25.
A Universal Language for Finding Mass Spectrometry Data Patterns.
Jarmusch AK, Aron AT, Petras D, Phelan VV, Bittremieux W, Acharya DD, Ahmed MMA, Bauermeister A, Bertin MJ, Boudreau PD, Borges RM, Bowen BP, Brown CJ, Chagas FO, Clevenger KD, Correia MSP, Crandall WJ, Crüsemann M, Damiani T, Fiehn O, Garg N, Gerwick WH, Gilbert JR, Globisch D, Gomes PWP, Heuckeroth S, James CA, Jarmusch SA, Kakhkhorov SA, Kang KB, Kersten RD, Kim H, Kirk RD, Kohlbacher O, Kontou EE, Liu K, Lizama-Chamu I, Luu GT, Luzzatto-Knaan T, Marty MT, McAvoy AC, McCall LI, Mohamed OG, Nahor O, Niedermeyer THJ, Northen TR, Overdahl KE, Pluskal T, Rainer J, Reher R, Rodriguez E, Sachsenberg TT, Sanchez LM, Schmid R, Stevens C, Tian Z, Tripathi A, Tsugawa H, Nishida K, Matsuzawa Y, van der Hooft JJJ, Vicini A, Walter A, Weber T, Xiong Q, Xu T, Zhao HN, Dorrestein PC, Mingxun Wang.
Submitted, preprint available at https://www.biorxiv.org/content/10.1101/2022.08.06.503000v1
24.
Discovery of homogentisic acid as a precursor in trimethoprim metabolism and natural product biosynthesis.
McAvoy AC, Threatt PH, Kapcia III2 J, Garg N.
Under review,
23.
Advances in immunity ‘omics in response to coral disease outbreaks.
Traylor-Knowles N, Baker AC, Beavers KM, Garg N, Guyon JR, Hawthorn A, MacKnight NJ, Medina M, Mydlarz LD, Peters EC, Stewart JM, Studivan MS, Voss JD.
Frontiers in Marine Science, 2022; doi: 10.3389/fmars.2022.952199.
22.
Metabolomics analysis of bacterial pathogen Burkholderia thailandensis and mammalian host cells in co-culture.
Aiosa N, Sinha A, Jaiyesimi OA, da Silva RR, Branda SS, Garg N.
ACS Infectious Disease, 2022; 8(8): 1646–1662
21.
A silent biosynthetic gene cluster from a methanotrophic bacterium potentiates discovery of a substrate promiscuous proteusin cyclodehydratase.
ACS Chemical Biology, 2022; 17(6); 1577–1585
Nguyen NA, Cong Y, Hurrell RC, Arias N, Garg N, Puri AW, Schmidt EW, Agarwal V
20.
Metabolomics approaches to dereplicate natural products from coral-derived bioactive bacteria.
Journal of Natural Products, 2022; 85(3): 462-478
Deutsch JM, Mandelare-Ruiz P, Yang Y, Foster G, Routhu A, Houk J, Flor YTDL, Ushijima B, Meyer JL, Paul VJ, Garg N.
19.
Stereochemical assignment and absolute abundance of non-proteinogenic amino acid homoarginine in marine sponges.
ACS Omega 2021; 6(48): 33200–33205
Mohanty I, Moore SG, Biggs JS, Freeman CJ, Gaul DA, Garg N, Agarwal V
18.
GNPS Dashboard: collaborative exploration of mass spectrometry data in the web browser.
Nature Methods, 2021; 19:134-136
Petras D, Phelan VV, Acharya D, Allen AE, Aron AT, Bandeira N, Bowen BP, Belle-Oudry D, Boecker S, Cummings Jr DA, Deutsch JM, Fahy E, Garg N, Gregor R, Handelsman J, Navarro-Hoyos M, Jarmusch AK, Jarmusch SA, Louie K, Maloney KN, Marty MT, Meijler MM, Mizrahi I, Neve RL, Northen TR, Molina-Santiago C, Panitchpakdi M, Pullman B, Puri AW, Schmid R, Subramaniam S, Thukral M, Vasquez-Castro F, Dorrestein PC, Wang M
17.
Metabolomic profiling of Burkholderia cenocepacia in synthetic cystic fibrosis sputum medium reveals environment-specific production of virulence factors.
Scientific Reports, 2021; 11:21419
Jaiyesimi OA*, McAvoy AC*, Fogg DN, and Garg N.
*equal contribution
16.
Molecular networking-based strategies in mass spectrometry coupled with in silico dereplication of peptidic natural products and gene cluster analysis.
Methods in Enzymology, 2021; 663:273-302
McAvoy AC, Garg N.
15.
Metabolomics of healthy and stony coral tissue loss disease affected Montastraea cavernosa corals.
Deutsch JM, Jaiyesimi OA, Pitts K, Houk J, Ushijima B, Walker BK, Paul VJ, and Garg N.
Frontiers in Marine Science, 2021; 8:714778
14.
Metabolomics in functional interrogation of individual holobiont members.
mSystems, 2021; 6(4): e00841-21
Garg N.
13.
Enzymatic synthesis assisted discovery of proline-rich macrocyclic peptides in marine sponges.
ChemBioChem, 2021; 22(16): 2614 – 2618
Mohanty I, Nguyen NA, Moore SG, Biggs JS, Gaul DA, Garg N, Agarwal V.
12.
An obligate peptidyl brominase underlies the discovery of highly distributed biosynthetic gene clusters in marine sponge microbiomes.
Journal of the American Chemical Society, 2021; 143(27): 10221–10231
Nguyen NA, Lin Z, Mohanty I, Garg N, Schmidt EW, Agarwal V.
11.
The role of algal chemical defenses in the feeding preferences of he long-spined sea urchin Diadema antillarum.
Aquatic Ecology, 2021; 55: 941–953
Spiers LJ, Harrison SJ, Deutsch JM, Garg N, Paul VJ.
10.
Presence of bromotyrosine alkaloids in marine sponges is independent of metabolomic and microbiome architectures.
mSystems, 2021; 6(2): e01387-20
Mohanty I, Tapadar S, Moore SG, Biggs JS, Freeman CJ, Gaul DA, Garg N*, Agarwal V*.
*co-corresponding authors
9.
A community resource for paired genomic and metabolomic data mining.
Nature Chemical Biology, 2021; 17: 63–368
Schorn MA, Verhoeven S, Ridder L, Huber F, Acharya DD, Aksenov AA, Aleti G, Moghaddam JA, Aron AT, Aziz S, Bauermeister A, Bauman KD, Baunach M, Beemelmanns C, Beman JM, Berlanga-Clavero MV, Blacutt AA, Bode HB, Boullie A, Brejnrod A, Bugni TS, Calteau A, Cao L, Carrion VJ, Castelo-Branco R, Chanana S, Chase AB, Chevrette MG, Costa-Lotufo LV, Crawford JM, Currie CR, Cuypers B, Dang T, de Rond T, Demko AM, Dittmann E, Du C, Drozd C, Dujardin J-C, Dutton RJ, Edlund A, Fewer DP, Garg N, Gauglitz JM, Gentry EC, Gerwick L, Glukhov E, Gross H, Gugger M, Guillén Matus DG, Helfrich EJN, Hempel B-F, Hur J-S, Iorio M, Jensen PR, Kang KB, Kaysser L, Kelleher NL, Kim CS, Kim KH, Koester I, König GM, Leao T, Lee SR, Lee Y-Y, Li X, Little JC, Maloney KN, Männle D, Martin C, McAvoy AC, Metcalf W, Mohimani H, Molina-Santiago C, Moore BS, Mullowney MW, Muskat M, Nothias LF, O'Neill EC, Parkinson EI, Petras D, Piel J, Pierce EC, Pires K, Reher R, Romero D, Roper MC, Rust M, Saad H, Saenz C, Sanchez LM, Sørensen SJ, Sosio M, Suessmuth RD, Sweeney D, Tahlan K, Thomson RJ, Tobias NJ, Trindade-Silva AE, van Wezel GP, Wang M, Weldon KC, Zhang F, Ziemert N, Duncan KR, Crüsemann M, Rogers S, Dorrestein PC, Medema MH, van der Hooft JJJ.
8.
Feature-based molecular networking in the GNPS analysis environment.
Nature Methods, 2020; 17: 905–908
Nothias L, 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, Gouellec AL, Ludwig M, H. CM, 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.
7.
Precursor-guided mining of marine sponge metabolomes lends insight into biosynthesis of pyrrole-imidazole alkaloids.
ACS Chemical Biology, 2020; 15(8): 2185–2194
Mohanty I, Moore SG, Yi D, Biggs JS, Gaul DA, Garg N, Agarwal V.
6.
Differences in Cystic Fibrosis-Associated Burkholderia spp. Bacteria Metabolomes after Exposure to the Antibiotic Trimethoprim.
ACS Infectious Diseases, 2020; 6(5):1154-1168
McAvoy AC, Jaiyesimi O, Threatt PH, Seladi T, Goldberg JB, da Silva RR, Garg N.
5.
Multi-Omic Profiling of Melophlus Sponges Reveals Diverse Metabolomic and Microbiome Architectures that Are Non-overlapping with Ecological Neighbors.
Marine Drugs, 2020;18(2): E124
Mohanty I, Podell S, Biggs JS, Garg N, Allen EE, Agarwal V.
4.
Molecular and Microbial Microenvironments in Chronically Diseased Lungs Associated with Cystic Fibrosis.
mSystems, 2019; 4:e00375-19
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.
3.
Mass spectrometry-based integration and expansion of the chemical diversity harbored within a marine sponge.
Journal of the American Society for Mass Spectrometry, 2019; 30(8):1373-1384
Cantrell TP, Freeman CJ, Paul VJ, Agarwal V, Garg N.
2.
The chemical topology of a bacterial swarm.
Journal of Biological Chemistry, 2018; 293(24):9553-9554
Garg N, Whiteley M.
1.
Chemoenzymatic synthesis of starting materials and characterization of halogenases requiring acyl carrier protein-tethered substrates.
Methods in Enzymology, 2018; 604:333-366
Thapa HR, Lail AJ, Garg N, Agarwal V.
PRIOR WORK
31.
Structural and mechanistic investigations of protein S-glycosyltransferases.
Cell Chemical Biology, 2021; 28(12), 1740–1749.
Fujinami D, Garcia de Gonzalo CV, Biswas S, Hao Y, Wang H, Garg N, Lukk T, Nair SK, van der Donk WA.
30.
LanCLs add glutathione to dehydroamino acids generated at phosphorylated sites in the proteome.
Cell, 2021; 184(10): 2680-2695.e26
Lai K-Y, Galan SRG, Zeng Y, Zhou H, He C, Raj R, Riedl J, Liu S, Chooi KP, Garg N, Zeng M, Jones LH, Hutchings GJ, Mohammed S, Nair SK, Chen J, Davis BG, van der Donk WA.
29.
Global chemical effects of the microbiome include new bile-acid conjugations.
Nature, 2020; 579:123–129.
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.
28.
Creating a 3D microbial and chemical snapshot of a human habitat.
Scientific Reports, 2018; 8(1):3669.
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.
27.
Three dimensional microbiome and metabolome cartography of a diseased human lung.
Cell Host & Microbe, 2017; 22(5):705-716.
Garg N, Wang M, Hyde E, da Silva RR, Melnik A, Protsyuk I, Bouslimani A, Lim YW, Wong R, Humphrey G, Ackerman G, Spivey T, Brouha SS, Bandeira N, Lin GY, Rohwer F, Conrad DJ, Alexandrov T, Knight R, Dorrestein PC.
Work presented in this study has been highlighted by Nature Medicine news: doi:10.1038/nm0815-837
Highlighted by UC SanDiego Health
26.
Metabolic Fingerprints from the Human Oral Microbiome Reveal a Vast Knowledge Gap of Secreted Small Peptidic Molecules.
Edlund A, Garg N, He X, Shi W, Dorrestein PC, McLean JS.
mSystems, 2017; 2(4):e00058-17.
Highlighted as Editor's Pick.
25.
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, Ackerman G, Amir A, Duggan BM, Ryazanov S, Gerwick L, Knight R, Alexandrov T, Bandeira N, Gerwick WH, Dorrestein, PC.
eLIFE, 2017; 6:e24214.
*Denotes equal contribution author.
24.
Multi-omics analysis of periodontal pocket microbial communities pre- and post-treatment.
Califf KJ, Schwarzberg-Lipson K, Garg N, Gibbons SM, Caporaso JG, Slots J, Cohen C, Dorrestein PC, Kelley ST.
mSystems, 2017; 2(3):e00016-17.
23.
Two flavoenzymes catalyze the post-translational generation of 5-chlorotryptophan and 2-aminovinyl-cysteine during NAI-107 biosynthesis.
Ortega MA, Cogan DP, Mukherjee S, Garg N, Li B, Thibodeaux GN, Maffioli S, Donadio S, Sosio M, Escano J, Smith L, Nair SK, van der Donk WA.
ACS Chemical Biology, 2017; 12(2):548-557.
22.
Natural Products as mediators of disease.
Garg N, Luzzatto-Knaan T, Melnik AV, Caraballo-Rodríguez AM, Floros DJ, Petras D, Gregor R, Dorrestein PC, Phelan VV.
Natural Products Reports, 2017; 34:194-219.
21.
Dereplication of peptidic natural products through database search of mass spectra.
Mohimani H, Gurevich A, Alla Mikheenko, Garg N, Louis-Felix Nothias, Akihiro Ninomiya, Kentaro Takada, Dorrestein PC, Pevzner PA.
Nature Chemical Biology, 2017; 13(1):30-37.
20.
Mass Spectrometry-Based Visualization of Molecules Associated with Human Habitats.
Petras D, Nothias LF, Quinn RA, Alexandrov T, Bandeira N, Bouslimani A, Castro-Falcón G, Chen L, Dang T, Floros DJ, Hook V, Garg N et al.
Analytical Chemistry, 2016; 88(22):10775-10784.
19.
Spatial Molecular Architecture of the Microbial Community of Peltigera Lichen.
Garg N, Zeng Y, Edlund A, Melnik AV, Sanchez LM, Mohimani H, Gurevich A, Miao V, Schiffler S, Lim YW, Luzzatto-Knaan T, Cai S, Rohwer F, Pezner PA, Cichewicz RH, Alexandrov T, Dorrestein PC.
mSystems, 2016; 1(6): e00139-16.
Highlighted as Editor's Pick.
18.
Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking.
Wang M*, Carver JJ*, Phelan VV*, Sanchez LM*, Garg N*, Peng Y*, Nguyen DD, Watrous J, Kapono CA, Luzzatto-Knaan T, Porto C, Bouslimani A, Melnik AV, Meehan MJ, Liu W-T, Crüsemann M, Boudreau PD, Esquenazi E, Sandoval-Calderón M, Kersten RD, Pace LA, Quinn RA, Duncan KR, Hsu C-C, Floros DJ, Gavilan RG, Kleigrewe K, Northen T, Dutton RJ, Parrot D, Carlson EE, Aigle B, Michelsen CF, Jelsbak L, Sohlenkamp C, Pevzner P, Edlund A, McLean J, Piel J, Murphy BT, Gerwick L, Liaw C-C, YangY-L, Humpf H-U, Månsson M, Keyzers RA, Sims AC, Johnson AR, Sidebottom AM, Sedio BE, Klitgaard A, Larson CB, Boya CA, Torres-Mendoza D, Gonzalez DJ, Silva DB, Marques LM, Demarque DP, Pociute E, O'Neill EC, Briand E, Helfrich EJN, Granatosky EA, Glukhov E, Ryffel F, Houson H, Mohimani H, Kharbush JJ, Zeng Y, Vorholt JA, Kurita KL, Charusanti P, McPhail KL, Nielsen KF, Vuong L, Elfeki M, Traxler MF, Engene N, Koyama N, Vining OB, Baric R, Silva RR, Mascuch SJ, Tomasi S, Jenkins S, Macherla V, Hoffman T, Agarwal V, Williams PG, Dai J, Neupane R, Gurr J, Rodríguez AMC, Lamsa A, Zhang C, Dorrestein K, Duggan BM, Almaliti J, Allard P-M, Phapale P, Nothias L-F, Alexandrov T, Litaudon M, Wolfender J-L, Kyle JE, Metz TO, Peryea T, Nguyen D-T, VanLeer D, Shinn P, Jadhav A, Müller R, Waters KM, Shi W, Liu X, Zhang L, Knight R, Jensen PR, Palsson BO, Pogliano K, Linington RG, Gutiérrez M, Lopes NP, Gerwick WH, Moore BS, Dorrestein PC, Bandeira N.
Nature Biotechnology, 2016; 34(8):828-837.
*Denotes equal contribution.
17.
Microbiome-wide association studies link dynamic microbial consortia to disease.
Gilbert JA, Quinn RA, Debelius J, Xu ZZ, Morton J, Garg N, Jansson JK, Dorrestein PC, Knight R.
Nature, 2016; 535: 94–103.
16.
Characterization of the stereochemical configuration of lanthionine formation by the lanthipeptide synthetase GeoM.
Garg N, Chen T, Goto Y, van der Donk WA. (2016).
Biopolymers . 2016; 106(6):834-842.
15.
Microbial, Host and Xenobiotic Diversity in the Cystic Fibrosis Sputum Metabolome.
Quinn RA, Phelan VV, Whiteson KL, Garg N, Bailey BA, Lim YW, Conrad DJ, Dorrestein PC, Rohwer FL.
The ISME Journal, 2016; 10(6):1483-98.
14.
Chemoenzymatic Synthesis of Acyl Coenzyme A Substrates Enables in Situ Labeling of Small Molecules and Proteins.
Agarwal V, Diethelm S, Ray L, Garg N, Awakawa T, Dorrestein PC, Moore BS.
Organic Letters, 2015; 17(18):4452-4455.
13.
Minimum Information about a Biosynthetic Gene cluster.
Medema MH, Kottmann R, Yilmaz P, Cummings M, Biggins JB, Blin K, de Bruijn I, Chooi YH, Claesen J, Coates RC, Cruz-Morales P, Duddela S, Düsterhus S, Edwards DJ, Fewer DP, Garg N et al.
Nature Chemical Biology, 2015; 11(9):625-631.
12.
Mass spectral similarity for untargeted metabolomics data analysis of complex mixtures.
Garg N, Kapono CA, Lim YW, Koyama N, Vermeij MJA, Conrad D, Rohwer F, Dorrestein PC.
International Journal of Mass Spectrometry, 2015; 377: 719-727.
11.
Specialized Metabolites from the Microbiome in Health and Disease.
Sharon G*, Garg N*, Debelius J*, Knight R, Dorrestein PC, Mazmanian SK.
Cell Metabolism, 2014; 20(5):719-730.
*Denotes equal contribution.
10.
Substrate specificity of the lanthipeptide peptidase ElxP and the oxidoreductase ElxO.
Ortega MA, Velásquez JE, Garg N, Zhang Q, Joyce R, Nair SK, van der Donk WA.
ACS Chemical Biology, 2014; 9(8):1718-1725.
9.
Mass spectrometry of natural products: current, emerging and future technologies.
Bouslimani A, Sanchez LM, Garg N, Dorrestein PC.
Natural Product Reports, 2014; 31(6):718-729.
8.
The Intestinal Metabolome: An Intersection Between Microbiota and Host.
Ursell LK, Haiser HJ, Treuren WV, Garg N, Reddivari L, Vanamala J, Dorrestein PC, Turnbaugh PJ, Knight R.
Gastroenterology, 2014; 146(6):1470-1476.
7.
Chemical Rescue and Inhibition Studies to Determine the Role of Arg301 in Phosphite Dehydrogenase.
Hung JE, Fogle EJ, Garg N, Chekan JA, Nair SK, van der Donk WA.
PLoS One, 2014; 9(1):e87134.
6.
Mode of Action and Structure-Activity Relationship Studies of Geobacillin I.
Garg N, Oman TJ, Andrew Wang TS, De Gonzalo CV, Walker S, van der Donk WA.
The Journal of Antibiotics, 2014; 67:133-136.
5.
In vitro activity of the nisin dehydratase NisB.
Garg N, Salazar-Ocampo LMA, van der Donk WA.
Proceedings of the National Academy of Sciences of the USA, 2013; 110(18):7258-7263.
4.
Lantibiotics from Geobacillus thermodenitrificans.
Garg N, Tang W, Goto Y, Nair SK, van der donk WA.
Proceedings of the National Academy of Sciences of the USA, 2012; 109(14):5241-5246.
Highlighted by ACS Chemical and Engineering News:
http://cen.acs.org/articles/90/i13/Thermally-Stable-Nisin-Analogs-Found.html
Highlighted by the University of Illinois News Bureau:
https://news.illinois.edu/view/6367/205107
3.
Cloning, sequence analysis, expression of Cyathus bulleri laccase in Pichia pastoris and characterization of recombinant laccase.
Garg N, Bieler N, Kenzom T, Chhabra M, Ansorge-Schumacher M, Mishra S.
BMC Biotechnology, 2012; 12:75-84.
2.
Production of lantipeptides in Escherichia coli.
Shi Y, Yang X, Garg N, van der Donk WA.
Journal of the American Chemical Society, 2011; 133: 2338-2341.
1.
Laccase of Cyathus bulleri: structural, catalytic characterization and expression in Escherichia coli.
Salony, Garg N, Baranwal R, Chhabra M, Mishra S, Chaudhuri TK, Bisaria VS.
Biochimica et Biophysica Acta, 2008; 1784(2): 259-268.
A Universal Language for Finding Mass Spectrometry Data Patterns.
Jarmusch AK, Aron AT, Petras D, Phelan VV, Bittremieux W, Acharya DD, Ahmed MMA, Bauermeister A, Bertin MJ, Boudreau PD, Borges RM, Bowen BP, Brown CJ, Chagas FO, Clevenger KD, Correia MSP, Crandall WJ, Crüsemann M, Damiani T, Fiehn O, Garg N, Gerwick WH, Gilbert JR, Globisch D, Gomes PWP, Heuckeroth S, James CA, Jarmusch SA, Kakhkhorov SA, Kang KB, Kersten RD, Kim H, Kirk RD, Kohlbacher O, Kontou EE, Liu K, Lizama-Chamu I, Luu GT, Luzzatto-Knaan T, Marty MT, McAvoy AC, McCall LI, Mohamed OG, Nahor O, Niedermeyer THJ, Northen TR, Overdahl KE, Pluskal T, Rainer J, Reher R, Rodriguez E, Sachsenberg TT, Sanchez LM, Schmid R, Stevens C, Tian Z, Tripathi A, Tsugawa H, Nishida K, Matsuzawa Y, van der Hooft JJJ, Vicini A, Walter A, Weber T, Xiong Q, Xu T, Zhao HN, Dorrestein PC, Mingxun Wang.
Submitted, preprint available at https://www.biorxiv.org/content/10.1101/2022.08.06.503000v1
24.
Discovery of homogentisic acid as a precursor in trimethoprim metabolism and natural product biosynthesis.
McAvoy AC, Threatt PH, Kapcia III2 J, Garg N.
Under review,
23.
Advances in immunity ‘omics in response to coral disease outbreaks.
Traylor-Knowles N, Baker AC, Beavers KM, Garg N, Guyon JR, Hawthorn A, MacKnight NJ, Medina M, Mydlarz LD, Peters EC, Stewart JM, Studivan MS, Voss JD.
Frontiers in Marine Science, 2022; doi: 10.3389/fmars.2022.952199.
22.
Metabolomics analysis of bacterial pathogen Burkholderia thailandensis and mammalian host cells in co-culture.
Aiosa N, Sinha A, Jaiyesimi OA, da Silva RR, Branda SS, Garg N.
ACS Infectious Disease, 2022; 8(8): 1646–1662
21.
A silent biosynthetic gene cluster from a methanotrophic bacterium potentiates discovery of a substrate promiscuous proteusin cyclodehydratase.
ACS Chemical Biology, 2022; 17(6); 1577–1585
Nguyen NA, Cong Y, Hurrell RC, Arias N, Garg N, Puri AW, Schmidt EW, Agarwal V
20.
Metabolomics approaches to dereplicate natural products from coral-derived bioactive bacteria.
Journal of Natural Products, 2022; 85(3): 462-478
Deutsch JM, Mandelare-Ruiz P, Yang Y, Foster G, Routhu A, Houk J, Flor YTDL, Ushijima B, Meyer JL, Paul VJ, Garg N.
19.
Stereochemical assignment and absolute abundance of non-proteinogenic amino acid homoarginine in marine sponges.
ACS Omega 2021; 6(48): 33200–33205
Mohanty I, Moore SG, Biggs JS, Freeman CJ, Gaul DA, Garg N, Agarwal V
18.
GNPS Dashboard: collaborative exploration of mass spectrometry data in the web browser.
Nature Methods, 2021; 19:134-136
Petras D, Phelan VV, Acharya D, Allen AE, Aron AT, Bandeira N, Bowen BP, Belle-Oudry D, Boecker S, Cummings Jr DA, Deutsch JM, Fahy E, Garg N, Gregor R, Handelsman J, Navarro-Hoyos M, Jarmusch AK, Jarmusch SA, Louie K, Maloney KN, Marty MT, Meijler MM, Mizrahi I, Neve RL, Northen TR, Molina-Santiago C, Panitchpakdi M, Pullman B, Puri AW, Schmid R, Subramaniam S, Thukral M, Vasquez-Castro F, Dorrestein PC, Wang M
17.
Metabolomic profiling of Burkholderia cenocepacia in synthetic cystic fibrosis sputum medium reveals environment-specific production of virulence factors.
Scientific Reports, 2021; 11:21419
Jaiyesimi OA*, McAvoy AC*, Fogg DN, and Garg N.
*equal contribution
16.
Molecular networking-based strategies in mass spectrometry coupled with in silico dereplication of peptidic natural products and gene cluster analysis.
Methods in Enzymology, 2021; 663:273-302
McAvoy AC, Garg N.
15.
Metabolomics of healthy and stony coral tissue loss disease affected Montastraea cavernosa corals.
Deutsch JM, Jaiyesimi OA, Pitts K, Houk J, Ushijima B, Walker BK, Paul VJ, and Garg N.
Frontiers in Marine Science, 2021; 8:714778
14.
Metabolomics in functional interrogation of individual holobiont members.
mSystems, 2021; 6(4): e00841-21
Garg N.
13.
Enzymatic synthesis assisted discovery of proline-rich macrocyclic peptides in marine sponges.
ChemBioChem, 2021; 22(16): 2614 – 2618
Mohanty I, Nguyen NA, Moore SG, Biggs JS, Gaul DA, Garg N, Agarwal V.
12.
An obligate peptidyl brominase underlies the discovery of highly distributed biosynthetic gene clusters in marine sponge microbiomes.
Journal of the American Chemical Society, 2021; 143(27): 10221–10231
Nguyen NA, Lin Z, Mohanty I, Garg N, Schmidt EW, Agarwal V.
11.
The role of algal chemical defenses in the feeding preferences of he long-spined sea urchin Diadema antillarum.
Aquatic Ecology, 2021; 55: 941–953
Spiers LJ, Harrison SJ, Deutsch JM, Garg N, Paul VJ.
10.
Presence of bromotyrosine alkaloids in marine sponges is independent of metabolomic and microbiome architectures.
mSystems, 2021; 6(2): e01387-20
Mohanty I, Tapadar S, Moore SG, Biggs JS, Freeman CJ, Gaul DA, Garg N*, Agarwal V*.
*co-corresponding authors
9.
A community resource for paired genomic and metabolomic data mining.
Nature Chemical Biology, 2021; 17: 63–368
Schorn MA, Verhoeven S, Ridder L, Huber F, Acharya DD, Aksenov AA, Aleti G, Moghaddam JA, Aron AT, Aziz S, Bauermeister A, Bauman KD, Baunach M, Beemelmanns C, Beman JM, Berlanga-Clavero MV, Blacutt AA, Bode HB, Boullie A, Brejnrod A, Bugni TS, Calteau A, Cao L, Carrion VJ, Castelo-Branco R, Chanana S, Chase AB, Chevrette MG, Costa-Lotufo LV, Crawford JM, Currie CR, Cuypers B, Dang T, de Rond T, Demko AM, Dittmann E, Du C, Drozd C, Dujardin J-C, Dutton RJ, Edlund A, Fewer DP, Garg N, Gauglitz JM, Gentry EC, Gerwick L, Glukhov E, Gross H, Gugger M, Guillén Matus DG, Helfrich EJN, Hempel B-F, Hur J-S, Iorio M, Jensen PR, Kang KB, Kaysser L, Kelleher NL, Kim CS, Kim KH, Koester I, König GM, Leao T, Lee SR, Lee Y-Y, Li X, Little JC, Maloney KN, Männle D, Martin C, McAvoy AC, Metcalf W, Mohimani H, Molina-Santiago C, Moore BS, Mullowney MW, Muskat M, Nothias LF, O'Neill EC, Parkinson EI, Petras D, Piel J, Pierce EC, Pires K, Reher R, Romero D, Roper MC, Rust M, Saad H, Saenz C, Sanchez LM, Sørensen SJ, Sosio M, Suessmuth RD, Sweeney D, Tahlan K, Thomson RJ, Tobias NJ, Trindade-Silva AE, van Wezel GP, Wang M, Weldon KC, Zhang F, Ziemert N, Duncan KR, Crüsemann M, Rogers S, Dorrestein PC, Medema MH, van der Hooft JJJ.
8.
Feature-based molecular networking in the GNPS analysis environment.
Nature Methods, 2020; 17: 905–908
Nothias L, 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, Gouellec AL, Ludwig M, H. CM, 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.
7.
Precursor-guided mining of marine sponge metabolomes lends insight into biosynthesis of pyrrole-imidazole alkaloids.
ACS Chemical Biology, 2020; 15(8): 2185–2194
Mohanty I, Moore SG, Yi D, Biggs JS, Gaul DA, Garg N, Agarwal V.
6.
Differences in Cystic Fibrosis-Associated Burkholderia spp. Bacteria Metabolomes after Exposure to the Antibiotic Trimethoprim.
ACS Infectious Diseases, 2020; 6(5):1154-1168
McAvoy AC, Jaiyesimi O, Threatt PH, Seladi T, Goldberg JB, da Silva RR, Garg N.
5.
Multi-Omic Profiling of Melophlus Sponges Reveals Diverse Metabolomic and Microbiome Architectures that Are Non-overlapping with Ecological Neighbors.
Marine Drugs, 2020;18(2): E124
Mohanty I, Podell S, Biggs JS, Garg N, Allen EE, Agarwal V.
4.
Molecular and Microbial Microenvironments in Chronically Diseased Lungs Associated with Cystic Fibrosis.
mSystems, 2019; 4:e00375-19
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.
3.
Mass spectrometry-based integration and expansion of the chemical diversity harbored within a marine sponge.
Journal of the American Society for Mass Spectrometry, 2019; 30(8):1373-1384
Cantrell TP, Freeman CJ, Paul VJ, Agarwal V, Garg N.
2.
The chemical topology of a bacterial swarm.
Journal of Biological Chemistry, 2018; 293(24):9553-9554
Garg N, Whiteley M.
1.
Chemoenzymatic synthesis of starting materials and characterization of halogenases requiring acyl carrier protein-tethered substrates.
Methods in Enzymology, 2018; 604:333-366
Thapa HR, Lail AJ, Garg N, Agarwal V.
PRIOR WORK
31.
Structural and mechanistic investigations of protein S-glycosyltransferases.
Cell Chemical Biology, 2021; 28(12), 1740–1749.
Fujinami D, Garcia de Gonzalo CV, Biswas S, Hao Y, Wang H, Garg N, Lukk T, Nair SK, van der Donk WA.
30.
LanCLs add glutathione to dehydroamino acids generated at phosphorylated sites in the proteome.
Cell, 2021; 184(10): 2680-2695.e26
Lai K-Y, Galan SRG, Zeng Y, Zhou H, He C, Raj R, Riedl J, Liu S, Chooi KP, Garg N, Zeng M, Jones LH, Hutchings GJ, Mohammed S, Nair SK, Chen J, Davis BG, van der Donk WA.
29.
Global chemical effects of the microbiome include new bile-acid conjugations.
Nature, 2020; 579:123–129.
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.
28.
Creating a 3D microbial and chemical snapshot of a human habitat.
Scientific Reports, 2018; 8(1):3669.
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.
27.
Three dimensional microbiome and metabolome cartography of a diseased human lung.
Cell Host & Microbe, 2017; 22(5):705-716.
Garg N, Wang M, Hyde E, da Silva RR, Melnik A, Protsyuk I, Bouslimani A, Lim YW, Wong R, Humphrey G, Ackerman G, Spivey T, Brouha SS, Bandeira N, Lin GY, Rohwer F, Conrad DJ, Alexandrov T, Knight R, Dorrestein PC.
Work presented in this study has been highlighted by Nature Medicine news: doi:10.1038/nm0815-837
Highlighted by UC SanDiego Health
26.
Metabolic Fingerprints from the Human Oral Microbiome Reveal a Vast Knowledge Gap of Secreted Small Peptidic Molecules.
Edlund A, Garg N, He X, Shi W, Dorrestein PC, McLean JS.
mSystems, 2017; 2(4):e00058-17.
Highlighted as Editor's Pick.
25.
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, Ackerman G, Amir A, Duggan BM, Ryazanov S, Gerwick L, Knight R, Alexandrov T, Bandeira N, Gerwick WH, Dorrestein, PC.
eLIFE, 2017; 6:e24214.
*Denotes equal contribution author.
24.
Multi-omics analysis of periodontal pocket microbial communities pre- and post-treatment.
Califf KJ, Schwarzberg-Lipson K, Garg N, Gibbons SM, Caporaso JG, Slots J, Cohen C, Dorrestein PC, Kelley ST.
mSystems, 2017; 2(3):e00016-17.
23.
Two flavoenzymes catalyze the post-translational generation of 5-chlorotryptophan and 2-aminovinyl-cysteine during NAI-107 biosynthesis.
Ortega MA, Cogan DP, Mukherjee S, Garg N, Li B, Thibodeaux GN, Maffioli S, Donadio S, Sosio M, Escano J, Smith L, Nair SK, van der Donk WA.
ACS Chemical Biology, 2017; 12(2):548-557.
22.
Natural Products as mediators of disease.
Garg N, Luzzatto-Knaan T, Melnik AV, Caraballo-Rodríguez AM, Floros DJ, Petras D, Gregor R, Dorrestein PC, Phelan VV.
Natural Products Reports, 2017; 34:194-219.
21.
Dereplication of peptidic natural products through database search of mass spectra.
Mohimani H, Gurevich A, Alla Mikheenko, Garg N, Louis-Felix Nothias, Akihiro Ninomiya, Kentaro Takada, Dorrestein PC, Pevzner PA.
Nature Chemical Biology, 2017; 13(1):30-37.
20.
Mass Spectrometry-Based Visualization of Molecules Associated with Human Habitats.
Petras D, Nothias LF, Quinn RA, Alexandrov T, Bandeira N, Bouslimani A, Castro-Falcón G, Chen L, Dang T, Floros DJ, Hook V, Garg N et al.
Analytical Chemistry, 2016; 88(22):10775-10784.
19.
Spatial Molecular Architecture of the Microbial Community of Peltigera Lichen.
Garg N, Zeng Y, Edlund A, Melnik AV, Sanchez LM, Mohimani H, Gurevich A, Miao V, Schiffler S, Lim YW, Luzzatto-Knaan T, Cai S, Rohwer F, Pezner PA, Cichewicz RH, Alexandrov T, Dorrestein PC.
mSystems, 2016; 1(6): e00139-16.
Highlighted as Editor's Pick.
18.
Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking.
Wang M*, Carver JJ*, Phelan VV*, Sanchez LM*, Garg N*, Peng Y*, Nguyen DD, Watrous J, Kapono CA, Luzzatto-Knaan T, Porto C, Bouslimani A, Melnik AV, Meehan MJ, Liu W-T, Crüsemann M, Boudreau PD, Esquenazi E, Sandoval-Calderón M, Kersten RD, Pace LA, Quinn RA, Duncan KR, Hsu C-C, Floros DJ, Gavilan RG, Kleigrewe K, Northen T, Dutton RJ, Parrot D, Carlson EE, Aigle B, Michelsen CF, Jelsbak L, Sohlenkamp C, Pevzner P, Edlund A, McLean J, Piel J, Murphy BT, Gerwick L, Liaw C-C, YangY-L, Humpf H-U, Månsson M, Keyzers RA, Sims AC, Johnson AR, Sidebottom AM, Sedio BE, Klitgaard A, Larson CB, Boya CA, Torres-Mendoza D, Gonzalez DJ, Silva DB, Marques LM, Demarque DP, Pociute E, O'Neill EC, Briand E, Helfrich EJN, Granatosky EA, Glukhov E, Ryffel F, Houson H, Mohimani H, Kharbush JJ, Zeng Y, Vorholt JA, Kurita KL, Charusanti P, McPhail KL, Nielsen KF, Vuong L, Elfeki M, Traxler MF, Engene N, Koyama N, Vining OB, Baric R, Silva RR, Mascuch SJ, Tomasi S, Jenkins S, Macherla V, Hoffman T, Agarwal V, Williams PG, Dai J, Neupane R, Gurr J, Rodríguez AMC, Lamsa A, Zhang C, Dorrestein K, Duggan BM, Almaliti J, Allard P-M, Phapale P, Nothias L-F, Alexandrov T, Litaudon M, Wolfender J-L, Kyle JE, Metz TO, Peryea T, Nguyen D-T, VanLeer D, Shinn P, Jadhav A, Müller R, Waters KM, Shi W, Liu X, Zhang L, Knight R, Jensen PR, Palsson BO, Pogliano K, Linington RG, Gutiérrez M, Lopes NP, Gerwick WH, Moore BS, Dorrestein PC, Bandeira N.
Nature Biotechnology, 2016; 34(8):828-837.
*Denotes equal contribution.
17.
Microbiome-wide association studies link dynamic microbial consortia to disease.
Gilbert JA, Quinn RA, Debelius J, Xu ZZ, Morton J, Garg N, Jansson JK, Dorrestein PC, Knight R.
Nature, 2016; 535: 94–103.
16.
Characterization of the stereochemical configuration of lanthionine formation by the lanthipeptide synthetase GeoM.
Garg N, Chen T, Goto Y, van der Donk WA. (2016).
Biopolymers . 2016; 106(6):834-842.
15.
Microbial, Host and Xenobiotic Diversity in the Cystic Fibrosis Sputum Metabolome.
Quinn RA, Phelan VV, Whiteson KL, Garg N, Bailey BA, Lim YW, Conrad DJ, Dorrestein PC, Rohwer FL.
The ISME Journal, 2016; 10(6):1483-98.
14.
Chemoenzymatic Synthesis of Acyl Coenzyme A Substrates Enables in Situ Labeling of Small Molecules and Proteins.
Agarwal V, Diethelm S, Ray L, Garg N, Awakawa T, Dorrestein PC, Moore BS.
Organic Letters, 2015; 17(18):4452-4455.
13.
Minimum Information about a Biosynthetic Gene cluster.
Medema MH, Kottmann R, Yilmaz P, Cummings M, Biggins JB, Blin K, de Bruijn I, Chooi YH, Claesen J, Coates RC, Cruz-Morales P, Duddela S, Düsterhus S, Edwards DJ, Fewer DP, Garg N et al.
Nature Chemical Biology, 2015; 11(9):625-631.
12.
Mass spectral similarity for untargeted metabolomics data analysis of complex mixtures.
Garg N, Kapono CA, Lim YW, Koyama N, Vermeij MJA, Conrad D, Rohwer F, Dorrestein PC.
International Journal of Mass Spectrometry, 2015; 377: 719-727.
11.
Specialized Metabolites from the Microbiome in Health and Disease.
Sharon G*, Garg N*, Debelius J*, Knight R, Dorrestein PC, Mazmanian SK.
Cell Metabolism, 2014; 20(5):719-730.
*Denotes equal contribution.
10.
Substrate specificity of the lanthipeptide peptidase ElxP and the oxidoreductase ElxO.
Ortega MA, Velásquez JE, Garg N, Zhang Q, Joyce R, Nair SK, van der Donk WA.
ACS Chemical Biology, 2014; 9(8):1718-1725.
9.
Mass spectrometry of natural products: current, emerging and future technologies.
Bouslimani A, Sanchez LM, Garg N, Dorrestein PC.
Natural Product Reports, 2014; 31(6):718-729.
8.
The Intestinal Metabolome: An Intersection Between Microbiota and Host.
Ursell LK, Haiser HJ, Treuren WV, Garg N, Reddivari L, Vanamala J, Dorrestein PC, Turnbaugh PJ, Knight R.
Gastroenterology, 2014; 146(6):1470-1476.
7.
Chemical Rescue and Inhibition Studies to Determine the Role of Arg301 in Phosphite Dehydrogenase.
Hung JE, Fogle EJ, Garg N, Chekan JA, Nair SK, van der Donk WA.
PLoS One, 2014; 9(1):e87134.
6.
Mode of Action and Structure-Activity Relationship Studies of Geobacillin I.
Garg N, Oman TJ, Andrew Wang TS, De Gonzalo CV, Walker S, van der Donk WA.
The Journal of Antibiotics, 2014; 67:133-136.
5.
In vitro activity of the nisin dehydratase NisB.
Garg N, Salazar-Ocampo LMA, van der Donk WA.
Proceedings of the National Academy of Sciences of the USA, 2013; 110(18):7258-7263.
4.
Lantibiotics from Geobacillus thermodenitrificans.
Garg N, Tang W, Goto Y, Nair SK, van der donk WA.
Proceedings of the National Academy of Sciences of the USA, 2012; 109(14):5241-5246.
Highlighted by ACS Chemical and Engineering News:
http://cen.acs.org/articles/90/i13/Thermally-Stable-Nisin-Analogs-Found.html
Highlighted by the University of Illinois News Bureau:
https://news.illinois.edu/view/6367/205107
3.
Cloning, sequence analysis, expression of Cyathus bulleri laccase in Pichia pastoris and characterization of recombinant laccase.
Garg N, Bieler N, Kenzom T, Chhabra M, Ansorge-Schumacher M, Mishra S.
BMC Biotechnology, 2012; 12:75-84.
2.
Production of lantipeptides in Escherichia coli.
Shi Y, Yang X, Garg N, van der Donk WA.
Journal of the American Chemical Society, 2011; 133: 2338-2341.
1.
Laccase of Cyathus bulleri: structural, catalytic characterization and expression in Escherichia coli.
Salony, Garg N, Baranwal R, Chhabra M, Mishra S, Chaudhuri TK, Bisaria VS.
Biochimica et Biophysica Acta, 2008; 1784(2): 259-268.