Publikationen

Joint publications of the participating research groups within the Leibniz ScienceCampus InterACt

2023

  • Sadegh S, Skelton J, Anastasi E, Maier A, Adamowicz K, Möller A, Kriege NM, Kronberg J, Haller T, Kacprowski T, Wipat A, Baumbach J, Blumenthal DB. (2023) Lacking mechanistic disease definitions and corresponding association data hamper progress in network medicine and beyond. Nat Commun. 2023 Mar 25;14(1):1662. doi: 10.1038/s41467-023-37349-4

  • Vieyres G, Pietschmann T. (2023) The role of human lipoproteins for hepatitis C virus persistence. Curr Opin Virol. 2023 Apr 7;60:101327. doi: 10.1016/j.coviro.2023.101327

  • Wichers-Misterek JS, Binder AM, Mesén-Ramírez P, Dorner LP, Safavi S, Fuchs G, Lenz TL, Bachmann A, Wilson D, Frischknecht F, Gilberger TW. (2023) A Microtubule-Associated Protein Is Essential for Malaria Parasite Transmission. mBio. 2023 Feb 28;14(1):e0331822. doi: 10.1128/mbio.03318-22

  • Yu D, Chojnowski G, Rosenthal M, Kosinski J. (2023) AlphaPulldown-a python package for protein-protein interaction screens using AlphaFold-Multimer. Bioinformatics. 2023 Jan 1;39(1):btac749. doi: 10.1093/bioinformatics/btac749

2022

  • Adamowicz K, Maier A, Baumbach J, Blumenthal DB. Online in silico validation of disease and gene sets, clusterings or subnetworks with DIGEST. Brief Bioinform. 2022 Jul 18;23(4):bbac247. doi: 10.1093/bib/bbac247

  • 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

  • Galindez G, Sadegh S, Baumbach J, Kacprowski T, List M. (2022) Network-based approaches for modeling disease regulation and progression. Comput Struct Biotechnol J. 2022 Dec 16;21:780-795. doi: 10.1016/j.csbj.2022.12.022

  • 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

  • Ostendorp A, Ostendorp S, Zhou Y, Chaudron Z, Wolffram L, Rombi K, von Pein L, Falke S, Jeffries CM, Svergun DI, Betzel C, Morris RJ, Kragler F, Kehr J. (2022) Intrinsically disordered plant protein PARCL colocalizes with RNA in phase-separated condensates whose formation can be regulated by mutating the PLD. J Biol Chem. 2022 Dec;298(12):102631. doi: 10.1016/j.jbc.2022.102631.

  • 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

  • Weber L, Vieyres G. (2002) The Railmap of Type I Interferon Induction: Subcellular Network Plan and How Viruses Can Change Tracks. Cells. 2022 Oct 6;11(19):3149. doi: 10.3390/cells11193149

  • 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

Leibniz ScienceCampus InterACt

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20251 Hamburg

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Campus Speaker

Prof. Dr. Kay Grünewald

Campus Coordinator

Dr. Ronja Markworth

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