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Zasha Weinberg, Ph.D. - Publications

Affiliations: 
2005 University of Washington, Seattle, Seattle, WA 
Area:
Computer Science, Molecular Biology, Genetics
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46 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Eckert I, Friedrich R, Weinberg CE, Weinberg Z. Discovery of natural non-circular permutations in non-coding RNAs. Nucleic Acids Research. 51: 2850-2861. PMID 36912096 DOI: 10.1093/nar/gkad137  0.553
2022 Lenkeit F, Eckert I, Sinn M, Hauth F, Hartig JS, Weinberg Z. A variant of guanidine-IV riboswitches exhibits evidence of a distinct ligand specificity. Rna Biology. 20: 10-19. PMID 36548032 DOI: 10.1080/15476286.2022.2160562  0.409
2022 Liao C, Sharma S, Svensson SL, Kibe A, Weinberg Z, Alkhnbashi OS, Bischler T, Backofen R, Caliskan N, Sharma CM, Beisel CL. Spacer prioritization in CRISPR-Cas9 immunity is enabled by the leader RNA. Nature Microbiology. 7: 530-541. PMID 35314780 DOI: 10.1038/s41564-022-01074-3  0.353
2021 Roth A, Weinberg Z, Vanderschuren K, Murdock MH, Breaker RR. Natural circularly permuted group II introns in bacteria produce RNA circles. Iscience. 24: 103431. PMID 34901790 DOI: 10.1016/j.isci.2021.103431  0.303
2021 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 Research. 49: 6375-6388. PMID 34096583 DOI: 10.1093/nar/gkab454  0.573
2020 Lenkeit F, Eckert I, Hartig JS, Weinberg Z. Discovery and characterization of a fourth class of guanidine riboswitches. Nucleic Acids Research. PMID 33237283 DOI: 10.1093/nar/gkaa1102  0.432
2020 Kalvari I, Nawrocki EP, Ontiveros-Palacios N, Argasinska J, Lamkiewicz K, Marz M, Griffiths-Jones S, Toffano-Nioche C, Gautheret D, Weinberg Z, Rivas E, Eddy SR, Finn RD, Bateman A, Petrov AI. Rfam 14: expanded coverage of metagenomic, viral and microRNA families. Nucleic Acids Research. PMID 33211869 DOI: 10.1093/nar/gkaa1047  0.402
2020 Eckert I, Weinberg Z. Discovery of 20 novel ribosomal leader candidates in bacteria and archaea. Bmc Microbiology. 20: 130. PMID 32448158 DOI: 10.1186/S12866-020-01823-6  0.472
2019 Wu D, von Roepenack-Lahaye E, Buntru M, de Lange O, Schandry N, Pérez-Quintero AL, Weinberg Z, Lowe-Power TM, Szurek B, Michael AJ, Allen C, Schillberg S, Lahaye T. A Plant Pathogen Type III Effector Protein Subverts Translational Regulation to Boost Host Polyamine Levels. Cell Host & Microbe. PMID 31628081 DOI: 10.1016/J.Chom.2019.09.014  0.309
2019 Weinberg CE, Weinberg Z, Hammann C. Novel ribozymes: discovery, catalytic mechanisms, and the quest to understand biological function. Nucleic Acids Research. 47: 9480-9494. PMID 31504786 DOI: 10.1093/Nar/Gkz737  0.605
2018 Weickhmann AK, Keller H, Wurm JP, Strebitzer E, Juen MA, Kremser J, Weinberg Z, Kreutz C, Duchardt-Ferner E, Wöhnert J. The structure of the SAM/SAH-binding riboswitch. Nucleic Acids Research. PMID 30590743 DOI: 10.2210/Pdb6Hag/Pdb  0.422
2017 Arachchilage GM, Sherlock ME, Weinberg Z, Breaker RR. SAM-VI RNAs Selectively Bind S-adenosylmethionine and Exhibit Similarities to SAM-III Riboswitches. Rna Biology. 0. PMID 29106323 DOI: 10.1080/15476286.2017.1399232  0.598
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 Research. PMID 28977401 DOI: 10.1093/Nar/Gkx699  0.614
2017 Weinberg Z, Nelson JW, Lünse CE, Sherlock ME, Breaker RR. Bioinformatic analysis of riboswitch structures uncovers variant classes with altered ligand specificity. Proceedings of the National Academy of Sciences of the United States of America. PMID 28265071 DOI: 10.1073/Pnas.1619581114  0.484
2016 Lünse CE, Weinberg Z, Breaker RR. Numerous small hammerhead ribozyme variants associated with Penelope-like retrotransposons cleave RNA as dimers. Rna Biology. 0. PMID 27858507 DOI: 10.1080/15476286.2016.1251002  0.548
2015 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. Nature Chemical Biology. 11: 606-10. PMID 26167874 DOI: 10.1038/Nchembio.1846  0.559
2015 Furukawa K, Ramesh A, Zhou Z, Weinberg Z, Vallery T, Winkler WC, Breaker RR. Bacterial riboswitches cooperatively bind Ni(2+) or Co(2+) ions and control expression of heavy metal transporters. Molecular Cell. 57: 1088-98. PMID 25794617 DOI: 10.1016/J.Molcel.2015.02.009  0.35
2014 McCown PJ, Liang JJ, Weinberg Z, Breaker RR. Structural, functional, and taxonomic diversity of three preQ1 riboswitch classes. Chemistry & Biology. 21: 880-9. PMID 25036777 DOI: 10.1016/J.Chembiol.2014.05.015  0.361
2014 Roth A, Weinberg Z, Chen AG, Kim PB, Ames TD, Breaker RR. A widespread self-cleaving ribozyme class is revealed by bioinformatics. Nature Chemical Biology. 10: 56-60. PMID 24240507 DOI: 10.1038/Nchembio.1386  0.569
2013 Nelson JW, Sudarsan N, Furukawa K, Weinberg Z, Wang JX, Breaker RR. Riboswitches in eubacteria sense the second messenger c-di-AMP. Nature Chemical Biology. 9: 834-9. PMID 24141192 DOI: 10.1038/Nchembio.1363  0.456
2013 Gu H, Furukawa K, Weinberg Z, Berenson DF, Breaker RR. Small, highly active DNAs that hydrolyze DNA. Journal of the American Chemical Society. 135: 9121-9. PMID 23679108 DOI: 10.1021/Ja403585E  0.308
2012 Baker JL, Sudarsan N, Weinberg Z, Roth A, Stockbridge RB, Breaker RR. Widespread genetic switches and toxicity resistance proteins for fluoride. Science (New York, N.Y.). 335: 233-5. PMID 22194412 DOI: 10.1126/Science.1215063  0.565
2011 Birmingham A, Clemente JC, Desai N, Gilbert J, Gonzalez A, Kyrpides N, Meyer F, Nawrocki E, Sterk P, Stombaugh J, Weinberg Z, Wendel D, Leontis NB, Zirbel C, Knight R, et al. Meeting report of the RNA Ontology Consortium January 8-9, 2011. Standards in Genomic Sciences. 4: 252-6. PMID 21677862 DOI: 10.4056/Sigs.1724282  0.565
2011 Perreault J, Weinberg Z, Roth A, Popescu O, Chartrand P, Ferbeyre G, Breaker RR. Identification of hammerhead ribozymes in all domains of life reveals novel structural variations. Plos Computational Biology. 7: e1002031. PMID 21573207 DOI: 10.1371/Journal.Pcbi.1002031  0.568
2011 Gardner PP, Barquist L, Bateman A, Nawrocki EP, Weinberg Z. RNIE: genome-wide prediction of bacterial intrinsic terminators. Nucleic Acids Research. 39: 5845-52. PMID 21478170 DOI: 10.1093/Nar/Gkr168  0.454
2011 Weinberg Z, Breaker RR. R2R--software to speed the depiction of aesthetic consensus RNA secondary structures. Bmc Bioinformatics. 12: 3. PMID 21205310 DOI: 10.1186/1471-2105-12-3  0.612
2010 Lee ER, Baker JL, Weinberg Z, Sudarsan N, Breaker RR. An allosteric self-splicing ribozyme triggered by a bacterial second messenger. Science (New York, N.Y.). 329: 845-8. PMID 20705859 DOI: 10.1126/Science.1190713  0.521
2010 Ames TD, Rodionov DA, Weinberg Z, Breaker RR. A eubacterial riboswitch class that senses the coenzyme tetrahydrofolate. Chemistry & Biology. 17: 681-5. PMID 20659680 DOI: 10.1016/J.Chembiol.2010.05.020  0.637
2010 Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR. Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes. Genome Biology. 11: R31. PMID 20230605 DOI: 10.1186/Gb-2010-11-3-R31  0.673
2009 Weinberg Z, Perreault J, Meyer MM, Breaker RR. Exceptional structured noncoding RNAs revealed by bacterial metagenome analysis. Nature. 462: 656-9. PMID 19956260 DOI: 10.1038/Nature08586  0.634
2009 Meyer MM, Ames TD, Smith DP, Weinberg Z, Schwalbach MS, Giovannoni SJ, Breaker RR. Identification of candidate structured RNAs in the marine organism 'Candidatus Pelagibacter ubique'. Bmc Genomics. 10: 268. PMID 19531245 DOI: 10.1186/1471-2164-10-268  0.661
2009 Tseng HH, Weinberg Z, Gore J, Breaker RR, Ruzzo WL. Finding non-coding RNAs through genome-scale clustering. Journal of Bioinformatics and Computational Biology. 7: 373-88. PMID 19340921 DOI: 10.1142/S0219720009004126  0.717
2008 Daub J, Gardner PP, Tate J, Ramsköld D, Manske M, Scott WG, Weinberg Z, Griffiths-Jones S, Bateman A. The RNA WikiProject: community annotation of RNA families. Rna (New York, N.Y.). 14: 2462-4. PMID 18945806 DOI: 10.1261/Rna.1200508  0.594
2008 Sudarsan N, Lee ER, Weinberg Z, Moy RH, Kim JN, Link KH, Breaker RR. Riboswitches in eubacteria sense the second messenger cyclic di-GMP. Science (New York, N.Y.). 321: 411-3. PMID 18635805 DOI: 10.1126/Science.1159519  0.512
2008 Weinberg Z, Regulski EE, Hammond MC, Barrick JE, Yao Z, Ruzzo WL, Breaker RR. The aptamer core of SAM-IV riboswitches mimics the ligand-binding site of SAM-I riboswitches. Rna (New York, N.Y.). 14: 822-8. PMID 18369181 DOI: 10.1261/Rna.988608  0.717
2008 Regulski EE, Moy RH, Weinberg Z, Barrick JE, Yao Z, Ruzzo WL, Breaker RR. A widespread riboswitch candidate that controls bacterial genes involved in molybdenum cofactor and tungsten cofactor metabolism. Molecular Microbiology. 68: 918-32. PMID 18363797 DOI: 10.1111/J.1365-2958.2008.06208.X  0.753
2007 Weinberg Z, Barrick JE, Yao Z, Roth A, Kim JN, Gore J, Wang JX, Lee ER, Block KF, Sudarsan N, Neph S, Tompa M, Ruzzo WL, Breaker RR. Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline. Nucleic Acids Research. 35: 4809-19. PMID 17621584 DOI: 10.1093/Nar/Gkm487  0.771
2007 Yao Z, Barrick J, Weinberg Z, Neph S, Breaker R, Tompa M, Ruzzo WL. A computational pipeline for high- throughput discovery of cis-regulatory noncoding RNA in prokaryotes. Plos Computational Biology. 3: e126. PMID 17616982 DOI: 10.1371/Journal.Pcbi.0030126  0.769
2007 Yao Z, Barrick J, Weinberg Z, Neph S, Breaker R, Tompa M, Ruzzo WL. A computational pipeline for high-throughput discovery of cis-regulatory noncoding RNA in prokaryotes Plos Computational Biology. 3: 1212-1223. DOI: 10.1371/journal.pcbi.0030126  0.693
2006 Eisen JA, Coyne RS, Wu M, Wu D, Thiagarajan M, Wortman JR, Badger JH, Ren Q, Amedeo P, Jones KM, Tallon LJ, Delcher AL, Salzberg SL, Silva JC, Haas BJ, ... ... Weinberg Z, et al. Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote. Plos Biology. 4: e286. PMID 16933976 DOI: 10.1371/Journal.Pbio.0040286  0.643
2006 Yao Z, Weinberg Z, Ruzzo WL. CMfinder--a covariance model based RNA motif finding algorithm. Bioinformatics (Oxford, England). 22: 445-52. PMID 16357030 DOI: 10.1093/Bioinformatics/Btk008  0.755
2006 Weinberg Z, Ruzzo WL. Sequence-based heuristics for faster annotation of non-coding RNA families. Bioinformatics (Oxford, England). 22: 35-9. PMID 16267089 DOI: 10.1093/Bioinformatics/Bti743  0.747
2005 Barrick JE, Sudarsan N, Weinberg Z, Ruzzo WL, Breaker RR. 6S RNA is a widespread regulator of eubacterial RNA polymerase that resembles an open promoter. Rna (New York, N.Y.). 11: 774-84. PMID 15811922 DOI: 10.1261/Rna.7286705  0.758
2004 Mandal M, Lee M, Barrick JE, Weinberg Z, Emilsson GM, Ruzzo WL, Breaker RR. A glycine-dependent riboswitch that uses cooperative binding to control gene expression. Science (New York, N.Y.). 306: 275-9. PMID 15472076 DOI: 10.1126/Science.1100829  0.669
2004 Weinberg Z, Ruzzo WL. Exploiting conserved structure for faster annotation of non-coding RNAs without loss of accuracy. Bioinformatics (Oxford, England). 20: i334-41. PMID 15262817 DOI: 10.1093/bioinformatics/bth925  0.711
2004 Weinberg Z, Ruzzo WL. Faster genome annotation of non-coding RNA families without loss of accuracy Proceedings of the Annual International Conference On Computational Molecular Biology, Recomb. 8: 243-251.  0.468
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