Publications by the Knop Lab

search pubmed for current publications by M. Knop

Accurate and sensitive interactome profiling usong a quantitative protein-fragment complementation essay.
Lazarewicz N, Le Dez G, Cerjani R, Runeshaw L, Meurer M, Knop M, Wysocki R, Rabut G. Cell Rep Methods. 2024 Oct 21;4(10):100880. doi: 10.1016/j.crmeth.2024.100880. PMID: 39437715 Free PMC article. Here, we constructed genome-wide libraries of yeast strains to systematically probe protein-protein interactions using NanoLuc Binary Technology (NanoBiT), a quantitative protein-fragment complementation assay (PCA) based on the NanoLuc luciferase. ...

Inhibtion of 26S proteasome activity by a-synuclein is mediated by the proteosomal chaperone Rpn14/PAAF1.
Galka D, Ali TT, Bast A, Niederleithinger M, Gerhardt E, Motosugi R, Sakata E, Knop M, Outeiro TF, Popova B, Braus GH. Aging Cell. 2024 May;23(5):e14128. doi: 10.1111/acel.14128. Epub 2024 Feb 28. PMID: 38415292 Free PMC article. Altered proteostasis depends on alpha-syn protein levels and the impact of alpha-syn on other components of the proteostasis network. Budding yeast Saccharomyces cerevisiae was used as eukaryotic reference organism to study the consequences of alpha-syn expre …

Correction: Comparison of Four Active SARS-CoV-2 Surveillance Strategies in Representative Population Sample Points: Two-Factor Factorial Randomized Controlled Trail.
Deckert A, Anders S, Morales I, De Allegri M, Nguyen HT, Souares A, McMahon S, Meurer M, Burk R, Lou D, Brugnara L, Sand M, Koeppel L, Maier-Hein L, Ross T, Adler TJ, Brenner S, Dyer C, Herbst K, Ovchinnikova S, Marx M, Schnitzler P, Knop M, Bärnighausen T, Denkinger CM. JMIR Public Health Surveill. 2024 Feb 16;10:e57203. doi: 10.2196/57203. PMID: 38364221 Free PMC article.

Proteome-wide tagging with an H2O2 biosensor reveals highly localized and dynamic redox microenvironments.
Kritsiligkou P, Bosch K, Shen TK, Meurer M, Knop M, Dick TP. Proc Natl Acad Sci U S A. 2023 Nov 28;120(48):e2314043120. doi: 10.1073/pnas.2314043120. Epub 2023 Nov 22. PMID: 37991942 Free PMC article. To identify endogenous "hotspots" of H(2)O(2) generation on the scale of individual proteins and protein complexes, we generated a yeast library in which the H(2)O(2) sensor HyPer7 was fused to the C-terminus of all protein-coding open reading frames (ORFs). ...

Multiplexed protein stability (MPS) profiling of terminal degrons using fluorescent timer libraries in Saccharomyces cerevisiae.
Reinbold C, Kong KE, Kats I, Khmelinskii A, Knop M. Methods Enzymol. 2023;686:321-344. doi: 10.1016/bs.mie.2023.02.017. Epub 2023 Apr 4. PMID: 37532406 Here we present a protocol for Multiplexed Protein Stability (MPS) profiling of tFT-libraries encoding large numbers of different protein N-termini fused to tFT in the yeast Saccharomyces cerevisiae. This protocol includes fluorescence cell sorting based prof …

Building yeast libraries to dissect terminal degrons with fluorescent timers.
Kong KE, Reinbold C, Knop M, Khmelinskii A. Methods Enzymol. 2023;686:297-319. doi: 10.1016/bs.mie.2023.02.012. Epub 2023 Mar 24. PMID: 37532405 Here, we describe common types of libraries used to identify and dissect degrons located at protein termini using MPS profiling in budding yeast, and provide protocols for their construction....

Comparison of Four Active SARS-CoV-2 Surveillance Strategies in Representative Population Sample Points: Two-Factor Factorial Randomized Controlled Trial.
Deckert A, Anders S, Morales I, De Allegri M, Nguyen HT, Souares A, McMahon S, Meurer M, Burk R, Lou D, Brugnara L, Sand M, Koeppel L, Maier-Hein L, Ross T, Adler TJ, Brenner S, Dyer C, Herbst K, Ovchinnikova S, Marx M, Schnitzler P, Knop M, Bärnighausen T, Denkinger CM. JMIR Public Health Surveill. 2023 Aug 17;9:e44204. doi: 10.2196/44204. PMID: 37235704 Free PMC article. Clinical Trial. 8

Scalable RT-LAMP-based SARS-CoV-2 testing for infection surveillance with applications in pandemic preparedness.
Lou D, Meurer M, Ovchinnikova S, Burk R, Denzler A, Herbst K, Papaioannou IA, Duan Y, Jacobs ML, Witte V, Ürge D, Kirrmaier D, Krogemann M, Gubicza K, Boerner K, Bundschuh C, Weidner NM, Merle U, Knorr B, Welker A, Denkinger CM, Schnitzler P, Kräusslich HG, Dao Thi VL, De Allegri M, Nguyen HT, Deckert A, Anders S, Knop M. EMBO Rep. 2023 May 4;24(5):e57162. doi: 10.15252/embr.202357162. Epub 2023 Mar 23. PMID: 36951170 Free PMC article.

Components of TOR and MAP kinase signaling control chemotropism and pathogenicity in the fungal pathogen Verticillium dahliae.
Vangalis V, Markakis EA, Knop M, Pietro AD, Typas MA, Papaioannou IA. Microbiol Res. 2023 Jun;271:127361. doi: 10.1016/j.micres.2023.127361. Epub 2023 Mar 12. PMID: 36921400 Free article.

From disgusting and complicated to simple and brilliant: Implementation perspectives and lessons learned from users and rejectors of mail-in SARS-CoV-2 gargle tests. .
Röhr F, Uellner F, Deckert A, Anders S, Burk R, Knop M, Brugnara L, Bärnighausen T, Jahn A, McMahon S, Souares A. Front Public Health. 2023 Jan 5;10:1024525. doi: 10.3389/fpubh.2022.1024525. eCollection 2022. PMID: 36684995 Free PMC article.

Cost and cost-effectiveness of four different SARS-CoV-2 active surveillance strategies: evidence from a randomised control trial in Germany.
Nguyen HT, Denkinger CM, Brenner S, Koeppel L, Brugnara L, Burk R, Knop M, Bärnighausen T, Deckert A, De Allegri M. Eur J Health Econ. 2023 Dec;24(9):1545-1559. doi: 10.1007/s10198-022-01561-8. Epub 2023 Jan 19. PMID: 36656403 Free PMC article. Clinical Trial.

SWR1 chromatin remodeling complex prevents mitotic slippage during spindle position checkpoint arrest.
Caydasi AK, Khmelinskii A, Darieva Z, Kurtulmus B, Knop M, Pereira G. Mol Biol Cell. 2023 Feb 1;34(2):ar11. doi: 10.1091/mbc.E20-03-0179. Epub 2022 Dec 21. PMID: 36542480 Free PMC article. Faithful chromosome segregation in budding yeast requires correct positioning of the mitotic spindle along the mother to daughter cell polarity axis. ...

Integrated genomic surveillance enables tracing of person-to-person SARS-CoV-2 transmission chains during community transmission and reveals extensive onward transmission of travel-imported infections, Germany, June to July 2021.
Houwaart T, Belhaj S, Tawalbeh E, Nagels D, Fröhlich Y, Finzer P, Ciruela P, Sabrià A, Herrero M, Andrés C, Antón A, Benmoumene A, Asskali D, Haidar H, von Dahlen J, Nicolai J, Stiller M, Blum J, Lange C, Adelmann C, Schroer B, Osmers U, Grice C, Kirfel PP, Jomaa H, Strelow D, Hülse L, Pigulla M, Kreuzer P, Tyshaieva A, Weber J, Wienemann T, Kohns Vasconcelos M, Hoffmann K, Lübke N, Hauka S, Andree M, Scholz CJ, Jazmati N, Göbels K, Zotz R, Pfeffer K, Timm J, Ehlkes L, Walker A, Dilthey AT; German COVID-19 OMICS Initiative (DeCOI); German COVID-19 OMICs Initiative (DeCOI). Euro Surveill. 2022 Oct;27(43):2101089. doi: 10.2807/1560-7917.ES.2022.27.43.2101089. PMID: 36305336 Free PMC article.

Rapid comparative evaluation of SARS-CoV-2 rapid point-of-care antigen tests.
Denzler A, Jacobs ML, Witte V, Schnitzler P, Denkinger CM, Knop M. Infection. 2022 Oct;50(5):1281-1293. doi: 10.1007/s15010-022-01810-1. Epub 2022 Apr 9. PMID: 35397099 Free PMC article.

Up-regulation of ubiquitin-proteasome activity upon loss of NatA-dependent N-terminal acetylation.
Kats I, Reinbold C, Kschonsak M, Khmelinskii A, Armbruster L, Ruppert T, Knop M. Life Sci Alliance. 2021 Nov 11;5(2):e202000730. doi: 10.26508/lsa.202000730. Print 2022 Feb. PMID: 34764209 Free PMC article.

Sex without crossing over in the yeast Saccharomycodes ludwigii.
Papaioannou IA, Dutreux F, Peltier FA, Maekawa H, Delhomme N, Bardhan A, Friedrich A, Schacherer J, Knop M. Genome Biol. 2021 Nov 3;22(1):303. doi: 10.1186/s13059-021-02521-w. PMID: 34732243 Free PMC article. BACKGROUND: Intermixing of genomes through meiotic reassortment and recombination of homologous chromosomes is a unifying theme of sexual reproduction in eukaryotic organisms and is considered crucial for their adaptive evolution. Previous studies of the budding yeast spec …

Early IFN-? signatures and persistent dysfunction are distinguishing features of NK cells in severe COVID-19.
Krämer B, Knoll R, Bonaguro L, ToVinh M, Raabe J, Astaburuaga-García R, Schulte-Schrepping J, Kaiser KM, Rieke GJ, Bischoff J, Monin MB, Hoffmeister C, Schlabe S, De Domenico E, Reusch N, Händler K, Reynolds G, Blüthgen N, Hack G, Finnemann C, Nischalke HD, Strassburg CP, Stephenson E, Su Y, Gardner L, Yuan D, Chen D, Goldman J, Rosenstiel P, Schmidt SV, Latz E, Hrusovsky K, Ball AJ, Johnson JM, Koenig PA, Schmidt FI, Haniffa M, Heath JR, Kümmerer BM, Keitel V, Jensen B, Stubbemann P, Kurth F, Sander LE, Sawitzki B; Deutsche COVID-19 OMICS Initiative (DeCOI); Aschenbrenner AC, Schultze JL, Nattermann J. Immunity. 2021 Nov 9;54(11):2650-2669.e14. doi: 10.1016/j.immuni.2021.09.002. Epub 2021 Sep 4. PMID: 34592166 Free PMC article.

The NADPH Oxidase A of Verticillium dahliae Is Essential for Pathogenicity, Normal Development, and Stress Tolerance, and It Interacts with Yap1 to Regulate Redox Homeostasis.
Vangalis V, Papaioannou IA, Markakis EA, Knop M, Typas MA. J Fungi (Basel). 2021 Sep 9;7(9):740. doi: 10.3390/jof7090740. PMID: 34575778 Free PMC article.

Alpha-Synuclein Decreases the Abundance of Proteasome Subunits and Alters Ubiquitin Conjugates in Yeast.
Popova B, Galka D, Häffner N, Wang D, Schmitt K, Valerius O, Knop M, Braus GH. Cells. 2021 Aug 28;10(9):2229. doi: 10.3390/cells10092229. PMID: 34571878 Free PMC article. To address the role of S129 phosphorylation on protein dynamics further we investigated the wild type and S129A variants using yeast and a tandem fluorescent timer protein reporter approach to monitor protein turnover and stability. Overexpression of both variants leads to …

Effectiveness and cost-effectiveness of four different strategies for SARS-CoV-2 surveillance in the general population (CoV-Surv Study): study protocol for a two-factorial randomized controlled multi-arm trial with cluster sampling.
Deckert A, Anders S, De Allegri M, Nguyen HT, Souares A, McMahon S, Meurer M, Burk R, Sand M, Koeppel L, Hein LM, Roß T, Adler T, Siems T, Brugnara L, Brenner S, Herbst K, Kirrmaier D, Duan Y, Ovchinnikova S, Boerner K, Marx M, Kräusslich HG, Knop M, Bärnighausen T, Denkinger C. Trials. 2021 Sep 26;22(1):656. doi: 10.1186/s13063-021-05619-5. PMID: 34565421 Free PMC article.

Starvation-induced cell fusion and heterokaryosis frequently escape imperfect allorecognition systems in an asexual fungal pathogen.
Vangalis V, Likhotkin I, Knop M, Typas MA, Papaioannou IA. BMC Biol. 2021 Aug 24;19(1):169. doi: 10.1186/s12915-021-01101-5. PMID: 34429100 Free PMC article.

Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection Clusters Based on Integrated Genomic Surveillance, Outbreak Analysis and Contact Tracing in an Urban Setting.
Walker A, Houwaart T, Finzer P, Ehlkes L, Tyshaieva A, Damagnez M, Strelow D, Duplessis A, Nicolai J, Wienemann T, Tamayo T, Kohns Vasconcelos M, Hülse L, Hoffmann K, Lübke N, Hauka S, Andree M, Däumer MP, Thielen A, Kolbe-Busch S, Göbels K, Zotz R, Pfeffer K, Timm J, Dilthey AT; German COVID-19 OMICS Initiative (DeCOI). Clin Infect Dis. 2022 Mar 23;74(6):1039-1046. doi: 10.1093/cid/ciab588. PMID: 34181711 Free PMC article.

Swarm Learning for decentralized and confidential clinical machine learning.
Sarveswara R, Händler K, Pickkers P, Aziz NA, Ktena S, Tran F, Bitzer M, Ossowski S, Casadei N, Herr C, Petersheim D, Behrends U, Kern F, Fehlmann T, Schommers P, Lehmann C, Augustin M, Rybniker J, Altmüller J, Mishra N, Bernardes JP, Krämer B, Bonaguro L, Schulte-Schrepping J, De Domenico E, Siever C, Kraut M, Desai M, Monnet B, Saridaki M, Siegel CM, Drews A, Nuesch-Germano M, Theis H, Heyckendorf J, Schreiber S, Kim-Hellmuth S; COVID-19 Aachen Study (COVAS); Nattermann J, Skowasch D, Kurth I, Keller A, Bals R, Nürnberg P, Rieß O, Rosenstiel P, Netea MG, Theis F, Mukherjee S, Backes M, Aschenbrenner AC, Ulas T; Deutsche COVID-19 Omics Initiative (DeCOI); Breteler MMB, Giamarellos-Bourboulis EJ, Kox M, Becker M, Cheran S, Woodacre MS, Goh EL, Schultze JL. Nature. 2021 Jun;594(7862):265-270. doi: 10.1038/s41586-021-03583-3. Epub 2021 May 26. PMID: 34040261 Free PMC article.

Timer-based proteomic profiling of the ubiquitin-proteasome system reveals a substrate receptor of the GID ubiquitin ligase.
Kong KE, Fischer B, Meurer M, Kats I, Li Z, Rühle F, Barry JD, Kirrmaier D, Chevyreva V, San Luis BJ, Costanzo M, Huber W, Andrews BJ, Boone C, Knop M, Khmelinskii A. Mol Cell. 2021 Jun 3;81(11):2460-2476.e11. doi: 10.1016/j.molcel.2021.04.018. Epub 2021 May 10. PMID: 33974913 Free PMC article. Here we systematically characterized the UPS in Saccharomyces cerevisiae. Using fluorescent timers, we determined how loss of individual UPS components affects yeast proteome turnover, detecting phenotypes for 76% of E2, E3, and deubiquitinating enzymes. ... ...

Colorimetric RT-LAMP and LAMP-sequencing forDetecting SARS-CoV-2 RNA in Clinical Samples.
Herbst K, Meurer M, Kirrmaier D, Anders S, Knop M, Thi VLD. Bio Protoc. 2021 Mar 20;11(6):e3964. doi: 10.21769/BioProtoc.3964. eCollection 2021 Mar 20. PMID: 33855122 Free PMC article.

Establishment of conidial fusion in the asexual fungus Verticillium dahliae as a useful system for the study of non-sexual genetic interactions.
Vangalis V, Knop M, Typas MA, Papaioannou IA. Curr Genet. 2021 Jun;67(3):471-485. doi: 10.1007/s00294-021-01157-4. Epub 2021 Feb 13. PMID: 33582843 Free PMC article.

N(alpha)-terminal acetylation of proteins by NatA and NatB serves distinct physiological roles in Saccharomyces cerevisiae.
Friedrich UA, Zedan M, Hessling B, Fenzl K, Gillet L, Barry J, Knop M, Kramer G, Bukau B. Cell Rep. 2021 Feb 2;34(5):108711. doi: 10.1016/j.celrep.2021.108711. PMID: 33535049 Free article. We investigate the roles of the two major Nats of S. cerevisiae, NatA and NatB, by performing transcriptome, translatome, and proteome profiling of natAdelta and natBdelta mutants. ...

Effectiveness and cost-effectiveness of four different strategies for SARS-CoV-2 surveillance in the general population (CoV-Surv Study): a structured summary of a study protocol for a cluster-randomised, two-factorial controlled trial.
Deckert A, Anders S, de Allegri M, Nguyen HT, Souares A, McMahon S, Boerner K, Meurer M, Herbst K, Sand M, Koeppel L, Siems T, Brugnara L, Brenner S, Burk R, Lou D, Kirrmaier D, Duan Y, Ovchinnikova S, Marx M, Kräusslich HG, Knop M, Bärnighausen T, Denkinger C. Trials. 2021 Jan 8;22(1):39. doi: 10.1186/s13063-020-04982-z. PMID: 33419461 Free PMC article.

CRISPR/Cas12a-mediated labeling of MET receptor enables quantitative single-molecule imaging of endogenous protein organization and dynamics.
Baldering TN, Karathanasis C, Harwardt MIE, Freund P, Meurer M, Rahm JV, Knop M, Dietz MS, Heilemann M. iScience. 2020 Dec 7;24(1):101895. doi: 10.1016/j.isci.2020.101895. eCollection 2021 Jan 22. PMID: 33364584 Free PMC article.

Hex1, the Major Component of Woronin Bodies, Is Required for Normal Development, Pathogenicity, and Stress Response in the Plant Pathogenic Fungus Verticillium dahliae.
Vangalis V, Papaioannou IA, Markakis EA, Knop M, Typas MA. J Fungi (Basel). 2020 Dec 7;6(4):344. doi: 10.3390/jof6040344. PMID: 33297524 Free PMC article.

Extensive 5'-surveillance guards against non-canonical NAD-caps of nuclear mRNAs in yeast.
Zhang Y, Kuster D, Schmidt T, Kirrmaier D, Nübel G, Ibberson D, Benes V, Hombauer H, Knop M, Jäschke A. Nat Commun. 2020 Nov 2;11(1):5508. doi: 10.1038/s41467-020-19326-3. PMID: 33139726 Free PMC article. The ubiquitous redox coenzyme nicotinamide adenine dinucleotide (NAD) acts as a non-canonical cap structure on prokaryotic and eukaryotic ribonucleic acids. Here we find that in budding yeast, NAD-RNAs are abundant (>1400 species), short (<170 nt), and mostly corresp …

Single-Color Fluorescence Lifetime Cross-Correlation Spectroscopy In Vivo.
Štefl M, Herbst K, Rübsam M, Benda A, Knop M. Biophys J. 2020 Oct 6;119(7):1359-1370. doi: 10.1016/j.bpj.2020.06.039. Epub 2020 Aug 20. PMID: 32919495 Free PMC article.

SARS-CoV-2 RNA Extraction Using Magnetic Beads for Rapid Large-Scale Testing by RT-qPCR and RT-LAMP.
Klein S, Müller TG, Khalid D, Sonntag-Buck V, Heuser AM, Glass B, Meurer M, Morales I, Schillak A, Freistaedter A, Ambiel I, Winter SL, Zimmermann L, Naumoska T, Bubeck F, Kirrmaier D, Ullrich S, Barreto Miranda I, Anders S, Grimm D, Schnitzler P, Knop M, Kräusslich HG, Dao Thi VL, Börner K, Chlanda P. Viruses. 2020 Aug 7;12(8):863. doi: 10.3390/v12080863. PMID: 32784757 Free PMC article.

A colorimetric RT-LAMP assay and LAMP-sequencing for detecting SARS-CoV-2 RNA in clinical samples.
Dao Thi VL, Herbst K, Boerner K, Meurer M, Kremer LP, Kirrmaier D, Freistaedter A, Papagiannidis D, Galmozzi C, Stanifer ML, Boulant S, Klein S, Chlanda P, Khalid D, Barreto Miranda I, Schnitzler P, Kräusslich HG, Knop M, Anders S. Sci Transl Med. 2020 Aug 12;12(556):eabc7075. doi: 10.1126/scitranslmed.abc7075. Epub 2020 Jul 27. PMID: 32719001 Free PMC article.

Exploring whole-genome duplicate gene retention with complex genetic interaction analysis.
Kuzmin E, VanderSluis B, Nguyen Ba AN, Wang W, Koch EN, Usaj M, Khmelinskii A, Usaj MM, van Leeuwen J, Kraus O, Tresenrider A, Pryszlak M, Hu MC, Varriano B, Costanzo M, Knop M, Moses A, Myers CL, Andrews BJ, Boone C. Science. 2020 Jun 26;368(6498):eaaz5667. doi: 10.1126/science.aaz5667. PMID: 32586993 Free PMC article. We describe a systematic complex genetic interaction analysis with yeast paralogs derived from the whole-genome duplication event. Mapping of digenic interactions for a deletion mutant of each paralog, and of trigenic interactions for the double mutant, provides insight in …

Proteasome-dependent protein quality control of the peroxisomal membrane protein Pxa1p.
Devarajan S, Meurer M, van Roermund CWT, Chen X, Hettema EH, Kemp S, Knop M, Williams C. Biochim Biophys Acta Biomembr. 2020 Sep 1;1862(9):183342. doi: 10.1016/j.bbamem.2020.183342. Epub 2020 May 13. PMID: 32416190 Free article. Here we have investigated the degradation of Pxa1p, a fatty acid transporter in the yeast Saccharomyces cerevisiae. Pxa1p is a homologue of the human protein ALDP and mutations in ALDP result in the severe disorder ALD. ...

CRISPR-Cas12a-assisted PCR tagging of mammalian genes.
Fueller J, Herbst K, Meurer M, Gubicza K, Kurtulmus B, Knopf JD, Kirrmaier D, Buchmuller BC, Pereira G, Lemberg MK, Knop M. J Cell Biol. 2020 Jun 1;219(6):e201910210. doi: 10.1083/jcb.201910210. PMID: 32406907 Free PMC article.

CDK1 couples proliferation with protein synthesis.
Haneke K, Schott J, Lindner D, Hollensen AK, Damgaard CK, Mong4is C, Knop M, Palm W, Ruggieri A, Stoecklin G. J Cell Biol. 2020 Mar 2;219(3):e201906147. doi: 10.1083/jcb.201906147. PMID: 32040547 Free PMC article.

ESCRT machinery mediates selective microautophagy of endoplasmatic reticulum in yeast.
Schäfer JA,Schessner JP, Bircham PW, Tsuji T, Funaya C, Pajonik O, Schaeff K, Ruffini G, Papagiannidis D, Knop M, Fujimoto T, Schuck S. EMBO J. 2019 Dec 5:e102586. doi:10.15252/embj. 2019102586 [Epub ahead of print] PMID:31802527.

Pooled clone collections by multiplexed CRISPR-Cas12a-assisted gene tagging in yeast .
Buchmuller BC, Herbst K, Meurer M, Kirrmaier D, Sass E, Levy ED, Knop M. Nat Commun. 2019 Jul 4;10(1): 2960. doi:10.1038/s41467-019-10816-7. PMID:31273196.

Cooperation of mitochondrial and ER factors in quality control of tail-anchored proteins.
Dederer V, Khmelinskii A, Huhn AG, Okreglak V, Knop M, Lemberg MK. Elife. 2019 Jun 7;8. pii: E45506. doi:10.7554/eLife.45506. PMID:31172943.

Self-Learning Microfluidic Platform for Single-Cell Imaging and Classification in Flow.
Constantinou I, Jendrusvh M, Aspert T, Görlitz F, Schulze A, Charvin G, , Knop M. Micromachines (Basel). 2019 May 9. 10(5).pii: E311. doi:10.3390/mi10050311. PMID:31075890.

YeastRGB: comparing the abundance and localization of yeast proteins across cells and libraries.
Dubreuil B, Sass E, Nadav Y, Heidenreich M, Georgeson JM, Weill U, Duan Y, Meurer M, Schuldiner M, Knop M, Levy ED. Nucleic Acids Res.2018 Oct 24. doi: 10.1093/nar/gky941. [Epub ahead of print] PubMed PMID:30357397.

Monitoring Protein Dynamics in Protein O-Mannosyltransferase Mutants In Vivo by Tandem Fluorescent Protein Timers.
Castells-Ballester J, Zatorska E, Meurer M, Neubert P, Metschies A, Knop M,Strahl S. Molecules. 2018 Oct 12;23(10). pii:E2622. doi: 10.3390/molecules23102622. PubMed PMID: 30322079; PubMed Central PMCID: PMC6222916.

Bicoid gradient formation mechanism and dynamics revealed by protein lifetime analysis.
Durrieu L, Kirrmaier D, Schneidt T, Kats I, Raghavan S, Hufnagel L, Saunders TE, Knop M. Mol Syst Biol. 2018 Sep 4;14(9):e8355. doi:10.15252/msb.20188355. PubMed PMID: 30181144; PubMed Central PMCID: PMC6121778.

Genome-wide C-SWAT library for high-throughput yeast genome tagging.
Meurer M, Duan Y, Sass E, Kats I, Herbst K, Buchmuller BC, Dederer V, Huber F, Kirrmaier D, Štefl M, Van Laer K, Dick TP, Lemberg MK, Khmelinskii A, Levy ED, Knop M. Nat Methods. 2018 Aug;15(8):598-600. doi: 10.1038/s41592-018-0045-8. Epub 2018 Jul 9. PubMed PMID: 29988096.

Determinants of the cytosolic turnover of mitochondrial intermembrane space proteins.
Kowalski L, Bragoszewski P, Khmelinskii A, Glow E, Knop M, Chacinska A. BMC Biol. 2018 Jun 22;16(1):66. doi: 10.1186/s12915-018-0536-1. PubMed PMID: 29929515; PubMed Central PMCID: PMC6013907.

Mapping Degradation Signals and Pathways in a Eukaryotic N-terminome.
Kats I, Khmelinskii A, Kschonsak M, Huber F, Knieß RA, Bartosik A, Knop M. Mol Cell. 2018 May 3;70(3):488-501.e5. doi: 10.1016/j.molcel.2018.03.033. PubMed PMID:29727619.

Cells Escape an Operational Mitotic Checkpoint through a Stochastic Process.
Bonaiuti P, Chiroli E, Gross F, Corno A, Vernieri C, Štefl M, Cosentino Lagomarsino M, Knop M, Ciliberto A. Curr Biol. 2018 Jan 8;28(1):28-37.e7.doi: 10.1016/j.cub.2017.11.031. Epub 2017 Dec 14. PubMed PMID: 29249657.

Upregulation of SPS100 gene expression by an antisense RNA via a switch of mRNA isoforms with different stabilities .
Bunina D, Štefl M, Huber F, Khmelinskii A, Meurer M, Barry JD, Kats I,Kirrmaier D, Huber W, Knop M. Nucleic Acids Res. 2017 Nov 2;45(19):11144-11158. doi: 10.1093/nar/gkx737. PubMed PMID:28977638; PubMed Central PMCID: PMC5737743.

Characterization of spindle pole body duplication reveals a regulatory role for nuclear pore complexes.
Rüthnick D, Neuner A, Dietrich F, Kirrmaier D, Engel U, Knop M, Schiebel E. J Cell Biol. 2017 Aug 7;216(8):2425-2442. doi:10.1083/jcb.201612129. Epub 2017 Jun 28. PubMed PMID: 28659328; PubMed Central PMCID: PMC5551709.

Alterations in cellular metabolism triggered by URA7 or GLN3 inactivation cause imbalanced dNTP pools and increased mutagenesis .
Schmidt TT, Reyes G, Gries K, Ceylan CÜ, Sharma S, Meurer M, Knop M, Chabes A, Hombauer H. Proc Natl Acad Sci U S A. 2017 May 30;114(22):E4442-E4451. doi: 10.1073/pnas.1618714114.Epub 2017 Apr 17. PubMed PMID: 28416670; PubMed Central PMCID: PMC5465912.

Temporal and compartment-specific signals coordinate mitotic exit with spindle position. .
Caydasi AK, Khmelinskii A, Duenas-Sanchez R, Kurtulmus B, Knop M, Pereira G. Nat Commun. 2017 Jan 24;8:14129. doi:10.1038/ncomms14129. PubMed PMID:28117323; PubMed Central PMCID: PMC5286211.

The regulatable MAL32 promoter in Saccharomyces cerevisiae: characteristics and tools to facilitate its use.
Meurer M, Chevyreva V, Cerulus B, Knop M. Yeast. 2017 Jan;34(1):39-49. doi: 10.1002/yea.3214. Epub 2016 Nov 23. PubMed PMID:27714848.

πSPIM: high NA high resolution isotropic light-sheet imaging in cell culture dishes.
Theer P, Dragneva D, Knop M. Sci Rep. 2016 Sep 13;6:32880. doi:10.1038/srep32880. PubMed PMID: 27619647; PubMed Central PMCID: PMC5020645.

Protein Abundance Control by Non-coding Antisense Transcription.
Huber F, Bunina D, Gupta I, Khmelinskii A, Meurer M, Theer P, Steinmetz LM, Knop M. Cell Rep. 2016 Jun 21;15(12):2625-36. doi: 10.1016/j.celrep.2016.05.043. Epub 2016 Jun 9. PubMed PMID: 27292640; PubMed Central PMCID: PMC4920891.

One library to make them all: streamlining the creation of yeast libraries via a SWAp-Tag strategy.
Yofe I, Weill U, Meurer M, Chuartzman S, Zalckvar E, Goldman O, Ben-Dor S, Schütze C, Wiedemann N, Knop M, Khmelinskii A, Schuldiner M. . Nat Methods. 2016 Apr;13(4):371-378. doi: 10.1038/nmeth.3795. Epub 2016 Feb 29. PubMed PMID: 26928762; PubMed Central PMCID: PMC4869835.

Comprehensive study on critical micellar concentrations of SDS in acetonitrile-water-solvents.
Šteflová J, Štefl M, Walz S, Knop M, Trapp O. Electrophoresis. 2016 May;37(10):1287-95. doi: 10.1002/elps.201500553. Epub 2016 Mar 14. PMID: 26842727

Incomplete proteasomal degradation of green fluorescent proteins in the context of tandem fluorescent protein timers.
Khmelinskii A, Meurer M, Ho CT, Besenbeck B, Füller J, Lemberg MK, Bukau B, Mogk A, Knop M. Mol Biol Cell. 2016 Jan 15;27(2):360-70. doi: 10.1091/mbc.E15-07-0525. Epub 2015 Nov 25. PubMed PMID: 26609072; PubMed Central PMCID: PMC4713137.

Systemic control of protein synthesis through sequestration of translation and ribosome biogenesis factors during severe heat stress.
Cherkasov V, Grousl T, Theer P, Vainshtein Y, Glässer C, Mongis C, Kramer G, Stoecklin G, Knop M, Mogk A, Bukau B. FEBS Lett. 2015 Nov 30;589(23):3654-64. doi: 10.1016/j.febslet.2015.10.010. Epub 2015 Oct 17. PubMed PMID: 26484595.

Live-cell multiphoton fluorescence correlation spectroskopy with an improved large Stokes shift fluorescent protein .
Guan Y, Meurer M, Raghavan S, Rebane A, Lindquist JR, Santos S, Kats I, Davidson MW, Mazitschek R, Hughes TE, Drobizhev M, Knop M, Shah JV. Mol Biol Cell. 2015 Jun1;26(11):2054-66.doi:10.1091/mbc.E14-10-1473.Epub 2015 Apri 15 2014 Dec 18;516(7531):410-3. doi: PMID:25877871.

Protein quality control at the inner nuclear membrane.
Khmelinskii A, Blaszczak E, Pantazopoulou M, Fischer B, Omnus DJ, Le Dez G, Brossard A, Gunnarsson A, Barry JD, Meurer M, Kirrmaier D, Boone C, Huber W, Rabut G, Ljungdahl PO, Knop M.
Nature. 2014 Dec 18;516(7531):410-3. doi: 10.1038/nature14096.

PCR Duplication: A One-Step Cloning-Free Method to Generate Duplicated Chromosomal Loci and Interference-Free Expression Reporters in Yeast.
Huber F, Meurer M, Bunina D, Kats I, Maeder CI, Stefl M, Mongis C, Knop M.
PLoS One. 2014 Dec 10;9(12):e114590. doi: 10.1371/journal.pone.0114590. eCollection 2014.

A memory system of negative polarity cues prevents replicative aging.
Meitinger F, Khmelinskii A, Morlot S, Kurtulmus B, Palani S, Andres-Pons A, Hub B, Knop M, Charvin G, Pereira G.
Cell. 2014 Nov 20;159(5):1056-69. doi: 10.1016/j.cell.2014.10.014. Epub 2014 Nov 13.

Quantification of cytosolic interactions identifies Ede1 oligomers as key organizers of endocytosis.
Boeke D, Trautmann S, Meurer M, Wachsmuth M, Godlee C, Knop M, Kaksonen M.
Mol Syst Biol. 2014 Nov 3;10:756. doi: 10.15252/msb.20145422.


PSFj: know your fluorescence microscope.
Theer P, Mongis C, Knop M.
Nat Methods. 2014 Oct;11(10):981-2. doi: 10.1038/nmeth.3102. No abstract available.

Analysis of protein dynamics with tandem fluorescent protein timers.
Khmelinskii A, Knop M.
Methods Mol Biol. 2014;1174:195-210. doi: 10.1007/978-1-4939-0944-5_13.

Tracking protein turnover and degradation by microscopy: photo-switchable versus time-encoded fluorescent proteins.
Knop M, Edgar BA.
Open Biol. 2014 Apr 16;4:140002. doi: 10.1098/rsob.140002.

Analytical model for macromolecular partitioning during yeast cell division
Kinkhabwala, A, Khmelinskii, A, and Knop, M. BMC Biophysics 2014, 7:10

Determinants of robustness in spindle assembly checkpoint signalling
Heinrich, S, Geissen, EM, Kamenz, J, Trautmann, S, Widmer, C, Drewe, P, Knop, M, Radde, N, Hasenauer, J, Hauf, S
Nat Cell Biol. 2013 Nov;15(11):1328-39. doi: 10.1038/ncb2864. Epub 2013 Oct 27.

Directional tissue migration through a self-generated chemokine gradient.
Donà E, Barry JD, Valentin G, Quirin C, Khmelinskii A, Kunze A, Durdu S, Newton LR, Fernandez-Minan A, Huber W, Knop M, Gilmour D.
Nature. 2013 Nov 14;503(7475):285-9. doi: 10.1038/nature12635. Epub 2013 Sep 25.

When yeast cells meet, karyogamy!: an example of nuclear migration slowly resolved.
Gibeaux R, Knop M.
Nucleus. 2013 May-Jun;4(3):182-8. doi: 10.4161/nucl.25021. Epub 2013 May 15. Review.

Spindle pole body-anchored Kar3 drives the nucleus along microtubules from another nucleus in preparation for nuclear fusion during yeast karyogamy.
Gibeaux R, Politi AZ, Nédélec F, Antony C, Knop M.
Genes Dev. 2013 Feb 1;27(3):335-49. doi: 10.1101/gad.206318.112.

Tandem fluorescent protein timers for in vivo analysis of protein dynamics.
Khmelinskii A, Keller PJ, Bartosik A, Meurer M, Barry JD, Mardin BR, Kaufmann A, Trautmann S, Wachsmuth M, Pereira G, Huber W, Schiebel E, Knop M.
Nat Biotechnol. 2012 Jun 24;30(7):708-14. doi: 10.1038/nbt.2281.

TIPI: TEV protease-mediated induction of protein instability.
Taxis C, Knop M.
Methods Mol Biol. 2012;832:611-26. doi: 10.1007/978-1-61779-474-2_43.

Seamless gene tagging by endonuclease-driven homologous recombination.
Khmelinskii A, Meurer M, Duishoev N, Delhomme N, Knop M.
PLoS One. 2011;6(8):e23794. doi: 10.1371/journal.pone.0023794. Epub 2011 Aug 22.

Exploiting spore-autonomous fluorescent protein expression to quantify meiotic chromosome behaviors in Saccharomyces cerevisiae.
Thacker D, Lam I, Knop M, Keeney S.
Genetics. 2011 Oct;189(2):423-39. doi: 10.1534/genetics.111.131326. Epub 2011 Aug 11.

Quantitative fluorescence imaging of protein diffusion and interaction in living cells.
Capoulade J, Wachsmuth M, Hufnagel L, Knop M.
Nat Biotechnol. 2011 Aug 7;29(9):835-9. doi: 10.1038/nbt.1928.

Yeast cell morphology and sexual reproduction--a short overview and some considerations.
Knop M.
C R Biol. 2011 Aug-Sep;334(8-9):599-606. doi: 10.1016/j.crvi.2011.05.007. Epub 2011 Jul 1. Review.

Genomic promoter replacement cassettes to alter gene expression in the yeast Saccharomyces cerevisiae.
Kaufmann A, Knop M.
Methods Mol Biol. 2011;765:275-94. doi: 10.1007/978-1-61779-197-0_16.

Artificial tethering to nuclear pores promotes partitioning of extrachromosomal DNA during yeast asymmetric cell division.
Khmelinskii A, Meurer M, Knop M, Schiebel E.
Curr Biol. 2011 Jan 11;21(1):R17-8. doi: 10.1016/j.cub.2010.11.034.

Segregation of yeast nuclear pores.
Khmelinskii A, Keller PJ, Lorenz H, Schiebel E, Knop M.
Nature. 2010 Jul 22;466(7305):E1. doi: 10.1038/nature09255.

Evolution of mutational robustness in the yeast genome: a link to essential genes and meiotic recombination hotspots.
Keller PJ, Knop M.
PLoS Genet. 2009 Jun;5(6):e1000533. doi: 10.1371/journal.pgen.1000533. Epub 2009 Jun 26.

Efficient protein depletion by genetically controlled deprotection of a dormant N-degron.
Taxis C, Stier G, Spadaccini R, Knop M.
Mol Syst Biol. 2009;5:267. doi: 10.1038/msb.2009.25. Epub 2009 Apr 28.

The SpoMBe pathway drives membrane bending necessary for cytokinesis and spore formation in yeast meiosis.
Maier P, Rathfelder N, Maeder CI, Colombelli J, Stelzer EH, Knop M.
EMBO J. 2008 Sep 17;27(18):2363-74. doi: 10.1038/emboj.2008.168. Epub 2008 Aug 28.

Reconstitution of Mdm2-dependent post-translational modifications of p53 in yeast.
Di Ventura B, Funaya C, Antony C, Knop M, Serrano L.
PLoS One. 2008 Jan 30;3(1):e1507. doi: 10.1371/journal.pone.0001507.

Spatial regulation of Fus3 MAP kinase activity through a reaction-diffusion mechanism in yeast pheromone signalling.
Maeder CI, Hink MA, Kinkhabwala A, Mayr R, Bastiaens PI, Knop M.
Nat Cell Biol. 2007 Nov;9(11):1319-26. Epub 2007 Oct 21.

Cytokinesis in yeast meiosis depends on the regulated removal of Ssp1p from the prospore membrane.
Maier P, Rathfelder N, Finkbeiner MG, Taxis C, Mazza M, Le Panse S, Haguenauer-Tsapis R, Knop M.
EMBO J. 2007 Apr 4;26(7):1843-52. Epub 2007 Mar 8.

Dynamic organization of the actin cytoskeleton during meiosis and spore formation in budding yeast.
Taxis C, Maeder C, Reber S, Rathfelder N, Miura K, Greger K, Stelzer EH, Knop M.
Traffic. 2006 Dec;7(12):1628-42.

Evolution of the hemiascomycete yeasts: on life styles and the importance of inbreeding.
Knop M.
Bioessays. 2006 Jul;28(7):696-708. Review.

Nud1p, the yeast homolog of Centriolin, regulates spindle pole body inheritance in meiosis.
Gordon O, Taxis C, Keller PJ, Benjak A, Stelzer EH, Simchen G, Knop M.
EMBO J. 2006 Aug 23;25(16):3856-68. Epub 2006 Aug 3.

System of centromeric, episomal, and integrative vectors based on drug resistance markers for Saccharomyces cerevisiae.
Taxis C, Knop M.
Biotechniques. 2006 Jan;40(1):73-8.

Spore number control and breeding in Saccharomyces cerevisiae: a key role for a self-organizing system.
Taxis C, Keller P, Kavagiou Z, Jensen LJ, Colombelli J, Bork P, Stelzer EH, Knop M.
J Cell Biol. 2005 Nov 21;171(4):627-40. Epub 2005 Nov 14.

Human Lsg1 defines a family of essential GTPases that correlates with the evolution of compartmentalization.
Reynaud EG, Andrade MA, Bonneau F, Ly TB, Knop M, Scheffzek K, Pepperkok R.
BMC Biol. 2005 Oct 7;3:21.

Differential requirement for phospholipase D/Spo14 and its novel interactor Sma1 for regulation of exocytotic vesicle fusion in yeast meiosis.
Riedel CG, Mazza M, Maier P, Körner R, Knop M.
J Biol Chem. 2005 Nov 11;280(45):37846-52. Epub 2005 Sep 7.

Molecular interactions position Mso1p, a novel PTB domain homologue, in the interface of the exocyst complex and the exocytic SNARE machinery in yeast.
Knop M, Miller KJ, Mazza M, Feng D, Weber M, Keränen S, Jäntti J.
Mol Biol Cell. 2005 Oct;16(10):4543-56. Epub 2005 Jul 19.

A versatile toolbox for PCR-based tagging of yeast genes: new fluorescent proteins, more markers and promoter substitution cassettesJanke C, Magiera MM, Rathfelder N, Taxis C, Reber S, Maekawa H, Moreno-Borchart A, Doenges G, Schwob E, Schiebel E, Knop M. Yeast. 2004 Aug;21(11):947-62.

Prospore membrane formation: how budding yeast gets shaped in meiosis.
Moreno-Borchart AC, Knop M.
Microbiol Res. 2003;158(2):83-90. Review.

Yeast Cdk1 translocates to the plus end of cytoplasmic microtubules to regulate bud cortex interactions.
Maekawa H, Usui T, Knop M, Schiebel E.
EMBO J. 2003 Feb 3;22(3):438-49.

Improved version of the red fluorescent protein (drFP583/DsRed/RFP).
Knop M, Barr F, Riedel CG, Heckel T, Reichel C.
Biotechniques. 2002 Sep;33(3):592, 594, 596-8 passim.

Prospore membrane formation linked to the leading edge protein (LEP) coat assembly.
Moreno-Borchart AC, Strasser K, Finkbeiner MG, Shevchenko A, Shevchenko A, Knop M.
EMBO J. 2001 Dec 17;20(24):6946-57.

A screen for genes required for meiosis and spore formation based on whole-genome expression.
Rabitsch KP, Tóth A, Gálová M, Schleiffer A, Schaffner G, Aigner E, Rupp C, Penkner AM, Moreno-Borchart AC, Primig M, Esposito RE, Klein F, Knop M, Nasmyth K.
Curr Biol. 2001 Jul 10;11(13):1001-9.

Role of the spindle pole body of yeast in mediating assembly of the prospore membrane during meiosis.
Knop M, Strasser K.
EMBO J. 2000 Jul 17;19(14):3657-67.

Microtubule organization by the budding yeast spindle pole body.
Knop M, Pereira G, Schiebel E.
Biol Cell. 1999 May-Jun;91(4-5):291-304. Review.

Interaction of the yeast gamma-tubulin complex-binding protein Spc72p with Kar1p is essential for microtubule function during karyogamy.
Pereira G, Grueneberg U, Knop M, Schiebel E.
EMBO J. 1999 Aug 2;18(15):4180-95.

Epitope tagging of yeast genes using a PCR-based strategy: more tags and improved practical routines.
Knop M, Siegers K, Pereira G, Zachariae W, Winsor B, Nasmyth K, Schiebel E.
Yeast. 1999 Jul;15(10B):963-72.

Spc29p is a component of the Spc110p subcomplex and is essential for spindle pole body duplication.
Elliott S, Knop M, Schlenstedt G, Schiebel E.
Proc Natl Acad Sci U S A. 1999 May 25;96(11):6205-10.

Receptors determine the cellular localization of a gamma-tubulin complex and thereby the site of microtubule formation.
Knop M, Schiebel E.
EMBO J. 1998 Jul 15;17(14):3952-67.

Spc98p directs the yeast gamma-tubulin complex into the nucleus and is subject to cell cycle-dependent phosphorylation on the nuclear side of the spindle pole body.
Pereira G, Knop M, Schiebel E.
Mol Biol Cell. 1998 Apr;9(4):775-93.

Spc98p and Spc97p of the yeast gamma-tubulin complex mediate binding to the spindle pole body via their interaction with Spc110p.
Knop M, Schiebel E.
EMBO J. 1997 Dec 1;16(23):6985-95.

The spindle pole body component Spc97p interacts with the gamma-tubulin of Saccharomyces cerevisiae and functions in microtubule organization and spindle pole body duplication.
Knop M, Pereira G, Geissler S, Grein K, Schiebel E.
EMBO J. 1997 Apr 1;16(7):1550-64.

N-Glycosylation affects endoplasmic reticulum degradation of a mutated derivative of carboxypeptidase yscY in yeast.
Knop M, Hauser N, Wolf DH.
Yeast. 1996 Sep 30;12(12):1229-38.

The spindle pole body component Spc98p interacts with the gamma-tubulin-like Tub4p of Saccharomyces cerevisiae at the sites of microtubule attachment.
Geissler S, Pereira G, Spang A, Knop M, Souès S, Kilmartin J, Schiebel E.
EMBO J. 1996 Aug 1;15(15):3899-911. Erratum in: EMBO J 1996 Sep 16;15(18):5124.

Der1, a novel protein specifically required for endoplasmic reticulum degradation in yeast.
Knop M, Finger A, Braun T, Hellmuth K, Wolf DH.
EMBO J. 1996 Feb 15;15(4):753-63.

Analysis of two mutated vacuolar proteins reveals a degradation pathway in the endoplasmic reticulum or a related compartment of yeast.
Finger A, Knop M, Wolf DH.
Eur J Biochem. 1993 Dec 1;218(2):565-74.

Vacuolar/lysosomal proteolysis: proteases, substrates, mechanisms.
Knop M, Schiffer HH, Rupp S, Wolf DH.
Curr Opin Cell Biol. 1993 Dec;5(6):990-6. Review.