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Publikationen von Dr. Fedor Alexandrov

Buchkapitel (2)

  1. E. Ovchinnikova, N. Montazeri, F. Alexandrov, J. Hobbs, M. C. McCord, R. Mulkar-Mehta .
    Abductive Reasoning with a Large Knowledge Base for Discourse Processing.
    Computing Meaning, 47, S. 107-127, Springer Verlag, 2013.

    DOI: 10.1007/978-94-007-7284-7_7

  2. J. H. Kobarg, F. Alexandrov.
    Efficient spatial segmentation of hyper-spectral 3D volume data.
    Algorithms from and for Nature and Life, B. Lausen, D. Van den Poel, A. Ultsch (Hrsg.), Studies in Classification, Data Analysis, and Knowledge Organization, S. 95-103, Springer Verlag, 2013.

    DOI: 10.1007/978-3-319-00035-0_9

Zeitschriftenartikel (41)

  1. J. Oetjen, D. Lachmund, A. Palmer, F. Alexandrov, M. Becker, T. Boskamp, P. Maaß.
    An approach to optimize sample preparation for MALDI imaging MS of FFPE sections using fractional factorial design of experiments.
    Analytical and Bioanalytical Chemistry, 408(24):6729-40, 2016.

    DOI: 10.1007/s00216-016-9793-4

  2. F. Hoffmann, J. M. Lotz, J. Lotz, S. Heldmann, D. Trede, J. Oetjen, M. Becker, G. Ernst, P. Maaß, F. Alexandrov, O. Guntinas-Lichius, H. Thiele, F. von Eggeling.
    Integration of 3D multimodal imaging data of a head and neck cancer and advanced feature recognition.
    BBA - Proteins and Proteomics, , 2016.

    DOI: 10.1016/j.bbapap.2016.08.018

  3. J. Oetjen, K. Veselkov, J. Watrous, J. McKenzie, M. Becker, L. Hauberg-Lotte, J. H. Kobarg, A. K. Mróz, N. Strittmatter, F. Hoffmann, D. Trede, A. Palmer, S. Schiffler, K. Steinhorst, M. Aichler, R. Goldin, O. Guntinas-Lichius, F. von Eggeling, H. Thiele, K. Mädler, A. Walch, P. Maaß, P. C. Dorrestein, Z. Takats, F. Alexandrov.
    Benchmark datasets for 3D MALDI- and DESI-imaging mass spectrometry.
    GigaScience, 4, 2015.

    DOI: 10.1186/s13742-015-0059-4

  4. C. Song, M. Mazzola, X. Cheng, J. Oetjen, F. Alexandrov, P. C. Dorrestein, J. Watrous, M. van der Voort, J. M. Raaijmakers.
    Molecular and chemical dialogues in bacteria-protozoa interactions.
    Scientific Reports, Article ID 12837 5, 2015.

    DOI: 10.1038/srep12837

  5. G. Ernst, O. Guntinas-Lichius, L. Hauberg-Lotte, D. Trede, M. Becker, F. Alexandrov, F. von Eggeling.
    Histomolecular interpretation of pleomorphic adenomas of the salivary gland by matrix-assisted laser desorption ionization imaging and spatial segmentation.
    Head & Neck, 37(7), 2014.

    DOI: 10.1002/hed.23713

  6. O. Klein, K. Strohschein, G. Nebrich, J. Oetjen, D. Trede, H. Thiele, F. Alexandrov, P. Giavalisco, G. N. Duda, P. Roth von, S. Geissler, J. Klose, T. Winkler.
    MALDI imaging mass spectrometry: Discrimination of pathophysiological regions in traumatized skeletal muscle by characteristic peptide signatures.
    Proteomics, 14(20):2249-2260, 2014.

    DOI: 10.1002/pmic.201400088

  7. F. Alexandrov, I. Cherniavskii, M. Becker, F. von Eggeling.
    Analysis and interpretation of imaging mass spectrometry data by clustering mass-to-charge images according to their spatial similarity.
    Analytical Chemistry, 85(23):11189-11195, 2013.

    DOI: 10.1021/ac401420z

  8. A. Bartels, P. Dülk, D. Trede, F. Alexandrov, P. Maaß.
    Compressed sensing in imaging mass spectrometry.
    Inverse Problems, 29(12), 125015 (24pp), IOPscience, 2013.

    Selected as one of the highlights among all articles published in IOP "Inverse Problems" in 2013.

    DOI: 10.1088/0266-5611/29/12/125015

  9. C. M. Rath, J. Y. Yang, F. Alexandrov, P. C. Dorrestein.
    Data-independent microbial metabolomics with ambient ionization mass spectrometry.
    Journal of Mass Spectrometry, 24(8):1167-1176, 2013.

    DOI: 10.1007/s13361-013-0608-y

  10. F. Alexandrov.
    Imaging mass spectrometry reveals modified forms of histone H4 as new biomarkers of microvascular invasion in hepatocellular carcinomas.
    Hepatology, 58(3):983-94, 2013.

    DOI: 10.1002/hep.26433

  11. J. Watrous, F. Alexandrov, P. C. Dorrestein.
    Interspecies interactions stimulate diversification of the Streptomyces coelicolor secreted metabolome.
    mBio, 4(4):e00459-13, 2013.

    DOI: 10.1128/mBio.00459-13

  12. F. Alexandrov, P. E. . Bourne.
    Learning how to run a lab: interviews with Principal Investigators.
    POLS Computational Biology, 9(11), e1003349 S., 2013.

    DOI: 10.1371/journal.pcbi.1003349

  13. J. Watrous, P. Roach, B. S. Heath, F. Alexandrov, J. Laskin, P. C. Dorrestein.
    Metabolic Profiling Directly from the Petri Dish Using Nanospray Desorption Electrospray Ionization Imaging Mass Spectrometry.
    Analytical Chemistry, 85(21), 10385–10391, 2013.

    DOI: 10.1021/ac4023154

  14. J. Watrous, F. Alexandrov, P. C. Dorrestein.
    Microbial metabolic exchange in 3D.
    ISME Journal, 7(4):770-780, 2013.

    DOI: 10.1038/ismej.2012.155

  15. J. Oetjen, M. Aichler, D. Trede, J. Strehlow, J. Berger, S. Heldmann, M. Becker, M. Gottschalk, J. H. Kobarg, S. Wirtz, S. Schiffler, H. Thiele, A. Walch, P. Maaß, F. Alexandrov.
    MRI-compatible pipeline for three-dimensional MALDI imaging mass spectrometry using PAXgene fixation .
    Journal of Proteomics, 90:52-60, 2013.

    DOI: 10.1016/j.jprot.2013.03.013

  16. F. Alexandrov, M. Becker, A. C. Crecelius.
    Phenalenone-type phytoalexins mediate resistance of banana plants (Musa spp.) to the burrowing nematode Radopholus similis.
    Proceedings of the National Academy of Sciences of the United States of America , , 2013.

    DOI: 10.1073/pnas.1314168110

  17. F. Alexandrov, P. Lasch.
    Segmentation of Confocal Raman Microspectroscopic Imaging Data Using Edge-Preserving Denoising and Clustering.
    Analytical Chemistry, 85(12):5676-83, 2013.

    DOI: 10.1021/ac303257d

  18. F. Alexandrov, A. Bartels.
    Testing for presence of known and unknown molecules in imaging mass spectrometry.
    Bioinformatics, 29(18):2335-2342, 2013.

    DOI: 10.1093/bioinformatics/btt388

  19. F. Alexandrov.
    The Young PI Buzz: Learning from the Organizers of the Junior Principal Investigator Meeting at ISMB-ECCB 2013.
    POLS Computational Biology, 9(11), e10003350 S., 2013.

    DOI: 10.1371/journal.pcbi.1003350

  20. M. Lagarrigue, F. Alexandrov, G. Dieuset, A. Perrin, R. Lavigne, S. Baulac, H. Thiele, B. Martin.
    A new analysis workflow for MALDI imaging mass spectrometry: application to the discovery and identification of potential markers of Childhood Absence Epilepsy.
    Journal of Proteome Research, 11(11):5453-5463, 2012.

    DOI: 10.1021/pr3006974

  21. F. Alexandrov, S. Bianconcini, E. B. Dagum, P. Maaß, T. S. McElroy.
    A review of some modern approaches to the problem of trend extraction.
    Econometric Reviews, 31(6):593-624, Taylor & Francis, 2012.

    DOI: 10.1080/07474938.2011.608032

  22. A. C. Crecelius, F. Alexandrov, U. S. Schubert.
    Application of MALDI-MSI for photolithographic structuring.
    Analytical Chemistry, 84(16):6921-6925, 2012.

    DOI: 10.1021/ac301616v

  23. D. Trede, S. Schiffler, M. Becker, S. Wirtz, K. Steinhorst, J. Strehlow, M. Aichler, J. H. Kobarg, J. Oetjen, A. Dyatlov, S. Heldmann, A. Walch, H. Thiele, P. Maaß, F. Alexandrov.
    Exploring Three-Dimensional Matrix-Assisted Laser Desorption/Ionization Imaging Mass Spectrometry Data: Three-Dimensional Spatial Segmentation of Mouse Kidney.
    Analytical Chemistry, 84(14):6079-6087, 2012.

    DOI: 10.1021/ac300673y

  24. D. Trede, F. Alexandrov, C. Sagiv, P. Maaß.
    Magnification of Label Maps with a Topology-Preserving Level-Set Method.
    IEEE Transactions on Image Processing, 21(9):4040-4053 , 2012.

    DOI: 10.1109/TIP.2012.2199325

  25. F. Alexandrov.
    MALDI imaging mass spectrometry: statistical data analysis and current computational challenges.
    BMC Bioinformatics, 13 (Suppl 16): S11; IF2.8 , 2012.

    DOI: 10.1186/1471-2105-13-S16-S11

  26. F. Alexandrov, M. Becker, O. Guntinas-Lichius, G. Ernst, F. von Eggeling.
    MALDI-imaging segmentation is a powerful tool for spatial functional proteomic analysis of human larynx carcinoma.
    Journal of Cancer Research and Clinical Oncology, 139(1):85-95, 2012.

    DOI: 10.1007/s00432-012-1303-2

  27. N. Bandeira, J. Watrous, P. Roach, F. Alexandrov, B. S. Heath, J. Y. Yang, R. D. Kersten, M. van der Voort, K. Pogliano, H. Gross, J. M. Raaijmakers, B. S. Moore, J. Laskin, P. C. Dorrestein.
    Mass spectral molecular networking of living microbial colonies.
    Proceedings of the National Academy of Sciences of the United States of America , 109(26):1743-1752, 2012.

    DOI: 10.1073/pnas.1203689109

  28. C. M. Rath, F. Alexandrov, S. K. Higginbottom, J. Song, J. L. Sonnenburg, M. E. Milla, M. A. Fischbach, P. C. Dorrestein.
    Molecular analysis of model gut microbiotas by imaging mass spectrometry and nano-desorption electrospray ionization reveals dietary metabolite transformations.
    Analytical Chemistry, 84(21):9259-9267, 2012.

    DOI: 10.1021/ac302039u

  29. D. Trede, J. H. Kobarg, J. Oetjen, H. Thiele, P. Maaß, F. Alexandrov.
    On the Importance of Mathematical Methods for Analysis of MALDI-Imaging Mass Spectrometry Data.
    Journal of Integrative Bioinformatics, 9(1), 189 S., 2012.

    DOI: 10.2390/biecoll-jib-2012-189
    online unter: JIB open access

  30. J. Bruand, F. Alexandrov, S. Sistla, M. Wisztorski, C. Meriaux, M. Becker, M. Salzet, I. Fournier, E. Macagno, V. Bafna.
    AMASS: algorithm for MSI (mass spectrometric imaging) analysis by semi-supervised segmentation.
    Journal of Proteome Research, 10(10):4734-4743, 2011.

    DOI: 10.1021/pr2005378

  31. A. C. Crecelius, F. Alexandrov, U. S. Schubert.
    Application of MALDI-MSI to monitor surface changes of UV irradiated poly(styrene) films.
    Rapid Communications in Mass Spectrometry, 25(19):2809-14, 2011.

    DOI: 10.1002/rcm.5164

  32. F. Alexandrov, J. H. Kobarg.
    Efficient spatial segmentation of large imaging mass spectrometry datasets with spatially aware clustering.
    Bioinformatics, 27(13):i230-i238, 2011.

    DOI: 10.1093/bioinformatics/btr246

  33. M. Komori, Y. Matsuyama, T. Nirasawa, H. Thiele, M. Becker, F. Alexandrov, T. Saida, M. Tanaka, H. Matsuo, H. Tomimoto, R. Takahashi, K. Tashiro, M. Ikegawa, T. Kondo.
    Proteomic pattern analysis discriminates among multiple sclerosis-related disorders.
    Annals of Neurology, 71(5):614-623, 2011.

    DOI: 10.1002/ana.22633

  34. F. Alexandrov, S. Meding, D. Trede, J. H. Kobarg, B. Balluff, A. Walch, H. Thiele, P. Maaß.
    Super-resolution segmentation of imaging mass spectrometry data: Solving the issue of low lateral resolution.
    Journal of Proteomics, 75(1):237-245, Elsevier, 2011.

    DOI: 10.1016/j.jprot.2011.08.002

  35. J. Watrous, F. Alexandrov, P. C. Dorrestein.
    The evolving field of imaging mass spectrometry and its impact on future biological research.
    Journal of Mass Spectrometry, 46(2):209-222, 2011.
  36. F. Alexandrov, M. Becker, S. Deininger, G. Ernst, L. Wehder, M. Grasmair, F. von Eggeling, H. Thiele, P. Maaß.
    Spatial segmentation of imaging mass spectrometry data with edge-preserving image denoising and clustering.
    Journal of Proteome Research, 9(12):6535-6546, 2010.

    DOI: 10.1021/pr100734z

  37. C. I. Balog, F. Alexandrov, R. J. Derks, P. J. Hensbergen, G. J. van Dam, E. M. Tukahebwa, N. B. Kabatereine, H. Thiele, B. J. Vennervald, O. A. Mayboroda, A. M. Deelder.
    The feasibility of mass spectrometry and advanced data processing for monitoring Schistosoma mansoni infection.
    Proteomics - Clinical Applications, 4(5):499-510, 2010.
  38. F. Alexandrov.
    A method of trend extraction using Singular Spectrum Analysis.
    RevStat, 7(1):1-22, 2009.
  39. F. Alexandrov, J. Decker, B. Mertens, A. M. Deelder, H. Thiele, P. Maaß, R. A. E. M. Tollenaar.
    Biomarker discovery in MALDI-TOF serum protein profiles using discrete wavelet transformation.
    Bioinformatics, 25(5):643-649, 2009.

    DOI: 10.1093/bioinformatics/btn662

  40. F. Alexandrov, N. Golyandina, A. Spirov.
    Singular Spectrum Analysis of gene expression profiles of early Drosophila embryo: exponential-in-distance patterns.
    Research Letters in Signal Processing, Article ID 825758, 5 S., 2008.
  41. A. C. Crecelius, F. Alexandrov, U. S. Schubert.
    Application of MALDI-MSI to monitor surface changes of UV irradiated poly(styrene) films.
    Research Letters in Signal Processing, 25(19):2809-14.

Tagungsbeiträge (13)

  1. A. Bartels, D. Trede, F. Alexandrov, P. Maaß.
    Hybrid Regularization and Sparse Reconstruction of Imaging Mass Spectrometry Data.
    10th International Conference on Sampling Theory and Applications (SampTA'13), 01.07.-05.07.2013, Bremen, Deutschland.

    online unter: http://www.eurasip.org/Proceedings/Ext/SampTA2013/papers/p189-bartels.pdf

  2. I. Chernyavsky, F. Alexandrov, P. Maaß.
    A Two-Step Soft Segmentation Procedure for MALDI Imaging Mass Spectrometry Data.
    German Conference on Bioinformatics 2012.

    DOI: 10.4230/OASIcs.GCB.2012.39

  3. E. Ovchinnikova, N. Montazeri, F. Alexandrov, J. Hobbs, M. C. McCord, R. Mulkar-Mehta .
    Abductive reasoning with a large knowledge base for discourse processing.
    Int. Conf. on Computational Semantics (IWCS'11), 12.01.-14.01.2011.
    Proc. Int. Conf. on Computational Semantics (IWCS'11), S. 225-234, 2011.
  4. D. Trede, J. H. Kobarg, K. Steinhorst, F. Alexandrov.
    Mathematical Methods for Imaging Mass Spectrometry.
    14th Joint International IMEKO TC1+TC7+TC13 Symposium, 31.08.-02.09.2011, Jena, Deutschland.

    Best Paper Award at IMEKO Symposium Jena

    online unter: URN: urn:nbn:de:gbv:ilm1-2011imeko-082:8

  5. E. Ovchinnikova, S. Borgo, A. Oltramari, L. Vieu, F. Alexandrov.
    Data-driven and ontological analysis of FrameNet for natural language reasoning.
    7th Int. Conf. on Language Resources and Evaluation (LREC'10), 2010.
  6. F. Alexandrov, O. Keszöcze, S. Schiffler, K. Steinhorst.
    Peak detection in mass spectrometry data using sparse coding.
  7. F. Alexandrov, O. Keszöcze, S. Schiffler, K. Steinhorst, D. Lorenz.
    An active set approach to the elastic-net and its applications in mass spectrometry.
    Second Workshop "Signal Processing with Adaptive Sparse Structured Representations" (SPARS′09), 06.04.-09.04.2009, St. Malo, Frankreich.

    online unter: http://hal.inria.fr/inria-00369397/en/

  8. E. Ovchinnikova, F. Alexandrov, T. Wandmacher.
    Automatic acquisition of the argument-predicate relations from a frame-annotated corpus.
    Conference on Empirical Methods in Natural Language Processing (EMNLP’09), 2009.
  9. F. Alexandrov.
    Self-taught learning for classification of mass spectrometry data: a case study of colorectal cancer.
    German Conference on Bioinformatics'09.
    Lecture Notes in Informatics 157, S. 45-54, 2009.
  10. F. Alexandrov.
    A method of trend extraction using Singular Spectrum Analysis.
    International Conference on Computational Statistics, 24.08-29.08.2008, Porto, Portugal.
    Erscheint in Proceedings of COMPSTAT'08.
  11. F. Alexandrov, N. Golyandina, A. Timofeyev.
    Dependence of accuracy of ESPRIT estimates on signal eigenvalues: the case of a noisy sum of two real exponentials.
    79th Annual Meeting of the International Association of Applied Mathematics and Mechanics, 31.03-04.04.2008, Bremen, Deutschland.
    Proceedings in Applied Mathematics and Mechanics, 8(1):10761–10762, 2008.

    DOI: 10.1002/pamm.200810761

  12. T. Wandmacher, E. Ovchinnikova, F. Alexandrov.
    Does latent semantic analysis reflect human associations?
    20th European Summer School in Logic, Language and Information, 04.08.-15.08.2008, Hamburg, Deutschland.
    Proceedings of the 20th European Summer School in Logic, Language and Information, M. Baroni, S. Evart, A. Lenci (Hrsg.), S. 63-70, 2008.
  13. K. Bredies, F. Alexandrov, J. Decker, D. Lorenz, H. Thiele.
    Sparse deconvolution for peak picking and ion charge estimation in mass spectrometry.
    15th European Conference on Mathematics in Industry'08, 30.06.-04.07.2008, London, Großbritannien.
    Erscheint in Proceedings of 15th European Conference on Mathematics in Industry'08.

Sonstiges (2)

  1. K. Steinhorst, O. Keszöcze, F. Alexandrov.
    Mass spectrometry and wavelet approximation.
    Projektbericht, Universität Bremen, 2008.
  2. C. Evers, K. Hachmann, M. Linden, A. Luttmann, K. Bredies, P. Maaß, F. Alexandrov.
    The Technomatika toolbox: LCMS peakpicking and alignment.
    Projektbericht, Universität Bremen, 2008.