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Items: 1 to 50 of 250

1.

Dereplication of microbial metabolites through database search of mass spectra.

Mohimani H, Gurevich A, Shlemov A, Mikheenko A, Korobeynikov A, Cao L, Shcherbin E, Nothias LF, Dorrestein PC, Pevzner PA.

Nat Commun. 2018 Oct 2;9(1):4035. doi: 10.1038/s41467-018-06082-8.

2.

Qiita: rapid, web-enabled microbiome meta-analysis.

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.

Nat Methods. 2018 Oct;15(10):796-798. doi: 10.1038/s41592-018-0141-9. Epub 2018 Oct 1.

PMID:
30275573
3.

Computational Removal of Undesired Mass Spectral Features Possessing Repeat Units via a Kendrick Mass Filter.

da Silva RR, Vargas F, Ernst M, Nguyen NH, Bolleddu S, Del Rosario KK, Tsunoda SM, Dorrestein PC, Jarmusch AK.

J Am Soc Mass Spectrom. 2018 Sep 28. doi: 10.1007/s13361-018-2069-9. [Epub ahead of print]

PMID:
30267361
4.

Niche partitioning of a pathogenic microbiome driven by chemical gradients.

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.

Sci Adv. 2018 Sep 26;4(9):eaau1908. doi: 10.1126/sciadv.aau1908. eCollection 2018 Sep.

5.

Pumilacidins from the Octocoral-Associated Bacillus sp. DT001 Display Anti-Proliferative Effects in Plasmodium falciparum.

Torres-Mendoza D, Coronado LM, Pineda LM, Guzmán HM, Dorrestein PC, Spadafora C, Gutiérrez M.

Molecules. 2018 Aug 29;23(9). pii: E2179. doi: 10.3390/molecules23092179.

6.

Before platelets: the production of platelet-activating factor during growth and stress in a basal marine organism.

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.

Proc Biol Sci. 2018 Aug 15;285(1884). pii: 20181307. doi: 10.1098/rspb.2018.1307.

7.

Targeted Isolation of Neuroprotective Dicoumaroyl Neolignans and Lignans from Sageretia theezans Using in Silico Molecular Network Annotation Propagation-Based Dereplication.

Kang KB, Park EJ, da Silva RR, Kim HW, Dorrestein PC, Sung SH.

J Nat Prod. 2018 Aug 24;81(8):1819-1828. doi: 10.1021/acs.jnatprod.8b00292. Epub 2018 Aug 14.

PMID:
30106290
8.

Are microbiome studies ready for hypothesis-driven research?

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.

Curr Opin Microbiol. 2018 Aug;44:61-69. doi: 10.1016/j.mib.2018.07.002. Epub 2018 Jul 27. Review.

PMID:
30059804
9.

Author Correction: Inflammation-induced IgA+ cells dismantle anti-liver cancer immunity.

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.

Nature. 2018 Sep;561(7721):E1. doi: 10.1038/s41586-018-0304-y.

PMID:
29973714
10.

Intermittent Hypoxia and Hypercapnia, a Hallmark of Obstructive Sleep Apnea, Alters the Gut Microbiome and Metabolome.

Tripathi A, Melnik AV, Xue J, Poulsen O, Meehan MJ, Humphrey G, Jiang L, Ackermann G, McDonald D, Zhou D, Knight R, Dorrestein PC, Haddad GG.

mSystems. 2018 Jun 5;3(3). pii: e00020-18. doi: 10.1128/mSystems.00020-18. eCollection 2018 May-Jun.

11.

The role of inter-species interactions in Salinispora specialized metabolism.

Patin NV, Floros DJ, Hughes CC, Dorrestein PC, Jensen PR.

Microbiology. 2018 Jul;164(7):946-955. doi: 10.1099/mic.0.000679. Epub 2018 Jun 7.

PMID:
29877785
12.

American Gut: an Open Platform for Citizen Science Microbiome Research.

McDonald D, Hyde E, Debelius JW, Morton JT, Gonzalez A, Ackermann G, Aksenov AA, Behsaz B, Brennan C, Chen Y, DeRight Goldasich L, Dorrestein PC, Dunn RR, Fahimipour AK, Gaffney J, Gilbert JA, Gogul G, Green JL, Hugenholtz P, Humphrey G, Huttenhower C, Jackson MA, Janssen S, Jeste DV, Jiang L, Kelley ST, Knights D, Kosciolek T, Ladau J, Leach J, Marotz C, Meleshko D, Melnik AV, Metcalf JL, Mohimani H, Montassier E, Navas-Molina J, Nguyen TT, Peddada S, Pevzner P, Pollard KS, Rahnavard G, Robbins-Pianka A, Sangwan N, Shorenstein J, Smarr L, Song SJ, Spector T, Swafford AD, Thackray VG, Thompson LR, Tripathi A, Vázquez-Baeza Y, Vrbanac A, Wischmeyer P, Wolfe E, Zhu Q; American Gut Consortium , Knight R.

mSystems. 2018 May 15;3(3). pii: e00031-18. doi: 10.1128/mSystems.00031-18. eCollection 2018 May-Jun.

13.

Best practices for analysing microbiomes.

Knight R, Vrbanac A, Taylor BC, Aksenov A, Callewaert C, Debelius J, Gonzalez A, Kosciolek T, McCall LI, McDonald D, Melnik AV, Morton JT, Navas J, Quinn RA, Sanders JG, Swafford AD, Thompson LR, Tripathi A, Xu ZZ, Zaneveld JR, Zhu Q, Caporaso JG, Dorrestein PC.

Nat Rev Microbiol. 2018 Jul;16(7):410-422. doi: 10.1038/s41579-018-0029-9. Review.

PMID:
29795328
14.

Propagating annotations of molecular networks using in silico fragmentation.

da Silva RR, Wang M, Nothias LF, van der Hooft JJJ, Caraballo-Rodríguez AM, Fox E, Balunas MJ, Klassen JL, Lopes NP, Dorrestein PC.

PLoS Comput Biol. 2018 Apr 18;14(4):e1006089. doi: 10.1371/journal.pcbi.1006089. eCollection 2018 Apr.

15.

Experimental Chagas disease-induced perturbations of the fecal microbiome and metabolome.

McCall LI, Tripathi A, Vargas F, Knight R, Dorrestein PC, Siqueira-Neto JL.

PLoS Negl Trop Dis. 2018 Mar 12;12(3):e0006344. doi: 10.1371/journal.pntd.0006344. eCollection 2018 Mar.

16.

Bioactivity-Based Molecular Networking for the Discovery of Drug Leads in Natural Product Bioassay-Guided Fractionation.

Nothias LF, Nothias-Esposito M, da Silva R, Wang M, Protsyuk I, Zhang Z, Sarvepalli A, Leyssen P, Touboul D, Costa J, Paolini J, Alexandrov T, Litaudon M, Dorrestein PC.

J Nat Prod. 2018 Apr 27;81(4):758-767. doi: 10.1021/acs.jnatprod.7b00737. Epub 2018 Mar 2.

PMID:
29498278
17.

Creating a 3D microbial and chemical snapshot of a human habitat.

Kapono CA, Morton JT, Bouslimani A, Melnik AV, Orlinsky K, Knaan TL, Garg N, Vázquez-Baeza Y, Protsyuk I, Janssen S, Zhu Q, Alexandrov T, Smarr L, Knight R, Dorrestein PC.

Sci Rep. 2018 Feb 27;8(1):3669. doi: 10.1038/s41598-018-21541-4.

18.

Chemical signaling at the eukaryotic/prokaryotic interface.

Dorrestein PC, Balskus EP.

Chem Soc Rev. 2018 Mar 5;47(5):1572-1573. doi: 10.1039/c8cs90021c. No abstract available.

PMID:
29479607
19.

Tundrenone: An Atypical Secondary Metabolite from Bacteria with Highly Restricted Primary Metabolism.

Puri AW, Mevers E, Ramadhar TR, Petras D, Liu D, Piel J, Dorrestein PC, Greenberg EP, Lidstrom ME, Clardy J.

J Am Chem Soc. 2018 Feb 14;140(6):2002-2006. doi: 10.1021/jacs.7b12240. Epub 2018 Jan 30.

20.

Transcriptomics-guided bottom-up and top-down venomics of neonate and adult specimens of the arboreal rear-fanged Brown Treesnake, Boiga irregularis, from Guam.

Pla D, Petras D, Saviola AJ, Modahl CM, Sanz L, Pérez A, Juárez E, Frietze S, Dorrestein PC, Mackessy SP, Calvete JJ.

J Proteomics. 2018 Mar 1;174:71-84. doi: 10.1016/j.jprot.2017.12.020. Epub 2017 Dec 29.

PMID:
29292096
21.

3D molecular cartography using LC-MS facilitated by Optimus and 'ili software.

Protsyuk I, Melnik AV, Nothias LF, Rappez L, Phapale P, Aksenov AA, Bouslimani A, Ryazanov S, Dorrestein PC, Alexandrov T.

Nat Protoc. 2018 Jan;13(1):134-154. doi: 10.1038/nprot.2017.122. Epub 2017 Dec 21.

PMID:
29266099
22.

Homospermidine Lipids: A Compound Class Specifically Formed during Fruiting Body Formation of Myxococcus xanthus DK1622.

Hoffmann M, Auerbach D, Panter F, Hoffmann T, Dorrestein PC, Müller R.

ACS Chem Biol. 2018 Jan 19;13(1):273-280. doi: 10.1021/acschembio.7b00816. Epub 2017 Dec 28.

PMID:
29185703
23.

Erratum: Inflammation-induced IgA+ cells dismantle anti-liver cancer immunity.

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.

Nature. 2017 Dec 21;552(7685):430. doi: 10.1038/nature25028. Epub 2017 Nov 22.

PMID:
29168501
24.

Inflammation-induced IgA+ cells dismantle anti-liver cancer immunity.

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.

Nature. 2017 Nov 16;551(7680):340-345. doi: 10.1038/nature24302. Epub 2017 Nov 8. Erratum in: Nature. 2017 Nov 22;:. Nature. 2018 Sep;561(7721):E1.

25.

Significance estimation for large scale metabolomics annotations by spectral matching.

Scheubert K, Hufsky F, Petras D, Wang M, Nothias LF, Dührkop K, Bandeira N, Dorrestein PC, Böcker S.

Nat Commun. 2017 Nov 14;8(1):1494. doi: 10.1038/s41467-017-01318-5.

26.

Meta-mass shift chemical profiling of metabolomes from coral reefs.

Hartmann AC, Petras D, Quinn RA, Protsyuk I, Archer FI, Ransome E, Williams GJ, Bailey BA, Vermeij MJA, Alexandrov T, Dorrestein PC, Rohwer FL.

Proc Natl Acad Sci U S A. 2017 Oct 31;114(44):11685-11690. doi: 10.1073/pnas.1710248114. Epub 2017 Oct 12.

27.

Three-Dimensional Microbiome and Metabolome Cartography of a Diseased Human Lung.

Garg N, Wang M, Hyde E, da Silva RR, Melnik AV, Protsyuk I, Bouslimani A, Lim YW, Wong R, Humphrey G, Ackermann G, Spivey T, Brouha SS, Bandeira N, Lin GY, Rohwer F, Conrad DJ, Alexandrov T, Knight R, Dorrestein PC.

Cell Host Microbe. 2017 Nov 8;22(5):705-716.e4. doi: 10.1016/j.chom.2017.10.001. Epub 2017 Oct 19.

28.

Impacts of the Human Gut Microbiome on Therapeutics.

Vázquez-Baeza Y, Callewaert C, Debelius J, Hyde E, Marotz C, Morton JT, Swafford A, Vrbanac A, Dorrestein PC, Knight R.

Annu Rev Pharmacol Toxicol. 2018 Jan 6;58:253-270. doi: 10.1146/annurev-pharmtox-042017-031849. Epub 2017 Oct 2.

PMID:
28968189
29.

Environmentally Friendly Procedure Based on Supercritical Fluid Chromatography and Tandem Mass Spectrometry Molecular Networking for the Discovery of Potent Antiviral Compounds from Euphorbia semiperfoliata.

Nothias LF, Boutet-Mercey S, Cachet X, De La Torre E, Laboureur L, Gallard JF, Retailleau P, Brunelle A, Dorrestein PC, Costa J, Bedoya LM, Roussi F, Leyssen P, Alcami J, Paolini J, Litaudon M, Touboul D.

J Nat Prod. 2017 Oct 27;80(10):2620-2629. doi: 10.1021/acs.jnatprod.7b00113. Epub 2017 Sep 19.

PMID:
28925702
30.

Mass Spectrometry-Based Chemical Cartography of a Cardiac Parasitic Infection.

McCall LI, Morton JT, Bernatchez JA, de Siqueira-Neto JL, Knight R, Dorrestein PC, McKerrow JH.

Anal Chem. 2017 Oct 3;89(19):10414-10421. doi: 10.1021/acs.analchem.7b02423. Epub 2017 Sep 22.

PMID:
28892370
31.

Total Synthesis and Biological Assessment of Novel Albicidins Discovered by Mass Spectrometric Networking.

von Eckardstein L, Petras D, Dang T, Cociancich S, Sabri S, Grätz S, Kerwat D, Seidel M, Pesic A, Dorrestein PC, Royer M, Weston JB, Süssmuth RD.

Chemistry. 2017 Nov 2;23(61):15316-15321. doi: 10.1002/chem.201704074. Epub 2017 Oct 12.

PMID:
28876492
32.

The medical threat of mamba envenoming in sub-Saharan Africa revealed by genus-wide analysis of venom composition, toxicity and antivenomics profiling of available antivenoms.

Ainsworth S, Petras D, Engmark M, Süssmuth RD, Whiteley G, Albulescu LO, Kazandjian TD, Wagstaff SC, Rowley P, Wüster W, Dorrestein PC, Arias AS, Gutiérrez JM, Harrison RA, Casewell NR, Calvete JJ.

J Proteomics. 2018 Feb 10;172:173-189. doi: 10.1016/j.jprot.2017.08.016. Epub 2017 Aug 24.

PMID:
28843532
33.

A metabolomics guided exploration of marine natural product chemical space.

Floros DJ, Jensen PR, Dorrestein PC, Koyama N.

Metabolomics. 2016 Sep;12(9). pii: 145. doi: 10.1007/s11306-016-1087-5. Epub 2016 Aug 9.

34.

Discovery and Synthesis of Caracolamide A, an Ion Channel Modulating Dichlorovinylidene Containing Phenethylamide from a Panamanian Marine Cyanobacterium cf. Symploca Species.

Naman CB, Almaliti J, Armstrong L, Caro-Díaz EJ, Pierce ML, Glukhov E, Fenner A, Spadafora C, Debonsi HM, Dorrestein PC, Murray TF, Gerwick WH.

J Nat Prod. 2017 Aug 25;80(8):2328-2334. doi: 10.1021/acs.jnatprod.7b00367. Epub 2017 Aug 7.

PMID:
28783331
35.

Metabolic Fingerprints from the Human Oral Microbiome Reveal a Vast Knowledge Gap of Secreted Small Peptidic Molecules.

Edlund A, Garg N, Mohimani H, Gurevich A, He X, Shi W, Dorrestein PC, McLean JS.

mSystems. 2017 Jul 18;2(4). pii: e00058-17. doi: 10.1128/mSystems.00058-17. eCollection 2017 Jul-Aug.

36.

Multi-omics Analysis of Periodontal Pocket Microbial Communities Pre- and Posttreatment.

Califf KJ, Schwarzberg-Lipson K, Garg N, Gibbons SM, Caporaso JG, Slots J, Cohen C, Dorrestein PC, Kelley ST.

mSystems. 2017 Jun 20;2(3). pii: e00016-17. doi: 10.1128/mSystems.00016-17. eCollection 2017 May-Jun.

37.

Imaging mass spectrometry and MS/MS molecular networking reveals chemical interactions among cuticular bacteria and pathogenic fungi associated with fungus-growing ants.

Boya P CA, Fernández-Marín H, Mejía LC, Spadafora C, Dorrestein PC, Gutiérrez M.

Sci Rep. 2017 Jul 17;7(1):5604. doi: 10.1038/s41598-017-05515-6.

38.

Molecular inter-kingdom interactions of endophytes isolated from Lychnophora ericoides.

Caraballo-Rodríguez AM, Dorrestein PC, Pupo MT.

Sci Rep. 2017 Jul 14;7(1):5373. doi: 10.1038/s41598-017-05532-5.

39.

Top-Down Atmospheric Ionization Mass Spectrometry Microscopy Combined With Proteogenomics.

Hsu CC, Baker MW, Gaasterland T, Meehan MJ, Macagno ER, Dorrestein PC.

Anal Chem. 2017 Aug 15;89(16):8251-8258. doi: 10.1021/acs.analchem.7b01096. Epub 2017 Jul 24.

PMID:
28692290
40.

Coupling Targeted and Untargeted Mass Spectrometry for Metabolome-Microbiome-Wide Association Studies of Human Fecal Samples.

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.

Anal Chem. 2017 Jul 18;89(14):7549-7559. doi: 10.1021/acs.analchem.7b01381. Epub 2017 Jul 6.

PMID:
28628333
41.

The WinCF Model - An Inexpensive and Tractable Microcosm of a Mucus Plugged Bronchiole to Study the Microbiology of Lung Infections.

Comstock WJ, Huh E, Weekes R, Watson C, Xu T, Dorrestein PC, Quinn RA.

J Vis Exp. 2017 May 8;(123). doi: 10.3791/55532.

PMID:
28518116
42.

Digitizing mass spectrometry data to explore the chemical diversity and distribution of marine cyanobacteria and algae.

Luzzatto-Knaan T, Garg N, Wang M, Glukhov E, Peng Y, Ackermann G, Amir A, Duggan BM, Ryazanov S, Gerwick L, Knight R, Alexandrov T, Bandeira N, Gerwick WH, Dorrestein PC.

Elife. 2017 May 11;6. pii: e24214. doi: 10.7554/eLife.24214.

43.

A Maldiisotopic Approach to Discover Natural Products: Cryptomaldamide, a Hybrid Tripeptide from the Marine Cyanobacterium Moorea producens.

Kinnel RB, Esquenazi E, Leao T, Moss N, Mevers E, Pereira AR, Monroe EA, Korobeynikov A, Murray TF, Sherman D, Gerwick L, Dorrestein PC, Gerwick WH.

J Nat Prod. 2017 May 26;80(5):1514-1521. doi: 10.1021/acs.jnatprod.7b00019. Epub 2017 Apr 27.

44.

Mass Spectrometry Based Molecular 3D-Cartography of Plant Metabolites.

Floros DJ, Petras D, Kapono CA, Melnik AV, Ling TJ, Knight R, Dorrestein PC.

Front Plant Sci. 2017 Mar 29;8:429. doi: 10.3389/fpls.2017.00429. eCollection 2017.

45.

Expanding the Chemical Repertoire of the Endophyte Streptomyces albospinus RLe7 Reveals Amphotericin B as an Inducer of a Fungal Phenotype.

Chagas FO, Caraballo-Rodríguez AM, Dorrestein PC, Pupo MT.

J Nat Prod. 2017 May 26;80(5):1302-1309. doi: 10.1021/acs.jnatprod.6b00870. Epub 2017 Apr 4.

PMID:
28375005
46.

Prioritizing Natural Product Diversity in a Collection of 146 Bacterial Strains Based on Growth and Extraction Protocols.

Crüsemann M, O'Neill EC, Larson CB, Melnik AV, Floros DJ, da Silva RR, Jensen PR, Dorrestein PC, Moore BS.

J Nat Prod. 2017 Mar 24;80(3):588-597. doi: 10.1021/acs.jnatprod.6b00722. Epub 2016 Nov 11.

47.

Antimicrobials from human skin commensal bacteria protect against Staphylococcus aureus and are deficient in atopic dermatitis.

Nakatsuji T, Chen TH, Narala S, Chun KA, Two AM, Yun T, Shafiq F, Kotol PF, Bouslimani A, Melnik AV, Latif H, Kim JN, Lockhart A, Artis K, David G, Taylor P, Streib J, Dorrestein PC, Grier A, Gill SR, Zengler K, Hata TR, Leung DY, Gallo RL.

Sci Transl Med. 2017 Feb 22;9(378). pii: eaah4680. doi: 10.1126/scitranslmed.aah4680.

48.

Balance Trees Reveal Microbial Niche Differentiation.

Morton JT, Sanders J, Quinn RA, McDonald D, Gonzalez A, Vázquez-Baeza Y, Navas-Molina JA, Song SJ, Metcalf JL, Hyde ER, Lladser M, Dorrestein PC, Knight R.

mSystems. 2017 Jan 17;2(1). pii: e00162-16. doi: 10.1128/mSystems.00162-16. eCollection 2017 Jan-Feb.

49.

Erratum: Indexing the Pseudomonas specialized metabolome enabled the discovery of poaeamide B and the bananamides.

Nguyen DD, Melnik AV, Koyama N, Lu X, Schorn M, Fang J, Aguinaldo K, Lincecum TL Jr, Ghequire MG, Carrion VJ, Cheng TL, Duggan BM, Malone JG, Mauchline TH, Sanchez LM, Kilpatrick AM, Raaijmakers JM, De Mot R, Moore BS, Medema MH, Dorrestein PC.

Nat Microbiol. 2017 Jan 23;2:17010. doi: 10.1038/nmicrobiol.2017.10. No abstract available.

PMID:
28112718
50.

From single cells to our planet-recent advances in using mass spectrometry for spatially resolved metabolomics.

Petras D, Jarmusch AK, Dorrestein PC.

Curr Opin Chem Biol. 2017 Feb;36:24-31. doi: 10.1016/j.cbpa.2016.12.018. Epub 2017 Jan 10. Review.

PMID:
28086192

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