Publications

✉ corresponding / co-corresponding author
* co-first author

    • I. Eckert, R. Friedrich, C.E. Weinberg, Z. Weinberg✉ (2023) Discovery of natural non-circular permutations in non-coding RNAs, Nucleic Acids Res, online ahead of print.
    • F. Lenkeit, I. Eckert, M. Sinn, F. Hauth, J.S. Hartig, Z. Weinberg✉ (2023)
      A variant of guanidine-IV riboswitches exhibits evidence of a distinct ligand specificity, RNA Biol., 20:10-19.
    • C. Liao, S. Sharma, S.L. Svensson, A. Kibe, Z. Weinberg, O.S. Alkhnbashi, T. Bischler, R. Backofen, N. Caliskan, C.M. Sharma, C.L. Beisel (2022) Spacer prioritization in CRISPR-Cas9 immunity is enabled by the leader RNA, Nature Microbiol, 7:530-541.
    • C.E. Weinberg, V.J. Olzog, I. Eckert, Z. Weinberg✉ (2021) Identification of over 200-fold more hairpin ribozymes than previously known in diverse circular RNAs, Nucleic Acids Res, 49:6375-6388.
    • M. Sinn, F. Hauth, F. Lenkeit, Z. Weinberg, J.S. Hartig (2021) Widespread Bacterial Utilization of Guanidine as Nitrogen Source, Mol Microbiol, doi:10.1111/mmi.14702.
    • A. Roth*, Z. Weinberg*, K. Vanderschuren, M.H. Murdock, R.R. Breaker (2021) Natural circularly permuted group II introns in bacteria produce RNA circles,  iScience, in press.
    • F. Lenkeit, I. Eckert, J.S. Hartig, Z. Weinberg✉  (2020) Discovery and characterization of a fourth class of guanidine riboswitches, Nucleic Acids Res., 48:12889-12899.
    • I. Eckert, Z. Weinberg✉ (2020) Discovery of 20 novel ribosomal leader candidates in bacteria and archaea, BMC Microbiol., 20:130.
    • I. Kalvari, E.P. Nawrocki, N. Ontiveros-Palacios, J. Argasinska, K. Lamkiewicz, M. Marz, S. Griffiths-Jones, C. Toffano-Nioche, D. Gautheret, Z. Weinberg, E. Rivas, S.R. Eddy, R.D. Finn, A. Bateman, A.I. Petrov (2020) Rfam 14: expanded coverage of metagenomic, viral and microRNA families, Nucleic Acids Res., 49:D192-D200.
    • RNAcentral Consortium (2020) RNAcentral 2021: secondary structure integration, improved sequence search and new member databases, Nucleic Acids Res., 49:D212-D220.
    • D. Wu, E. von Roepenack-Lahaye, M. Buntru, O. de Lange, N. Schandry, A.L. Pérez-Quintero, Z. Weinberg, T.M. Lowe-Power, B. Szurek, A.J. Michael, C. Allen, S. Schillberg, T. Lahaye (2019) A plant pathogen type III effector protein subverts translational regulation to boost host polyamine levels, Cell Host Microbe, 26:638-649.
    • C.E. Weinberg, Z. Weinberg✉, C. Hammann (2019) Novel ribozymes: discovery, catalytic mechanisms and the quest to understand biological function, Nucleic Acids Res., 47:9480-9494.
    • A.K. Weickhmann, H. Keller, J.P. Wurm, E. Strebitzer, M.A. Juen, J. Kremser, Z. Weinberg, C. Kreutz, E. Duchardt-Ferner, J. Wöhnert. (2019) The structure of the SAM/SAH-binding riboswitch, Nucleic Acids Res. 47:2654-2665.
    • G. Mirihana Arachchilage, M.E. Sherlock, Z. Weinberg, R.R. Breaker (2018) SAM-VI RNAs selectively bind S-adenosylmethionine and exhibit similarities to SAM-III riboswitches, RNA Biol, 15:371-378.
    • Z. Weinberg✉, C.E. Lünse, K.A. Corbino, T.D. Ames, J.W. Nelson, A. Roth, K.R. Perkins, M.E. Sherlock, R.R. Breaker (2017) Detection of 224 candidate structured RNAs by comparative analysis of specific subsets of intergenic regions, Nucleic Acids Res, 45:10811-10823.
    • Z. Weinberg*, J.W. Nelson*, C.E. Lünse, M.E. Sherlock, R.R. Breaker (2017) Bioinformatic analysis of riboswitch structures uncovers variant classes with altered ligand specificity, Proc Natl Acad Sci USA, 114:E2077-2085.
    • C.E. Lünse, Z. Weinberg, R.R. Breaker (2016) Numerous small hammerhead ribozyme variants associated with Penelope-like retrotransposons cleave RNA as dimers, RNA Biol, 14:1499-1507.
    • Z. Weinberg*, P.B. Kim*, T.H. Chen, S. Li, K.A. Harris, C.E. Lünse, R.R. Breaker (2015) New classes of self-cleaving ribozymes revealed by comparative genomics analysis, Nat Chem Biol, 11: 606-610.
    • K. Furukawa, A. Ramesh, Z. Zhou, Z. Weinberg, T. Vallery, W.C. Winkler, R.R. Breaker (2015) Bacterial riboswitches cooperatively bind Ni2+ or Co2+ ions and control expression of heavy metal transporters, Mol Cell, 57: 1088-1098.
    • P.J. McCown, J.J. Liang, Z. Weinberg, R.R. Breaker (2014) Structural, functional, and taxonomic diversity of three preQ1 riboswitch classes, Chem Biol, 21:880-889.
    • A. Roth*, Z. Weinberg*, A.G. Chen, P.B. Kim, T.D. Ames and R.R. Breaker (2014) A widespread self-cleaving ribozyme class is revealed by bioinformatics, Nat Chem Biol, 10:56-60.
    • J.W. Nelson, N. Sudarsan, K. Furukawa, Z. Weinberg, J.X. Wang, R.R. Breaker (2013) Riboswitches in eubacteria sense the second messenger c-di-AMP, Nat Chem Biol, 9:834-839.
    • H. Gu, K. Furukawa, Z. Weinberg, D.F. Berenson and R.R. Breaker (2013) Small, highly active DNAs that hydrolyze DNA, J. Am Chem Soc, 135:9121-0129.
    • R.B. Stockbridge, H.H. Lim, R. Otten, C. Williams, T. Shane, Z. Weinberg, C. Miller (2012) Fluoride resistance and transport by riboswitch-controlled CLC antiporters, Proc Natl Acad Sci USA, 109:15289-15294.
    • J.L. Baker, N. Sudarsan, Z. Weinberg, A. Roth, R.B. Stockbridge, R.R. Breaker (2012) Widespread genetic switches and toxicity resistance proteins for fluoride, Science, 335:223-225.
    • A. Birmingham, J.C. Clemente, N. Desai, J. Gilbert, A. Gonzalez, N. Kyrpides, F. Meyer, E. Nawrocki, P. Sterk, J. Stombaugh, Z. Weinberg, D. Wendel, N.B. Leontis, C. Zirbel, R. Knight, A. Laederach (2011) Meeting report of the RNA Ontology Consortium January 8-9, 2011, Stand Genomic Sci, 4: 252-256.
    • J. Perreault, Z. Weinberg, A. Roth, O. Popescu, P. Chartrand, G. Ferbeyre, R.R. Breaker (2011) Identification of hammerhead ribozymes in all domains of life reveals novel structural variations, PLoS Comput Biol, 7: e1002031.
    • P.P. Gardner, L. Barquist, A. Bateman, E.P. Nawrocki, Z. Weinberg (2011) RNIE: genome-wide prediction of bacterial intrinsic terminators, Nucleic Acids Res, 39: 5845.
    • Z. Weinberg✉, R.R. Breaker (2011) R2R—software to speed the depiction of aesthetic consensus RNA secondary structure, BMC Bioinformatics, 12: 3.
    • E.R. Lee, J.L. Baker, Z. Weinberg, N. Sudarsan, R.R. Breaker (2010) An allosteric self-splicing ribozyme triggered by a bacterial second messenger, Science, 329: 845-848.
    • T.D. Ames, D.A. Rodionov, Z. Weinberg, R.R. Breaker (2010) A eubacterial riboswitch class that senses the coenzyme tetrahydrofolate, Chem Biol, 17:681-685.
    • Z. Weinberg✉, J.X. Wang, J. Bogue, J. Yang, K. Corbino, R.H. Moy, R.R. Breaker (2010) Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes, Genome Biol, 11:R31.
    • Z. Weinberg, J. Perreault, M.M. Meyer, R.R. Breaker (2009) Extraordinary structured noncoding RNAs revealed by bacterial metagenome analysis, Nature, 462:656-659.
    • M.M. Meyer, T.D. Ames, D.P. Smith, Z. Weinberg, M.S. Schwalbach, S.J. Giovanni, R.R. Breaker (2009), Identification of candidate structured RNAs in the marine organism ‘Candidatus Pelagibacter ubique’, BMC Genomics, 10:268.
    • H.H. Tseng, Z. Weinberg, J. Gore, R.R. Breaker, W.L. Ruzzo (2009), Finding non-coding RNAs through genome-scale clustering, J Bioinform Comput Biol, 7:373-388.
    • J. Daub, P.P. Gardner, J. Tate, D. Ramsköld, M. Manske, W.G. Scott, Z. Weinberg, S. Griffiths-Jones, A. Bateman (2008), The RNA WikiProject: community annotation of RNA families, RNA, 14:2462-2464.
    • N. Sudarsan, E.R. Lee, Z. Weinberg, R.H. Moy, J.N. Kim, K.H. Link, R.R. Breaker (2008), Riboswitches in eubacteria sense the second messenger cyclic di-GMP, Science, 321:411-413.
    • Z. Weinberg, E.E. Regulski, M.C. Hammond, J.E. Barrick, Z. Yao, W.L. Ruzzo, R.R. Breaker (2008) The aptamer core of SAM-IV riboswitches mimics the ligand-binding site of SAM-I riboswitches, RNA, 14:822-828.
    • E.E. Regulski, R.H. Moy, Z. Weinberg, J.E. Barrick, Z. Yao, W.L. Ruzzo, R.R. Breaker (2008) A widespread riboswitch candidate that controls bacterial genes involved in molybdenum cofactor and tungsten cofactor metabolism,
      Mol Microbiol, 68:918-932.
    • Z. Weinberg✉, J.E. Barrick, Z. Yao, et al. (2007) Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline, Nucleic Acids Res, 35:4809-4819.
    • Z. Yao, J.E. Barrick, Z. Weinberg, S. Neph, R.R. Breaker, M. Tompa, W.L. Ruzzo (2007) A computational pipeline for high-throughput discovery of cis-regulatory noncoding RNA in prokaryotes, PLoS Comput Biol, 3:e126.
    • J.A. Eisen, et al. (2006) Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote, PLoS Biol, 4:e286.
    • Z. Weinberg, W.L. Ruzzo (2006) Sequence-based heuristics for faster annotation of non-coding RNA families, Bioinformatics, 22:35-39.
    • Z. Yao, Z. Weinberg, W.L. Ruzzo (2006) CMfinder—a covariance model based RNA motif finding algorithm, Bioinformatics, 22:445-452.
    • J.E. Barrick, N. Sudarsan, Z. Weinberg, W.L. Ruzzo, R.R. Breaker (2005) 6S RNA is a widespread regulator of eubacterial RNA polymerase that resembles an open promoter, RNA, 11:774-784.
    • M. Mandal, M. Lee, J.E. Barrick, Z. Weinberg, G.M. Emilsson, W.L. Ruzzo, R.R.
      Breaker (2004)  A glycine-dependent riboswitch that uses cooperative binding to control gene expression, Science, 306: 275-279.
    • Z. Weinberg, W.L. Ruzzo (2004) Exploiting conserved structure for faster
      annotation of non-coding RNAs without loss of accuracy, 12th International
      Conference on Intelligent Systems  for Molecular Biology (ISMB) and Bioinformatics, 20 (suppl. 1): i334-i341.
    • Z. Weinberg, W.L. Ruzzo (2004) Faster genome annotation of non-coding RNA
      families without loss of accuracy, Proc. Eighth Annual Inter. Conf. on
      Computational Molecular Biology (RECOMB), ACM Press, pp. 243-251.
    • J. T.-L. Wang, X. Wang, D. Shasha, B.A. Shapiro, K. Zhang, X. Zheng, Q. Ma, Z. Weinberg (2000) An approximate search engine for structural databases, SIGMOD Conference 2000: 584.