Publications
2024
K. Grützmann, K. Salomo, A. Krüger, A. Lohse-Fischer, K. Erdmann, M. Seifert, G Baretton, D. Aust, D. William, E. Schröck, C. Thomas, S. Füssel: Identification of novel snoRNA-based biomarkers for clear cell renal cell carcinoma from urine-derived extracellular vesicles, Biology Direct , 2024, 19, 38. [pdf]
T. Kraft, K. Grützmann, M. Meinhardt, F. Meier, D. Westphal, M. Seifert: Personalized identification and characterization of genome-wide gene expression differences between patient-matched intracranial and extracranial melanoma metastasis pairs, Acta Neuropathologica Communications, 2024, 12:67. [pdf]
K. Grützmann, T. Kraft, M. Meinhardt, F. Meier, D. Westphal, M. Seifert: Network-based analysis of heterogeneous patient-matched brain and extracranial melanoma metastasis pairs reveals three homogeneous subgroups, Computational and Structural Biotechnology Journal, 2024, 23, 1036 - 1050. [pdf]
F. Broghammer, I. Korovina, M. Gouda, M. Celotti, J. van Es, I. Lange, C. Brunner, J. Mircetic, R. P. Coppes, O. Gires, A. Dahl, M. Seifert, N. Cordes: Resistance of HNSCC cell models to pan-FGFR inhibition depends on the EMT phenotype associating with clinical outcome, Molecular Cancer, 2024, 23, 39. [pdf]
I. Korovina, M. Elser, O. Borodins, M. Seifert, H. Willers, N. Cordes: β1 integrin mediates unresponsiveness to PI3Kα inhibition for radiochemosensitization of 3D HNSCC models, Biomedicine & Pharmacotherapy, 2024, 171, 116217. [pdf]
2023
O. Borodins, F. Broghammer, M. Seifert, N. Cordes: Meta-analysis of expression and targeting of cell adhesion associated genes in nine cancer types – a one research lab re-evaluation, Computational and Structural Biotechnology Journal, 2023, 21, 2824 - 2836. [pdf]
D. Westphal, M. Meinhardt, K. Grützmann, L. Schöne, J. Steininger, L. T. Neuhaus, M. Wiegel, D. Schrimpf, D. E. Aust, E. Schröck, G. B. Baretton, S. Beissert, T. A. Juratli, G. G. Schackert, J. Gravemeyer, J. C. Becker, A. von Deimling, C. Koelsche, B. Klink, F. Meier*, A. Schulz*, M. H. Muders*, M. Seifert*: Identification of Epigenetically Regulated Genes Distinguishing Intracranial From Extracranial Metastases, Journal of Investigative Dermatology, 2023, 143(7), 1233 - 1245.e17. [pdf] (*shared senior authorship)
T. Kraft, K. Grützmann, M. Meinhardt, F. Meier, D. Westphal, M. Seifert: Patient-specific identification of genome-wide DNA-methylation differences between intracranial and extracranial melanoma metastases, Scientific Reports, 2023, 13, 444. [pdf]
2022
N. Mikhaylenko, L. Wahnschaffe, M. Herling, I. Roeder, M. Seifert: Computational gene expression analysis reveals distinct molecular subgroups of T-cell prolymphocytic leukemia, PLoS ONE, 2022, 17(9): e0274463. [pdf]
D. Westphal, M. Seifert: Interview with Dana Westphal and Michael Seifert: "Interdisciplinarity is the only way to answer complex questions" - Interdisziplinary junior research alliance is investigating new therapeutic approaches to melanoma brain metastases, gesundhyte.de, Issue 14 June 2022, 73-76. [pdf]
M. Seifert: Computational Cancer Research: Network-based analysis of cancer data disentangles clinically relevant alterations from molecular measurements, Habilitation thesis, 2022, Medical Faculty TU Dresden. [pdf]
O.A. Sidorova, S. Sayed, M. Paszkowski-Rogacz, M. Seifert, A. Camgöz, I. Roeder, M. Bornhäuser, C. Thiede, F. Buchholz: RNAi-mediated screen of primary AML cells nominates MDM4 as a therapeutic target in NK-AML with DNMT3A mutations, Cells, 2022, 11(5), 854. [pdf]
A. Schwarz, I. Roeder, M. Seifert: Comparative gene expression analysis reveals similarities and differences of chronic myeloid leukemia phases, Cancers, 2022, 14(1), 256. [pdf]
2021
D. Westphal, M. Seifert: Interview mit Dana Westphal und Michael Seifert: "komplexe fragestellungen kann man nur durch interdisziplinarität beantworten" - Interdisziplinärer Juniorverbund forscht an neuen Therapieansätzen für Melanom-Hirnmetastasen, gesundhyte.de, Ausgabe 14 Dezember 2021, 73-76. [pdf]
T. Braun, A. Dechow, G. Friedrich, M. Seifert, J. Stachelscheid and M. Herling: Advanced pathogenetic concepts in T-cell prolymphocytic leukemia and their translational impact, Frontiers in Oncology, 2021, 11:775363. [pdf]
D. Westphal, R. Wehner, F. Meier, M. Karreman, M. Seifert: e:Med-Juniorverbund: MelBrainSys - Modellbasierte Vorhersage und experimentelle Validierung neuer therapeutischer Interventionen für Melanom-Hirnmetastasen, Spitzenforschung in der onkologischen Dermatologie. Innovationen und Auszeichnungen 2021, ALPHA Informations-GmbH, Lampertheim, 38-48. [pdf]
2020
R. J. P. Brown, B. Tegtmeyer, J. Sheldon, T. Khera, Anggakusuma, D. Todt, G. Vieyres, R. Weller, S. Joecks, Y. Zhang, S. Sake, D. Bankwitz, K. Welsch, C. Ginkel, M. Engelmann, G. Gerold, E. Steinmann, Q. Yuan, M. Ott, F. W. R. Vondran, T. Krey, L. J. Ströh, C. Miskey, Z. Ivics, V. Herder, W. Baumgärtner, C. Lauber, M. Seifert, A. W. Tarr, C. P. McClure, G. Randall, Y. Baktash, A. Ploss, V. L. D. Thi, E. Michailidis, M. Saeed, L. Verhoye, P. Meuleman, N. Goedecke, D. Wirth, C. M. Rice, T. Pietschmann: Liver-expressed Cd302 and Cr1l limit hepatitis C virus cross-species transmission to mice, Sci. Adv., 2020, 6:eabd3233. [pdf]
S. Cirak, L.-L. Becker, H. Dafsari, J. Schallner, D. Abdin, M. Seifert, F. Petit, T. Smol, L. Bok, L. Rodan, I. Krapels, S. Spranger, B. Weschke, K. Johnson, V. Straub, A. Kaindl, N. Di Donato, M. von der Hagen: The clinical phenotype continuum in DYNC1H1-related disorders - genomic profiling and proposal for a novel classification, Journal of Human Genetics, 2020, 65, 1003 - 1017. [pdf]
C. Lauber, N. Correia, A. Trumpp, M. A. Rieger, A. Dolnik, L. Bullinger, I. Roeder, and M. Seifert: Survival differences and associated molecular signatures of DNMT3A-mutant acute myeloid leukemia patients, Scientific Reports, 2020, 10:12761. [pdf]
M. Seifert, G. Schackert, A. Temme, E. Schröck, A. Deutsch, B. Klink: Molecular characterization of astrocytoma progression towards secondary glioblastomas utilizing patient-matched tumor pairs, Cancers, 12(6), 2020, 1696. [pdf]
P. Johansson, L. Klein-Hitpass, B. Budeus, M. Kuhn, C. Lauber, M. Seifert, I. Roeder, R. Pförtner, M. Stuschke, U. Dührsen, A. Eckstein, J. Dürig, R. Küppers : Identifying genetic lesions in ocular adnexal extranodal marginal zone lymphomas of the MALT subtype by whole genome, whole exome and targeted sequencing, Cancers, 2020, 12(4), 986. [pdf]
2019
E. Kolbe, S. Aleithe, C. Rennert, L. Spormann, F. Ott, D. Meierhofer, R. Gajowski, C. Stöpel, S. Hoehme, M. Kücken, L. Brusch, M. Seifert, W. von Schoenfels, C. Schafmayer, M. Brosch, U. Hofmann, G. Damm, D. Seehofer, J. Hampe, R. Gebhardt, M. Matz-Soja: Mutual Zonated Interactions of Wnt and Hh Signaling Are Orchestrating the Metabolism of the Adult Liver in Mice and Human, Cell Reports, 2019, 29(13), 4553-4567, e7. [pdf][pubmed]
J. Biedermann, M. Preussler, M. Conde, M. Peitzsch, S. Richter, R. Wiedemuth, K. Abou-El-Ardat, A. Krüger, M. Meinhardt, G. Schackert, W. Leenders, C. Herold-Mende, S. Niclou, R. Bjerkvig, G. Eisenhofer, A. Temme, M. Seifert, L. Kunz-Schughart, E. Schröck, B. Klink: Mutant IDH1 differently affects redox-state and metabolism in glial cells of normal and tumor origin, Cancers, 2019, 11(12), 2028. [pdf]
M. Seifert, C. Peitzsch, I. Gorodetska, C. Börner, B. Klink, A. Dubrovska : Network-based analysis of prostate cancer cell lines reveals novel marker gene candidates associated with radioresistance and patient relapse, PLoS Computational Biology, 2019, 15(11): e1007460. [pdf]
F. Zakrzewski, L. Gieldon, A. Rump, M. Seifert, K. Grützmann, A. Krüger, S. Loos, S. Zeugner, K. Hackmann, J. Porrmann, J. Wagner, K. Kast, P. Wimberger, G. Baretton, E. Schröck, D. Aust, B. Klink: Targeted capture-based NGS is superior to multiplex PCR-based NGS for hereditary BRCA1 and BRCA2 gene analysis in FFPE tumor samples, BMC Cancer, 2019, 19:396. [pdf]
Y. Liu, Y. Mi, T. Mueller, S. Kreibich, E. G. Williams, A. Van Drogen, C. Borel, M. Frank, P.-L. Germain, I. Bludau, M. Mehnert, M. Seifert, M. Emmenlauer, I. Sorg, F. Bezrukov, F. S. Bena, H. Zhou, C. Dehio, G. Testa, J. Saez-Rodriguez, S. E. Antonarakis, W.-D. Hardt, R. Aebersold: Multi-omic measurements of heterogeneity in HeLa cells across laboratories, Nature Biotechnology, 2019, 37(3), 314-322. [pdf][pubmed][preprint]
C. Lauber, M. Seifert, R. Bartenschlager, S. Seitz: Discovery of highly divergent lineages of plant-associated astro-like viruses sheds light on the emergence of potyviruses, Virus Research, 2019, 260, 38-48. [pdf]
2018
J. Gladitz, B. Klink, M. Seifert: Network-based analysis of oligodendrogliomas predicts novel cancer gene candidates within the region of the 1p/19q co-deletion, Acta Neuropathologica Communications, 2018, 6:49. [pdf]
L. Mäder, A. E. Blank, D. Capper, J. Jangsong, P. Baumgarten, N. M. Wirsik, C. Zachskorn, J. Ehlers, M. Seifert, B. Klink, S. Liebner, S. Niclou, U. Naumann, P. N. Harter, M. Mittelbronn: Pericytes/vessel-associated mural cells (VAMCs) are the major source of key epithelial-mesenchymal transition (EMT) factors SLUG and TWIST in human glioma, Oncotarget, 2018, 9:24041-24053. [pdf]
C. Lauber, B. Klink, M. Seifert: Comparative analysis of histologically classified oligodendrogliomas reveals characteristics molecular differences between subgroups, BMC Cancer, 2018, 18:399. [pdf]
E. Klapproth, E. Dickreuter, F. Zakrzewski, M. Seifert, A. Petzold, A. Dahl, E. Schröck, B. Klink, N. Cordes: Whole exome sequencing identifies mTOR and KEAP1 as potential targets for radiosensitization of HNSCC cells refractory to EGFR and β1 integrin inhibition, Oncotarget, 2018, 9:18099-18114. [pdf]
M. Seifert, and A. Beyer: regNet: An R package for network-based propagation of gene expression alterations, Bioinformatics, 2018, 34(2), 308-311. [pdf][tool]
2017
J. C. L. Alfonso, K. Talkenberger, M. Seifert, B. Klink, A. Hawkins-Daarud, K. R. Swanson, H. Hatzikirou, A. Deutsch: The biology and mathematical modelling of glioma invasion: a review, J. R. Soc. Interface, 2017, 14:20170490. [pdf]
T. Buder, A. Deutsch, M. Seifert*, A. Voss-Böhme*: CellTrans: An R package to quantify stochastic cell state transitions, Bioinformatics and Biology Insights, 2017:11. (*shared senior authorship) [pdf]
A. Vehlow, E. Klapproth, K. Storch, E. Dickreuter, M. Seifert, A. Dietrich, R. Bütof, A. Temme, N. Cordes: Adhesion- and stress-related adaptation of glioma radiochemoresistance is circumvented by β1 integrin/JNK co-targeting, Oncotarget,2017, 8:49224-49237. [pdf][pubmed]
K. Abou-El-Ardat, M. Seifert, K. Becker, S. Eisenreich, M. Lehmann, K. Hackmann, A. Rump, G. Meijer, B. Carvalho, A. Temme, G. Schackert, E. Schröck, D. Krex, B. Klink: Comprehensive molecular characterization of multifocal glioblastoma proves their monoclonal origin and reveals novel insights into clonal evolution and heterogeneity of glioblastomas, Neuro-Oncology, 2017, 19(4), 546-557. [pdf][pubmed]
2016
M. Seifert, B. Friedrich, A. Beyer: Importance of rare gene copy number alterations for personalized tumor characterization and survival analysis, Genome Biology, 2016, 17:204. [pdf][Poster Price at SBMC 2016]
2015
M. Seifert, M. Garbe, B. Friedrich, M. Mittelbronn, B. Klink: Comparative Transcriptomics Reveals Similarities and Differences between Astrocytoma Grades, BMC Cancer, 2015, 15:952. [pdf][pubmed]
M. Seifert, B. Friedrich, A. Beyer: Importance of rare copy number mutations for personalized tumor characterization, ISMB/ECCB 2015, Late Breaking Research, Dublin, Ireland, July 12-14. [pdf]
2014
2013
U. Biswas, C. Blei, J. Lange, E. Christodoulou, M. Seifert, A. Beyer, R. Jessberger: Meiotic cohesin SMC1β provides prophase I centromeric cohesion and is required for multiple synapsis-associated functions, PLoS Genetics, 2013, 9(12): e1003985. [pdf][pubmed]
O. M. Aliyu*, M. Seifert*, J. M. Corral, J. Fuchs, and T. F. Sharbel : Copy number variation in transcriptionally active regions of sexual and apomictic Boechera demonstrates independently-derived apomictic lineages, Plant Cell, 2013, 25(10), 3808-3823. (*contributed equally) [pdf][pubmed]
C. Bérard, M. Seifert, T. Mary-Huard, and M.-L. Martin-Magniette: MultiChIPmixHMM: an R package for ChIP-chip data analysis modeling spatial dependencies and multiple replicates, BMC Bioinformatics, 2013, 14:271, doi:10.1186/1471-2105-14-271. [pdf][pubmed]
M. Seifert: Hidden Markov Models with Applications in Computational Biology, SVH-Verlag, 2013, ISBN 978-3-8381-3604-2, 176 pages. [home]
N. Aghaeepour, G. Finak, The FlowCAP Consortium, The DREAM Consortium, H. Hoos, T.R. Mosmann, R. Brinkman, R. Gottardo, R.H. Scheuermann: Critical assessment of automated flow cytometry analysis techniques, Nature Methods, 2013, 10(3), 228-238. (M. Seifert is part of the The DREAM Consortium) [pdf][pubmed]
J. Grau, J. Keilwagen, A. Gohr, I.A. Paponov, S. Posch, M. Seifert, M. Strickert, and I. Grosse: Dispom: A discriminative de-novo motif discovery tool based on the Java Jstacs library, Journal of Bioinformatics and Computational Biology, 2013, 11(1). [pdf]
2012
M. Seifert, S. Cortijo, M. Colome-Tache, F. Johannes, F. Roudier, and V. Colot: MeDIP-HMM: Genome-wide identification of distinct DNA methylation states from high-density tiling arrays, Bioinformatics, 2012, 28(22), 2930-2939.[pdf] [pubmed]
G. Mönke, M. Seifert, J. Keilwagen, M. Mohr, I. Grosse, U. Hähnel, A. Junker, B. Weisshaar, U. Conrad, H. Bäumlein, and L. Altschmied: Toward the identification and regulation of the Arabidopsis thaliana ABI3 regulon, Nucleic Acids Research, 2012, 40(17), 8240-8254. [pdf][pubmed]
A. Junker, G. Mönke, T. Rutten, J. Keilwagen, M. Seifert, M. Ngyuen Thi, S. Balzergue, J.-P. Renou, P. Viehoever, U. Hähnel, J. Ludwig-Müller, L. Altschmied, U. Conrad, B. Weisshaar, and H. Bäumlein: Elongation-related functions of LEAFY COTYLEDON1 during the development of Arabidopsis thaliana, The Plant Journal, 2012, 71(3), 427-42. [pubmed]
M. Strickert, and M. Seifert: Posterior regularization and attribute assessment of under-determined linear mappings, Proceedings of the ESANN 2012: European Symposium on Artificial Neural Networks, Computational Intelligence and Machine Learning, Bruges, Belgium, 25 to 27 April 2012, ISBN 978-2-87419-049-0, 67-72. [pdf]
M. Seifert, A. Gohr, M. Strickert, and I. Grosse: Parsimonious higher-order Hidden Markov Models for improved Array-CGH analysis with applications to Arabidopsis thaliana, PLoS Computational Biology, 2012, 8(1), e1002286. [pdf][pubmed]
2011
M. Seifert, M. Strickert, A. Schliep, and I. Grosse: Exploiting prior knowledge and gene distances in the analysis of tumor expression profiles with extended Hidden Markov Models, Bioinformatics, 2011, 27(12), 1645-1652. [pdf][pubmed]
A. Banaei, F. Roudier, M. Seifert, C. Berard, M.-L. M. Magniette, R. K. Ashtiyani, A. Houben, V. Colot, and M. F. Mette: Additive inheritance of histone modifications in Arabidopsis thaliana intraspecific hybrids, The Plant Journal, 2011, 67(4), 691-700. [pdf][pubmed]
2010
M. Seifert: Extensions of Hidden Markov Models for the analysis of DNA microarray data, PhD thesis, 2010, Martin Luther University Halle-Wittenberg. [pdf]
2009
M. Seifert, J. Keilwagen, M. Strickert, and I. Grosse: Utilizing gene pair orientations for HMM-based analysis of promoter array ChIP-chip data, Bioinformatics, 2009, 25(16), 2118-2125. [pdf][pubmed]
M. Seifert, A. Banaei, J. Keilwagen, M.F. Mette, A. Houben, F. Roudier, V. Colot, I. Grosse, and M. Strickert: Array-based genome comparison of Arabidopsis ecotypes using Hidden Markov Models, In Proceedings of the Second International Conference on Bio-inspired Systems and Signal Processing, 2009, Porto, Portugal, 3-11. [pdf][home]
2006 - 2008
M. Seifert, J. Keilwagen, M. Strickert, and I. Grosse: Utilizing promoter pair orientations for HMM-based analysis of promoter array ChIP-chip data, In Proceedings of the German Conference on Bioinformatics 2008, Dresden, Germany, 116-127. [pdf][home]
M. Seifert: Analyzing microarray data using homogeneous and inhomogeneous Hidden Markov Models, Diploma thesis, 2006, Martin Luther University Halle-Wittenberg, Library: Heide-Süd, Book number: MI Dipl 2006 Seif.