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Alexandrov Team

Spatial and single-cell metabolomics

Publications

Publisher Correction: LifeTime and improving European healthcare through cell-based interceptive medicine.

Rajewsky N, Almouzni G, Gorski SA, Aerts S, Amit I, Bertero MG, Bock C, Bredenoord AL, Cavalli G, Chiocca S, Clevers H, De Strooper B, Eggert A, Ellenberg J, Fernández XM, Figlerowicz M, Gasser SM, Hubner N, Kjems J, Knoblich JA, Krabbe G, Lichter P, Linnarsson S, Marine JC, Marioni JC, Marti-Renom MA, Netea MG, Nickel D, Nollmann M, Novak HR, Parkinson H, Piccolo S, Pinheiro I, Pombo A, Popp C, Reik W, Roman-Roman S, Rosenstiel P, Schultze JL, Stegle O, Tanay A, Testa G, Thanos D, Theis FJ, Torres-Padilla ME, Valencia A, Vallot C, van Oudenaarden A, Vidal M, Voet T, LifeTime Community Working Groups

Nature 2021

33731935. doi:10.1038/s41586-021-03287-8.

A multimodal and integrated approach to interrogate human kidney biopsies with rigor and reproducibility: guidelines from the kidney precision medicine project.

El-Achkar TM, Eadon MT, Menon R, Lake BB, Sigdel TK, Alexandrov T, Parikh S, Zhang G, Dobib D, Dunn KW, Otto EA, Anderton CR, Carson JM, Luo J, Park C, Hamidi H, Zhou J, Hoover P, Schroeder A, Joanes M, Azeloglu EU, Sealfon R, Winfree S, Steck B, He Y, D'Agati VD, Iyengar R, Troyanskaya OG, Barisoni L, Gaut J, Zhang K, Laszik Z, Rovin B, Dagher PC, Sharma K, Sarwal M, Hodgin JB, Alpers CE, Kretzer M, Jain S, The Kidney Precision Medicine Project F

Physiological genomics 2020

33197228. doi:10.1152/physiolgenomics.00104.2020.

Feature-based molecular networking in the GNPS analysis environment.

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

Nature methods 2020

32839597. doi:10.1038/s41592-020-0933-6.

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

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

Nature reviews. Nephrology 2020

32939051. doi:10.1038/s41581-020-00335-w.

Life time and improving European healthcare through cell-based interceptive medicine.

Rajewsky N, Almouzni G, Gorski SA, Aerts S, Amit I, Bertero MG, Bock C, Bredenoord AL, Cavalli G, Chiocca S, Clevers H, De Strooper B, Eggert A, Ellenberg J, Fernández XM, Figlerowicz M, Gasser SM, Hubner N, Kjems J, Knoblich JA, Krabbe G, Lichter P, Linnarsson S, Marine JC, Marioni J, Marti-Renom MA, Netea MG, Nickel D, Nollmann M, Novak HR, Parkinson H, Piccolo S, Pinheiro I, Pombo A, Popp C, Reik W, Roman-Roman S, Rosenstiel P, Schultze JL, Stegle O, Tanay A, Testa G, Thanos D, Theis FJ, Torres-Padilla ME, Valencia A, Vallot C, van Oudenaarden A, Vidal M, Voet T

Nature 2020

32894860. doi:10.1038/s41586-020-2715-9.

ColocAI: artificial intelligence approach to quantify co-localization between mass spectrometry images.

Katja Ovchinnikova, Alexander Rakhlin, Lachlan Stuart, Sergey Nikolenko, Theodore Alexandrov

2019

doi:10.1101/758425.

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

Katja Ovchinnikova, Vitaly Kovalev, Lachlan Stuart, Theodore Alexandrov

2019

doi:10.1101/518977.

Spatial single-cell profiling of intracellular metabolomes in situ.

Rappez L, Stadler M, Triana S, Phapale P, Heikenwalder M, Alexandrov T

2019

doi:10.1101/510222.

METASPACE: A community-populated knowledge base of spatial metabolomes in health and disease.

Theodore Alexandrov, Katja Ovchnnikova, Andrew Palmer, Vitaly Kovalev, Artem Tarasov, Lachlan Stuart, Renat Nigmetzianov, Dominik Fay, Key METASPACE Contributors

2019

doi:10.1101/539478.

Data-driven restoring of metabolite annotations significantly improves sensitivity.

Silva ASC, Palmer A, Kovalev V, Tarasov A, Alexandrov T, Martens L, Degroeve S

ANALYTICAL CHEMISTRY 2018

doi:10.1021/acs.analchem.8b03224.

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, Hoffner N, Jiang Y, Kapono CA, Koester I, Knight R, Leber CA, Ling TJ, Luzzatto-Knaan T, McCall LI, McGrath AP, Meehan MJ, Merritt JK, Mills RH, Morton J, Podvin S, Protsyuk I, Purdy T, Satterfield K, Searles S, Shah S, Shires S, Steffen D, White M, Todoric J, Tuttle R, Wojnicz A, Sapp V, Vargas F, Yang J, Zhang C, Dorrestein PC

Analytical chemistry 2016

27732780. doi:10.1021/acs.analchem.6b03456.

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 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

Nature biotechnology 2016

27504778. doi:10.1038/nbt.3597.

Where imaging mass spectrometry stands: here are the numbers

Palmer A, Trede D, Alexandrov T

International Urogynecology Journal 2016

doi:10.1007/s11306-016-1047-0.

Benchmark datasets for 3D MALDI- and DESI-imaging mass spectrometry.

Oetjen J, Veselkov K, Watrous J, McKenzie JS, Becker M, Hauberg-Lotte L, Kobarg JH, Strittmatter N, Mróz AK, Hoffmann F, Trede D, Palmer A, Schiffler S, Steinhorst K, Aichler M, Goldin R, Guntinas-Lichius O, von Eggeling F, Thiele H, Maedler K, Walch A, Maass P, Dorrestein PC, Takats Z, Alexandrov T

GigaScience 2015

25941567. doi:10.1186/s13742-015-0059-4.

Molecular cartography of the human skin surface in 3D.

Bouslimani A, Porto C, Rath CM, Wang M, Guo Y, Gonzalez A, Berg-Lyon D, Ackermann G, Moeller Christensen GJ, Nakatsuji T, Zhang L, Borkowski AW, Meehan MJ, Dorrestein K, Gallo RL, Bandeira N, Knight R, Alexandrov T, Dorrestein PC

Proceedings of the National Academy of Sciences of the United States of America 2015

25825778. doi:10.1073/pnas.1424409112.

Phenalenone-type phytoalexins mediate resistance of banana plants (Musa spp.) to the burrowing nematode Radopholus similis.

Hölscher D, Dhakshinamoorthy S, Alexandrov T, Becker M, Bretschneider T, Buerkert A, Crecelius AC, De Waele D, Elsen A, Heckel DG, Heklau H, Hertweck C, Kai M, Knop K, Krafft C, Maddula RK, Matthäus C, Popp J, Schneider B, Schubert US, Sikora RA, Svatoš A, Swennen RL

Proceedings of the National Academy of Sciences of the United States of America 2013

24324151. doi:10.1073/pnas.1314168110.

Compressed sensing in imaging mass spectrometry

Bartels A, Dulk P, Trede D, Alexandrov T, Maass P

INVERSE PROBLEMS 2013

doi:10.1088/0266-5611/29/12/125015.

Abductive Reasoning with a Large Knowledge Base for Discourse Processing

Ovchinnikova E, Montazeri N, Alexandrov T, Hobbs J, McCord M, Mulkar-Mehta R

2013

doi:10.1007/978-94-007-7284-7_7.

Mass spectral molecular networking of living microbial colonies.

Watrous J, Roach P, Alexandrov T, Heath BS, Yang JY, Kersten RD, van der Voort M, Pogliano K, Gross H, Raaijmakers JM, Moore BS, Laskin J, Bandeira N, Dorrestein PC

Proceedings of the National Academy of Sciences of the United States of America 2012

22586093. doi:10.1073/pnas.1203689109.

A Review of Some Modern Approaches to the Problem of Trend Extraction

Alexandrov T, Bianconcini S, Dagum EB, Maass P, McElroy TS

ECONOMETRIC REVIEWS 2012

doi:10.1080/07474938.2011.608032.

A Method of Trend Extraction Using Singular Spectrum Analysis

Alexandrov T

REVSTAT-STATISTICAL JOURNAL 2009

doi:.


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