2015

Palmer A, Ovchinnikova E, Thune M, Lavigne R, Guevel B, Dyatlov A, Vitek O, Pineau C, Boren M, Alexandrov T.
Using collective expert judgements to evaluate quality measures of mass spectrometry images.
Bioinformatics, 2015, 31 (12): i375-i384. 
http://bioinformatics.oxfordjournals.org/content/31/12/i375.full.pdf+html

Diehl HC, Beine B, Elm J, Trede D, Ahrens M, Eisenacher M, Marcus K, Meyer HE, Henkel C.
The challenge of on-tissue digestion for MALDI MSI- a comparison of different protocols to improve imaging experiments.
Anal Bioanal Chem. 2015 Mar;407(8):2223-43.
doi: 10.1007/s00216-014-8345-z.

Boulimani 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 P.
Molecular cartography of the human skin surface in 3D.
PNAS, 112(17), E2120-E2129.
http://www.pnas.org/content/early/2015/03/26/1424409112

Palmer A, Alexandrov T.
Serial 3D imaging mass spectrometry at its tipping point.
Analytical Chemistry, 87(8):4055-62.
http://pubs.acs.org/doi/pdf/10.1021/ac504604g

Oetjen J, Veselkov K, Watrous J, McKenzie JS, Becker M, Hauberg-Lotte L, Strittmatter N, Mróz AK, Hoffmann F, Trede D, Kobarg JH, Palmer Schiffler S, Steinhorst K, Aichler M, Goldin R, Guntinas-Lichius O, von Eggeling F, Thiele H, Maedler K, Walch A, Maass P, Dorrestein P, Takats Z, Alexandrov T.
Benchmark datasets for 3D MALDI- and DESI-Imaging Mass Spectrometry.

2014

Krasny L, Hoffmann F, Ernst G, Trede D, Alexandrov T, Havlicek V, Guntinas-Lichius O, von Eggeling F, Crecelius AC.
Spatial segmentation of MALDI FT-ICR MSI data: A powerful tool to explore head and neck tumor in situ lipidome.

Laouirem S, Le Faouder J, Alexandrov T, Mestivier D, Léger T, Baudin X, Mebarki M, Paradis V, Camadro J, Bedossa P.
MALDI imaging mass spectrometry reveals novel ubiquitin modification as a biomarker of cirrhosis progressing to hepatocellular carcinoma.

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

Lagarrigue M, Lavigne R, Tabet E, Genet V, Thomé JF, Rondel K, Guével B, Multigner L, Samson M, Pineau C.
Localization and in situ absolute quantification of chlordecone in the mouse liver by MALDI Imaging.
http://pubs.acs.org/doi/abs/10.1021/ac500313s.

Bouslimani A, Sanchez LM, Garg N, Dorrestein PC.
Mass spectrometry of natural products: current, emerging and future technologies.
Faouder JF, Laouirem S, Alexandrov T, Ben-Harzallah S, Albuquerque M, Bedossa P, Paradis V.
Tumoral heterogeneity of intrahepatic cholangiocarcinomas revealed by MALDI imaging mass spectrometry.
DOI: 10.1002/pmic.201300463.

Ernst G, Guntinas-Lichius O, Hauberg-Lotte L, Trede D, Becker M, Alexandrov T, von Eggeling F.
Histomolecular interpretation of pleomorphic adenomas of the salivary gland by MALDI imaging and spatial segmentation.
2014 Jun 19.
DOI: 10.1002/hed.23713

2013

Hoelscher D,  Dhakshinamoorthy S, Alexandrov A, Becker M, Bretschneider T, Buerkert A, Crecelius AC, De Waele D, Elsen A, Heckel DG, Heklau H, Hertweck H, Kai M, Knop K, Krafft C, Maddula RK, Matthaeus C, Popp J, Schneider B, Schubert US, Sikora RA, Svatos A, Swennen RL.
Phenalenone-type phytoalexins mediate resistance of banana plants (Musa spp.) to the burrowing nematode Radopholus similis.
PNAS, 

De Ridder J, Bromberg, Y, Michaut M, Satagopam VP, Corpas M, Macintyre G, Alexandrov T.
The young PI buzz: Learning from the organizers of the Junior Principal Investigator Meeting at ISMB-ECCB 2013.
PLoS Computational Biology, 9(11): e1003350.
DOI: 10.1371/journal.pcbi.1003350

Alexandrov T, Bourne PE.
Learning how to run a lab: Interviews with principal investigators.
PLoS Computational Biology, 9(11): e1003349.
DOI: 10.1371/journal.pcbi.1003349

Bartels A, Duelk P, Trede D, Alexandrov T, Maass P.
Compressed sensing in imaging mass spectrometry.
Inverse Problems, 2013;29(12).
doi:10.1088/0266-5611/29/12/125015

Alexandrov T, Chernyavsky I, Becker M, van Eggeling F, Nikolenko S.
Analysis and interpretation of imaging mass spectrometry data by clustering mass-to-charge images according to their spatial similarity.
Analytical chemistry, 2013;85(23):11189–11195.
DOI: 10.1021/ac401420z

Alexandrov T, and Bartels A.
Testing for presence of known and unknown molecules in imaging mass spectrometry.
Bioinformatics, 2013;29(18):2335-2342.
http://bioinformatics.oxfordjournals.org/content/early/2013/07/27/bioinformatics.btt388

Alexandrov T, and Lasch P.
Segmentation of Confocal Raman Microspectroscopic Imaging Data using Edge-Preserving Denoising and Clustering.
Analytical Chemistry, 2013;85(12):5676–5683.
http://pubs.acs.org/doi/abs/10.1021/ac303257d.

Rath CM, Yang JY, Alexandrov T, and Dorrestein PC.
Data-independent microbial metabolomics with ambient ionization mass spectrometry.
Journal of American Society for Mass Spectrometry,  2013;24(8):1167-76.
http://link.springer.com/article/10.1007%2Fs13361-013-0608-y

Pote N, Alexandrov T, Lefaouder J, Laouirem S, Léger T, Mebarki M, Belghiti J, Camadro JM, Bedossa P, and Paradis V.
Imaging mass spectrometry reveals modified forms of Histone H4 as new biomarkers of microvascular invasion in hepatocellular carcinomas.
Hepathology, 2013;58(3):983-994.
http://onlinelibrary.wiley.com/doi/10.1002/hep.26433/abstract

Watrous JD, Roach P, Heath B, Alexandrov T, Laskin J, Dorrestein PC.
Metabolic profiling directly from the Petri dish using nanoDESI imaging mass spectrometry.
Analytical Chemistry, 2013;85(21):10385-10391.
http://pubs.acs.org/doi/abs/10.1021/ac4023154

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, and Alexandrov T.
MRI-compatible pipeline for three-dimensional MALDI imaging mass spectrometry using PAXgene fixation.
Journal of Proteomics, 2013;90:52-60.
http://www.sciencedirect.com/science/article/pii/S1874391913001607

Traxler MF, Watrous JD, Alexandrov T, Dorrestein PC, Kolter R.
Interspecies interactions stimulate diversification of the Streptomyces coelicolor secreted metabolome.
mBio, 4(4):e00459-13.
http://mbio.asm.org/content/4/4/e00459-13

Watrous JD, Phelan W, Hsu CC, Moree WJ, Duggan BM, Alexandrov T, and Dorrestein PC.
Microbial metabolic exchange in 3D.
ISME J., 7(4): 770-780.
doi: 10.1038/ismej.2012.155.
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