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Metabolomics Core Facility

This facility provides services for analysis of metabolites and lipids.

Publications

Metabolic decisions in development and disease-a Keystone Symposia report.

Cable J, Pourquié O, Wellen KE, Finley LWS, Aulehla A, Gould AP, Teleman A, Tu WB, Garrett WS, Miguel-Aliaga I, Perrimon N, Hooper LV, Walhout AJM, Wei W, Alexandrov T, Erez A, Ralser M, Rabinowitz JD, Hemalatha A, Gutiérrez-Pérez P, Chandel NS, Rutter J, Locasale JW, Landoni JC, Christofk H

Annals of the New York Academy of Sciences 2021

34414571. doi:10.1111/nyas.14678.

Single-cell transcriptomics reveals immune response of intestinal cell types to viral infection.

Triana S, Stanifer ML, Metz-Zumaran C, Shahraz M, Mukenhirn M, Kee C, Serger C, Koschny R, Ordonez-Rueda D, Paulsen M, Benes V, Boulant S, Alexandrov T

MOLECULAR SYSTEMS BIOLOGY 2021

doi:10.15252/msb.20209833.

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.


Metabolic decisions in development and disease-a Keystone Symposia report.

Cable J, Pourquié O, Wellen KE, Finley LWS, Aulehla A, Gould AP, Teleman A, Tu WB, Garrett WS, Miguel-Aliaga I, Perrimon N, Hooper LV, Walhout AJM, Wei W, Alexandrov T, Erez A, Ralser M, Rabinowitz JD, Hemalatha A, Gutiérrez-Pérez P, Chandel NS, Rutter J, Locasale JW, Landoni JC, Christofk H

Annals of the New York Academy of Sciences 2021

34414571. doi:10.1111/nyas.14678.

Single-cell transcriptomics reveals immune response of intestinal cell types to viral infection.

Triana S, Stanifer ML, Metz-Zumaran C, Shahraz M, Mukenhirn M, Kee C, Serger C, Koschny R, Ordonez-Rueda D, Paulsen M, Benes V, Boulant S, Alexandrov T

MOLECULAR SYSTEMS BIOLOGY 2021

doi:10.15252/msb.20209833.

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.

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