Publications

Total: 19 publication(s)

2020

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 HC, McCall LI, McSayles J, Meyer SW, Mohimani H, Morsy M, Moyone 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. (2020)

Feature-based molecular networking in the GNPS analysis environment.

Nat Methods 17(9):905-908. doi: 10.1038/s41592-020-0933-6
Europe PMC | doi

Ong E, Wang LL, Schaub J, O'Toole JF, Steck B, Rosenberg AZ, Dowd F, Hansen J, Barisoni L, Jain S, de Boer IH, Valerius MT, Waikar SS, Park C, Crawford DC, Alexandrov T, Anderton CR, Stoeckert C, Weng C, Diehl AD, Mungall CJ, Haendel M, Robinson PN, Himmelfarb J, Iyengar R, Kretzler M, Mooney S, He Y, Kidney Precision Medicine Project. (2020)

Modelling kidney disease using ontology: insights from the Kidney Precision Medicine Project.

Nat Rev Nephrol 16(11) doi: 10.1038/s41581-020-00335-w
Europe PMC | doi

Phapale P, Rai V, Mohanty AK, Srivastava S. (2020)

Untargeted metabolomics workshop report: quality control considerations from sample preparation to data analysis.

J Am Soc Mass Spectrom 31(9):2006-2010. doi: 10.1021/jasms.0c00224
Europe PMC | doi

Ovchinnikova K, Stuart L, Rakhlin A, Nikolenko S, Alexandrov T. (2020)

ColocML: machine learning quantifies co-localization between mass spectrometry images.

Bioinformatics 36(10):3215-3224. doi: 10.1093/bioinformatics/btaa085
Europe PMC | doi


2019

Li Y, Kuhn M, Gavin AC, Bork P. (2019)

Identification of metabolites from tandem mass spectra with a machine learning approach utilizing structural features.

Bioinformatics 36(4):1213-1218. doi: 10.1093/bioinformatics/btz736
Europe PMC | doi

Rusu P, Shao C, Neuerburg A, Acikgöz AA, Wu Y, Zou P, Phapale P, Shankar TS, Döring K, Dettling S, Körkel-Qu H, Bekki G, Costa B, Guo T, Friesen O, Schlotter M, Heikenwalder M, Tschaharganeh DF, Bukau B, Kramer G, Angel P, Herold-Mende C, Radlwimmer B, Liu HK. (2019)

GPD1 specifically marks dormant glioma stem cells with a distinct metabolic profile.

Cell Stem Cell 25(2):241-257.e8. doi: 10.1016/j.stem.2019.06.004
Europe PMC | doi

Cooke A, Schwarzl T, Huppertz I, Kramer G, Mantas P, Alleaume AM, Huber W, Krijgsveld J, Hentze MW. (2019)

The RNA-binding protein YBX3 controls amino acid levels by regulating SLC mRNA abundance.

Cell Rep 27(11):3097-3106.e5. doi: 10.1016/j.celrep.2019.05.039
Europe PMC | doi

Villani A, Benjaminsen J, Moritz C, Henke K, Hartmann J, Norlin N, Richter K, Schieber NL, Franke T, Schwab Y, Peri F. (2019)

Clearance by microglia depends on packaging of phagosomes into a unique cellular compartment.

Dev. Cell 49(1):77-88.e7. doi: 10.1016/j.devcel.2019.02.014
Europe PMC | doi

Katja Ovchinnikova, Vitaly Kovalev, Lachlan Stuart, Theodore Alexandrov. (2019)

Recognizing off-sample mass spectrometry images with machine and deep learning.

bioRxiv 518977 doi: 10.1101/518977
doi

Rappez L, Stadler M, Triana S, Phapale P, Heikenwalder M, Alexandrov T. (2019)

Spatial single-cell profiling of intracellular metabolomes in situ.

bioRxiv doi: 10.1101/510222
doi


2018

Hauke S, Keutler K, Phapale P, Yushchenko DA, Schultz C. (2018)

Endogenous Fatty Acids are Essential Signaling Factors of Pancreatic β-Cells and Insulin Secretion.

Diabetes 67(10) doi: 10.2337/db17-1215
Europe PMC | doi

Palmer A, Phapale P, Fay D, Alexandrov T. (2018)

Curatr: a web application for creating, curating and sharing a mass spectral library.

Bioinformatics 34(8):1436-1438. doi: 10.1093/bioinformatics/btx786
Europe PMC | doi

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. (2018)

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

Sci Rep 8(1) doi: 10.1038/s41598-018-21541-4
Europe PMC | doi

Protsyuk I, Melnik AV, Nothias LF, Rappez L, Phapale P, Aksenov AA, Bouslimani A, Ryazanov S, Dorrestein PC, Alexandrov T. (2018)

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

Nat Protoc 13(1):134-154. doi: 10.1038/nprot.2017.122
Europe PMC | doi


2017

Palmer A, Phapale P, Fay D, Alexandrov T. (2017)

Curatr: a web application for creating, curating, and sharing a mass spectral library.

Bioinformatics 34(8) doi: 10.1093/bioinformatics/btx786
Europe PMC | doi

Havas KM, Milchevskaya V, Radic K, Alladin A, Kafkia E, Garcia M, Stolte J, Klaus B, Rotmensz N, Gibson TJ, Burwinkel B, Schneeweiss A, Pruneri G, Patil KR, Sotillo R, Jechlinger M. (2017)

Metabolic shifts in residual breast cancer drive tumor recurrence

J Clin Invest 127(6):2091-2105. doi: 10.1172/JCI89914
Europe PMC | doi

Kaczmarska Z, Ortega E, Goudarzi A, Huang H, Kim S, Márquez JA, Zhao Y, Khochbin S, Panne D. (2017)

Structure of p300 in complex with acyl-CoA variants

Nat. Chem. Biol. 13(1):21-29. doi: 10.1038/nchembio.2217
Europe PMC | doi

Palmer A, Phapale P, Chernyavsky I, Lavigne R, Fay D, Tarasov A, Kovalev V, Fuchser J, Nikolenko S, Pineau C, Becker M, Alexandrov T. (2017)

FDR-controlled metabolite annotation for high-resolution imaging mass spectrometry.

Nat. Methods 14(1):57-60. doi: 10.1038/nmeth.4072
Europe PMC | doi


2016

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 WT, Crüsemann M, Boudreau PD, Esquenazi E, Sandoval-Calderón M, Kersten RD, Pace LA, Quinn RA, Duncan KR, Hsu CC, 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 CC, Yang YL, Humpf HU, Maansson M, Keyzers RA, Sims AC, Johnson AR, Sidebottom AM, Sedio BE, Klitgaard A, Larson CB, Boya P CA, Torres-Mendoza D, Gonzalez DJ, Silva DB, Marques LM, Demarque DP, Pociute E, O'Neill EC, Briand E, Helfrich EJ, 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 AM, Lamsa A, Zhang C, Dorrestein K, Duggan BM, Almaliti J, Allard PM, Phapale P, Nothias LF, Alexandrov T, Litaudon M, Wolfender JL, Kyle JE, Metz TO, Peryea T, Nguyen DT, VanLeer D, Shinn P, Jadhav A, Müller R, Waters KM, Shi W, Liu X, Zhang L, Knight R, Jensen PR, Palsson BØ, Pogliano K, Linington RG, Gutiérrez M, Lopes NP, Gerwick WH, Moore BS, Dorrestein PC, Bandeira N. (2016)

Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking.

Nat. Biotechnol. 34(8):828-837. doi: 10.1038/nbt.3597
Europe PMC | doi