Gameiro E, Juárez-Núñez KA, Fung JJ, Shankar S, Luke B and Khmelinskii A ( 2024 ) Genome-wide conditional degron libraries for functional genomics. bioRxiv , doi: https://doi.org/10.1101/2024.05.29.596381 Link


Kong KYE, Reinbold C, Knop M and Khmelinskii A ( 2023 ) Building yeast libraries to dissect terminal degrons with fluorescent timers. Methods Enzymol , 686:297–319 Link

Kong KYE*, Shankar S*, Rühle F and Khmelinskii A ( 2023 ) Orphan quality control by an SCF ubiquitin ligase directed to pervasive C-degrons. Nat Commun , 14:8363  (*indicates joint contribution)  Link

Reinbold C, Kong KYE, Kats I, Khmelinskii A and Knop M ( 2023 ) Multiplexed protein stability (MPS) profiling of terminal degrons using fluorescent timer libraries in Saccharomyces cerevisiae. Methods Enzymol , 686:321–344 Link

Sanchez N, de Leon N, Valle R, Fung JJ, Khmelinskii A and Roncero C ( 2023 ) Multiple quality control mechanisms monitor yeast chitin synthase folding in the endoplasmic reticulum. Mol Biol Cell , 34:mbc.E23-05-0186 Link

Schindler N*, Tonn M*, Kellner V, Fung JJ, Lockhart A, Vydzhak O, Juretschke T, Möckel S, Beli P, Khmelinskii A and Luke B ( 2023 ) Genetic requirements for repair of lesions caused by single genomic ribonucleotides in S phase. Nat Commun , 14:1227  (* indicates joint contribution)  Link


Caydasi AK, Khmelinskii A, Darieva Z, Kurtulmus B, Knop M and Pereira G ( 2022 ) SWR1 chromatin remodeling complex prevents mitotic slippage during spindle position checkpoint arrest. Mol Biol Cell , 34:ar11 Link

Fung JJ*, Blöcher-Juárez K* and Khmelinskii A ( 2022 ) High-throughput analysis of protein turnover with tandem fluorescent protein timers - the unfolded protein response: methods and protocols. Methods Mol Biol , 2378:85-100  (*indicates joint contribution)  Link


Kats I, Reinbold C, Kschonsak M, Khmelinskii A, Armbruster L, Ruppert T and Knop M ( 2021 ) Up-regulation of ubiquitin–proteasome activity upon loss of NatA-dependent N-terminal acetylation. Life Sci Alliance , 5:e202000730 Link

Kong KYE, Coelho JPL, Feige MJ and Khmelinskii A ( 2021 ) Quality control of mislocalized and orphan proteins. Exp Cell Res , 403:112617 Link

Kong KYE*, 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# and Khmelinskii A# ( 2021 ) Timer-based proteomic profiling of the ubiquitin-proteasome system reveals a substrate receptor of the GID ubiquitin ligase Mol Cell , 81:2460-2476.e11  (*indicates joint contribution, #indicates joint correspondence)  Link


Ivanova E and Khmelinskii A (2020) (Photo)convert to pooled visual screening. Mol Syst Biol, 16:e9640 Link

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 and Boone C (2020) Exploring whole-genome duplicate gene retention with complex genetic interaction analysis. Science, 368:eaaz5667 (*indicates joint contribution) Link

Renz C, Albanèse V, Tröster V, Albert TK, Santt O, Jacobs SC, Khmelinskii A, Léon S and Ulrich HD (2020) Ubc13-Mms2 cooperates with a family of RING E3s in membrane protein sorting. J Cell Sci, 133:jcs244566 Link


Caydasi AK, Khmelinskii A, Darieva Z, Kurtulmus B, Knop M and Pereira G (2019) SWR1 chromatin remodeling complex prevents mitotic slippage during spindle position checkpoint arrest. bioRxiv, 34:ar11 Link

Dederer V, Khmelinskii A, Huhn AG, Okreglak V, Knop M and Lemberg MK (2019) Cooperation of mitochondrial and ER factors in quality control of tail-anchored proteins. eLife, 8:e45506 Link

Renz C, Tröster V, Albert TK, Santt O, Jacobs SC, Khmelinskii A and Ulrich HD (2019) The ubiquitin-conjugating enzyme Ubc13-Mms2 cooperates with a family of FYVE-type-RING ubiquitin protein ligases in K63-polyubiquitylation at internal membranes. bioRxiv, 133:jcs244566 Link


Kats I, Khmelinskii A, Kschonsak M, Huber F, Knieß RA, Bartosik A and Knop M (2018) Mapping degradation signals and pathways in a eukaryotic N-terminome. Mol Cell, 70:488–501.e5 Link

Kowalski L, Bragoszewski P, Khmelinskii A, Glow E, Knop M and Chacinska A (2018) Determinants of the cytosolic turnover of mitochondrial intermembrane space proteins. BMC Biol, 16:66 Link

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# and Knop M# (2018) Genome-wide C-SWAT library for high-throughput yeast genome tagging. Nat Methods, 15:598–600 (#indicates joint correspondence) Link


Bunina D, Štefl M, Huber F, Khmelinskii A, Meurer M, Barry JD, Kats I, Kirrmaier D, Huber W and Knop M (2017) Upregulation of SPS100 gene expression by an antisense RNA via a switch of mRNA isoforms with different stabilities. Nucleic Acids Res, 45:11144–11158 Link

Caydasi AK, Khmelinskii A, Duenas-Sanchez R, Kurtulmus B, Knop M and Pereira G (2017) Temporal and compartment-specific signals coordinate mitotic exit with spindle position. Nat Commun, 8:14129 Link


Huber F, Bunina D, Gupta I, Khmelinskii A, Meurer M, Theer P, Steinmetz LM and Knop M (2016) Protein abundance control by non-coding antisense transcription. Cell Rep, 15:2625–2636 Link

Khmelinskii A, Meurer M, Ho C-T, Besenbeck B, Fuller J, Lemberg MK, Bukau B, Mogk A and Knop M (2016) Incomplete proteasomal degradation of green fluorescent proteins in the context of tandem fluorescent protein timers. Mol Biol Cell, 27:360–370 Link

Yofe I#, Weill U, Meurer M, Chuartzman S#, Zalckvar E, Goldman O, Ben-Dor S, Schütze C, Wiedemann N, Knop M, Khmelinskii A# and Schuldiner M# (2016) One library to make them all: Streamlining the creation of yeast libraries via a SWAp-Tag strategy. Nat Methods, 13:371–378 (#indicates joint correspondence) Link


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 and Knop M (2014) Protein quality control at the inner nuclear membrane. Nature, 516:410–413 (*indicates joint contribution) Link

Khmelinskii A and Knop M (2014) Analysis of protein dynamics with tandem fluorescent protein timers. Methods Mol Biol, 1174:195-210 Link

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

Meitinger F, Khmelinskii A, Morlot S, Kurtulmus B, Palani S, Andres-Pons A, Hub B, Knop M, Charvin G and Pereira G (2014) A memory system of negative polarity cues prevents replicative aging. Cell, 159:1056–1069 Link


Donà E, Barry JD, Valentin G, Quirin C, Khmelinskii A, Kunze A, Durdu S, Newton LR, Fernandez-Minan A, Huber W, Knop M and Gilmour D (2013) Directional tissue migration through a self-generated chemokine gradient. Nature, 503:285–289 Link


Khmelinskii A*, Keller PJ*, Bartosik A, Meurer M, Barry JD, Mardin BR, Kaufmann A, Trautmann S, Wachsmuth M, Pereira G, Huber W, Schiebel E and Knop M (2012) Tandem fluorescent protein timers for in vivo analysis of protein dynamics. Nat Biotechnol, 30:708–714 (*indicates joint contribution) Link


Khmelinskii A*, Meurer M*, Duishoev N, Delhomme N and Knop M (2011) Seamless gene tagging by endonuclease-driven homologous recombination. PLoS One, 6:e23794 (*indicates joint contribution) Link

Khmelinskii A, Meurer M, Knop M and Schiebel E (2011) Artificial tethering to nuclear pores promotes partitioning of extrachromosomal DNA during yeast asymmetric cell division. Curr Biol, 21:R17–R18 Link


Khmelinskii A, Keller PJ, Lorenz H, Schiebel E and Knop M (2010) Segregation of yeast nuclear pores. Nature, 466:E1 Link

Roostalu J#, Schiebel E and Khmelinskii A# (2010) Cell cycle control of spindle elongation. Cell Cycle, 9:1084–1090 (#indicates joint correspondence) Link


Khmelinskii A, Roostalu J, Roque H, Antony C and Schiebel E (2009) Phosphorylation-dependent protein interactions at the spindle midzone mediate cell cycle regulation of spindle elongation. Dev Cell, 17:244–256 Link

Khmelinskii A and Schiebel E (2009) Chromosome segregation: Monopolin goes spindle. Curr Biol, 19:R482–R484 Link


Khmelinskii A and Schiebel E (2008) Assembling the spindle midzone in the right place at the right time. Cell Cycle, 7:283–286 Link


Khmelinskii A*, Lawrence C*, Roostalu J and Schiebel E (2007) Cdc14-regulated midzone assembly controls anaphase B. J Cell Biol, 177:981–993 (*indicates joint contribution) Link