Publikationen

Gemeinsame Publikationen der beteiligten Arbeitsgruppen im Rahmen des Leibniz-WissenschaftsCampus InterACt

2022

Arend L, Bernett J, Manz Q, Klug M, Lazareva O, Baumbach J, Bongiovanni D, List M. (2022) A systematic comparison of novel and existing differential analysis methods for CyTOF data. Brief Bioinform. 2022 Jan 17;23(1):bbab471. doi: 10.1093/bib/bbab471
Boddin J, Ip WH, Wilkens B, von Stromberg K, Ching W, Koyuncu E, Bertzbach LD, Dobner T. (2022) A Single Amino Acid Switch in the Adenoviral DNA Binding Protein Abrogates Replication Center Formation and Productive Viral Infection. mBio. 2022 Mar 7:e0014422. doi: 10.1128/mbio.00144-22
Caragliano E, Bonazza S, Frascaroli G, Tang J, Soh TK, Grünewald K, Bosse JB, Brune W. (2022) Human cytomegalovirus forms phase-separated compartments at viral genomes to facilitate viral replication. Cell Reports. 2022 Mar 8. doi: 10.1016/j.celrep.2022.110469
Caragliano E, Brune W, Bosse JB. (2022) Herpesvirus Replication Compartments: Dynamic Biomolecular Condensates? Viruses. 2022 May 4;14(5):960. doi: 10.3390/v14050960
Degenhardt F, ... Özer O, ... Teles A, ... Azuure C, ... Lenz TL, ... Franke A. (2022) Detailed stratified GWAS analysis for severe COVID-19 in four European populations. Hum Mol Genet. 2022 Jul 15:ddac158. doi: 10.1093/hmg/ddac158
Falter C, Reumann S. (2022) The essential role of fungal peroxisomes in plant infection. Mol Plant Pathol. 2022 Jan 10. doi: 10.1111/mpp.13180
Fiedler M, Ip WH, Hofmann-Sieber H, Wilkens B, Nkrumah FK, Zhang W, Ehrhardt A, Bertzbach LD, Dobner T. (2022) Protein-Protein Interactions Facilitate E4orf6-Dependent Regulation of E1B-55K SUMOylation in HAdV-C5 Infection. Viruses. 2022 Feb 24;14(3):463. doi: 10.3390/v14030463
Flomm FJ, Soh TK, Schneider C, Wedemann L, Britt HM, Thalassinos K, Pfitzner S, Reimer R, Grünewald K, Bosse JB. (2022) Intermittent bulk release of human cytomegalovirus. PLoS Pathog. 2022 Aug 4;18(8):e1010575. doi: 10.1371/journal.ppat.1010575
Franken LE, Rosch R, Laugks U, Grünewald K. Protocol for live-cell fluorescence-guided cryoFIB-milling and electron cryo-tomography of virus-infected cells. STAR Protoc. 2022 Sep 21;3(4):101696. doi: 10.1016/j.xpro.2022.101696
Gudzuhn M, Alio I, Moll R, de Vries J, Boehlich J, Assmann M, Janneschütz J, Schützenmeister N, Himmelbach A, Poehlein A, Daniel R, Streit WR. (2022) Molecular Insight into Gene Response of Diorcinol- and Rubrolide-Treated Biofilms of the Emerging Pathogen Stenotrophomonas maltophilia. Microbiol Spectr. 2022 Apr 26:e0258221. doi: 10.1128/spectrum.02582-21
Ivanova ME, Lukoyanova N, Malhotra S, Topf M, Trapani JA, Voskoboinik I, Saibil HR. (2022) The pore conformation of lymphocyte perforin. Sci Adv 8(6):eabk3147. doi: 10.1126/sciadv.abk3147
Kolbe V, Ip WH, Kieweg-Thompson L, Lang J, Gruhne J, Meyer T, Wilkens B, Schie M, Thünauer R, Schreiner S, Bertzbach LD, Rodríguez E, Dobner T (2022). Conserved E1B-55K SUMOylation in different human adenovirus species is a potent regulator of intracellular localization. J Virol. 2022 Feb 9;96(3):e0083821. doi: 10.1128/JVI.00838-21
Kopicki JD, Saikia A, Niebling S, Günther C, Anjanappa R, Garcia-Alai M, Springer S, Uetrecht C. (2022) Opening opportunities for Kd determination and screening of MHC peptide complexes. Commun Biol. 2022 May 23;5(1):488. doi: 10.1038/s42003-022-03366-0
Nasirigerdeh R, Torkzadehmahani R, Matschinske J, Frisch T, List M, Späth J, Weiss S, Völker U, Pitkänen E, Heider D, Wenke NK, Kaissis G, Rueckert D, Kacprowski T, Baumbach J. (2022) sPLINK: a hybrid federated tool as a robust alternative to meta-analysis in genome-wide association studies. Genome Biol. 2022 Jan 24;23(1):32. doi: 10.1186/s13059-021-02562-1
Rose TD, Bechtler T, Ciora OA, Le KAL, Molnar F, Koehler N, Baumbach J, Röttger R, Pauling JK (2022) MoSBi: Automated signature mining for molecular stratification and subtyping. Proc Natl Acad Sci U.S.A. 2022 Apr 11; 119 (16) e2118210119. doi: 10.1073/pnas.2118210119
Schöning-Stierand K, Diedrich K, Ehrt C, Flachsenberg F, Graef J, Sieg J, Penner P, Poppinga M, Ungethüm A, Rarey M. (2022) ProteinsPlus: a comprehensive collection of web-based molecular modeling tools. Nucleic Acids Res. 2022 Apr 30:gkac305. doi: 10.1093/nar/gkac305
Wedemann L, Flomm FJ, Bosse JB. (2022) The unconventional way out-Egress of HCMV through multiviral bodies. Mol Microbiol. 2022 May 23. doi: 10.1111/mmi.14946
Yu D, Chojnowski G, Rosenthal M, Kosinski J (2022) AlphaPulldown – a Python package for protein-protein interaction screens using AlphaFold-Multimer. bioRxiv 2022.08.05.502961 doi: 10.1101/2022.08.05.502961

2021

Cook AD, Roberts AJ, Atherton J, Tewari R, Topf M, Moores CA. (2021) Cryo-EM structure of a microtubule-bound parasite kinesin motor and implications for its mechanism and inhibition. J Biol Chem 297(5):101063. doi: 10.1016/j.jbc.2021.101063
Cragnolini T, Kryshtafovych A, Topf M. (2021) Cryo-EM targets in CASP14. Proteins. 2021 Dec;89(12):1949-1958. doi: 10.1002/prot.26216
Cragnolini T, Sahota H, Joseph AP, Sweeney A, Malhotra S, Vasishtan D, Topf M. (2021) TEMPy2: a Python library with improved 3D electron microscopy density-fitting and validation workflows. Acta Crystallogr D Struct Biol 77(Pt 1):41–47. doi: 10.1107/S2059798320014928
Dülfer J, Yan H, Brodmerkel MN, Creutznacher R, Mallagaray A, Peters T, Caleman C, Marklund EG, Uetrecht C. (2021) Glycan-Induced Protein Dynamics in Human Norovirus P Dimers Depend on Virus Strain and Deamidation Status. Molecules. 2021 Apr 7;26(8):2125. doi: 10.3390/molecules26082125
Ferreira JL, Heincke D, Wichers JS, Liffner B, Wilson DW, Gilberger TW (2021). The Dynamic Roles of the Inner Membrane Complex in the Multiple Stages of the Malaria Parasite. Front Cell Infect Microbiol. 2021 Jan 8;10:611801.doi: 10.3389/fcimb.2020.611801
Günther S, Reinke PYA, Fernández-García Y, Lieske J, Lane TJ, Ginn HM, Koua FHM, Ehrt C, Ewert W, Oberthuer D, Yefanov O, Meier S, Lorenzen K, Krichel B, Kopicki JD, Gelisio L, Brehm W, Dunkel I, Seychell B, Gieseler H, Norton-Baker B, Escudero-Pérez B, Domaracky M, Saouane S, Tolstikova A, White TA, Hänle A, Groessler M, Fleckenstein H, Trost F, Galchenkova M, Gevorkov Y, Li C, Awel S, Peck A, Barthelmess M, Schlünzen F, Lourdu Xavier P, Werner N, Andaleeb H, Ullah N, Falke S, Srinivasan V, França BA, Schwinzer M, Brognaro H, Rogers C, Melo D, Zaitseva-Doyle JJ, Knoska J, Peña-Murillo GE, Mashhour AR, Hennicke V, Fischer P, Hakanpää J, Meyer J, Gribbon P, Ellinger B, Kuzikov M, Wolf M, Beccari AR, Bourenkov G, von Stetten D, Pompidor G, Bento I, Panneerselvam S, Karpics I, Schneider TR, Garcia-Alai MM, Niebling S, Günther C, Schmidt C, Schubert R, Han H, Boger J, Monteiro DCF, Zhang L, Sun X, Pletzer-Zelgert J, Wollenhaupt J, Feiler CG, Weiss MS, Schulz EC, Mehrabi P, Karničar K, Usenik A, Loboda J, Tidow H, Chari A, Hilgenfeld R, Uetrecht C, Cox R, Zaliani A, Beck T, Rarey M, Günther S, Turk D, Hinrichs W, Chapman HN, Pearson AR, Betzel C, Meents A. (2021) X-ray screening identifies active site and allosteric inhibitors of SARS-CoV-2 main protease. Science. 2021 May 7;372(6542):642-646. doi: 10.1126/science.abf7945
Herker E, Vieyres G, Beller M, Krahmer N, Bohnert M. (2021) Lipid Droplet Contact Sites in Health and Disease. Trends Cell Biol. 2021 May;31(5):345-358. doi: 10.1016/j.tcb.2021.01.004
Hessler G, Portheine SM, Gerlach EM, Lienemann T, Koch G, Voigt CA, Hoth S. (2021) PMR4-dependent cell wall depositions are a consequence but not the cause of temperature-induced autoimmunity. J Exp Bot. 2021 Sep 14:erab423. doi: 10.1093/jxb/erab423
Jung JM, Ching W, Baumdick ME, Hofmann-Sieber H, Bosse JB, Koyro T, Möller KJ, Wegner L, Niehrs A, Russu K, Ohms M, Zhang W, Ehrhardt A, Duisters K, Spierings E, Hölzemer A, Körner C, Jansen SA, Peine S, Königs I, Lütgehetmann M, Perez D, Reinshagen K, Lindemans CA, Altfeld M, Belderbos M, Dobner T, Bunders MJ. (2021) KIR3DS1 directs NK cell-mediated protection against human adenovirus infections. Sci Immunol. 2021 Sep 17;6(63):eabe2942. doi: 10.1126/sciimmunol.abe2942
Klose M, Scheungrab M, Luckner M, Wanner G, Linder S. (2021) FIB-SEM-based analysis of Borrelia intracellular processing by human macrophages. J Cell Sci. 2021 Feb 11;134(5):jcs252320. doi: 10.1242/jcs.252320
Knop J, Lienemann T, El-Kilani H, Falke S, Krings C, Sindalovskaya M, Bergler J, Betzel C, Hoth S. (2021) Structural Features of a Full-Length Ubiquitin Ligase Responsible for the Formation of Patches at the Plasma Membrane. Int J Mol Sci. 2021 Aug 31;22(17):9455. doi: 10.3390/ijms22179455
Krichel B, Bylapudi G, Schmidt C, Blanchet C, Schubert R, Brings L, Koehler M, Zenobi R, Svergun D, Lorenzen K, Madhugiri R, Ziebuhr J, Uetrecht C. (2021) Hallmarks of Alpha- and Betacoronavirus non-structural protein 7+8 complexes. Science advances, 7(10), eabf1004 doi: 10.1126/sciadv.abf1004
Louadi Z, Elkjaer ML, Klug M, Lio CT, Fenn A, Illes Z, Bongiovanni D, Baumbach J, Kacprowski T, List M, Tsoy O. (2021) Functional enrichment of alternative splicing events with NEASE reveals insights into tissue identity and diseases. Genome Biol 22, 327. doi: 10.1186/s13059-021-02538-1
Malhotra S, Joseph AP, Thiyagalingam J, Topf M. (2021) Assessment of protein-protein interfaces in cryo-EM derived assemblies. Nat Commun 12(1):3399 doi: 10.1038/s41467-021-23692-x
Manz Q, Tsoy O, Fenn A, Baumbach J, Völker U, List M, Kacprowski T (2021) ASimulatoR: splice-aware RNA-Seq data simulation. Bioinformatics 2021 Feb 27, btab142. doi: 10.1093/bioinformatics/btab142
Pfitzner S, Bosse JB, Hofmann-Sieber H, Flomm F, Reimer R, Dobner T, Grünewald K, Franken LE. (2021) Human Adenovirus Type 5 Infection Leads to Nuclear Envelope Destabilization and Membrane Permeability Independently of Adenovirus Death Protein. Int J Mol Sci. 2021 Dec 2;22(23):13034. doi: 10.3390/ijms222313034
Pogan R, Weiss VU, Bond K, Dülfer J, Krisp C, Lyktey N, Mueller-Guhl J, Zoratto S, Allmaier G, Jarrold MF, Munoz-Fontela C, Schlüter H, Uetrecht C. (2021) N-terminal VP1 truncations favor T=1 norovirus-like particles. Vaccines, 9:8 doi: 10.3390/vaccines9010008
Pražák V, Grünewald K, Kaufmann R. (2021) Correlative super-resolution fluorescence and electron cryo-microscopy based on cryo-SOFI. Methods Cell Biol. 2021;162:253-271. doi: 10.1016/bs.mcb.2020.10.021
Sadegh S, Skelton J, Anastasi E, Bernett J, Blumenthal DB, Galindez G, Salgado-Albarrán M, Lazareva O, Flanagan K, Cockell S, Nogales C, Casas AI, Schmidt HHHW, Baumbach J, Wipat A, Kacprowski T. (2021) Network medicine for disease module identification and drug repurposing with the NeDRex platform. Nat Commun. 2021 Nov 25;12(1):6848. doi: 10.1038/s41467-021-27138-2
Silvester E, Vollmer B, Pražák V, Vasishtan D, Machala EA, Whittle C, Black S, Bath J, Turberfield AJ, Grünewald K, Baker LA (2021) DNA origami signposts for identifying proteins on cell membranes by electron cryotomography. Cell. 184(4):1110-1121.e16. doi: 10.1016/j.cell.2021.01.033
Simanjuntak Y, Schamoni-Kast K, Grün A, Uetrecht C, Scaturro P (2021). Top-Down and Bottom-Up Proteomics Methods to Study RNA Virus Biology. Viruses. 2021 Apr 13;13(4):668. doi: 10.3390/v13040668
Tegtmeyer B, Vieyres G, Todt D, Lauber C, Ginkel C, Engelmann M, Herrmann M, Pfaller CK, Vondran FWR, Broering R, Vafadarnejad E, Saliba AE, Puff C, Baumgärtner W, Miskey C, Ivics Z, Steinmann E, Pietschmann T, Brown RJP. (2021) Initial HCV infection of adult hepatocytes triggers a temporally structured transcriptional program containing diverse pro- and anti-viral elements. J Virol. 2021 Mar 3;95(10):e00245-21. doi: 10.1128/JVI.00245-21
Vieyres G. (2021) PicPreview and PicSummary: Two Timesaving Plugins for the Fluorescence Microscopist. Cells, 2021 Apr 8;10(4):846. doi: 10.3390/cells10040846
Woitzik P, Linder S. (2021) Molecular Mechanisms of Borrelia burgdorferi Phagocytosis and Intracellular Processing by Human Macrophages. Biology (Basel). 2021 Jun 22;10(7):567. doi: 10.3390/biology10070567
Zolotareva O, Nasirigerdeh R, Matschinske J, Torkzadehmahani R, Bakhtiari M, Frisch T, Späth J, Blumenthal DB, Abbasinejad A, Tieri P, Kaissis G, Rückert D, Wenke NK, List M, Baumbach J. (2021) Flimma: a federated and privacy-aware tool for differential gene expression analysis. Genome Biol. 2021 Dec 14;22(1):338. doi: 10.1186/s13059-021-02553-2

2020

Alio I, Gudzuhn M, Pérez García P, Danso D, Schoelmerich M, Mamat U, Schaible UE, Steinmann J, Yero D, Gibert I, Kohl TA, Niemann S, Gröschel MI, Haerdter J, Hackl T, Vollstedt C, Bömeke M, Egelkamp R, Daniel R, Poehlein A, Streit WR. (2020) Phenotypic and transcriptomic analysis of seven clinical Stenotrophomonas maltophilia isolates identify a small set of shared and commonly regulated genes involved in biofilm lifestyle. Appl Environ Microbiol. 2020 Oct 23:AEM.02038-20. doi: 10.1128/AEM.02038-20.
Brown RJP, Tegtmeyer B, Sheldon J, Khera T, Anggakusuma, Todt D, Vieyres G, Weller R, Joecks S, Zhang Y, Sake S, Bankwitz D, Welsch K, Ginkel C, Engelmann M, Gerold G, Steinmann E, Yuan Q, Ott M, Vondran FWR, Krey T, Ströh LJ, Miskey C, Ivics Z, Herder V, Baumgärtner W, Lauber C, Seifert M, Tarr AW, McClure CP, Randall G, Baktash Y, Ploss A, Thi VLD, Michailidis E, Saeed M, Verhoye L, Meuleman P, Goedecke N, Wirth D, Rice CM, Pietschmann T. (2020) Liver-expressed Cd302 and Cr1l limit hepatitis C virus cross-species transmission to mice. Sci Adv. 2020 Nov 4;6(45):eabd3233. doi: 10.1126/sciadv.abd3233
Gröschel MI, Meehan CJ, Barilar I, Diricks M, Gonzaga A, Steglich M, Conchillo-Solé O, Scherer IC, Mamat U, Luz CF, De Bruyne K, Utpatel C, Yero D, Gibert I, Daura X, Kampmeier S, Rahman NA, Kresken M, van der Werf TS, Alio I, Streit WR, Zhou K, Schwartz T, Rossen JWA, Farhat MR, Schaible UE, Nübel U, Rupp J, Steinmann J, Niemann S, Kohl TA. (2020) The phylogenetic landscape and nosocomial spread of the multidrug-resistant opportunist Stenotrophomonas maltophilia. Nat Commun. 2020;11(1):2044. doi: 10.1038/s41467-020-15123-0
Joseph AP, Lagerstedt I, Jakobi A, Burnley T, Patwardhan A, Topf M, Winn M. (2020) Comparing Cryo-EM Reconstructions and Validating Atomic Model Fit Using Difference Maps. J Chem Inf Model 60(5):2552–2560. doi: 10.1021/acs.jcim.9b01103
Krichel B, Falke S, Hilgenfeld R, Redecke L, Uetrecht C. (2020) Processing of the SARS-CoV pp1a/ab nsp7-10 region. Biochem J, 477(5):1009-1019. doi: 10.1042/BCJ20200029
Louadi Z, Yuan K, Gress A, Tsoy O, Kalinina O, Baumbach J, Kacprowski T, List M (2020) DIGGER: Exploring the functional role of alternative splicing in protein interactions. Nucleic Acids Res. 2020 Sep 25:gkaa768 doi: 10.1093/nar/gkaa768
Pfitzner S, Hofmann-Sieber H, Bosse JB, Franken LE, Grünewald K, Dobner T (2020) Fluorescent protein tagging of adenoviral proteins pV and pIX reveals ‘late virion accumulation compartment’. PLOS Pathogens 16(6): e1008588. doi: 10.1371/journal.ppat.1008588
Sinnott M, Malhotra S, Madhusudhan MS, Thalassinos K, Topf M. (2020) Combining Information from Crosslinks and Monolinks in the Modeling of Protein Structures. Structure 28(9):1061-1070.e3. doi: 10.1016/j.str.2020.05.012
Vollmer B, Pražák V, Vasishtan D, Jefferys EE , Hernandez-Duran A, Vallbracht M, Klupp B, Mettenleiter TC, Backovic M, Rey FA, Topf M, Grünewald K (2020). The prefusion structure of herpes simplex virus glycoprotein B. Science Advances. eabc1726. doi: 10.1126/sciadv.abc1726
Wolff G, Limpens RWAL, Zevenhoven-Dobbe JC, Laugks U, Zheng S, de Jong AWM, Koning RI, Agard DA, Grünewald K, Koster AJ, Snijder EJ, Bárcena M. (2020) A molecular pore spans the double membrane of the coronavirus replication organelle. Science. 369(6509):1395-1398. doi: 10.1126/science.abd3629

Prof. Dr. Kay Grünewald

Dr. Ronja Markworth

Publikationen

2022

2021

2020

Leibniz-WissenschaftsCampus InterACt

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