EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany

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Biography

  • PhD 2007, St. Petersburg State University.
    Postdoctoral Researcher, University of Bremen.
    Group Leader, University of Bremen.
    Assistant Adjunct Professor, University of California San Diego.
    Team leader at EMBL since 2014.

Publications

Total: 51 publication(s)

2016

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. (2016)

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

Biochim. Biophys. Acta doi: 10.1016/j.bbapap.2016.08.018
Europe PMC | doi

Oetjen J, Lachmund D, Palmer A, Alexandrov T, Becker M, Boskamp T, Maass P. (2016)

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

Anal Bioanal Chem
Europe PMC

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.
Europe PMC

Andrew Palmer, Dennis Trede, Theodore Alexandrov. (2016)

Where imaging mass spectrometry stands: here are the numbers

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


2015

Song CX, Mazzola M, Cheng X, Oetjen J, Alexandrov T, Dorrestein P, Watrous J, van der Voort M, Raaijmakers JM. (2015)

Molecular and chemical dialogues in bacteria-protozoa interactions

Sci Rep 5 doi: 10.1038/srep12837
Europe PMC | doi

Palmer A, Ovchinnikova E, Thuné M, Lavigne R, Guével B, Dyatlov A, Vitek O, Pineau C, Borén M, Alexandrov T. (2015)

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

Bioinformatics 31(12):i375-i384. doi: 10.1093/bioinformatics/btv266
Europe PMC | doi

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. (2015)

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

Gigascience 4 doi: 10.1186/s13742-015-0059-4
Europe PMC | doi

Palmer AD, Alexandrov T. (2015)

Serial 3D Imaging Mass Spectrometry at Its Tipping Point

Anal. Chem. 87(8):4055-4062. doi: 10.1021/ac504604g
Europe PMC | doi

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. (2015)

Molecular cartography of the human skin surface in 3D.

Proc. Natl. Acad. Sci. U.S.A. doi: 10.1073/pnas.1424409112
Europe PMC | doi


2014

Laouirem S, Le Faouder J, Alexandrov T, Mestivier D, Léger T, Baudin X, Mebarki M, Paradis V, Camadro JM, Bedossa P. (2014)

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

J. Pathol. 234(4):452-463. doi: 10.1002/path.4398
Europe PMC | doi

Quinn RA, Alexandrov T. (2014)

The community ecology of microbial molecules.

J. Chem. Ecol. 40(11-12):1161-1162. doi: 10.1007/s10886-014-0528-8
Europe PMC | doi

Krasny L, Hoffmann F, Ernst G, Trede D, Alexandrov T, Havlicek V, Guntinas-Lichius O, von Eggeling F, Crecelius AC. (2014)

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

J. Am. Soc. Mass Spectrom. doi: 10.1007/s13361-014-1018-5
Europe PMC | doi

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. (2014)

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

Proteomics 14(20):2249-2260. doi: 10.1002/pmic.201400088
Europe PMC | doi

Ernst G, Guntinas-Lichius O, Hauberg-Lotte L, Trede D, Becker M, Alexandrov T, von Eggeling F. (2014)

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

Head Neck doi: 10.1002/hed.23713
Europe PMC | doi

Le Faouder J, Laouirem S, Alexandrov T, Ben-Harzallah S, Léger T, Albuquerque M, Bedossa P, Paradis V. (2014)

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

Proteomics 14(7-8):965-972. doi: 10.1002/pmic.201300463
Europe PMC | doi

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. (2014)

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

Proc. Natl. Acad. Sci. U.S.A. 111(1):105-110. doi: 10.1073/pnas.1314168110
Europe PMC | doi


2013

Alexandrov T, Chernyavsky I, Becker M, von Eggeling F, Nikolenko S. (2013)

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

Anal. Chem. 85(23):11189-11195. doi: 10.1021/ac401420z
Europe PMC | doi

Bartels A, Dulk P, Trede D, Alexandrov T, Maass P. (2013)

Compressed sensing in imaging mass spectrometry

INVERSE PROBL 29 doi: 10.1088/0266-5611/29/12/125015
doi

Watrous J, Roach P, Heath B, Alexandrov T, Laskin J, Dorrestein PC. (2013)

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

Anal. Chem. 85(21):10385-10391. doi: 10.1021/ac4023154
Europe PMC | doi

Alexandrov T, Bartels A. (2013)

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

Bioinformatics 29(18):2335-2342. doi: 10.1093/bioinformatics/btt388
Europe PMC | doi

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. (2013)

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

J Proteomics 90:52-60. doi: 10.1016/j.jprot.2013.03.013
Europe PMC | doi

Poté N, Alexandrov T, Le Faouder J, Laouirem S, Léger T, Mebarki M, Belghiti J, Camadro JM, Bedossa P, Paradis V. (2013)

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

Hepatology 58(3):983-994. doi: 10.1002/hep.26433
Europe PMC | doi

Rath CM, Yang JY, Alexandrov T, Dorrestein PC. (2013)

Data-independent microbial metabolomics with ambient ionization mass spectrometry.

J. Am. Soc. Mass Spectrom. 24(8):1167-1176. doi: 10.1007/s13361-013-0608-y
Europe PMC | doi

Alexandrov T, Lasch P. (2013)

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

Anal. Chem. 85(12):5676-5683. doi: 10.1021/ac303257d
Europe PMC | doi

Watrous JD, Phelan VV, Hsu CC, Moree WJ, Duggan BM, Alexandrov T, Dorrestein PC. (2013)

Microbial metabolic exchange in 3D.

ISME J 7(4):770-780. doi: 10.1038/ismej.2012.155
Europe PMC | doi

Alexandrov T, Becker M, Guntinas-Lichius O, Ernst G, von Eggeling F. (2013)

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

J. Cancer Res. Clin. Oncol. 139(1):85-95. doi: 10.1007/s00432-012-1303-2
Europe PMC | doi

Ovchinnikova E, Montazeri N, Alexandrov T, Hobbs J, McCord M, Mulkar-Mehta R. (2013)

Abductive Reasoning with a Large Knowledge Base for Discourse Processing

In: Bunt H, Bos J, Pulman S (eds.), Computing Meaning, vol 4. Text, Speech and Language Technology. Springer Netherlands. pp 107-127.doi: 10.1007/978-94-007-7284-7_7
doi


2012

Alexandrov T, Bourne PE. (2012)

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

PLoS Comput. Biol. 9(11) doi: 10.1371/journal.pcbi.1003349
Europe PMC | doi

de Ridder J, Bromberg Y, Michaut M, Satagopam VP, Corpas M, MacIntyre G, Alexandrov T. (2012)

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

PLoS Comput. Biol. 9(11) doi: 10.1371/journal.pcbi.1003350
Europe PMC | doi

Traxler MF, Watrous JD, Alexandrov T, Dorrestein PC, Kolter R. (2012)

Interspecies interactions stimulate diversification of the Streptomyces coelicolor secreted metabolome.

MBio 4(4) doi: 10.1128/mbio.00459-13
Europe PMC | doi

Lagarrigue M, Alexandrov T, Dieuset G, Perrin A, Lavigne R, Baulac S, Thiele H, Martin B, Pineau C. (2012)

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

J. Proteome Res. 11(11):5453-5463. doi: 10.1021/pr3006974
Europe PMC | doi

Rath CM, Alexandrov T, Higginbottom SK, Song J, Milla ME, Fischbach MA, Sonnenburg JL, Dorrestein PC. (2012)

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

Anal. Chem. 84(21):9259-9267. doi: 10.1021/ac302039u
Europe PMC | doi

Trede D, Alexandrov T, Sagiv C, Maass P. (2012)

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

IEEE Trans Image Process 21(9):4040-4053. doi: 10.1109/tip.2012.2199325
Europe PMC | doi

Crecelius AC, Steinacker R, Meier A, Alexandrov T, Vitz J, Schubert US. (2012)

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

Anal. Chem. 84(16):6921-6925. doi: 10.1021/ac301616v
Europe PMC | doi

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. (2012)

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

Anal. Chem. 84(14):6079-6087. doi: 10.1021/ac300673y
Europe PMC | doi

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. (2012)

Mass spectral molecular networking of living microbial colonies.

Proc. Natl. Acad. Sci. U.S.A. 109(26):E1743-52. doi: 10.1073/pnas.1203689109
Europe PMC | doi

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. (2012)

Proteomic pattern analysis discriminates among multiple sclerosis-related disorders.

Ann. Neurol. 71(5):614-623. doi: 10.1002/ana.22633
Europe PMC | doi

Alexandrov T, Bianconcini S, Dagum EB, Maass P, McElroy TS. (2012)

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

ECONOMET REV 31:593-624. doi: 10.1080/07474938.2011.608032
doi


2011

Alexandrov T. (2011)

MALDI imaging mass spectrometry: statistical data analysis and current computational challenges.

BMC Bioinformatics 13 Suppl 16 doi: 10.1186/1471-2105-13-s16-s11
Europe PMC | doi

Alexandrov T, Meding S, Trede D, Kobarg JH, Balluff B, Walch A, Thiele H, Maass P. (2011)

Super-resolution segmentation of imaging mass spectrometry data: Solving the issue of low lateral resolution.

J Proteomics 75(1):237-245. doi: 10.1016/j.jprot.2011.08.002
Europe PMC | doi

Trede D, Kobarg JH, Oetjen J, Thiele H, Maass P, Alexandrov T. (2011)

On the importance of mathematical methods for analysis of MALDI-imaging mass spectrometry data.

J Integr Bioinform 9(1) doi: 10.2390/biecoll-jib-2012-189
Europe PMC | doi

Bruand J, Alexandrov T, Sistla S, Wisztorski M, Meriaux C, Becker M, Salzet M, Fournier I, Macagno E, Bafna V. (2011)

AMASS: algorithm for MSI analysis by semi-supervised segmentation.

J. Proteome Res. 10(10):4734-4743. doi: 10.1021/pr2005378
Europe PMC | doi

Crecelius AC, Alexandrov T, Schubert US. (2011)

Application of matrix-assisted laser desorption/ionization mass spectrometric imaging to monitor surface changes of UV-irradiated poly(styrene) films.

Rapid Commun. Mass Spectrom. 25(19):2809-2814. doi: 10.1002/rcm.5164
Europe PMC | doi

Alexandrov T, Kobarg JH. (2011)

Efficient spatial segmentation of large imaging mass spectrometry datasets with spatially aware clustering.

Bioinformatics 27(13):i230-8. doi: 10.1093/bioinformatics/btr246
Europe PMC | doi

Watrous JD, Alexandrov T, Dorrestein PC. (2011)

The evolving field of imaging mass spectrometry and its impact on future biological research.

J Mass Spectrom 46(2):209-222. doi: 10.1002/jms.1876
Europe PMC | doi


2010

Alexandrov T, Becker M, Deininger SO, Ernst G, Wehder L, Grasmair M, von Eggeling F, Thiele H, Maass P. (2010)

Spatial segmentation of imaging mass spectrometry data with edge-preserving image denoising and clustering.

J. Proteome Res. 9(12):6535-6546. doi: 10.1021/pr100734z
Europe PMC | doi

Balog CI, Alexandrov T, Derks RJ, Hensbergen PJ, van Dam GJ, Tukahebwa EM, Kabatereine NB, Thiele H, Vennervald BJ, Mayboroda OA, Deelder AM. (2010)

The feasibility of MS and advanced data processing for monitoring Schistosoma mansoni infection.

Proteomics Clin Appl 4(5):499-510. doi: 10.1002/prca.200900158
Europe PMC | doi


2009

Alexandrov T. (2009)

A Method of Trend Extraction Using Singular Spectrum Analysis

REVSTAT-STAT J 7:1-22.

Alexandrov T, Decker J, Mertens B, Deelder AM, Tollenaar RA, Maass P, Thiele H. (2009)

Biomarker discovery in MALDI-TOF serum protein profiles using discrete wavelet transformation.

Bioinformatics 25(5):643-649. doi: 10.1093/bioinformatics/btn662
Europe PMC | doi

Alexandrov T, Golyandina N, Timofeyev A. (2009)

Dependence of accuracy of ESPRIT estimates on signal eigenvalues: the case of a noisy sum of two real exponentials.

Proc Appl Math Mech 8(1):10761-10762. doi: 10.1002/pamm.200810761
Europe PMC | doi


2008

Alexandrov T, Golyandina N, Spirov A. (2008)

Singular Spectrum Analysis of Gene Expression Profiles of Early Drosophila embryo: Exponential-in-Distance Patterns.

Res Lett Signal Process 2008 doi: 10.1155/2008/825758
Europe PMC | doi