______________________________ Publications 2020 ______________________________

  • Spilger R, Imle A, Lee JY, Müller B, Fackler OT, Bartenschlager RRohr K (2020). A Recurrent Neural Network for Particle Tracking in Microscopy Images Using Future Information, Track Hypotheses, and Multiple Detections. IEEE Transactions on Image Processing 29:1, 3681-3694, DOI: 10.1109/TIP.2020.2964515
  • Wiegand T, Fratini M, Frey F, Yserentant K, Liu Y, Weber E, Galior K, Ohmes J, Braun F, Herten DP, Boulant S, Schwarz US, Salaita K, Cavalcanti-Adam EA, Spatz JP (2020). Forces during cellular uptake of viruses and nanoparticles at the ventral side. Nat Commun. 2020 Jan 2;11(1):32. doi: 10.1038/s41467-019-13877-w
  • Ananth S, Morath K, Trautz B, Tibroni N, Shytaj IA, Obermaier B, Stolp B, Lusic M, Fackler OT (2020). Multifunctional Roles of the N-Terminal Region of HIV-1SF2Nef Are Mediated by Three Independent Protein Interaction Sites. J. Virol. 94:e01398-19, https://doi.org/10.1128/JVI.01398-19

 ______________________________ Publications 2019 ______________________________

  • Wollmann T, Ritter C, Dohrke JN, Lee JY, Bartenschlager R, Rohr K (2019). DetNet: Deep Neural Network for Particle Detection in Fluorescence Microscopy Images. IEEE International Symposium on Biomedical Imaging (ISBI 2019), Venice, Italy, April 8-11, 2019
  • Mücksch F, Citir M, Lüchtenborg C, Glass B, Traynor-Kaplan A, Schultz C, Brügger BKräusslich HG (2019). Quantification of phosphoinositides reveals strong enrichment of PIP2 in HIV-1 compared to producer cell membranes. Scientific Reports 9:17661, https://doi.org/10.1038/s41598-019-53939-z
  • Zila V, Müller TG, Laketa V, Müller B, Kräusslich HG (2019). Analysis of CA Content and CPSF6 Dependence of Early HIV-1 Replication Complexes in SupT1-R5 Cells. MBio, doi 10.1128/mBio.02501-19
  • Muenchau S, Deutsch R, de Castro IJ, Hielscher T, Heber N, Niesler B, Lusic M, Stanifer ML, Boulant S (2019). Hypoxic Environment Promotes Barrier Formation in Human Intestinal Epithelial Cells through Regulation of MicroRNA 320a Expression. Mol Cell Biol. Jun 27;39(14). pii: e00553-18. doi: 10.1128/MCB.00553-18
  • Fröhlich B, Jäger J, Lansche C, Sanchez CP, Cyrklaff M, Buchholz B, Soubeiga ST, Simpore J, Ito H, Schwarz US, Lanzer M, Tanaka M (2019). Hemoglobin S and C affect biomechanical membrane properties of P. falciparum-infected erythrocytes. Commun Biol. Aug 13;2:311. doi: 10.1038/s42003-019-0556-6
  • Gabel M, Hohl T, Imle A, Fackler OT, Graw F (2019). FAMoS: A Flexible and dynamic Algorithm for Model Selection to analyse complex systems dynamics. PLoS Comput Biol 15: e1007230. https://doi.org/10.1371/journal.pcbi.1007230
  • Fu RM, Decker CC, Dao Thi VL (2019). Cell Culture Models for Hepatitis E Virus. Viruses 11, 608; doi:10.3390/v11070608
  • Kummer S, Avinoam O, Kräusslich HG (2019). IFITM3 Clusters on Virus Containing Endosomes and Lysosomes Early in the Influenza A Infection of Human Airway Epithelial Cells. Viruses 2019, 11(6), 548; doi.org/10.3390/v11060548
  • Ritter C, Wollmann T, Bernhard P, Gunkel M, Braun DM, Lee JY, Meiners J, Simon R, Sauter G, Erfle H, Rippe K, Bartenschlager R, Rohr K (2019). Hyperparameter optimization for image analysis: application to prostate tissue images and live cell data of virus-infected cells. Int. J. CARS, 14:1847, doi.org/10.1007/s11548-019-02010-3
  • Spreng B, Fleckenstein H, Kübler P, Di Biagio C, Benz M, Patra P, Schwarz US, Cyrklaff M, Frischknecht F (2019). Microtubule number and length determine cellular shape and function in Plasmodium. The EMBO Journal (2019) e100984. doi 10.15252/embj.2018100984. Published online 24.05.2019
  • Płaszczyca A, Scaturro P, Neufeldt CJ, Cortese M, Cerikan B, Ferla S, Brancale A, Pichlmair A, Bartenschlager R (2019). A novel interaction between dengue virus nonstructural protein 1 and the NS4A-2K-4B precursor is required for viral RNA replication but not for formation of the membranous replication organelle. PLoS Pathog 15(5): e1007736, doi.org/10.1371/journal.ppat.1007736, May 9, 2019
  • Sanchez CP, Karathanasis C, Sanchez R, Cyrklaff M, Jäger J, Buchholz B, Schwarz US, Heilemann M, Lanzer M (2019). Single-molecule imaging and quantification of the immune-variant adhesin VAR2CSA on knobs of Plasmodium falciparum-infected erythrocytes. Comm. Biol. 2:172, doi.org/10.1038/s42003-019-0429-z
  • Imle A, Kumberger P, Schnellbächer N, Fehr J, Carillo-Bustamante P, Ales J, Schmidt P, Ritter C, Godinez W J, Müller B, Rohr K, Hamprecht FA, Schwarz U, Graw F, Fackler, OT (2019). Experimental and computational analyses reveal that environmental restrictions shape HIV-1 spread in 3D cultures. Nat Comm. 10:2144
  • Reinkemeier CD, Girona GE, Lemke EA (2019). Designer membraneless organelles enable codon reassignment of selected mRNAs in eukaryotes.
    Science, published online 15 March 2019. DOI:10.1126/science.aaw2644
  • Stanifer ML, Pervolaraki K, Boulant S (2019). Differential regulation of type I and type III interferon signaling. Int. J. Mol. Sci.  2019 Mar 21;20(6). pii: E1445. doi: 10.3390/ijms20061445
  • Frey F, Ziebert F, Schwarz US (2019). Stochastic Dynamics of Nanoparticle and Virus Uptake. Physical Review Letters 122, 088102 (2019), doi: 10.1103/PhysRevLett.122.088102
  • Müller TG, Sakin V, Müller B (2019). A Spotlight on Viruses-Application of Click Chemistry to Visualize Virus-Cell Interactions. Molecules. 2019 Jan 29;24(3). pii: E481. doi: 10.3390/molecules24030481. Review.
  • Bejarano, DA, Peng, K, Laketa V, Börner K, Jost KL, Lucic B, Glass B, Lusic B, Müller B, Kräusslich HG (2019). HIV-1 nuclear import in macrophages is regulated by CPSF6-capsid interactions at the Nuclear Pore Complex. Elife, 2019 Jan 23;8. pii: e41800. doi: 10.7554/eLife.41800. [Epub ahead of print]
  • Tsopoulidis N, Kaw S, Laketa V, Kutscheidt S, Baarlink C, Stolp B, Grosse R, Fackler OT (2019). T cell receptor–triggered nuclear actin network formation drives CD4+ T cell effector functions. Sci. Immunol. 4, eaav1987


 ______________________________ Publications 2018 ______________________________

  • Spilger R, Wollmann T, Qiang Y, Imle A, Lee JY, Müller B, Fackler OT, Bartenschlager R, Rohr K (2018). Deep Particle Tracker: Automatic Tracking of Particles in Fluorescence Microscopy Images Using Deep Learning. In: Stoyanov D. et al. (eds) Deep Learning in Medical Image Analysis and Multimodal Learning for Clinical Decision Support. DLMIA 2018, ML-CDS 2018. Lecture Notes in Computer Science, vol 11045. Springer, Cham, https://doi.org/10.1007/978-3-030-00889-5_15
  • Schult P, Roth H, Adams RL, Mas C, Imbert L, Orlik C, Ruggieri A, Pyle AM, Lohmann V (2018). MicroRNA-122 amplifies hepatitis C virus translation by shaping the structure of the internal ribosomal entry site. Nature Comm. 9:2613, doi: 10.1038/s41467-018-05053-3
  • Bejarano DA, Puertas MC, Börner K, Picado JM, Müller B, Kräusslich HG (2018). Detailed Characterization of Early HIV-1 ReplicationDynamics in Primary Human Macrophages. Viruses 2018, 10, 620; doi:10.3390/v10110620
  • Ritter C, Imle A, Lee JY, Müller B, Fackler OT, Bartenschlager R, Rohr K (2018). Two-Filter Probabilistic Data Association for Tracking of Virus Particles in Fluorescence Microscopy Images. Proc. IEEE International Symposium on Biomedical Imaging (ISBI 2018), Washington, D.C., USA, April 4-7
  • Pervolaraki K, Rastgou Talemi S, Albrecht D, Bormann F, Bamford C, Mendoza JL, Garcia KC, McLauchlan J, Höfer T, Stanifer ML, Boulant S (2018). Differential induction of interferon stimulated genes between type I and type III interferons is independent of interferon receptor abundance. PLoS Pathog. 2018 Nov 28;14(11):e1007420. doi: 10.1371/journal.ppat.1007420
  • Lansche C, Dasanna AK, Quadt K., Fröhlich B, Missirlis D, Tétard M, Gamain B, Buchholz B, Sanchez CP, Tanaka M, Schwarz US, Lanzer M (2018). The sickle cell trait affects contact dynamics and endothelial cell activation in Plasmodium falciparum-infected erythrocytes. Comm. Biol. 1:211, doi: 10.1038/s42003-018-0223-3
  • Klug D, Kehrer J, Frischknecht F, Singer M (2018). A synthetic promoter for multi-stage expression to probe complementary functions of Plasmodium adhesins. J Cell Sci. 2018 Oct 22;131(20). pii: jcs210971. doi: 10.1242/jcs.210971
  • Neufeldt CJ, Cortese M, Acosta EG, Bartenschlager R (2018). Rewiring cellular networks by members of the Flaviviridae family. Nat Rev Microbiol. 2018 Feb 12;16(3):125-142. doi: 10.1038/nrmicro.2017.170
  • Santarella-Mellwig R, Haselmann U, Schieber NL, Walther P, Schwab Y, Antony C, Bartenschlager R, Romero-Brey I (2018). Correlative Light Electron Microscopy (CLEM) for Tracking and Imaging Viral Protein Associated Structures in Cryo-immobilized Cells. J Vis Exp. 2018 Sep 7;(139). doi: 10.3791/58154
  • Lamas-Murua M, Stolp B, Kaw S, Thoma J, Tsopoulidis N, Trautz B, Ambiel I, Reif T, Arora S, Imle A, Tibroni N, Wu J, Cui G, Stein JV, Tanaka M, Lyck R, Fackler OT (2018). HIV-1 Nef Disrupts CD4+ T Lymphocyte Polarity, Extravasation, and Homing to Lymph Nodes via Its Nef-Associated Kinase Complex Interface. J Immunol. 2018 Nov 1;201(9):2731-2743. doi: 10.4049/jimmunol.1701420. Epub 2018 Sep 26.
  • Fratini M, Wiegand T, Funaya C, Jiang Z, Shah PNM, Spatz JP, Cavalcanti-Adam EA, Boulant S (2018). Surface Immobilization of Viruses and Nanoparticles Elucidates Early Events in Clathrin-Mediated Endocytosis. ACS Infect Dis. 2018 Nov 9;4(11):1585-1600. doi: 10.1021/acsinfecdis.8b00134. Epub 2018 Sep 26
  • Bejarano DA, Puertas MC, Börner K, Martinez-Picado J. Müller B, Kräusslich HG (2018). Detailed Characterization of Early HIV-1 Replication Dynamics in Primary Human Macrophages. Viruses. 2018 Nov 10;10(11). pii: E620. doi: 10.3390/v10110620
  • Zhang Z, Filzmayer C, Ni Y, Sültmann H, Mutz P, Hiet MS, Vondran FWR, Bartenschlager R, Urban S (2018). Hepatitis D Virus replication is sensed by MDA5 and induces IFN-β/λ responses in hepatocytes. J Hepatol. 2018 Mar 8, doi: 10.1016/j.jhep.2018.02.021
  • Bucher D, Frey F,  Sochacki KA, Kummer S,  Bergeest JP,  Godinez WJ,  Kräusslich HGRohr K, Taraska JW,  Schwarz US, Boulant S (2018). Clathrin-adaptor ratio and membrane tension regulate the flat-to-curved transition of the clathrin coat during endocytosis. Nature comm 9, doi:10.1038/s41467-018-03533-0
  • Stoeck IK, Lee JY, Tabata K, Romero-Brey I, Paul D, Schult P, Lohmann V, Kaderali L, Bartenschlager R (2018). Hepatitis C Virus Replication Depends on Endosomal Cholesterol Homeostasis. J Virol. 92(1). pii: e01196-17. doi: 10.1128/JVI.01196-17
  • Kozma E, Paci G, Estrada Girona G, Lemke EA, Kele P (2018). Fluorogenic Tetrazine-Siliconrhodamine Probe for the Labeling of Noncanonical Amino Acid Tagged Proteins. Methods Mol Biol. 2018;1728:337-363. doi: 10.1007/978-1-4939-7574-7_22
  • Muthinja JM, Ripp J, Krüger T, Imle A, Haraszti T, Fackler OT, Spatz JP, Engstler M, Frischknecht F (2018). Tailored environments to study motile cells and pathogens. Cell Microbiol. 20(3). doi: 10.1111/cmi.12820. Epub 2018 Jan 29. Review
  • Uhlmann V, Haubold C, Hamprecht FA, Unser M (2018). DiversePathsJ: diverse shortest paths for bioimage analysis. Bioinformatics. 34(3): 538–540


 ______________________________ Publications 2017 ______________________________

  • Ulman V, Maška M, Magnusson KEG, Ronneberger O, Haubold C, Harder N, Matula Pavel, Matula Petr, Svoboda D, Radojevic M, Smal I, Rohr K, Jaldén J, Blau HM, Dzyubachyk O, Lelieveldt B, Xiao P, Li Y, Cho S-Y, Dufour AC, Olivo-Marin J-C, Reyes-Aldasoro CC, Solis-Lemus JA, Bensch R, Brox T, Stegmaier J, Mikut R, Wolf S, Hamprecht FA, Esteves T, Quelhas P, Demirel Ö, Malmström L, Jug F, Tomancak P, Meijering E, Muñoz-Barrutia A, Kozubek M, Ortiz-de-Solorzano C (2017). An objective comparison of cell-tracking algorithms. Nature Methods 14: 1141–1152
  • Kaufmann SHE, Dorhoi A, Hotchkiss RS, Bartenschlager R (2017). Host-directed therapies for bacterial and viral infections. Nat Rev Drug Discov. 2017 Sep 22. doi: 10.1038/nrd.2017.162
  • Stoeck IK, Lee JY, Tabata K, Romero-Brey I, Paul D, Schult P, Lohmann V, Kaderali L, Bartenschlager R (2017). Hepatitis C Virus Replication Depends on Endosomal Cholesterol Homeostasis. J Virol. 2017 92(1). doi: 10.1128/JVI.01196-17
  • Donkers JM, Zehnder B, van Westen GJP, Kwakkenbos MJ, IJzerman AP, Oude Elferink RPJ, Beuers U, Urban S, van de Graaf SFJ (2017). Reduced hepatitis B and D viral entry using clinically applied drugs as novel inhibitors of the bile acid transporter NTCP. Sci Rep. 7(1):15307. doi: 10.1038/s41598-017-15338-0
  • Doerflinger SY, Cortese M, Romero-Brey I, Menne Z, Tubiana T, Schenk C, White PA, Bartenschlager R, Bressanelli S, Hansman GS, Lohmann V (2017). Membrane alterations induced by nonstructural proteins of human norovirus. PLoS Pathog. 13(10):e1006705. doi: 10.1371/journal.ppat.1006705
  • Senís E, Mockenhaupt S, Rupp D, Bauer T, Paramasivam N, Knapp B, Gronych J, Grosse S, Windisch MP, Schmidt F, Theis FJ, Eils R, Lichter P, Schlesner M, Bartenschlager R, Grimm D (2017). TALEN/CRISPR-mediated engineering of a promoterless anti-viral RNAi hairpin into an endogenous miRNA locus. Nucleic Acids Res. 45(1):e3. doi: 10.1093/nar/gkw805
  • Grosse S, Penaud-Budloo M, Herrmann AK, Börner K, Fakhiri J, Laketa V, Krämer C, Wiedtke E, Gunkel M, Ménard L, Ayuso E, Grimm D (2017). Relevance of Assembly-Activating Protein for Adeno-associated Virus Vector Production and Capsid Protein Stability in Mammalian and Insect Cells. J Virol. 91(20). pii: e01198-17. doi: 10.1128/JVI.01198-17
  • Grimm D, Büning H (2017). Small But Increasingly Mighty: Latest Advances in AAV Vector Research, Design, and Evolution. Hum Gene Ther. 28(11):1075-1086. doi: 10.1089/hum.2017.172
  • Sá E Cunha C, Nyboer B, Heiss K, Sanches-Vaz M, Fontinha D, Wiedtke E, Grimm D, Przyborski JM, Mota MM, Prudêncio M, Mueller AK (2017). Plasmodium berghei EXP-1 interacts with host Apolipoprotein H during Plasmodium liver-stage development. Proc Natl Acad Sci U S A 114(7):E1138-E1147. doi: 10.1073/pnas.1606419114
  • Amoasii L, Long C, Li H, Mireault AA, Shelton JM, Sanchez-Ortiz E, McAnally JR, Bhattacharyya S, Schmidt F, Grimm D, Hauschka SD, Bassel-Duby R, Olson EN (2017). Single-cut genome editing restores dystrophin expression in a new mouse model of muscular dystrophy. Sci Transl Med. 9(418), doi: 10.1126/scitranslmed.aan8081
  • Cyrklaff M, Frischknecht F, Kudryashev M (2017). Functional insights into pathogen biology from 3D electron microscopy. FEMS Microbiol Rev. 41(6):828-853. doi: 10.1093/femsre/fux041
  • Tektonidis M, Rohr K (2017). Diffeomorphic Multi-Frame Non-Rigid Registration of Cell Nuclei in 2D and 3D Live Cell Images, IEEE Transactions on Image Processing 26:3, 1405-1417
  • Moreau CA, Bhargav SP, Kumar H, Quadt KA, Piirainen H, Strauss L, Kehrer J, Streichfuss M, Spatz JP, Wade RC, Kursula I, Frischknecht F (2017). A unique profilin-actin interface is important for malaria parasite motility. PLOS Pathogens 13: e1006412
  • Pallarola D, Platzman I, Bochen A, Cavalcanti-Adam EA, Axmann M, Kessler H, Geiger B, Spatz JP (2017). Focal adhesion stabilization by enhanced integrin-cRGD binding affinity. BioNanoMaterials, 18(1-2):20160014
  • Weiss M, Frohnmayer JP, Benk LT, Haller B, Janiesch J-W, Heitkamp T, Börsch M, Lira RB, Dimova R, Lipowsky R, Bodenschatz E, Baret J-C, Vidakovic-Koch T, Sundmacher K, Platzman I, Spatz JP (2017). Sequential bottom-up assembly of mechanically stabilized cell-like proteoliposomes by microfluidics. Nature Materials 17(1):89-96
  • Oria R, Wiegand T, Escribano J, Elosegui-Artola A, Uriarte JJ, Moreno-Pulido C, Platzman I, Delcanale P, Albertazzi, L, Navajas D, Trepat X, Garcia-Aznar JM, Cavalcanti-Adam EA*, Roca-Cusachs P* (2017). Force loading explains spatial sensing of ligands by cells. Nature, 2017 Dec 6. doi: 10.1038/nature24662
  • Higaki Y, Fröhlich B, Yamamoto A, Murakami R, Kaneko M, Takahara A, Tanaka M (2017). Ion-Specific Modulation of Interfacial Interaction Potentials between Solid Substrates and Cell-Sized Particles Mediated via Zwitterionic, Super-Hydrophilic Poly(sulfobetaine) Brushes. J Phys Chem B 121: 1396-1404
  • Frank V, Chushkin Y, Fröhlich B, Abuillan W, Rieger H, Becker AS, Yamamoto A, Rossetti FF, Kaufmann S, Lanzer M, Zontone F, Tanaka M (2017). Lens-Free Tomographic Imaging of Near Surface Structures of Frozen Hydrated Malaria-Infected Human Erythrocytes by Coherent X-Ray Diffraction Microscopy. Sci Rep, 7(1):14081, doi:10.1038/s41598-017-14586-4
  • Dasanna AK, Lansche C, Lanzer M, Schwarz US (2017). Rolling adhesion of schizont stage malaria-infected red blood cells in shear flow. Biophysical J, 112:1908-1919
  • Stanifer ML, Kischnick C, Rippert A, Albrecht D, Boulant S (2017). Reovirus inhibits interferon production by sequestering IRF3 into viral factories. Sci Rep. 7(1):10873. doi: 10.1038/s41598-017-11469-6
  • Martínez C, Rodiño-Janeiro BK, Lobo B, Stanifer ML, Klaus B, Granzow M, González-Castro AM, Salvo-Romero E, Alonso-Cotoner C, Pigrau M, Roeth R, Rappold G, Huber W, González-Silos R, Lorenzo J, de Torres I, Azpiroz F, Boulant S, Vicario M, Niesler B, Santos J (2017). miR-16 and miR-125b are involved in barrier function dysregulation through the modulation of claudin-2 and cingulin expression in the jejunum in IBS with diarrhoea. Gut. 66(9):1537-1538. doi: 10.1136/gutjnl-2016-311477
  • Pervolaraki K, Stanifer ML, Münchau S, Renn LA, Albrecht D, Kurzhals S, Senís E, Grimm D, Schröder-Braunstein J, Rabin RL, Boulant S (2017). Type I and type III interferons display different dependency on mitogen-activated protein kinases to mount an antiviral state in the human gut. Front Immunol. 21;8:459
  • Shah PNM, Stanifer ML, Höhn K, Engel U, Haselmann U, Bartenschlager R, Kräusslich HG, Krijnse-Locker J, Boulant S. (2017). Genome packaging of Reovirus is mediated by the scaffolding property of the microtubule network. Cell Microbiol. 2017 Jul 3. doi: 10.1111/cmi.12765
  • Bankwitz D, Doepke M, Hueging K, Weller R, Bruening J, Behrendt P, Lee JY, Vondran FWR, Manns MP, Bartenschlager R, Pietschmann T. (2017). Maturation of secreted HCV particles by incorporation of secreted apoE protects from antibodies by enhancing infectivity. J Hepatol. 2017 Apr 21. pii: S0168-8278(17)30251-9. doi: 10.1016/j.jhep.2017.04.010
  • Beier T, Pape C, Rahaman N, Prange T, Berg S, Bock DD, Cardona A, Knott GW, Plaza SM, Scheffer LK, Koethe U, Kreshuk A, Hamprecht FA (2017). Multicut brings automated neurite segmentation closer to human performance. Nature Methods, 14(2):101-102
  • Mücksch F, Laketa V, Müller B, Schultz C, Kräusslich HG (2017). Synchronized HIV assembly by tunable PIP2 changes reveals PIP2 requirement for stable Gag anchoring. Elife. pii: e25287. doi: 10.7554/eLife.25287.
  • Sakin V, Hanne J, Dunder J, Anders-Össwein M, Laketa V, Nikic I, Kräusslich HG, Lemke EA, Müller B (2017). A Versatile Tool for Live-Cell Imaging and Super-Resolution Nanoscopy Studies of HIV-1 Env Distribution and Mobility. Cell Chem Biol. 2017 May 18;24(5):635-645.e5
  • Cortese M, Goellner S, Acosta EG, Neufeldt CJ, Oleksiuk O, Lampe M, Haselmann U, Funaya C, Schieber N, Ronchi P, Schorb M, Pruunsild P, Schwab Y, Chatel-Chaix L, Ruggieri A, Bartenschlager R (2017). Ultrastructural Characterization of Zika Virus Replication Factories. Cell Rep. 2017 Feb 28;18(9):2113-2123. doi: 10.1016/j.celrep.2017.02.014
  • Muthinja MJ, Ripp J, Hellmann JK, Haraszti T, Dahan N, Lemgruber L, Battista A, Schütz L, Fackler OT, Schwarz US, Spatz JP, Frischknecht F (2017). Microstructured Blood Vessel Surrogates Reveal Structural Tropism of Motile Malaria Parasites. Advanced Healthcare Materials. (published online) doi: 10.1002/adhm.201601178
  • Klug D, Frischknecht F (2017). Motility precedes egress of malaria parasites from oocysts. Elife, 6, e19157. doi: 10.7554/eLife.19157
  • Roth, H, Magg, V, Uch, F, Mutz, P, Klein, P, Haneke, K, Lohmann, V, Bartenschlager, R, Fackler, OT, Locker, N, Stoecklin, G, Ruggieri, A (2017). Flavivirus infection uncouples translation suppression from cellular stress responses. mBio, 8:e02150-16. doi.org/10.1128/mBio.02150-16


______________________________ Publications 2016 ______________________________

  • FEBSletters_coverSpecial issue in FEBS Letters: Volume 590, Issue Supplement 13, July 2016

    Members of SFB1129 and external experts contributed to a special issue of FEBS Letters edited by Oliver Fackler and Hans-Georg Kräusslich and entitled “Integrative analysis of pathogen replication and spread”.

    Articles in this special issue highlight important recent developments that facilitate the quantitative analyses of pathogen-host interactions across scales and at maximum tempo-spatial resolution in physiologically relevant cell systems. Contributions to the special issue also identify key challenges for the field that are being addressed by SFB1129. All articles of this issue can be accessed and freely downloaded under this link.

  • Michler T, Große S, Mockenhaupt S, Röder N, Stückler F, Knapp B, Ko C, Heikenwalder M, Protzer U, Grimm D (2016). Blocking sense-strand activity improves potency, safety and specificity of anti-hepatitis B virus short hairpin RNA. EMBO Mol Med. 8(9):1082-98. doi: 10.15252/emmm.201506172
  • Lempp FA, Ni Y, Urban S (2016). Hepatitis delta virus: insights into a peculiar pathogen and novel treatment options. Nat Rev Gastroenterol Hepatol 13:580-589
  • Nikić I, Estrada Girona G, Kang JH, Paci G, Mikhaleva S, Koehler C, Shymanska NV, Ventura Santos C, Spitz D, Lemke EA* (2016). Debugging Eukaryotic Genetic Code Expansion for Site-Specific Click-PAINT Super-Resolution Microscopy. Angew Chem Int Ed Engl. 55(52):16172-16176
  • Jaiswal A, Godinez WJ, Lehmann MJ, Rohr K (2016). Direct Combination of Multi-Scale Detection and Multi-Frame Association for Tracking of Virus Particles in Microscopy Image Data, Proc. IEEE Internat. Symposium on Biomedical Imaging: From Nano to Macro (ISBI 2016), Prague, Czech Republic, April 13-16
  • Stanifer ML, Rippert A, Kazakov A, Willemsen J, Bucher D, Bender S, Bartenschlager R, Binder M, Boulant S (2016). Reovirus intermediate subviral particles constitute a strategy to infect intestinal epithelial cells by exploiting TGF-β dependent pro-survival signaling. Cell Microbiol. 18(12):1831-1845
  • Meijering E, Carpenter AE, Peng H, Hamprecht FA, Olivo-Marin JC (2016). Imagining the future of bioimage analysis. Nat. Biotechnol. Volume 34 (12):1250-1255
  • Beier T, Andres B, Köthe U, Hamprecht FA (2016). An efficient fusion move algorithm for the minimum cost lifted multicut problem. In European Conference on Computer Vision (pp. 715-730). Springer International Publishing.
  • Cyrklaff M, Srismith S, Nyboer B, Burda K, Hoffmann A, Lasitschka F, Adjalley S, Bisseye C, Simpore J, Mueller AK, Sanchez CP, Frischknecht F, Lanzer M (2016). Oxidative insult can induce malaria-protective trait of sickle and fetal erythrocytes. Nat. Commun. 7, 13401 doi: 10.1038/ncomms13401 (2016)
  • Waldecker M, Dasanna AK, Lansche C, Linke M, Srismith S, Cyrklaff M, Sanchez CP, Schwarz US, Lanzer M (2016). Differential time-dependent volumetric and surface area changes and delayed induction of new permeation pathways in P. falciparum-infected hemoglobinopathic erythrocytes. Cell Microbiol. doi: 10.1111/cmi.12650
  • Bane KS, Lepper S, Kehrer J, Sattler JM, Singer M, Reinig M, Klug D, Heiss K, Baum J, Mueller AK, Frischknecht F (2016). The actin-filament binding protein coronin regulates motility in Plasmodium sporozoites, PLoS Pathog. 2016 Jul 13;12(7):e1005710. doi: 10.1371/journal.ppat.1005710
  • Hentzschel F, Herrmann AK, Mueller AK, Grimm D (2016). Plasmodium meets AAV – the (un)likely marriage of parasitology and virology, and how to make the match. FEBS Lett., 2016. doi: 10.1002/1873-3468.12187
  • Kumar H, Sattler JM, Singer M, Heiss K, Reinig M, Hammerschmidt-Kamper C, Heussler V, Mueller AK, Frischknecht F (2016). Protective efficacy and safety of liver stage attenuated malaria parasites. Sci. Rep. 6:26824. doi: 10.1038/srep26824
  • Zayas M, Long G, Madan V, Bartenschlager R (2016). Coordination of Hepatitis C Virus Assembly by Distinct Regulatory Regions in Nonstructural Protein 5A. PLoS Pathog. 12(1):e1005376
  • Romero-Brey I, Bartenschlager R (2016). Endoplasmic Reticulum: The Favorite Intracellular Niche for Viral Replication and Assembly. Viruses. 2016 Jun 7;8(6). pii: E160. doi: 10.3390/v8060160. Review
  • Kehrer J, Singer M, Lemgruber L, Silva PA, Frischknecht F, Mair GR. (2016). A Putative Small Solute Transporter Is Responsible for the Secretion of G377 and TRAP-Containing Secretory Vesicles during Plasmodium Gamete Egress and Sporozoite Motility. PLoS Pathog. 2016 Jul 18;12(7):e1005734. doi: 10.1371/journal.ppat.1005734
  • Chatel-Chaix L, Cortese M, Romero-Brey I, Bender S, Fischl W, Scaturro P, Fischer B, Ruggieri A, Bartenschlager R (2016). Dengue Virus Perturbs Mitochondrial Morphodynamics to Dampen Innate Immune Responses. Cell Host Microbe. 20, 342-356, doi: 10.1016/j.chom.2016.07.008
  • Schaufler V, Czichos-Medda H, Hirschfeld-Warnecken V, Neubauer S, Rechenmacher F, Medda R, Kessler H, Geiger B, Spatz JP, Cavalcanti-Adam EA (2016). Selective binding and lateral clustering of a5b1 and avb3 integrins: unraveling the spatial requirements for cell spreading and focal adhesion assembly. Cell Adhesion and Migration, March 22, 1-11
  • Haubold C, Schiegg M, Kreshuk A, Berg S, Köthe U, Hamprecht FA (2016). Segmenting and Tracking Multiple Dividing Targets Using ilastik, in: W.H. De Vos, S. Munck, J.-P. Timmermans (Eds.): Focus on Bio-Image Informatics, Springer Advances in Anatomy, Embryology and Cell Biology, Volume 219, pp. 199-229
  • Imle A, Stolp B, Böhmer V, Geyer M, Raz E, Fackler OT (2016). D186/D190 is an Allele-dependent Determinant of HIV-1 Nef Function. Virology 498:44-56
  • Schorb M, Gaechter L, Avinoam O, Sieckmann F, Clarke M, Bebeacua C, Bykov Y, Sonnen AFP, Lihl R, Briggs JAG (2016). New hardware and workflows for semi-automated correlative cryo-fluoresence and cryo-electron microscopy/tomography. Journal of Structural Biology, in press, doi:10.1016/j.jsb.2016.06.020
  • Bykov YS, Cortese M, Briggs JAG, Bartenschlager R (2016). Correlative light and electron microscopy methods for the study of virus-cell interactions (review). FEBS Lett. 590(13):1877-1895
  • Hanne J, Zila V, Heilemann M, Müller B, Kräusslich HG (2016). Super-resolved insights into human immunodeficiency virus biology. FEBS Lett. 590(13):1858-76
  • Sakin V, Paci G, Lemke EA, Müller B (2016). Labeling of virus components for advanced, quantitative imaging analyses. FEBS Lett. 590(13):1896-914
  • Frischknecht F, Fackler OT (2016). Experimental Systems for Studying Plasmodium-HIV coinfection. FEBS Lett, Mar 24. doi: 10.1002/1873-3468.12151
  • Pujol FM, Laketa V, Schmidt F, Mukenhirn M, Müller B, Boulant S, Grimm D, Keppler OT, Fackler OT (2016). HIV-1 Vpu Antagonizes CD317/tetherin by Adaptor protein-1-Mediated Exclusion from Virus Assembly Sites. J. Virol. 90:6709-6723
  • Kozma E, Nikic I, Varga BR, Aramburu IV, Kang JH, Fackler OT, Lemke EA, Kele P (2016). Hydrophilic trans-Cyclooctenylated Non-Canonical Amino Acids for Fast Intracellular Protein Labeling. Chembiochem. 2016 May 25. doi: 10.1002/cbic.201600284
  • Lee HY, Schierer S, Blume K, Dindorf J, Wittki S, Xiang W, Ostalecki C, Koliha N, Wild S, Schuler G, Fackler OT, Saksela K, Harrer T, Baur AS (2016). HIV-Nef and ADAM17-Containing Plasma Extracellular Vesicles Induce and Correlate with Immune Pathogenesis in Chronic HIV Infection. EBioMedicine, 6: 103–113
  • Zhang Z, Zehnder B, Damrau C, Urban S (2016). Visualization of Hepatitis B Virus Entry: Novel Tools and Approaches to Directly Follow Virus Entry into Hepatocytes. FEBS Letters. doi: 10.1002/1873-3468.12202
  • Helms G, Dasanna AK, Schwarz US, Lanzer M (2016). Modeling cytoadhesion of Plasmodium falciparuminfected erythrocytes and leukocytes—common principles and distinctive features. FEBS Letters. doi: 10.1002/1873-3468.12142
  • Quadt KA, Streichfuss M, Moreau CA, Spatz JP, Frischknecht F (2016). Coupling of Retrograde Flow to Force Production During Malaria Parasite Migration. ACS Nano, doi: 10:2091-2102; 10.1021/acsnano.5b06417


______________________________ Publications 2015 ______________________________

  • Grimm D, Zolotukhin S (2015). E Pluribus Unum: 50 Years of Research, Millions of Viruses, and One Goal–Tailored Acceleration of AAV Evolution. Mol Ther. 23(12):1819-31. doi: 10.1038/mt.2015.173
  • Milles S, Mercadante D, Aramburu IV, Jensen MR, Banterle B, Koehler C, Tyagi S, Clarke J, Shammas S, Blackledge M*, Gräter F*, Lemke EA* (2015). Plasticity of an ultrafast interaction between nucleoporin and transport receptors. Cell, 10.1016/j.cell.2015.09.047
  • Kilian N, Srismith S, Dittmer M, Ouermi D, Bisseye C, Simpore J, Cyrklaff M, Sanchez CP, Lanzer M (2015). Hemoglobin S and C affect protein export in Plasmodium falciparum-infected erythrocytes. Biol Open 4: 400-410
  • Rieger H, Yoshikawa HY, Quadt K, Nielsen MA, Sanchez CP, Salanti A, Tanaka M, Lanzer M (2015). Cytoadhesion of Plasmodium falciparum-infected erythrocytes to chondroitin-4-sulfate is cooperative and shear enhanced. Blood 125: 383-391
  • Paul D, Bartenschlager R (2015). Flaviviridae Replication Organelles: Oh, What a Tangled Web We Weave. Annu Rev Virol. 2(1):289-310
  • Rieger H, Yoshikawa HY, Quadt K, Nielsen MA, Sanchez CP, Salanti A, Tanaka M, Lanzer M (2015). Cytoadhesion of Plasmodium falciparum-infected erythrocytes to chondroitin-4-sulfate is cooperative and shear enhanced. Blood 125: 383-391
  • Kilian, N, Srismith, S, Dittmer, M, Ouermi, D, Bisseye, C, Simpore, J, Cyrklaff, M, Sanchez, CP, Lanzer, M (2015). Hemoglobin S and C affect protein export in Plasmodium falciparum-infected erythrocytes. Biol Open 4, 400-410
  • Chatel-Chaix L, Fischl W, Scaturro P, Cortese M, Kallis S, Bartenschlager M, Fischer B, Bartenschlager R (2015). A combined genetic-proteomic approach identifies residues within Dengue virus NS4B critical for interaction with NS3 and viral replication. J. Virol. 89(14):7170-86
  • Romero-Brey I, Berger C, Kallis S, Kolovou A, Paul D, Lohmann V, Bartenschlager R (2015). NS5A Domain 1 and Polyprotein Cleavage Kinetics Are Critical for Induction of Double-Membrane Vesicles Associated with Hepatitis C Virus Replication. Mbio 6(4):e00759
  • Madan V, Bartenschlager R (2015). Structural and Functional Properties of the Hepatitis C Virus p7 Viroporin. Viruses. 7(8):4461-81. Review
  • Grünvogel O, Esser-Nobis K, Reustle A, Schult P, Müller B, Metz P, Trippler M, Windisch MP, Frese M, Binder M, Fackler O, Bartenschlager R, Ruggieri A, Lohmann V. (2015). DDX60L Is an Interferon-Stimulated Gene Product Restricting Hepatitis C Virus Replication in Cell Culture. J. Virol. 89(20):10548-68*
  • Scaturro P, Cortese M, Chatel-Chaix L, Fischl W, Bartenschlager R (2015). Dengue Virus Non-structural Protein 1 Modulates Infectious Particle Production via Interaction with the Structural Proteins. PLoS Pathog. 11(11):e1005277. eCollection 2015 Nov
  • Romero-Brey I, Bartenschlager R. (2015). Viral Infection at High Magnification: 3D Electron Microscopy Methods to Analyze the Architecture of Infected Cells. Viruses.7(12):6316-45. Review
  • Cavalcanti-Adam EA, Spatz JP (2015). Receptor clustering control and associated force sensing by surface patterning: when force matters. Nanomedicine 10(5): 681-4
  • Chlanda P, Schraidt O, Kummer S, Riches J, Oberwinkler H, Prinz S, Kräusslich HG, Briggs JAG (2015). Structural analysis of the roles of influenza A virus membrane-associated proteins in assembly and morphology. J. Virol. 89:8957-8966
  • Jaiswal A, Godinez WJ, Eils R, Lehmann MJ, Rohr K (2015). Tracking Virus Particles in Fluorescence Microscopy Images Using Multi-Scale Detection and Multi-Frame Association. IEEE Transactions on Image Processing, 24(11):4122-4136, doi: 10.1109/TIP.2015.2458174
  • Singer M, Marshall J, Heiss K, Mair GR, Grimm D, Mueller AK, Frischknecht F (2015). Zinc finger nuclease-based double-strand breaks attenuate malaria parasites and reveal rare microhomology-mediated end joining. Genome Biology 16:249, doi: 10.1186/s13059-015-0811-1
  • Lempp FA, Mutz P, Lipps C, Wirth D, Bartenschlager R, Urban S (2015). Evidence that hepatitis B virus replication in mouse cells is limited by the lack of a host cell dependency factor. Journal of Hepatology (2015), doi: http://dx.doi.org/10.1016/j.jhep.2015.10.030
  • Milles S, Mercadante D, Aramburu IV, Ringkjøbing Jensen M, Banterle N, Koehler C, Tyagi S, Clarke J, Shammas SL, Blackledge M, Gräter F, Lemke EA (2015). Plasticity of an Ultrafast Interaction between Nucleoporins and Nuclear Transport Receptors. Cell 163:734–745
  • Verollet D, Souriant S, Bonnaud E, Jolicœur P, Raynaud-Messina B, Kinnaer C, Fourquaux I, Imle A, Benichou S, Fackler OT, Poincloux R, Maridonneau-Parini I (2015). HIV-1 reprograms the Migration of macrophages. Blood 125:1611-1522


______________________________ Publications 2014 ______________________________

  • Odendall C, Dixit E, Stavru F, Bierne H, Franz KM, Durbin AF, Boulant S, Gehrke L, Cossart P, Kagan JC (2014). Diverse intracellular pathogens activate type III interferon expression from peroxisomes. Nat Immunol. 8:717–726
  • Senís E, Fatouros C, Große S, Wiedtke E, Niopek D, Mueller AK, Börner K, Grimm D (2014). CRISPR/Cas9-mediated genome engineering: an adeno-associated viral (AAV) vector toolbox. Biotechnol J. (11):1402-12, doi:10.1002/biot.201400046
  • Hentzschel F, Hammerschmidt-Kamper C, Börner K, Heiss K, Knapp B, Sattler JM, Kaderali L, Castoldi M, Bindman JG, Malato Y, Willenbring H, Mueller AK, Grimm D (2014). Mol Ther. (12):2130-41, doi: 10.1038/mt.2014.172
  • Fackler OT, Murooka TT, Imle A, Mempel TR (2014). Adding new dimensions: Towards an integrative understanding of HIV-1 spread. Nat. Rev. Microbiol. 12:563-574
  • Battista A, Frischknecht F, Schwarz U (2014). Geometrical model for a Malaria parasite Migration in structured environments. Phys. Rev. E. 90:042720
  • Peng K, Muranyi W, Glass B, Laketa V, Yant SR, Tsai L, Cihlar T, Müller B, Kräusslich HG (2014). Quantitative microscopy of functional HIV post-entry complexes reveals association of replication with the viral capsid. Elife Dec 17;3:e04114