BioDecipher^®

References

JAK2-V617F promotes venous thrombosis through β1/β2 integrin activation.

Edelmann B, Gupta N, Schnoeder TM, Oelschlegel AM, Shahzad K, Goldschmidt J, Philipsen L, Weinert S, Ghosh A, Saalfeld FC, Nimmagadda SC, Müller P, Braun-Dullaeus R, Mohr J, Wolleschak D, Kliche S, Amthauer H, Heidel FH, Schraven B, Isermann B, Müller AJ, Fischer T. J Clin Invest. 2018 Oct 1;128(10):4359-4371. doi: 10.1172/JCI90312. Epub 2018 Jul 19.

Multiplexed histology analyses for the phenotypic and spatial characterization of human innate lymphoid cells.

Pascual-Reguant A, Köhler R, Mothes R, Bauherr S, Hernández DC, Uecker R, Holzwarth K, Kotsch K, Seidl M, Philipsen L, Müller W, Romagnani C, Niesner R, Hauser AE. Nat Commun. 2021 Mar 19;12(1):1737. doi: 10.1038/s41467-021-21994-8.

Multiplexed fluorescence microscopy reveals heterogeneity among stromal cells in mouse bone marrow sections.

Holzwarth K, Köhler R, Philipsen L, Tokoyoda K, Ladyhina V, Wählby C, Niesner RA, Hauser AE. Cytometry A. 2018 Jul;93(9):876-888. doi: 10.1002/cyto.a.23526. Epub 2018 Aug 14.

CD11c-expressing Ly6C+CCR2+ monocytes constitute a reservoir for efficient Leishmania proliferation and cell-to-cell transmission.

Heyde S, Philipsen L, Formaglio P, Fu Y, Baars I, Höbbel G, Kleinholz CL, Seiß EA, Stettin J, Gintschel P, Dudeck A, Bousso P, Schraven B, Müller AJ. PLoS Pathog. 2018 Oct 22;14(10):e1007374. doi: 10.1371/journal.ppat.1007374. eCollection 2018 Oct.

IL-7 derived from lymph node fibroblastic reticular cells is dispensable for naive T cell homeostasis but crucial for central memory T cell survival.

Knop L, Deiser K, Bank U, Witte A, Mohr J, Philipsen L, Fehling HJ, Müller AJ, Kalinke U, Schüler T. Eur J Immunol. 2020 Jun;50(6):846-857. doi: 10.1002/eji.201948368. Epub 2020 Mar 16.

Cold shock Y-box binding protein-1 acetylation status in monocytes is associated with systemic inflammation and vascular damage.

Ewert L, Fischer A, Brandt S, Scurt FG, Philipsen L, Müller AJ, Girndt M, Zenclussen AC, Lindquist JA, Gorny X, Mertens PR. Atherosclerosis. 2018 Nov;278:156-165. doi: 10.1016/j.atherosclerosis.2018.09.020. Epub 2018 Sep 22.

TCR signalling network organization at the immunological synapses of murine regulatory T cells.

van Ham M, Teich R, Philipsen L, Niemz J, Amsberg N, Wissing J, Nimtz M, Gröbe L, Kliche S, Thiel N, Klawonn F, Hubo M, Jonuleit H, Reichardt P, Müller AJ, Huehn J, Jänsch L. Eur J Immunol. 2017 Dec;47(12):2043-2058. doi: 10.1002/eji.201747041. Epub 2017 Sep 12.

Inflammatory cell infiltration and resolution of kidney inflammation is orchestrated by the cold-shock protein Y-box binding protein-1.

Bernhardt A, Fehr A, Brandt S, Jerchel S, Ballhause TM, Philipsen L, Stolze S, Geffers R, Weng H, Fischer KD, Isermann B, Brunner-Weinzierl MC, Batra A, Siegmund B, Zhu C, Lindquist JA, Mertens PR. Kidney Int. 2017 Nov;92(5):1157-1177. doi: 10.1016/j.kint.2017.03.035. Epub 2017 Jun 11.

Targeted antigen delivery to dendritic cells elicits robust antiviral T cell-mediated immunity in the liver.

Volckmar J, Gereke M, Ebensen T, Riese P, Philipsen L, Lienenklaus S, Wohlleber D, Klopfleisch R, Stegemann-Koniszewski S, Müller AJ, Gruber AD, Knolle P, Guzman CA, Bruder D. Sci Rep. 2017 Mar 7;7:43985. doi: 10.1038/srep43985.

Multimolecular analysis of stable immunological synapses reveals sustained recruitment and sequential assembly of signaling clusters.

Philipsen L, Engels T, Schilling K, Gurbiel S, Fischer KD, Tedford K, Schraven B, Gunzer M, Reichardt P. Mol Cell Proteomics. 2013 Sep;12(9):2551-67. doi: 10.1074/mcp.M112.025205. Epub 2013 Jun 10.

Analyzing human tissue samples of skin for different diseases

The CD11a binding site of efalizumab in psoriatic skin tissue as analyzed by Multi-Epitope Ligand Cartography robot technology. Introduction of a novel biological drug-binding biochip assay.

Bonnekoh B, Böckelmann R, Pommer AJ, Malykh Y, Philipsen L, Gollnick H. Skin Pharmacol Physiol. 2007;20(2):96-111. doi: 10.1159/000097982. Epub 2006 Dec 13.

Topo-proteomic in situ analysis of psoriatic plaque under efalizumab treatment.

Bonnekoh B, Pommer AJ, Böckelmann R, Hofmeister H, Philipsen L, Gollnick H. Skin Pharmacol Physiol. 2007;20(5):237-52. doi: 10.1159/000104422. Epub 2007 Jun 22.

In-situ-topoproteome analysis of cutaneous lymphomas: perspectives of assistance for dermatohistologic diagnostics by Multi Epitope Ligand Cartography (MELC).

Bonnekoh B, Pommer AJ, Böckelmann R, Philipsen L, Hofmeister H, Gollnick H. J Dtsch Dermatol Ges. 2008 Dec;6(12):1038-51. doi: 10.1111/j.1610-0387.2007.06754.x.

Analyzing human tissue samples of colon for different diseases

Proteomic analysis of the inflamed intestinal mucosa reveals distinctive immune response profiles in Crohn's disease and ulcerative colitis.

Berndt U, Bartsch S, Philipsen L, Danese S, Wiedenmann B, Dignass AU, Hämmerle M, Sturm A. J Immunol. 2007 Jul 1;179(1):295-304. doi: 10.4049/jimmunol.179.1.295.

Systematic high-content proteomic analysis reveals substantial immunologic changes in colorectal cancer.

Berndt U, Philipsen L, Bartsch S, Wiedenmann B, Baumgart DC, Hämmerle M, Sturm A. Cancer Res. 2008 Feb 1;68(3):880-8. doi: 10.1158/0008-5472.CAN-07-2923.

Comparative Multi-Epitope-Ligand-Cartography reveals essential immunological alterations in Barrett's metaplasia and esophageal adenocarcinoma.

Berndt U, Philipsen L, Bartsch S, Hu Y, Röcken C, Bertram W, Hämmerle M, Rösch T, Sturm A. Mol Cancer. 2010 Jul 6;9:177. doi: 10.1186/1476-4598-9-177.

XCOSM

J.A. Conchello, J.G. McNally: Fast regularization technique for expectation maximization algorithm for computational optical sectioning microscopy: Image acquisition and processing

C.J. Cogswell, G.S. Kino, T. Wilson (Eds.), Proc. SPIE, 2655 (1996), pp. 199-208

Multiplex bio imaging techniques

The first publication about multiple antigen mapping (MAM)

Multiple antigen-mapping microscopy of human tissue

W. Schubert, G. Burger, M. Oberholzer, G.P. Vooijs (Eds.), Excerpta medica, Elsevier, Amsterdam (1990), pp. 97-98 Adv. Analyt. Cell. Pathol.

Antigenic determinants of T lymphocyte alpha beta receptor and other leukocyte surface proteins as differential markers of skeletal muscle regeneration: detection of spatially and timely restricted patterns by MAM microscopy.

Schubert W. Eur J Cell Biol. 1992 Aug;58(2):395-410.

Introduction of MELC technology: Analyzing proteome topology and function by automated multidimensional fluorescence microscopy.

Schubert W, Bonnekoh B, Pommer AJ, Philipsen L, Böckelmann R, Malykh Y, Gollnick H, Friedenberger M, Bode M, Dress AW. Nat Biotechnol. 2006 Oct;24(10):1270-8. doi: 10.1038/nbt1250. Epub 2006 Oct 1.

A. Abbott: Mapping togetherness (Research highlight)

Nature, 443 (2006), p. 609 (referring to ref. 4)

Basic Protocols

Fluorescence detection of protein clusters in individual cells and tissue sections by using toponome imaging system: sample preparation and measuring procedures.

Friedenberger M, Bode M, Krusche A, Schubert W. Nat Protoc. 2007;2(9):2285-94. doi: 10.1038/nprot.2007.320.

Comparison of mRNA levels of whole organ immune cell population with its spatial distribution, introductions of MELC antibody library for murine immune cells Murine whole-organ immune cell populations revealed by multi-epitope-ligand cartography.

Eckhardt J, Ostalecki C, Kuczera K, Schuler G, Pommer AJ, Lechmann M. J Histochem Cytochem. 2013 Feb;61(2):125-33. doi: 10.1369/0022155412470140. Epub 2012 Nov 16.