@article{chan_brown_lowe_2012, title={Modeling the Thermoproteaceae RNase P RNA}, volume={9}, ISSN={["1547-6286"]}, DOI={10.4161/rna.21502}, abstractNote={The RNA component of the RNase P complex is found throughout most branches of the tree of life and is principally responsible for removing the 5′ leader sequence from pre-tRNA transcripts during tRNA maturation. RNase P RNA has a number of universal core features, however variations in sequence and structure found in homologs across the tree of life require multiple Rfam covariance search models to detect accurately. We describe a new Rfam search model to enable efficient detection of the diminutive archaeal Type T RNase P RNAs, which are missed by existing Rfam models. Using the new model, we establish effective score detection thresholds, and detect four new RNase P RNA genes in recently completed genomes from the crenarchaeal family Thermoproteaceae.}, number={9}, journal={RNA BIOLOGY}, author={Chan, Patricia P. and Brown, James W. and Lowe, Todd M.}, year={2012}, month={Sep}, pages={1155–1160} }
 @article{lai_chan_cozen_bernick_brown_gopalan_lowe_2010, title={Discovery of a minimal form of RNase P in Pyrobaculum}, volume={107}, ISSN={0027-8424 1091-6490}, url={http://dx.doi.org/10.1073/pnas.1013969107}, DOI={10.1073/pnas.1013969107}, abstractNote={RNase P RNA is an ancient, nearly universal feature of life. As part of the ribonucleoprotein RNase P complex, the RNA component catalyzes essential removal of 5′ leaders in pre-tRNAs. In 2004, Li and Altman computationally identified the RNase P RNA gene in all but three sequenced microbes: Nanoarchaeum equitans, Pyrobaculum aerophilum, and Aquifex aeolicus (all hyperthermophiles) [Li Y, Altman S (2004) RNA 10:1533–1540]. A recent study concluded that N. equitans does not have or require RNase P activity because it lacks 5′ tRNA leaders. The “missing” RNase P RNAs in the other two species is perplexing given evidence or predictions that tRNAs are trimmed in both, prompting speculation that they may have developed novel alternatives to 5′ pre-tRNA processing. Using comparative genomics and improved computational methods, we have now identified a radically minimized form of the RNase P RNA in five Pyrobaculum species and the related crenarchaea Caldivirga maquilingensis and Vulcanisaeta distributa, all retaining a conventional catalytic domain, but lacking a recognizable specificity domain. We confirmed 5′ tRNA processing activity by high-throughput RNA sequencing and in vitro biochemical assays. The Pyrobaculum and Caldivirga RNase P RNAs are the smallest naturally occurring form yet discovered to function as trans-acting precursor tRNA-processing ribozymes. Loss of the specificity domain in these RNAs suggests altered substrate specificity and could be a useful model for finding other potential roles of RNase P. This study illustrates an effective combination of next-generation RNA sequencing, computational genomics, and biochemistry to identify a divergent, formerly undetectable variant of an essential noncoding RNA gene.}, number={52}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Lai, L. B. and Chan, P. P. and Cozen, A. E. and Bernick, D. L. and Brown, J. W. and Gopalan, V. and Lowe, T. M.}, year={2010}, month={Dec}, pages={22493–22498} }
 @article{ellis_brown_brown_2010, title={The small nucleolar ribonucleoprotein (snoRNP) database}, volume={16}, ISSN={["1469-9001"]}, DOI={10.1261/rna.1871310}, abstractNote={Small nucleolar ribonucleoproteins (snoRNPs) are widely studied and characterized as guide RNAs for sequence-specific 2'-O-ribose methylation and psuedouridylation of ribosomal RNAs. In addition, snoRNAs have also been shown to interact with some tRNAs and direct alternative splicing in mRNA biogenesis. Recent advances in bioinformatics have resulted in new algorithms able to rapidly identify noncoding RNAs generally and snoRNAs specifically in genomic and metagenomic sequences, resulting in a rapid increase in the number and diversity of identified snoRNA sequences. The snoRNP database is a web-based collection of snoRNA and snoRNA-associated protein sequences from a wide range of species. The database currently contains 8994 snoRNA sequences from Bacteria, Archaea, and Eukaryotes and 589 snoRNA-associated protein sequences. The snoRNP database can be found at: http://evolveathome.com/snoRNA/snoRNA.php.}, number={4}, journal={RNA}, author={Ellis, J. Christopher and Brown, Daniel D. and Brown, James W.}, year={2010}, month={Apr}, pages={664–666} }
 @article{brown_birmingham_griffiths_jossinet_kachouri-lafond_knight_lang_leontis_steger_stombaugh_et al._2009, title={The RNA structure alignment ontology}, volume={15}, ISSN={["1469-9001"]}, DOI={10.1261/rna.1601409}, abstractNote={Multiple sequence alignments are powerful tools for understanding the structures, functions, and evolutionary histories of linear biological macromolecules (DNA, RNA, and proteins), and for finding homologs in sequence databases. We address several ontological issues related to RNA sequence alignments that are informed by structure. Multiple sequence alignments are usually shown as two-dimensional (2D) matrices, with rows representing individual sequences, and columns identifying nucleotides from different sequences that correspond structurally, functionally, and/or evolutionarily. However, the requirement that sequences and structures correspond nucleotide-by-nucleotide is unrealistic and hinders representation of important biological relationships. High-throughput sequencing efforts are also rapidly making 2D alignments unmanageable because of vertical and horizontal expansion as more sequences are added. Solving the shortcomings of traditional RNA sequence alignments requires explicit annotation of the meaning of each relationship within the alignment. We introduce the notion of "correspondence," which is an equivalence relation between RNA elements in sets of sequences as the basis of an RNA alignment ontology. The purpose of this ontology is twofold: first, to enable the development of new representations of RNA data and of software tools that resolve the expansion problems with current RNA sequence alignments, and second, to facilitate the integration of sequence data with secondary and three-dimensional structural information, as well as other experimental information, to create simultaneously more accurate and more exploitable RNA alignments.}, number={9}, journal={RNA}, author={Brown, James W. and Birmingham, Amanda and Griffiths, Paul E. and Jossinet, Fabrice and Kachouri-Lafond, Rym and Knight, Rob and Lang, B. Franz and Leontis, Neocles and Steger, Gerhard and Stombaugh, Jesse and et al.}, year={2009}, month={Sep}, pages={1623–1631} }
 @article{betancourt_loveless_brown_bishop_2008, title={Characterization of diazotrophs containing Mo-independent nitrogenases, isolated from diverse natural environments}, volume={74}, ISSN={["1098-5336"]}, DOI={10.1128/AEM.02694-07}, abstractNote={ABSTRACT Molybdenum-independent nitrogenases were first described in the nitrogen-fixing bacterium Azotobacter vinelandii and have since been described in other diazotrophic bacteria. Previously, we reported the isolation of seven diazotrophs with Mo-independent nitrogenases from aquatic environments. In the present study, we extend these results to include diazotrophs isolated from wood chip mulch, soil, “paraffin dirt,” and sediments from mangrove swamps. Mo-deficient, N-free media under both aerobic and anaerobic conditions were used for the isolations. A total of 26 isolates were genetically and physiologically characterized. Their phylogenetic placement was determined using 16S rRNA gene sequence analysis. Most of the isolates are members of the gamma subdivision of the class Proteobacteria and appear to be specifically related to fluorescent pseudomonads and azotobacteria. Two other isolates, AN1 and LPF4, are closely related to Enterobacter spp. and Paenibacillus spp., respectively. PCR and/or Southern hybridization were used to detect the presence of nitrogenase genes in the isolates. PCR amplification of vnfG and anfG was used to detect the genetic potential for the expression of the vanadium-containing nitrogenase and the iron-only nitrogenase in the isolates. This study demonstrates that diazotrophs with Mo-independent nitrogenases can be readily isolated from diverse natural environments.}, number={11}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Betancourt, Doris A. and Loveless, Telisa M. and Brown, James W. and Bishop, Paul E.}, year={2008}, month={Jun}, pages={3471–3480} }
 @article{ellis_barnes_brown_2007, title={Is Alba an RNase P subunit?}, volume={4}, ISSN={["1555-8584"]}, DOI={10.4161/rna.4.3.5347}, abstractNote={It has been suggested that Alba, a well-established chromatin protein in Archaea, is also a subunit of the archaeal RNase P holoenzyme, based on the observation that the homolog of this protein in humans has been shown to be associated with RNase P activity. Using the same biochemical methods we used previously to show that four other proteins homologous to eukaryotic RNase P proteins are bona fide RNase P subunits in Archaea, we could not detect any association of the Alba homolog in Methanothermobacter thermoautotrophicus (Mth1483p) with the RNase P holoenzyme. In addition, the presence of Mth1483p did not enhance the activity of RNase P holoenzyme reconstituted from recombinant subunits. In conclusion, we find no evidence that Alba is an RNase P subunit.}, number={3}, journal={RNA BIOLOGY}, author={Ellis, J. Chris and Barnes, Jeffrey and Brown, James W.}, year={2007}, pages={169–172} }
 @article{leontis_altman_berman_brenner_brown_engelke_harvey_holbrook_jossinet_lewis_et al._2006, title={The RNA Ontology Consortium: An open invitation to the RNA community}, volume={12}, ISSN={["1469-9001"]}, DOI={10.1261/rna.2343206}, abstractNote={The aim of the RNA Ontology Consortium (ROC) is to create an integrated conceptual framework-an RNA Ontology (RO)-with a common, dynamic, controlled, and structured vocabulary to describe and characterize RNA sequences, secondary structures, three-dimensional structures, and dynamics pertaining to RNA function. The RO should produce tools for clear communication about RNA structure and function for multiple uses, including the integration of RNA electronic resources into the Semantic Web. These tools should allow the accurate description in computer-interpretable form of the coupling between RNA architecture, function, and evolution. The purposes for creating the RO are, therefore, (1) to integrate sequence and structural databases; (2) to allow different computational tools to interoperate; (3) to create powerful software tools that bring advanced computational methods to the bench scientist; and (4) to facilitate precise searches for all relevant information pertaining to RNA. For example, one initial objective of the ROC is to define, identify, and classify RNA structural motifs described in the literature or appearing in databases and to agree on a computer-interpretable definition for each of these motifs. To achieve these aims, the ROC will foster communication and promote collaboration among RNA scientists by coordinating frequent face-to-face workshops to discuss, debate, and resolve difficult conceptual issues. These meeting opportunities will create new directions at various levels of RNA research. The ROC will work closely with the PDB/NDB structural databases and the Gene, Sequence, and Open Biomedical Ontology Consortia to integrate the RO with existing biological ontologies to extend existing content while maintaining interoperability.}, number={4}, journal={RNA}, author={Leontis, NB and Altman, RB and Berman, HM and Brenner, SE and Brown, JW and Engelke, DR and Harvey, SC and Holbrook, SR and Jossinet, F and Lewis, SE and et al.}, year={2006}, month={Apr}, pages={533–541} }
 @article{o'rourke_pitulle_hegarty_kraycirik_killary_grosenstein_brown_breitschwerdt_2005, title={Bartonella quintana in Cynomolgus Monkey (Macaca fascicularis)}, volume={11}, ISSN={1080-6040 1080-6059}, url={http://dx.doi.org/10.3201/eid1112.030045}, DOI={10.3201/eid1112.030045}, abstractNote={We identified a Bartonella quintana strain by polymerase chain reaction amplification, cloning, and sequencing of DNA extracted from lysed erythrocytes and cultured colonies grown from peripheral blood collected from a captive-bred cynomolgus monkey (Macaca fascicularis). This report describes naturally acquired B. quintana infection in a nonhuman primate.}, number={12}, journal={Emerging Infectious Diseases}, publisher={Centers for Disease Control and Prevention (CDC)}, author={O'Rourke, Laurie G. and Pitulle, Christian and Hegarty, Barbara C. and Kraycirik, Sharon and Killary, Karen A. and Grosenstein, Paul and Brown, James W. and Breitschwerdt, Edward B.}, year={2005}, month={Dec}, pages={1931–1934} }
 @article{marquez_harris_kelley_brown_dawson_roberts_pace_2005, title={Structural implications of novel diversity in eucaryal RNase P RNA}, volume={11}, number={5}, journal={RNA}, author={Marquez, S. M. and Harris, J. K. and Kelley, S. T. and Brown, J. W. and Dawson, S. C. and Roberts, E. C. and Pace, N. R.}, year={2005}, pages={739–751} }
 @article{tran_brown_maxwell_2004, title={Evolutionary origins of the RNA-guided nucleotide-modification complexes: from the primitive translation apparatus?}, volume={29}, ISSN={0968-0004}, url={http://dx.doi.org/10.1016/j.tibs.2004.05.001}, DOI={10.1016/j.tibs.2004.05.001}, abstractNote={Eukarya and Archaea possess scores of RNA-guided nucleotide-modification complexes that target specific ribonucleotides for 2′-O-methylation or pseudouridylation. Recent characterization of these RNA-modification machines has yielded striking results with implications for their evolutionary origins: the two main classes of nucleotide-modification complex in Archaea share a common ribonucleoprotein (RNP) core element that has evolved from a progenitor RNP. The fact that this common RNP element is also found in ribosomes suggests that the origin of the progenitor RNP lies in the primitive translation apparatus. Thus, the trans-acting, RNA-guided nucleotide-modification complexes of the modern RNP world seem to have evolved from cis-acting RNA or RNP elements contained in the primitive translation apparatus during the transition from the ancient RNA world to the modern RNP world.}, number={7}, journal={Trends in Biochemical Sciences}, publisher={Elsevier BV}, author={Tran, Elizabeth and Brown, James and Maxwell, E.Stuart}, year={2004}, month={Jul}, pages={343–350} }
 @article{ellis_brown_2003, title={Genes within genes within bacteria}, volume={28}, ISSN={["0968-0004"]}, DOI={10.1016/j.tibs.2003.08.002}, abstractNote={Recently, an unusual gene structure has been described in species of the genus Thermus, in which the rpmH (ribosomal protein L34) coding sequence was found to be entirely overlapped by the unusually large rnpA (RNase P protein subunit) sequence. Gene overlap is common in viruses, but has not been seen to this extent in any bacterium.}, number={10}, journal={TRENDS IN BIOCHEMICAL SCIENCES}, author={Ellis, JC and Brown, JW}, year={2003}, month={Oct}, pages={521–523} }
 @article{hall_brown_2002, title={Archaeal RNase P has multiple protein subunits homologous to eukaryotic nuclear RNase P proteins}, volume={8}, ISSN={["1469-9001"]}, DOI={10.1017/S1355838202028492}, abstractNote={Although archaeal RNase P RNAs are similar in both sequence and structure to those of Bacteria rather than eukaryotes, and heterologous reconstitution between the Bacillus subtilis RNase P protein and some archaeal RNase P RNAs has been demonstrated, no archaeal protein sequences with similarity to any known bacterial RNase P protein subunit have been identified, and the density of Methanothermobacter thermoautotrophicus RNase P in Cs2SO4 (1.42 g/mL) is inconsistent with a single small bacterial-like protein subunit. Four hypothetical open reading frames (MTH11, MTH687, MTH688, and MTH1618) were identified in the genome of M. thermoautotrophicus that have sequence similarity to four of the nine Saccharomyces cerevisiae RNase P protein subunits: Pop4p, Pop5p, Rpp1p, and Rpr2p, respectively. Polyclonal antisera generated to recombinant Mth11p, Mth687p, Mth688p, and Mth1618p each recognized a protein of the predicted molecular weight in western blots of partially purified M. thermoautotrophicus RNase P, and immunoprecipitated RNase P activity from the same partially purified preparation. RNase P in Archaea is therefore composed of an RNA subunit similar to bacterial RNase P RNA and multiple protein subunits similar to those in the eukaryotic nucleus.}, number={3}, journal={RNA}, author={Hall, TA and Brown, JW}, year={2002}, month={Mar}, pages={296–306} }
 @article{pitulle_strehse_brown_breitschwerdt_2002, title={Investigation of the phylogenetic relationships within the genus Bartonella based on comparative sequence analysis of the rnpB gene, 16S rDNA and 23S rDNA}, volume={52}, ISSN={["1466-5034"]}, DOI={10.1099/ijs.0.02281-0}, number={2002 Nov}, journal={INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY}, author={Pitulle, C and Strehse, C and Brown, JW and Breitschwerdt, EB}, year={2002}, month={Nov}, pages={2075–2080} }
 @article{waugh_gendron_altman_brown_case_gautheret_harvey_leontis_westbrook_westhof_et al._2002, title={RNAML: A standard syntax for exchanging RNA information}, volume={8}, ISSN={["1469-9001"]}, DOI={10.1017/S1355838202028017}, abstractNote={Analyzing a single data set using multiple RNA informatics programs often requires a file format conversion between each pair of programs, significantly hampering productivity. To facilitate the interoperation of these programs, we propose a syntax to exchange basic RNA molecular information. This RNAML syntax allows for the storage and the exchange of information about RNA sequence and secondary and tertiary structures. The syntax permits the description of higher level information about the data including, but not restricted to, base pairs, base triples, and pseudoknots. A class-oriented approach allows us to represent data common to a given set of RNA molecules, such as a sequence alignment and a consensus secondary structure. Documentation about experiments and computations, as well as references to journals and external databases, are included in the syntax. The chief challenge in creating such a syntax was to determine the appropriate scope of usage and to ensure extensibility as new needs will arise. The syntax complies with the eXtensible Markup Language (XML) recommendations, a widely accepted standard for syntax specifications. In addition to the various generic packages that exist to read and interpret XML formats, an XML processor was developed and put in the open-source MC-Core library for nucleic acid and protein structure computer manipulation.}, number={6}, journal={RNA}, author={Waugh, A and Gendron, P and Altman, R and Brown, JW and Case, D and Gautheret, D and Harvey, SC and Leontis, N and Westbrook, J and Westhof, E and et al.}, year={2002}, month={Jun}, pages={707–717} }
 @article{andrews_hall_brown_2001, title={Characterization of RNAse P holoenzymes from methanococcusjannaschii and methanothermobacter thermoautotrophicus}, volume={382}, number={8}, journal={Biological Chemistry Hoppe-Seyler}, author={Andrews, A. J. and Hall, T. A. and Brown, J. W.}, year={2001}, pages={1171–1177} }
 @article{harris_haas_williams_frank_brown_2001, title={New insight into RNase P RNA structure from comparative analysis of the archaeal RNA}, volume={7}, ISSN={["1469-9001"]}, DOI={10.1017/S1355838201001777}, abstractNote={A detailed comparative analysis of archaeal RNase P RNA structure and a comparison of the resulting structural information with that of the bacterial RNA reveals that the archaeal RNase P RNAs are strikingly similar to those of Bacteria. The differences between the secondary structure models of archaeal and bacterial RNase P RNA have largely disappeared, and even variation in the sequence and structure of the RNAs are similar in extent and type. The structure of the cruciform (P7-11) has been reevaluated on the basis of a total of 321 bacterial and archaeal sequences, leading to a model for the structure of this region of the RNA that includes an extension to P11 that consistently organizes the cruciform and adjacent highly-conserved sequences.}, number={2}, journal={RNA}, author={Harris, JK and Haas, ES and Williams, D and Frank, DN and Brown, JW}, year={2001}, month={Feb}, pages={220–232} }
 @inbook{hall_brown_2001, title={The ribonuclease P family}, volume={341}, booktitle={Ribonucleases: Pt. A}, publisher={San Diego, CA: Academic Press}, author={Hall, T. A. and Brown, J. W.}, year={2001}, pages={56–77} }
 @article{pannucci_haas_hall_harris_brown_1999, title={RNase P RNAs from some Archaea are catalytically active}, volume={96}, ISSN={["0027-8424"]}, DOI={10.1073/pnas.96.14.7803}, abstractNote={The RNA subunits of RNase Ps of Archaea and eukaryotes have been thought to depend fundamentally on protein for activity, unlike those of Bacteria that are capable of efficient catalysis in the absence of protein. Although the eukaryotic RNase P RNAs are quite different than those of Bacteria in both sequence and structure, the archaeal RNAs generally contain the sequences and structures of the bacterial, phylogenetically conserved catalytic core. A spectrum of archaeal RNase P RNAs were therefore tested for activity in a wide range of conditions. Many remain inactive in ionically extreme conditions, but catalytic activity could be detected from those of the methanobacteria, thermococci, and halobacteria. Chimeric holoenzymes, reconstituted from the Methanobacterium RNase P RNA and the Bacillus subtilis RNase P protein subunits, were functional at low ionic strength. The properties of the archaeal RNase P RNAs (high ionic-strength requirement, low affinity for substrate, and catalytic reconstitution by bacterial RNase P protein) are similar to synthetic RNase P RNAs that contain all of the catalytic core of the bacterial RNA but lack phylogenetically variable, stabilizing elements.}, number={14}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Pannucci, JA and Haas, ES and Hall, TA and Harris, JK and Brown, JW}, year={1999}, month={Jul}, pages={7803–7808} }
 @article{brown_1999, title={The Ribonuclease P Database}, volume={27}, ISSN={["0305-1048"]}, DOI={10.1093/nar/27.1.314}, abstractNote={Ribonuclease P is responsible for the 5'-maturation of tRNA precursors. Ribonuclease P is a ribonucleoprotein, and in bacteria the RNA subunit alone is catalytically active in vitro , i.e., it is a ribozyme. The Ribonuclease P Database is a compilation of ribonuclease P sequences, sequence alignments, secondary structures, three-dimensional models, and accessory information, available via the World Wide Web (http: //www.mbio.ncsu.edu/RNaseP/home.html ).}, number={1}, journal={NUCLEIC ACIDS RESEARCH}, author={Brown, JW}, year={1999}, month={Jan}, pages={314–314} }
 @article{haas_brown_1998, title={Evolutionary variation in bacterial RNase P RNAs}, volume={26}, ISSN={["0305-1048"]}, DOI={10.1093/nar/26.18.4093}, abstractNote={Sequences encoding RNase P RNAs from representatives of the last remaining classical phyla of Bacteria have been determined, completing a general phylogenetic survey of RNase P RNA sequence and structure. This broad sampling of RNase P RNAs allows some refinement of the secondary structure, and reveals patterns in the evolutionary variation of sequences and secondary structures. Although the sequences range from 100 to <25% identical to one another, and although only 40 of the nucleotides are invariant, there is considerable conservation of the underlying core of the RNA sequence. RNase P RNAs, like group I intron RNAs but unlike ribosomal RNAs, transfer RNAs or other highly conserved RNAs, are quite variable in secondary structure outside of this conserved structural core. Conservative regions of the RNA evolve by substitution of apparently interchangeable alternative structures, rather than the insertion and deletion of helical elements that occurs in the more variable regions of the RNA. In a remarkable case of convergent molecular evolution, most of the unusual structural elements of type B RNase P RNAs of the low G+C Gram-positive Bacteria have evolved independently in Thermomicrobium roseum , a member of the green non-sulfur Bacteria.}, number={18}, journal={NUCLEIC ACIDS RESEARCH}, author={Haas, ES and Brown, JW}, year={1998}, month={Sep}, pages={4093–4099} }
 @article{miller_plante_kim_brown_hemenway_1998, title={Stem-loop structure in the 5 ' region of potato virus X genome required for plus-strand RNA accumulation}, volume={284}, ISSN={["1089-8638"]}, DOI={10.1006/jmbi.1998.2174}, abstractNote={Computer-generated thermodynamic predictions and solution structure probing indicated two stem-loop structures, stem-loop 1 (SL1; nt 32-106) and stem-loop 2 (SL2; nt 143-183), within the 5' 230 nt of potato virus X (PVX) RNA. Because the existence of SL1 was further supported by covariation analysis of several PVX strains, the functional significance of this structure was investigated by site-directed mutational analysis in a tobacco protoplast system. In general, mutations that reduced genomic plus-strand RNA accumulation similarly affected coat protein accumulation, indicating that subgenomic plus-strand RNA was also affected. In contrast, minus-strand RNA levels remained relatively unchanged. Mutational analysis of the stem C (SC) region of SL1 indicated that pairing was more important than sequence, which was consistent with the covariation analysis. Alterations that increased length and stability of either SC or stem D (SD) were deleterious to plus-strand RNA accumulation. The formation of internal loop C between SC and SD, as well as specific nucleotides within this loop, were also required. Several modifications were made to the terminal GAAA tetraloop, a motif known for enhanced RNA stability. Both GANA and GAAG motifs resulted in wild-type levels of RNA accumulation. However, a UUCG tetraloop was detrimental, indicating that the sequence of this element was important beyond just providing stabilization of the structure. These data indicate that multiple features of SL1 are critical for accumulation of PVX plus-strand RNA.}, number={3}, journal={JOURNAL OF MOLECULAR BIOLOGY}, author={Miller, ED and Plante, CA and Kim, KH and Brown, JW and Hemenway, C}, year={1998}, month={Dec}, pages={591–608} }
 @article{brown_1998, title={The Ribonuclease P Database}, volume={26}, ISSN={["0305-1048"]}, DOI={10.1093/nar/26.1.351}, abstractNote={The Ribonuclease P Sequence database is a compilation of RNase P sequences, sequence alignments, secondary structures, three-dimensional models, and accessory information. In its initial form, the database contains information on RNase P RNA in bacteria and archaea, and RNase P protein in bacteria. The sequences themselves are presented phylogenetically ordered and aligned. The database also contains secondary structures of bacterial and archaeal RNAs, including specially annotated 'reference' secondary structures of Escherichia coli and Bacillus subtilis RNase P RNAs, a minimum phylogenetic consensus structure, and coordinates for models of three-dimensional structure.}, number={1}, journal={NUCLEIC ACIDS RESEARCH}, author={Brown, JW}, year={1998}, month={Jan}, pages={351–352} }
 @article{selvamurugan_joost_haas_brown_galvin_eliceiri_1997, title={Intracellular localization and unique conserved sequences of three small nucleolar RNAs}, volume={25}, ISSN={["0305-1048"]}, DOI={10.1093/nar/25.8.1591}, abstractNote={Three human small nucleolar RNAs (snoRNAs), E1, E2 and E3, were reported earlier that have unique sequences, interact directly with unique segments of pre-rRNA in vivo and are encoded in introns of protein genes. In the present report, human and frog E1, E2 and E3 RNAs injected into the cytoplasm of frog oocytes migrated to the nucleus and specifically to the nucleolus. This indicates that the nucleolar and nuclear localization signals of these snoRNAs reside within their evolutionarily conserved segments. Homologs of these snoRNAs from several vertebrates were sequenced and this information was used to develop RNA secondary structure models. These snoRNAs have unique phylogenetically conserved sequences.}, number={8}, journal={NUCLEIC ACIDS RESEARCH}, author={Selvamurugan, N and Joost, OH and Haas, ES and Brown, JW and Galvin, NJ and Eliceiri, GL}, year={1997}, month={Apr}, pages={1591–1596} }
 @article{brown_1997, title={The ribonuclease P database}, volume={25}, ISSN={["0305-1048"]}, DOI={10.1093/nar/25.1.263}, abstractNote={Ribonuclease P is responsible for the 5'-maturation of tRNA precursors. Ribonuclease P is a ribonucleoprotein, and in bacteria (and some Archaea) the RNA subunit alone is catalytically active in vitro, i.e. it is a ribozyme. The Ribonuclease P Database is a compilation of ribonuclease P sequences, sequence alignments, secondary structures, three-dimensional models and accessory information, available via the World Wide Web at the following URL: http://www.mbio.ncsu.edu/RNaseP/home .html}, number={1}, journal={NUCLEIC ACIDS RESEARCH}, author={Brown, JW}, year={1997}, month={Jan}, pages={263–264} }