At BC
Furumo Q, and Meyer MM: Analysis of 3′-seq data from multiple E. coli studies identifies diverging results sets and raw data characteristics despite similar collection conditions. [BioRxiv]
Korn RR, and Meyer MM: Deep mutational scanning of an S. pneumoniae FMN riboswitch reveals robustness during mouse infection but diverging adaptive landscapes in response to targeting antibiotics. [BioRxiv]
Mizrahi O, Corley M, Feldman O, Fröhlking T, Sun L, Ziesel A, Antczak M, Bernetti M, Elhajjajy SI, Huang W, Nguyen GG, Park SS, Perez Martell RI, Trinity L, Xu K, Zok T, Bussi G, Jabbari H, Orenstein Y, Aviran S, Meyer MM, Yeo G. Evaluation of novel computational methods to identify RNA-binding protein footprints from structural data. RNA. (2025) in press [pubmed][Epub ahead of print].
Eichelman, M and Meyer MM: Assessing the conservation and targets of putative sRNAs in Streptococcus pneumoniae. Microbiology Spectrum (2025) in press. [BioRxiv].
Furumo Q, and Meyer MM: PIPETS: a statistically informed gene annotation agnostic analysis method to study bacterial termination using 3′-end sequencing BMC Bioinformatics 25: 363 (2024). [pubmed][article]
Geiwitz M, Page OR, Marello T, Nichols ME, Kumar N, Hummel S Belosevich V, Ma Q, van Opijnen T, Batten B, Meyer MM, Burch KS: Graphene Multiplexed Sensor for Point-of-Need Viral Wastewater-Based Epidemiology. ACS Appl. Biol. Mater. in press (2024) [pubmed][medRxiv]
Warrier I, Perry A, Hubbell SM, Eichelman M, van Opijnen T, Meyer MM: RNA cis-regulators are important for Streptococcus pneumoniae in vivo success. PLoS Genetics 20(3): e1011188 (2024). [pubmed][article]
Mukherjee S, Retwitzer MD, Hubbell SM, Meyer MM, Barash D: A computational approach for the identification of distant homologs of bacterial riboswitches based on inverse RNA folding Brief Bioinform. 24(3):bbad110 (2023). [pubmed][article]
Meyer, MM: Revisiting the Relationships Between Genomic G+C content, RNA Secondary Structures, and Optimal Growth Temperature J. Mol. Evol. 89:165-171 (2021). [pubmed][article]
Gray EC, Beringer DM, Meyer MM: Siblings or doppelgängers? Deciphering the evolution of structured cis-regulatory RNAs beyond homology. Biochem. Soc. Trans. 48:1941-1951 (2020). [pubmed][article]
Ram-Mohan N and Meyer MM: Comparative Metatranscriptomics of Periodontitis Supports a Common Polymicrobial Shift in Metabolic Function and Identifies Novel Putative Disease-Associated ncRNAs. Front Microbiol. 11:482 (2020) [pubmed] [article]
Liberles DA, Chang B, Geiler-Samerotte K, Goldman A, Hey J, Kacar B, Meyer MM, Murphy W, Posada D, Storfer A: Emerging Frontiers in the Study of Molecular Evolution. J. Mol. Evol. 88: 211-226. (2020). [pubmed][article].
Crum M, Ram-Mohan N, Meyer MM: Regulatory Context Drives Conservation of Glycine Riboswitch Aptamers. PLoS Comp. Biol 15(12):e1007564 (2019) [pubmed] [article]
Warrier I, Ram Mohan N, Zhu Z, Hazery A, Echlin H, Rosch J, Meyer MM, van Opijnen T: The Transcriptional landscape of Streptococcus pneumoniae TIGR4 reveals a complex operon architecture and abundant riboregulation critical for growth and virulence. PLoS Pathogens 14(12):e1007461 (2018).[pubmed] [article]
Meyer MM: rRNA mimicry in RNA regulation of gene expression. In Regulating with RNA in Bacteria and Archaea. eds. Gisela Storz and Kai Papenfort. ASM Press (2018) [pubmed][article]
Babina AM, Parke DJ, Li GW, Meyer MM: Fitness advantages conferred by the L20-interacting RNA cis-regulator of ribosomal protein synthesis in Bacillus subtilis. RNA 24:11330-1143 (2018).[pubmed] [article]
Babina AM, Lea NL*, Meyer MM: In vivo Behavior of the Tandem Glycine Riboswitch in Bacillus subtilis. mBio 8(5):e01602-17 (2017). [pubmed][article]
Pei S, Slinger BL and Meyer MM: Recognizing RNA structural motifs in HT-SELEX data for ribosomal protein S15. BMC Bioinformatics 18(1):298 (2017). [pubmed] [article]
Slinger BL and Meyer MM: RNA regulators responding to ribosomal protein S15 are frequent in sequence space. Nucleic Acids Res 44:9331-9341 (2016). [pubmed] [article]
Meyer MM: The role of mRNA structure in bacterial translation regulation. Wiley Interdiscip. Rev. RNA. (2016). [pubmed]
Slinger BL, Newman H*, Lee Y*, Pei S, Meyer MM: Co-evolution of bacterial ribosomal protein S15 with diverse mRNA regulatory structures PLOS Genetics 11:e1005720 (2015).[pubmed] [article]
Babina AM, Soo MW*, Fu Y, Meyer MM: An S6:S18 complex inhibits translation of the E. coli rpsF operon. RNA 21:1-8 (2015). [pubmed] [article]
Pei S, Anthony J, Meyer MM: The structural ensemble neutrality as a feature for structured RNA classification BMC Genomics.16:77 (2015). [pubmed] [article]
Dotu I, Garcia-Martin JA, Dixon BL, Mechery V, Meyer MM, Clote P: Complete RNA inverse folding: computational design of functional hammerhead ribozymes. Nucleic Acids Research 42:11752-11762 (2015).[pubmed] [article]
Slinger BL, Deiorio-Hagger K, Anthony J, Gilligan M*,Meyer MM: Discovery and validation of novel and distinct RNA regulators for ribosomal protein S15 BMC Genomics 15:657 (2014). [pubmed] [article]
Fu Y, Deiorio-Haggar K, Soo MW*, Meyer MM: Bacterial RNA motif in the 5′ UTR of rpsF interacts with an S6:S18 complex RNA 20:168-176 (2014).[pubmed] [article]
Deiorio-Haggar K, Anthony J, Meyer MM: RNA structures regulating ribosomal protein biosynthesis in bacilli. RNA Biology 10(7):1180-1184 (2013). [pubmed] [article]
Fu Y, Deiorio-Haggar K, Anthony J, Meyer MM: Most RNAs regulating ribosomal protein biosythesis in E. coli are narrowly distrbuted to Gammaproteobacteria. Nucleic Acids Research 41(6):3491-3503 (2013). [pubmed] [article]
Miller C, Anthony J, Meyer MM, Marth G: Scribl: An HTML5 Canvas-based graphic library for visualizing genomic data over the web. Bioinformatics 29(3): 381-383 (2013). [pubmed] [article]
Zarringhalam K, Meyer MM, Dotu I, Chuang, JH, Clote P: Integrating chemical footprinting data into RNA secondary structure prediction. PLOS ONE 7 (10), e45160 (2012). [pubmed] [article]
*undergraduate author
Before BC
Meyer MM, Hammond MC, Salinas Y, Roth A, Sudarsan N, Breaker RR: Aspects of ligand identification of challenging riboswitch candidates. RNA Biology 2011, 8:1
Weinberg Z, Perreault P, Meyer MM, Breaker RR: Exceptional Structured Non-coding RNAs Revealed by Bacterial Metagenome Analysis. Nature 2009, 462:656-659.
Poiata E, Meyer MM, Ames TD, Breaker RR: A variant riboswitch aptamer class of S-adenosylmethionine common in marine bacteria. RNA 2009, 15:2046-2056.
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 2009, 10:268.
Tripp HJ, Schwalbach MS, Meyer MM, Kitner JB, Breaker RR, Giovannoni SJ: ‘Candidatus Pelagibacter ubique’ is a functional glycine-serine auxotroph with a glycine riboswitch preceding malate synthase. Environmental Microbiology 2009, 11:230-238.
Meyer MM, Roth A, Chervin S, Garcia GA, Breaker RR: Confirmation of a second natural preQ1-binding aptamer. RNA 2008 14:685-695.
Meyer MM, Hochrein L, Arnold FH: Structure-Guided Recombination of Distantly Related beta-lactamases. Prot. Eng. Des. Sel. 2006, 19:563-570.
Drummond DA, Silberg JJ, Meyer MM, Wilke CO, Arnold FH: On the conservative nature of intragenic recombination. Proc. Natl. Acad. Sci. 2005, 102:5380-5385.
Meyer MM, Silberg JJ, Voigt CA, Endelman JB, Mayo SL, Wang ZG, Arnold FH: Library analysis of SCHEMA-guided protein recombination. Protein Sci. 2003, 12:1686-1693.
Segura MJR, Lodeiro S, Meyer MM, Patel AJ, Matsuda SPT: Directed evolution experiments reveal mutations at cycloartenol synthase residue His477 that dramatically alter catalysis. Org. Lett. 2002, 4:4459 -4462.
Meyer MM, Xu R, Matsuda SPT: Directed evolution to generate cycloartenol synthase mutants that produce lanosterol. Org. Lett. 2002, 4: 1395-1398.
Meyer MM, Segura MJR, Wilson WK, Matsuda SPT: Oxidosqualene cyclase residues that promote formation of cycloartenol, lanosterol, and parkeol. Angew. Chem. 2000, 39: 4090-4092.
Segura MJR, Meyer MM, Matsuda SPT: Arabidopsis thaliana LUP1 converts oxidosqualene to multiple triterpene alcohols and a triterpene diol Org. Lett. 2000, 2: 2257-2259.
Matsuda SPT, Darr LB, Hart EA, Herrera JBR, McCann KE, Meyer MM, Pang J, Schepmann HR, Wilson WK: Steric bulk at cycloartenol synthase position 481 influences cyclization and deprotonation. Org. Lett. 2000, 2: 2261-2263.
Godzina SM, Lovato MA, Meyer MM, Foster KA, Wilson WK, Gu W, de Hostos EL, Matsuda SPT: Cloning and characterization of the Dictyostelium discoideum cycloartenol synthase cDNA. Lipids 2000, 36:249-255.