtilis. Biochemistry. 2003 Mar 18; 42(10):2971-81. Settembre EC, Dorrestein PC, Park JH, Augustine AM, Begley TP, Ealick SE. PMID: 12627963.
      View in: PubMed   Mentions: 33     Fields:    Translation:Cells
    345. Structure of oxalate decarboxylase from Bacillus subtilis at 1.75 A resolution. Biochemistry. 2002 Jun 18; 41(24):7659-69. Anand R, Dorrestein PC, Kinsland C, Begley TP, Ealick SE. PMID: 12056897.
      View in: PubMed   Mentions: 37     Fields:    Translation:Cells
    346. Synthesis and physical characterization of some new hydrophobic forms of the solvatochromic N,N-dialkyl-p-nitroanilines. J Org Chem. 2001 Jun 01; 66(11):4050-4. Mansour G, Creedon W, Dorrestein PC, Maxka J, MacDonald JC, Helburn R. PMID: 11375035.
      View in: PubMed   Mentions:    Fields:    
    347. The biosynthesis of nicotinamide adenine dinucleotides in bacteria. Vitam Horm. 2001; 61:103-19. Begley TP, Kinsland C, Mehl RA, Osterman A, Dorrestein P. PMID: 11153263.
      View in: PubMed   Mentions: 36     Fields:    Translation:Cells
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