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Alexey Melnik
Alexey Melnik
Verified email at ucsd.edu
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Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
E Bolyen, JR Rideout, MR Dillon, NA Bokulich, CC Abnet, GA Al-Ghalith, ...
Nature biotechnology 37 (8), 852-857, 2019
143182019
Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking
M Wang, JJ Carver, VV Phelan, LM Sanchez, N Garg, Y Peng, ...
Nature biotechnology 34 (8), 828-837, 2016
33552016
Best practices for analysing microbiomes
R Knight, A Vrbanac, BC Taylor, A Aksenov, C Callewaert, J Debelius, ...
Nature Reviews Microbiology 16 (7), 410-422, 2018
15062018
SIRIUS 4: a rapid tool for turning tandem mass spectra into metabolite structure information
K Dührkop, M Fleischauer, M Ludwig, AA Aksenov, AV Melnik, M Meusel, ...
Nature methods 16 (4), 299-302, 2019
10632019
Antimicrobials from human skin commensal bacteria protect against Staphylococcus aureus and are deficient in atopic dermatitis
T Nakatsuji, TH Chen, S Narala, KA Chun, AM Two, T Yun, F Shafiq, ...
Science translational medicine 9 (378), eaah4680, 2017
10362017
QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science
E Bolyen, JR Rideout, MR Dillon, NA Bokulich, C Abnet, GA Al-Ghalith, ...
PeerJ Preprints, 2018
9572018
Minimum information about a biosynthetic gene cluster
MH Medema, R Kottmann, P Yilmaz, M Cummings, JB Biggins, K Blin, ...
Nature chemical biology 11 (9), 625-631, 2015
8762015
American gut: an open platform for citizen science microbiome research
D McDonald, E Hyde, JW Debelius, JT Morton, A Gonzalez, G Ackermann, ...
Msystems 3 (3), 10.1128/msystems. 00031-18, 2018
6802018
Global chemical effects of the microbiome include new bile-acid conjugations
RA Quinn, AV Melnik, A Vrbanac, T Fu, KA Patras, MP Christy, Z Bodai, ...
Nature 579 (7797), 123-129, 2020
4012020
Mass spectrometry searches using MASST
M Wang, AK Jarmusch, F Vargas, AA Aksenov, JM Gauglitz, K Weldon, ...
Nature biotechnology 38 (1), 23-26, 2020
1952020
The impact of skin care products on skin chemistry and microbiome dynamics
A Bouslimani, R da Silva, T Kosciolek, S Janssen, C Callewaert, A Amir, ...
BMC biology 17, 1-20, 2019
1612019
Indexing the Pseudomonas specialized metabolome enabled the discovery of poaeamide B and the bananamides
DD Nguyen, AV Melnik, N Koyama, X Lu, M Schorn, J Fang, K Aguinaldo, ...
Nature microbiology 2 (1), 1-10, 2016
1422016
Prioritizing Natural Product Diversity in a Collection of 146 Bacterial Strains Based on Growth and Extraction Protocols
PCDBSM Max Crüsemann, Ellis C. O’Neill, Charles B. Larson, Alexey V. Melnik ...
Journal of Natural Product, 1021, 2016
129*2016
Pep2Path: automated mass spectrometry-guided genome mining of peptidic natural products
MH Medema, Y Paalvast, DD Nguyen, A Melnik, PC Dorrestein, E Takano, ...
PLoS computational biology 10 (9), e1003822, 2014
1122014
Three-dimensional microbiome and metabolome cartography of a diseased human lung
N Garg, M Wang, E Hyde, RR da Silva, AV Melnik, I Protsyuk, ...
Cell host & microbe 22 (5), 705-716. e4, 2017
1112017
Intermittent hypoxia and hypercapnia, a hallmark of obstructive sleep apnea, alters the gut microbiome and metabolome
A Tripathi, AV Melnik, J Xue, O Poulsen, MJ Meehan, G Humphrey, ...
Msystems 3 (3), 10.1128/msystems. 00020-18, 2018
1082018
Auto-deconvolution and molecular networking of gas chromatography–mass spectrometry data
AA Aksenov, I Laponogov, Z Zhang, SLF Doran, I Belluomo, D Veselkov, ...
Nature biotechnology 39 (2), 169-173, 2021
1052021
A Cutibacterium acnes antibiotic modulates human skin microbiota composition in hair follicles
J Claesen, JB Spagnolo, SF Ramos, KL Kurita, AL Byrd, AA Aksenov, ...
Science translational medicine 12 (570), eaay5445, 2020
1032020
3D molecular cartography using LC–MS facilitated by Optimus and'ili software
I Protsyuk, AV Melnik, LF Nothias, L Rappez, P Phapale, AA Aksenov, ...
Nature protocols 13 (1), 134-154, 2018
1012018
CA; Torres-Mendoza, D
M Wang, JJ Carver, VV Phelan, LM Sanchez, N Garg, Y Peng, ...
Gonzalez, DJ, 828-837, 0
96
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