Publications

Here you find our publications and selected highlighted papers. Leppek lab members designated in bold. *, ** authors contributed equally; ‡ co-corresponding authors

Please also visit PubMed and GoogleScholar for a full list.

Selected Publications

A versatile toolbox for determining IRES activity in cells and embryonic tissues.

Koch P*, Zhang Z*, Genuth NR*, Susanto TT, Haimann M, Khmelinskaia A, Byeon GW, Dey S, Barna M‡, Leppek K‡.
⟶ EMBO Journal 2025 Mar 13. (see Press & Media for press release)
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Combinatorial optimization of mRNA structure, stability, and translation for RNA-based therapeutics.

Leppek K*, Byeon GW*, Kladwang W*, Wayment-Steele HK*, Kerr CH*, Xu AF**, Kim DS**, Topkar VV, Choe C, Rothschild D, Tiu GC, Wellington-Oguri R, Fujii K, Sharma E, Watkins AM, Nicol JJ, Romano J, Tunguz B, Diaz F, Cai H, Guo P, Wu J, Meng F, Shi S, Eterna Participants, Dormitzer PR, Solórzano A, Barna M‡, Das R‡.
⟶ Nature Comm. 2022 Mar;13(1): 1536,1-22. (see Press & Media for press release)
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VELCRO-IP RNA-seq reveals ribosome expansion segment function in translation genome-wide.

Leppek K*, Byeon GW*, Fujii K, Barna M. (*authors contributed equally)
⟶ Cell Reports, 2021 Jan 19;34(3):108629.
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Gene- and species-specific Hox mRNA translation by ribosome expansion segments.

Leppek K, Fujii K, Quade N, Susanto TT, Boehringer D, Lenarčič T, Xue S, Genuth NR, Ban, N, Barna M.
⟶ Mol. Cell, 2020 Dec 17;80(6):980-995.e13.
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Functional 5’ UTR mRNA structures in eukaryotic translation regulation and how to find them.

Leppek K, Das R, Barna M.
⟶ Nat Rev Mol Cell Biol. 2018 Mar;19(3):158-174.
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Roquin promotes constitutive mRNA decay via a conserved class of stem-loop recognition motifs.

Leppek K, Schott J, Reitter S, Poetz F, Hammond MC, Stoecklin G.
⟶ Cell. 2013 May 9;153(4):869-81. (see Press & Media for press release)
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All Publications

2022-2025 (Leppek Lab)

A versatile toolbox for determining IRES activity in cells and embryonic tissues.

Koch P*, Zhang Z*, Genuth NR*, Susanto TT, Haimann M, Khmelinskaia A, Byeon GW, Dey S, Barna M‡, Leppek K‡. A versatile toolbox for determining IRES activity in cells and embryonic tissues.
EMBO J. 2025 Mar 13. doi: 10.1038/s44318-025-00404-5.

Combinatorial optimization of mRNA structure, stability, and translation for RNA-based therapeutics.

Leppek K*, Byeon GW*, Kladwang W*, Wayment-Steele HK*, Kerr CH*, Xu AF**, Kim DS**, Topkar VV, Choe C, Rothschild D, Tiu GC, Wellington-Oguri R, Fujii K, Sharma E, Watkins AM, Nicol JJ, Romano J, Tunguz B, Diaz F, Cai H, Guo P, Wu J, Meng F, Shi S, Eterna Participants, Dormitzer PR, Solórzano A, Barna M‡, Das R‡.
Nature Comm. 2022 Mar;13(1): 1536,1-22. doi: 10.1038/s41467-022-28776-w.

2015-2021 (Postdoc)

VELCRO-IP RNA-seq reveals ribosome expansion segment function in translation genome-wide.

Leppek K*, Byeon GW*, Fujii K, Barna M.
Cell Reports, 2021 Jan 19;34(3):108629. doi: 10.1016/j.celrep.2020.108629.

Gene- and species-specific Hox mRNA translation by ribosome expansion segments.

Leppek K, Fujii K, Quade N, Susanto TT, Boehringer D, Lenarčič T, Xue S, Genuth NR, Ban, N, Barna M.
Mol. Cell, 2020 Dec 17;80(6):980-995.e13. doi: 10.1016/j.molcel.2020.10.023.

An rRNA variant to deal with stress.

Leppek K, Barna M.
Nat Microbiol. 2019 Mar;4(3):382-383. doi: 10.1038/s41564-019-0396-7.

Functional 5’ UTR mRNA structures in eukaryotic translation regulation and how to find them.

Leppek K, Das R, Barna M.
Nat Rev Mol Cell Biol. 2018 Mar;19(3):158-174. doi: 10.1038/nrm.2017.103. (Epub Nov 22, 2017)

The Mammalian Ribo-interactome Reveals Ribosome Functional Diversity and Heterogeneity.

Simsek D, Tiu GC, Flynn RA, Byeon GW, Leppek K, Xu AF, Chang HY, Barna M.
Cell. 2017 Jun 1;169(6):1051-1065.e18. doi: 10.1016/j.cell.2017.05.022.

A distinct, sequence-induced conformation is required for recognition of the CDE RNA by Roquin.

Codutti L, Leppek K, Zálešák J, Windeisen V, Masiewicz P, Stoecklin G and Carlomagno T.
Structure. 2015 Aug 4;23(8):1437-1447. doi: 10.1016/j.str.2015.06.001.

2011-2014 (Ph.D.)

An optimized streptavidin-binding RNA aptamer for purification of ribonucleoprotein complexes identifies novel ARE-binding proteins.

Leppek K and Stoecklin G.
Nucl Acids Res. 2014 Jan;42(2):e13. doi: 10.1093/nar/gkt956. (Epub Oct 23, 2013)

Roquin promotes constitutive mRNA decay via a conserved class of stem-loop recognition motifs.

Leppek K, Schott J, Reitter S, Poetz F, Hammond MC, Stoecklin G.
Cell. 2013 May 9;153(4):869-81. doi: 10.1016/j.cell.2013.04.016.

Genome-wide assessment of AU-rich elements by the AREScore algorithm.

Spasic M, Friedel CC, Schott J, Kreth J, Leppek K, Hofmann S, Ozgur S, Stoecklin G.
PLoS Genet. 2012 Jan;8(1):e1002433. doi: 10.1371/journal.pgen.1002433.

Protein synthesis and translational control: at eye level with the ribosome.

Leppek K, Schott J, Stoecklin G.
EMBO Rep. 2011 Dec 1;12(12):1214-6. doi: 10.1038/embor.2011.224.

Before (B.Sc.)

A plant 5S ribosomal RNA mimic regulates alternative splicing of transcription factor IIIA pre-mRNAs.

Hammond MC, Wachter A, Breaker RR.
Nat Struct Mol Biol. 2009;16(5):541-549. doi:10.1038/nsmb.1588

Patents

“Gene-Product Expression Constructs and Systems”

Philipp Koch, Maria Barna, Kathrin Leppek
09/2024, US63/695,706, US/EU provisional patent, shared IP of Stanford/Uni Bonn

Publications

Selected Publications

A versatile toolbox for determining IRES activity in cells and embryonic tissues.

Combinatorial optimization of mRNA structure, stability, and translation for RNA-based therapeutics.

VELCRO-IP RNA-seq reveals ribosome expansion segment function in translation genome-wide.

Gene- and species-specific Hox mRNA translation by ribosome expansion segments.

Functional 5’ UTR mRNA structures in eukaryotic translation regulation and how to find them.

Roquin promotes constitutive mRNA decay via a conserved class of stem-loop recognition motifs.

All Publications

2022-2025 (Leppek Lab)

A versatile toolbox for determining IRES activity in cells and embryonic tissues.

Combinatorial optimization of mRNA structure, stability, and translation for RNA-based therapeutics.

2015-2021 (Postdoc)

VELCRO-IP RNA-seq reveals ribosome expansion segment function in translation genome-wide.

Gene- and species-specific Hox mRNA translation by ribosome expansion segments.

An rRNA variant to deal with stress.

Functional 5’ UTR mRNA structures in eukaryotic translation regulation and how to find them.

The Mammalian Ribo-interactome Reveals Ribosome Functional Diversity and Heterogeneity.

A distinct, sequence-induced conformation is required for recognition of the CDE RNA by Roquin.

2011-2014 (Ph.D.)

An optimized streptavidin-binding RNA aptamer for purification of ribonucleoprotein complexes identifies novel ARE-binding proteins.

Roquin promotes constitutive mRNA decay via a conserved class of stem-loop recognition motifs.

Genome-wide assessment of AU-rich elements by the AREScore algorithm.

Protein synthesis and translational control: at eye level with the ribosome.

Before (B.Sc.)

A plant 5S ribosomal RNA mimic regulates alternative splicing of transcription factor IIIA pre-mRNAs.

Patents

“Gene-Product Expression Constructs and Systems”

“Systems and Methods for Enhancing Gene Expression”

“Systems and methods to assess RNA stability”

“Systems and Methods for Producing RNA Constructs with Increased Translation and Stability”

“Systems and methods to assess RNA stability”