A call for accessible tools to unlock single-cell immunometabolism research.

Cosgrove J, Marçais A, Hartmann FJ, Bergthaler A, Zanoni I, Corrado M, Perié L, Cabezas-Wallscheid N, Bousso P, Alexandrov T, Kielian T, Martínez-Martín N, Opitz CA, Lyssiotis CA, Argüello RJ, Van den Bossche J

Nature metabolism, 2024

doi:10.1038/s42255-024-01031-w.

13C-SpaceM: Spatial single-cell isotope tracing reveals heterogeneity of de novo fatty acid synthesis in cancer.

Buglakova E, Ekelöf M, Schwaiger-Haber M, Schlicker L, Molenaar MR, Mohammed S, Stuart L, Eisenbarth A, Hilsenstein V, Patti GJ, Schulze A, Snaebjornsson MT, Alexandrov T

bioRxiv, 2024

doi:10.1101/2023.08.18.553810.

Large-scale evaluation of spatial metabolomics protocols and technologies.

Saharuka V, Vieira LM, Stuart L, Ekelöf M, Molenaar MR, Bailoni A, Ovchinnikova K, Soltwisch J, Bausbacher T, Jakob D, King M, Müller MA, Oetjen J, Pace C, Pinto FE, Strittmatter N, Velickovic D, Spengler B, Muddiman DC, Liebeke M, Janfelt C, Goodwin R, Eberlin LS, Anderton CR, Hopf C, Dreisewerd K, Alexandrov T

bioRxiv, 2024

doi:10.1101/2024.01.29.577354.

FOXO1-mediated lipid metabolism maintains mammalian embryos in dormancy.

van der Weijden VA, Stötzel M, Iyer DP, Fauler B, Gralinska E, Shahraz M, Meierhofer D, Vingron M, Rulands S, Alexandrov T, Mielke T, Bulut-Karslioglu A

Nature cell biology, 2024

doi:10.1038/s41556-023-01325-3.

Enablers and challenges of spatial omics, a melting pot of technologies.

Alexandrov T, Saez-Rodriguez J, Saka SK

Molecular systems biology, 2023

doi:10.15252/msb.202110571.

Spatial metabolomics: from a niche field towards a driver of innovation.

Alexandrov T

Nature metabolism, 2023

doi:10.1038/s42255-023-00881-0.

Endogenous adenine mediates kidney injury in diabetic models and predicts diabetic kidney disease in patients.

Sharma K, Zhang G, Hansen J, Bjornstad P, Lee HJ, Menon R, Hejazi L, Liu JJ, Franzone A, Looker HC, Choi BY, Fernandez R, Venkatachalam MA, Kugathasan L, Sridhar VS, Natarajan L, Zhang J, Sharma VS, Kwan B, Waikar SS, Himmelfarb J, Tuttle KR, Kestenbaum B, Fuhrer T, Feldman H, de Boer IH, Tucci FC, Sedor J, Heerspink HL, Schaub J, Otto EA, Hodgin JB, Kretzler M, Anderton CR, Alexandrov T, Cherney D, Lim SC, Nelson RG, Gelfond J, Iyengar R

The Journal of clinical investigation, 2023

doi:10.1172/jci170341.

Enhancing metabolite coverage in MALDI-MSI using laser post-ionisation (MALDI-2).

McKinnon JC, Milioli HH, Purcell CA, Chaffer CL, Wadie B, Alexandrov T, Mitchell TW, Ellis SR

Analytical methods : advancing methods and applications, 2023

doi:10.1039/d3ay01046e.

A pathogen-specific isotope tracing approach reveals metabolic activities and fluxes of intracellular Salmonella.

Mitosch K, Beyß M, Phapale P, Drotleff B, Nöh K, Alexandrov T, Patil KR, Typas A

PLoS biology, 2023

doi:10.1371/journal.pbio.3002198.

An atlas of healthy and injured cell states and niches in the human kidney.

Lake BB, Menon R, Winfree S, Hu Q, Melo Ferreira R, Kalhor K, Barwinska D, Otto EA, Ferkowicz M, Diep D, Plongthongkum N, Knoten A, Urata S, Mariani LH, Naik AS, Eddy S, Zhang B, Wu Y, Salamon D, Williams JC, Wang X, Balderrama KS, Hoover PJ, Murray E, Marshall JL, Noel T, Vijayan A, Hartman A, Chen F, Waikar SS, Rosas SE, Wilson FP, Palevsky PM, Kiryluk K, Sedor JR, Toto RD, Parikh CR, Kim EH, Satija R, Greka A, Macosko EZ, Kharchenko PV, Gaut JP, Hodgin JB, KPMP Consortium, Eadon MT, Dagher PC, El-Achkar TM, Zhang K, Kretzler M, Jain S

Nature, 2023

doi:10.1038/s41586-023-05769-3.

Sublethal necroptosis signaling promotes inflammation and liver cancer.

Vucur M, Ghallab A, Schneider AT, Adili A, Cheng M, Castoldi M, Singer MT, Büttner V, Keysberg LS, Küsgens L, Kohlhepp M, Görg B, Gallage S, Barragan Avila JE, Unger K, Kordes C, Leblond AL, Albrecht W, Loosen SH, Lohr C, Jördens MS, Babler A, Hayat S, Schumacher D, Koenen MT, Govaere O, Boekschoten MV, Jörs S, Villacorta-Martin C, Mazzaferro V, Llovet JM, Weiskirchen R, Kather JN, Starlinger P, Trauner M, Luedde M, Heij LR, Neumann UP, Keitel V, Bode JG, Schneider RK, Tacke F, Levkau B, Lammers T, Fluegen G, Alexandrov T, Collins AL, Nelson G, Oakley F, Mann DA, Roderburg C, Longerich T, Weber A, Villanueva A, Samson AL, Murphy JM, Kramann R, Geisler F, Costa IG, Hengstler JG, Heikenwalder M, Luedde T

Immunity, 2023

doi:10.1016/j.immuni.2023.05.017.

Are phosphatidic acids ubiquitous in mammalian tissues or overemphasized in mass spectrometry imaging applications?

Vandergrift GW, Lukowski JK, Taylor MT, Zemaitis KJ, Alexandrov T, Eder JG, Olson HM, Kyle JE, Anderton C

Analysis & sensing, 2023

doi:10.1002/anse.202200112.

Increasing quantitation in spatial single-cell metabolomics by using fluorescence as ground truth.

Molenaar MR, Shahraz M, Delafiori J, Eisenbarth A, Ekelöf M, Rappez L, Alexandrov T

Frontiers in molecular biosciences, 2022

doi:10.3389/fmolb.2022.1021889.

Developmental phenomics suggests that H3K4 monomethylation confers multi-level phenotypic robustness.

Gandara L, Tsai A, Ekelöf M, Galupa R, Preger-Ben Noon E, Alexandrov T, Crocker J

Cell reports, 2022

doi:10.1016/j.celrep.2022.111832.

An optimized approach and inflation media for obtaining complimentary mass spectrometry-based omics data from human lung tissue.

Lukowski JK, Olson H, Velickovic M, Wang J, Kyle JE, Kim YM, Williams SM, Zhu Y, Huyck HL, McGraw MD, Poole C, Rogers L, Misra R, Alexandrov T, Ansong C, Pryhuber GS, Clair G, Adkins JN, Carson JP, Anderton CR

Frontiers in molecular biosciences, 2022

doi:10.3389/fmolb.2022.1022775.

A user-friendly tool for cloud-based whole slide image segmentation with examples from renal histopathology.

Lutnick B, Manthey D, Becker JU, Ginley B, Moos K, Zuckerman JE, Rodrigues L, Gallan AJ, Barisoni L, Alpers CE, Wang XX, Myakala K, Jones BA, Levi M, Kopp JB, Yoshida T, Zee J, Han SS, Jain S, Rosenberg AZ, Jen KY, Sarder P, Kidney Precision Medicine Project

Communications medicine, 2022

doi:10.1038/s43856-022-00138-z.

A model for network-based identification and pharmacological targeting of aberrant, replication-permissive transcriptional programs induced by viral infection.

Laise P, Stanifer ML, Bosker G, Sun X, Triana S, Doldan P, La Manna F, De Menna M, Realubit RB, Pampou S, Karan C, Alexandrov T, Kruithof-de Julio M, Califano A, Boulant S, Alvarez MJ

Communications biology, 2022

doi:10.1038/s42003-022-03663-8.

Controlled humidity levels for fine spatial detail information in in enzyme-assisted N-Glycan MALDI MSI.

Veličković D, Sharma K, Alexandrov T, Hodgin JB, Anderton CR

Journal of the American Society for Mass Spectrometry, 2022

doi:10.1021/jasms.2c00120.

Rapid and automatic annotation of multiple on-tissue chemical modifications in mass spectrometry imaging with Metaspace.

Larson EA, Forsman TT, Stuart L, Alexandrov T, Lee YJ

Analytical chemistry, 2022

doi:10.1021/acs.analchem.2c00979.

A reference tissue atlas for the human kidney.

Hansen J, Sealfon R, Menon R, Eadon MT, Lake BB, Steck B, Anjani K, Parikh S, Sigdel TK, Zhang G, Velickovic D, Barwinska D, Alexandrov T, Dobi D, Rashmi P, Otto EA, Rivera M, Rose MP, Anderton CR, Shapiro JP, Pamreddy A, Winfree S, Xiong Y, He Y, de Boer IH, Hodgin JB, Barisoni L, Naik AS, Sharma K, Sarwal MM, Zhang K, Himmelfarb J, Rovin B, El-Achkar TM, Laszik Z, He JC, Dagher PC, Valerius MT, Jain S, Satlin LM, Troyanskaya OG, Kretzler M, Iyengar R, Azeloglu EU, Kidney Precision Medicine Project

Science advances, 2022

doi:10.1126/sciadv.abn4965.

Mapping the epithelial-immune cell interactome upon infection in the gut and the upper airways.

Poletti M, Treveil A, Csabai L, Gul L, Modos D, Madgwick M, Olbei M, Bohar B, Valdeolivas A, Turei D, Verstockt B, Triana S, Alexandrov T, Saez-Rodriguez J, Stanifer ML, Boulant S, Korcsmaros T

NPJ systems biology and applications, 2022

doi:10.1038/s41540-022-00224-x.

Quantification reveals early dynamics in Drosophila maternal gradients.

Shlemov A, Alexandrov T, Golyandina N, Holloway D, Baumgartner S, Spirov AV

PloS one, 2021

doi:10.1371/journal.pone.0244701.

SARS-CoV-2 infects the human kidney and drives fibrosis in kidney organoids.

Jansen J, Reimer KC, Nagai JS, Varghese FS, Overheul GJ, de Beer M, Roverts R, Daviran D, Fermin LAS, Willemsen B, Beukenboom M, Djudjaj S, von Stillfried S, van Eijk LE, Mastik M, Bulthuis M, Dunnen WD, van Goor H, Hillebrands JL, Triana SH, Alexandrov T, Timm MC, van den Berge BT, van den Broek M, Nlandu Q, Heijnert J, Bindels EMJ, Hoogenboezem RM, Mooren F, Kuppe C, Miesen P, Grünberg K, Ijzermans T, Steenbergen EJ, Czogalla J, Schreuder MF, Sommerdijk N, Akiva A, Boor P, Puelles VG, Floege J, Huber TB, COVID Moonshot consortium, van Rij RP, Costa IG, Schneider RK, Smeets B, Kramann R

Cell stem cell, 2021

doi:10.1016/j.stem.2021.12.010.

Single-cell proteo-genomic reference maps of the hematopoietic system enable the purification and massive profiling of precisely defined cell states.

Triana S, Vonficht D, Jopp-Saile L, Raffel S, Lutz R, Leonce D, Antes M, Hernández-Malmierca P, Ordoñez-Rueda D, Ramasz B, Boch T, Jann JC, Nowak D, Hofmann WK, Müller-Tidow C, Hübschmann D, Alexandrov T, Benes V, Trumpp A, Paulsen M, Velten L, Haas S

Nature immunology, 2021

doi:10.1038/s41590-021-01059-0.

Quantification of Duloxetine in the Bacterial Culture and Medium to Study Drug-gut Microbiome Interactions.

Phapale PB, Blasche S, Patil KR, Alexandrov T

Bio-protocol, 2021

doi:10.21769/BioProtoc.4214.

HERMES: a molecular-formula-oriented method to target the metabolome.

Giné R, Capellades J, Badia JM, Vughs D, Schwaiger-Haber M, Alexandrov T, Vinaixa M, Brunner AM, Patti GJ, Yanes O

Nature methods, 2021

doi:10.1038/s41592-021-01307-z.

Rapid automated annotation and analysis of N-glycan mass spectrometry imaging data sets using NGlycDB in METASPACE.

Veličković D, Bečejac T, Mamedov S, Sharma K, Ambalavanan N, Alexandrov T, Anderton CR

Analytical chemistry, 2021

doi:10.1021/acs.analchem.1c02347.

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

doi:10.1111/nyas.14678.

Facilitating imaging mass spectrometry of microbial specialized metabolites with METASPACE.

Nguyen DD, Saharuka V, Kovalev V, Stuart L, Del Prete M, Lubowiecka K, De Mot R, Venturi V, Alexandrov T

Metabolites, 2021

doi:10.3390/metabo11080477.

SpaceM reveals metabolic states of single cells.

Rappez L, Stadler M, Triana S, Gathungu RM, Ovchinnikova K, Phapale P, Heikenwalder M, Alexandrov T

Nature methods, 2021

doi:10.1038/s41592-021-01198-0.

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.

Single-cell analyses reveal SARS-CoV-2 interference with intrinsic immune response in the human gut.

Triana S, Metz-Zumaran C, Ramirez C, Kee C, Doldan P, Shahraz M, Schraivogel D, Gschwind AR, Sharma AK, Steinmetz LM, Herrmann C, Alexandrov T, Boulant S, Stanifer ML

Molecular systems biology, 2021

doi:10.15252/msb.202110232.

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

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

Adaptive pixel mass recalibration for mass spectrometry imaging based on locally endogenous biological signals.

La Rocca R, Kune C, Tiquet M, Stuart L, Eppe G, Alexandrov T, De Pauw E, Quinton L

Analytical chemistry, 2021

doi:10.1021/acs.analchem.0c05071.

Public LC-Orbitrap tandem mass spectral library for metabolite identification.

Phapale P, Palmer A, Gathungu RM, Kale D, Brügger B, Alexandrov T

Journal of proteome research, 2021

doi:10.1021/acs.jproteome.0c00930.

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

doi:10.1152/physiolgenomics.00104.2020.

DeepCycle reconstructs a cyclic cell cycle trajectory from unsegmented cell images using convolutional neural networks.

Rappez L, Rakhlin A, Rigopoulos A, Nikolenko S, Alexandrov T

Molecular systems biology, 2020

doi:10.15252/msb.20209474.

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

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

Storage conditions of human kidney tissue sections affect spatial lipidomics analysis reproducibility.

Lukowski JK, Pamreddy A, Velickovic D, Zhang G, Pasa-Tolic L, Alexandrov T, Sharma K, Anderton CR, Kidney Precision Medicine Project

Journal of the American Society for Mass Spectrometry, 2020

doi:10.1021/jasms.0c00256.

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

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

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

Spatial metabolomics and imaging mass spectrometry in the age of artificial intelligence.

Alexandrov T

Annual review of biomedical data science, 2020

doi:10.1146/annurev-biodatasci-011420-031537.

Critical role of type III interferon in controlling SARS-CoV-2 infection in human intestinal epithelial cells.

Stanifer ML, Kee C, Cortese M, Zumaran CM, Triana S, Mukenhirn M, Kraeusslich HG, Alexandrov T, Bartenschlager R, Boulant S

Cell reports, 2020

doi:10.1016/j.celrep.2020.107863.

Probing metabolism in time and space.

Alexandrov T

Science (New York, N.Y.), 2020

doi:10.1126/science.abb3094.

OffsampleAI: artificial intelligence approach to recognize off-sample mass spectrometry images.

Ovchinnikova K, Kovalev V, Stuart L, Alexandrov T

BMC bioinformatics, 2020

doi:10.1186/s12859-020-3425-x.

Response surface methodology as a new approach for finding optimal MALDI matrix spraying parameters for mass spectrometry imaging.

Veličković D, Zhang G, Bezbradica D, Bhattacharjee A, Paša-Tolić L, Sharma K, Alexandrov T, Anderton CR, Anderton CR

Journal of the American Society for Mass Spectrometry, 2020

doi:10.1021/jasms.9b00074.

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

Ovchinnikova K, Stuart L, Rakhlin A, Nikolenko S, Alexandrov T

Bioinformatics (Oxford, England), 2020

doi:10.1093/bioinformatics/btaa085.

DESI-MSI and METASPACE indicates lipid abnormalities and altered mitochondrial membrane components in diabetic renal proximal tubules.

Zhang G, Zhang J, DeHoog RJ, Pennathur S, Anderton CR, Venkatachalam MA, Alexandrov T, Eberlin LS, Sharma K

Metabolomics : Official journal of the Metabolomic Society, 2020

doi:10.1007/s11306-020-1637-8.

PySpacell: a python package for spatial analysis of cell images.

Rose F, Rappez L, Triana SH, Alexandrov T, Genovesio A

2019

doi:10.1002/cyto.a.23955.

Molecular and microbial microenvironments in chronically diseased lungs associated with cystic fibrosis.

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, Ackermann G, Humphrey G, Brouha SS, Spivey T, Lin GY, Bandeira N, Conrad DJ, Rohwer F, Knight R, Alexandrov T, Garg N, Dorrestein PC

mSystems, 2019

doi:10.1128/mSystems.00375-19.

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

biorxiv, 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.

Two-exponential models of gene expression patterns for noisy experimental data.

Alexandrov T, Golyandina N, Holloway D, Shlemov A, Spirov A

Journal of computational biology : a journal of computational molecular cell biology, 2018

doi:10.1089/cmb.2017.0063.

Data-driven rescoring of metabolite annotations significantly improves sensitivity.

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

Analytical chemistry, 2018

doi:10.1021/acs.analchem.8b03224.

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.

Bioactivity-based molecular networking for the discovery of drug leads in natural product bioassay-guided fractionation.

Nothias LF, Nothias-Esposito M, da Silva R, Wang M, Protsyuk I, Zhang Z, Sarvepalli A, Leyssen P, Touboul D, Costa J, Paolini J, Alexandrov T, Litaudon M, Dorrestein PC

Journal of natural products, 2018

doi:10.1021/acs.jnatprod.7b00737.

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

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

Scientific reports, 2018

doi:10.1038/s41598-018-21541-4.

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

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

Nature protocols, 2017

doi:10.1038/nprot.2017.122.

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

Palmer A, Phapale P, Fay D, Alexandrov T

Bioinformatics , 2017

doi:10.1093/bioinformatics/btx786.

Three-Dimensional Microbiome and Metabolome Cartography of a Diseased Human Lung.

Garg N, Wang M, Hyde E, da Silva RR, Melnik AV, Protsyuk I, Bouslimani A, Lim YW, Wong R, Humphrey G, Ackermann G, Spivey T, Brouha SS, Bandeira N, Lin GY, Rohwer F, Conrad DJ, Alexandrov T, Knight R, Dorrestein PC

Cell host & microbe, 2017

doi:10.1016/j.chom.2017.10.001.

Meta-mass shift chemical profiling of metabolomes from coral reefs.

Hartmann AC, Petras D, Quinn RA, Protsyuk I, Archer FI, Ransome E, Williams GJ, Bailey BA, Vermeij MJA, Alexandrov T, Dorrestein PC, Rohwer FL

Proceedings of the National Academy of Sciences of the United States of America, 2017

doi:10.1073/pnas.1710248114.

Coupling Targeted and Untargeted Mass Spectrometry for Metabolome-Microbiome-Wide Association Studies of Human Fecal Samples.

Melnik AV, da Silva RR, Hyde ER, Aksenov AA, Vargas F, Bouslimani A, Protsyuk I, Jarmusch AK, Tripathi A, Alexandrov T, Knight R, Dorrestein PC

Analytical chemistry, 2017

doi:10.1021/acs.analchem.7b01381.

Integration of 3D multimodal imaging data of a head and neck cancer and advanced feature recognition.

Lotz JM, Hoffmann F, Lotz J, Heldmann S, Trede D, Oetjen J, Becker M, Ernst G, Maas P, Alexandrov T, Guntinas-Lichius O, Thiele H, von Eggeling F

Biochimica et biophysica acta, 2016

doi:10.1016/j.bbapap.2016.08.018.

N-acyl Taurines and Acylcarnitines Cause an Imbalance in Insulin Synthesis and Secretion Provoking β Cell Dysfunction in Type 2 Diabetes.

Aichler M, Borgmann D, Krumsiek J, Buck A, MacDonald PE, Fox JEM, Lyon J, Light PE, Keipert S, Jastroch M, Feuchtinger A, Mueller NS, Sun N, Palmer A, Alexandrov T, Hrabe de Angelis M, Neschen S, Tschöp MH, Walch A

Cell metabolism, 2017

doi:10.1016/j.cmet.2017.04.012.

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, Ackermann G, Amir A, Duggan BM, Ryazanov S, Gerwick L, Knight R, Alexandrov T, Bandeira N, Gerwick WH, Dorrestein PC

eLife, 2017

doi:10.7554/eLife.24214.

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

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

Nature methods, 2016

doi:10.1038/nmeth.4072.

Spatial Molecular Architecture of the Microbial Community of a 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, Pevzner PA, Cichewicz RH, Alexandrov T, Dorrestein PC

mSystems, 2016

doi:10.1128/msystems.00139-16.

3D-Plant2cells project: Spatial metabolomic, spatial metagenomic, and 3D mass spectrometry imaging, to explore the impact of pesticides on plant metabolome and microbiota.

Nothias LF, Protsiuc I, Alexandrov T, Knight R, Brunelle A, Touboul D, Dorrestein PC

Planta medica, 2016

doi:10.1055/s-0036-1596119.

Data for spatial analysis of growth anomaly lesions on Montipora capitata coral colonies using 3D reconstruction techniques.

Burns JHR, Alexandrov T, Ovchinnikova K, Gates RD, Takabayashi M

Data in Brief, 2016

doi:10.1016/j.dib.2016.09.009.

Lifestyle chemistries from phones for individual profiling

Bouslimani A, Melnik AV, Xu ZJ, Amir A, da Silva RR, Wang M, Bandeira N, Alexandrov T, Knight R, Dorrestein PC

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2016

doi:10.1073/pnas.1610019113.

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

doi:10.1021/acs.analchem.6b03456.

Investigating the spatial distribution of growth anomalies affecting Montipora capitata corals in a 3-dimensional framework

Burns JHR, Alexandrov T, Ovchinnikova E, Gates RD, Takabayashi M

JOURNAL OF INVERTEBRATE PATHOLOGY, 2016

doi:10.1016/j.jip.2016.08.007.

An approach to optimize sample preparation for MALDI imaging MS of FFPE sections using fractional factorial design of experiments.

Oetjen J, Lachmund D, Palmer A, Alexandrov T, Becker M, Boskamp T, Maass P

Analytical and bioanalytical chemistry, 2016

doi:10.1007/s00216-016-9793-4.

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

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.

Molecular and chemical dialogues in bacteria-protozoa interactions

Song CX, Mazzola M, Cheng X, Oetjen J, Alexandrov T, Dorrestein P, Watrous J, van der Voort M, Raaijmakers JM

SCIENTIFIC REPORTS, 2015

doi:10.1038/srep12837.

Using collective expert judgements to evaluate quality measures of mass spectrometry images.

Palmer A, Ovchinnikova E, Thuné M, Lavigne R, Guével B, Dyatlov A, Vitek O, Pineau C, Borén M, Alexandrov T

Bioinformatics (Oxford, England), 2015

doi:10.1093/bioinformatics/btv266.

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

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

Serial 3D Imaging Mass Spectrometry at Its Tipping Point

Palmer AD, Alexandrov T

ANALYTICAL CHEMISTRY, 2015

doi:10.1021/ac504604g.

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

doi:10.1073/pnas.1424409112.

Spatial Segmentation of MALDI FT-ICR MSI Data: A Powerful Tool to Explore the Head and Neck Tumor In Situ Lipidome.

Krasny L, Hoffmann F, Ernst G, Trede D, Alexandrov T, Havlicek V, Guntinas-Lichius O, von Eggeling F, Crecelius AC

Journal of the American Society for Mass Spectrometry, 2014

doi:10.1007/s13361-014-1018-5.

Progression from cirrhosis to cancer is associated with early ubiquitin post-translational modifications: identification of new biomarkers of cirrhosis at risk of malignancy.

Laouirem S, Le Faouder J, Alexandrov T, Mestivier D, Léger T, Baudin X, Mebarki M, Paradis V, Camadro JM, Bedossa P

The Journal of pathology, 2014

doi:10.1002/path.4398.

The community ecology of microbial molecules.

Quinn RA, Alexandrov T

Journal of chemical ecology, 2014

doi:10.1007/s10886-014-0528-8.

MALDI imaging mass spectrometry: Discrimination of pathophysiological regions in traumatized skeletal muscle by characteristic peptide signatures.

Klein O, Strohschein K, Nebrich G, Oetjen J, Trede D, Thiele H, Alexandrov T, Giavalisco P, Duda GN, von Roth P, Geissler S, Klose J, Winkler T

Proteomics, 2014

doi:10.1002/pmic.201400088.

Histomolecular interpretation of pleomorphic adenomas of the salivary gland by matrix-assisted laser desorption ionization imaging and spatial segmentation.

Ernst G, Guntinas-Lichius O, Hauberg-Lotte L, Trede D, Becker M, Alexandrov T, von Eggeling F

Head & neck, 2014

doi:10.1002/hed.23713.

Tumoral heterogeneity of hepatic cholangiocarcinomas revealed by MALDI imaging mass spectrometry.

Le Faouder J, Laouirem S, Alexandrov T, Ben-Harzallah S, Léger T, Albuquerque M, Bedossa P, Paradis V

Proteomics, 2014

doi:10.1002/pmic.201300463.

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

doi:10.1073/pnas.1314168110.

Analysis and interpretation of imaging mass spectrometry data by clustering mass-to-charge images according to their spatial similarity.

Alexandrov T, Chernyavsky I, Becker M, von Eggeling F, Nikolenko S

Analytical chemistry, 2013

doi:10.1021/ac401420z.

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.

Metabolic profiling directly from the Petri dish using nanospray desorption electrospray ionization imaging mass spectrometry.

Watrous J, Roach P, Heath B, Alexandrov T, Laskin J, Dorrestein PC

Analytical chemistry, 2013

doi:10.1021/ac4023154.

Testing for presence of known and unknown molecules in imaging mass spectrometry.

Alexandrov T, Bartels A

Bioinformatics (Oxford, England), 2013

doi:10.1093/bioinformatics/btt388.

MRI-compatible pipeline for three-dimensional MALDI imaging mass spectrometry using PAXgene fixation.

Oetjen J, Aichler M, Trede D, Strehlow J, Berger J, Heldmann S, Becker M, Gottschalk M, Kobarg JH, Wirtz S, Schiffler S, Thiele H, Walch A, Maass P, Alexandrov T

Journal of proteomics, 2013

doi:10.1016/j.jprot.2013.03.013.

Imaging mass spectrometry reveals modified forms of histone H4 as new biomarkers of microvascular invasion in hepatocellular carcinomas.

Poté N, Alexandrov T, Le Faouder J, Laouirem S, Léger T, Mebarki M, Belghiti J, Camadro JM, Bedossa P, Paradis V

Hepatology (Baltimore, Md.), 2013

doi:10.1002/hep.26433.

Data-independent microbial metabolomics with ambient ionization mass spectrometry.

Rath CM, Yang JY, Alexandrov T, Dorrestein PC

Journal of the American Society for Mass Spectrometry, 2013

doi:10.1007/s13361-013-0608-y.

Segmentation of confocal Raman microspectroscopic imaging data using edge-preserving denoising and clustering.

Alexandrov T, Lasch P

Analytical chemistry, 2013

doi:10.1021/ac303257d.

Microbial metabolic exchange in 3D.

Watrous JD, Phelan VV, Hsu CC, Moree WJ, Duggan BM, Alexandrov T, Dorrestein PC

The ISME journal, 2013

doi:10.1038/ismej.2012.155.

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.

MALDI-imaging segmentation is a powerful tool for spatial functional proteomic analysis of human larynx carcinoma.

Alexandrov T, Becker M, Guntinas-Lichius O, Ernst G, von Eggeling F

Journal of cancer research and clinical oncology, 2013

doi:10.1007/s00432-012-1303-2.

Learning how to run a lab: interviews with principal investigators.

Alexandrov T, Bourne PE

PLoS computational biology, 2013

doi:10.1371/journal.pcbi.1003349.

The young PI buzz: learning from the organizers of the Junior Principal Investigator Meeting at ISMB-ECCB 2013.

de Ridder J, Bromberg Y, Michaut M, Satagopam VP, Corpas M, MacIntyre G, Alexandrov T

PLoS computational biology, 2013

doi:10.1371/journal.pcbi.1003350.

Interspecies interactions stimulate diversification of the Streptomyces coelicolor secreted metabolome.

Traxler MF, Watrous JD, Alexandrov T, Dorrestein PC, Kolter R

mBio, 2013

doi:10.1128/mbio.00459-13.

New analysis workflow for MALDI imaging mass spectrometry: application to the discovery and identification of potential markers of childhood absence epilepsy.

Lagarrigue M, Alexandrov T, Dieuset G, Perrin A, Lavigne R, Baulac S, Thiele H, Martin B, Pineau C

Journal of proteome research, 2012

doi:10.1021/pr3006974.

Molecular analysis of model gut microbiotas by imaging mass spectrometry and nanodesorption electrospray ionization reveals dietary metabolite transformations.

Rath CM, Alexandrov T, Higginbottom SK, Song J, Milla ME, Fischbach MA, Sonnenburg JL, Dorrestein PC

Analytical chemistry, 2012

doi:10.1021/ac302039u.

Magnification of label maps with a topology-preserving level-set method.

Trede D, Alexandrov T, Sagiv C, Maass P

IEEE transactions on image processing : a publication of the IEEE Signal Processing Society, 2012

doi:10.1109/tip.2012.2199325.

Application of matrix-assisted laser desorption/ionization mass spectrometric imaging for photolithographic structuring.

Crecelius AC, Steinacker R, Meier A, Alexandrov T, Vitz J, Schubert US

Analytical chemistry, 2012

doi:10.1021/ac301616v.

Exploring three-dimensional matrix-assisted laser desorption/ionization imaging mass spectrometry data: three-dimensional spatial segmentation of mouse kidney.

Trede D, Schiffler S, Becker M, Wirtz S, Steinhorst K, Strehlow J, Aichler M, Kobarg JH, Oetjen J, Dyatlov A, Heldmann S, Walch A, Thiele H, Maass P, Alexandrov T

Analytical chemistry, 2012

doi:10.1021/ac300673y.

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

doi:10.1073/pnas.1203689109.

Proteomic pattern analysis discriminates among multiple sclerosis-related disorders.

Komori M, Matsuyama Y, Nirasawa T, Thiele H, Becker M, Alexandrov T, Saida T, Tanaka M, Matsuo H, Tomimoto H, Takahashi R, Tashiro K, Ikegawa M, Kondo T

Annals of neurology, 2012

doi:10.1002/ana.22633.