Publications

corresponding author *; Weinberg Lab Members; contributed equally °

2023

Eckert I, Friedrich R, Weinberg CE*, Weinberg Z*. “Discovery of natural non-circular permuations in non-coding RNAs.” Nucleic Acids Res. 2023, accepted.

2022

Olzog VJ, Freist LI, Goldmann R, Fallmann J, Weinberg CE*. “Application of RtcB ligase to monitor self-cleaving ribozyme activity by RNA-seq.” Biological Chemistry, 403(8-9): 705-715, 2022. https://doi.org/10.1515/hsz-2021-0408.

2021

Olzog VJ, Gärtner C, Stadler PF, Fallmann J, Weinberg CE*. “cyPhyRNA-seq: A genome-scale RNA-seq method to detect active self-cleaving ribozymes by capturing RNAs with 2′,3′ cyclic phosphate and 5′ hydroxyl ends.” RNA Biology 2021, doi:10.1080/15476286.2021.1999105

Stitz M, Chapparo C, Lu Z, Olzog VJ, Weinberg CE, Blom J, Goesmann
A, Grunau C, Grevelding CG. “The new WEome of Schistosoma mansoni – Repetitively
organized, transcribed and mobile genetic DNA elements with functional
roles for schistosome biology and evolution.” Genome Biol Evol 2021; evab204, doi:
10.1093/gbe/evab204

Weinberg CE, Olzog VJ, Eckert I, Weinberg Z. “Identification of over 200-fold
more hairpin ribozymes than previously known in diverse circular RNAs.” Nucleic Acids Res. 2021;49(11):6375–6388.

Lihanova Y, Weinberg CE.* “Biochemical analysis of cleavage and ligation activities of the pistol ribozyme from Paenibacillus polymyxa.” RNA Biology. 2021 ; S.1-9. doi:10.1080/15476286.2021.1874706

Weinberg CE.* “Biological roles of self-cleaving ribozymes.” In: Müller, Masquida, Winkler (Eds.): Ribozymes, Vol. 2, 2021; https://doi.org/10.1002/9783527814527.ch2

2020

Günzel C, Kühnl F, Arnold A, Findeiß S, Weinberg CE, Stadler PF, Mörl M. “Beyond Plug and Pray: Context Sensitivity and in silico Design of Artificial Neomycin Riboswitches“, RNA Biology. 2020 DOI: 10.1080/15476286.2020.1816336

Malkowski S, Atilho R, Greenlee E, Weinberg CE, Breaker RR. “A rare bacterial RNA motif is implicated in the regulation of the purF gene whose encoded enzyme synthesizes phosphoribosylamine“. RNA. 2020 Aug 25: rna.077313.120.

2019

Weinberg CE*, Weinberg Z, Hammann C. “Novel ribozymes: Discovery, catalytic mechanisms, and the quest to understand biological functions.” Nucleic Acids Res. 2019;47(18):9480-9494.

Kirsch R°, Olzog VJ°, Bonin S, Weinberg CE, Betat H, Stadler PF, Mörl M. “A streamlined protocol for the detection of mRNA-sRNA interactions using AMT crosslinking in vitro.” Biotechniques 2019;67(4):178-183.

2017

Weinberg Z, Lünse CE, Corbino KA, Ames TD, Nelson JW, Roth A, Perkins KR, Sherlock ME, Breaker RR. “Detection of 224 candidate structured RNAs by comparative analysis of specific subsets of intergenic regions.” Nucleic Acids Res. 2017; 45(18):10811-10823.

Lorenz C, Lünse CE, Mörl M. “tRNA Modifications: Impact on Structure and Thermal Adaptation.” Biomolecules 2017;7(2)pii: E35.

Weinberg Z, Nelson JW, Lünse CE, Sherlock ME, Breaker RR. “Bioinformatic analysis of riboswitch structures uncovers variant classes with altered ligand specificity.” Proc Natl Acad Sci USA. 2017;114(11):E2077-E2085.

Lünse CE*, Mayer G. “Reporter-gene-based screening for TPP riboswitch activators.” In: Sass P, Ed. Antibiotics: Methods and Protocols. New York, NY: Springer New York, 2017:227-35.

2016

Lünse CE, Weinberg Z, Breaker RR. “Numerous small hammerhead ribozyme variants associated with Penelope-like elements cleave RNA as dimers.” RNA Biol. 2016;14(11):1499-1507.

Schüller A, Matzner D, Lünse CE, Wittmann V, Schumacher C, Unsleber S, Brötz-Oesterhelt H, Mayer C, Bierbaum G, Mayer G. “Activation of the glmS ribozyme confers bacterial growth inhibition.” ChemBioChem 2016;18(5):435-440.

2015

Li S, Lünse CE, Harris KA, Breaker RR. “Biochemical analysis of hatchet self-cleaving ribozymes.” RNA. 2015;21(11):1845-51.

Harris KA, Lünse CE, Li S, Brewer KI, Breaker RR. “Biochemical analysis of pistol self-cleaving ribozymes.” RNA. 2015;21(11):1952-8.

Weinberg Z, Kim PB, Chen TH, Li S, Harris KA, Lünse CE, Breaker RR. “New classes of self-cleaving ribozymes revealed by comparative genomics analysis.” Nat Chem Biol. 2015;11(8):606-610.

Nelson JW, Sudarsan N, Phillips GE, Stav S, Lünse CE, McCown PJ, Breaker RR. “Control of bacterial exoelectrogenesis by c-AMP-GMP.” Proc Natl Acad Sci USA. 2015;112(17):5389-94.

2014

Lünse CE, Scott FJ, Suckling CJ, Mayer G. “Novel TPP-riboswitch activators bypass metabolic enzyme dependency.” Front Chem. 2014;2:53.

Lünse CE, Mayer G. “Screening assays to identify artificial glmS ribozyme activators.” Methods Mol Biol 2014;1103:199-209.

Lünse CE, Schüller A, Mayer G. “The promise of riboswitches as potential antibacterial drug targets.” Int J Med Microbiol 2014;304(1):79-92.

2012

Lünse CE, Scott F, Suckling C, Mayer G. “Thiamine derivatives and their use as antibiotics.” EP 12 154 531.3, (filed on 08.02.2012)

2011

Mayer G, Müller J, Lünse CE. “RNA diagnostics: real-time RT-PCR strategies and promising novel target RNAs.” Wiley Interdiscip Rev RNA 2011;2(1):32-41.

Lünse CE, Schmidt MS, Wittmann V, Mayer G. “Carba-sugars activate the glmS-riboswitch of Staphylococcus aureus.”ACS Chem Biol. 2011;6(7):675-8.

2010

Lünse CE, Schmidt M, Wittman V, Mayer G. “Cyclohexane compounds and their use as antibiotics.” EP 10 194 929.5, (filed on 14.12.2010).

Lünse CE, Michlewski G, Hopp CS, Rentmeister A, Cáceres JF, Famulok M, Mayer G. “An aptamer targeting the apical-loop domain modulates pri-miRNA processing.” Angew Chem Int Ed Engl. 2010;49(27):4674-7.