Search Results - "Anton, Brian P."

Genome-wide identification of 5-methylcytosine sites in bacterial genomes by high-throughput sequencing of MspJI restriction fragments by Anton, Brian P, Fomenkov, Alexey, Wu, Victoria, Roberts, Richard J

“…Single-molecule Real-Time (SMRT) sequencing can easily identify sites of N6-methyladenine and N4-methylcytosine within DNA sequences, but similar…”
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Rapid identification of methylase specificity (RIMS-seq) jointly identifies methylated motifs and generates shotgun sequencing of bacterial genomes by Baum, Chloé, Lin, Yu-Cheng, Fomenkov, Alexey, Anton, Brian P, Chen, Lixin, Yan, Bo, Evans, Thomas C, Roberts, Richard J, Tolonen, Andrew C, Ettwiller, Laurence

“…Abstract DNA methylation is widespread amongst eukaryotes and prokaryotes to modulate gene expression and confer viral resistance. 5-Methylcytosine (m5C)…”
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The complex methylome of the human gastric pathogen Helicobacter pylori by Krebes, Juliane, Morgan, Richard D, Bunk, Boyke, Spröer, Cathrin, Luong, Khai, Parusel, Raphael, Anton, Brian P, König, Christoph, Josenhans, Christine, Overmann, Jörg, Roberts, Richard J, Korlach, Jonas, Suerbaum, Sebastian

“…The genome of Helicobacter pylori is remarkable for its large number of restriction-modification (R-M) systems, and strain-specific diversity in R-M systems…”
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A Survey of Archaeal Restriction-Modification Systems by Anton, Brian P, Roberts, Richard J

“…When compared with bacteria, relatively little is known about the restriction-modification (RM) systems of archaea, particularly those in taxa outside of the…”
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Genome-wide methylome analysis of two strains belonging to the hypervirulent Neisseria meningitidis serogroup W ST-11 clonal complex by Stenmark, Bianca, Eriksson, Lorraine, Thulin Hedberg, Sara, Anton, Brian P., Fomenkov, Alexey, Roberts, Richard J., Mölling, Paula

“…A rising incidence of meningococcal serogroup W disease has been evident in many countries worldwide. Serogroup W isolates belonging to the sequence type…”
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Biochemical Characterization of Hypothetical Proteins from Helicobacter pylori by Choi, Han-Pil, Juarez, Silvia, Ciordia, Sergio, Fernandez, Marisol, Bargiela, Rafael, Albar, Juan P, Mazumdar, Varun, Anton, Brian P, Kasif, Simon, Ferrer, Manuel, Steffen, Martin

“…The functional characterization of Open Reading Frames (ORFs) from sequenced genomes remains a bottleneck in our effort to understand microbial biology. In…”
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The complete methylome of Helicobacter pylori UM032 by Lee, Woon Ching, Anton, Brian P, Wang, Susana, Baybayan, Primo, Singh, Siddarth, Ashby, Meredith, Chua, Eng Guan, Tay, Chin Yen, Thirriot, Fanny, Loke, Mun Fai, Goh, Khean Lee, Marshall, Barry J, Roberts, Richard J, Vadivelu, Jamuna

“…The genome of the human gastric pathogen Helicobacter pylori encodes a large number of DNA methyltransferases (MTases), some of which are shared among many…”
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Complete Genome Sequence of ER2796, a DNA Methyltransferase-Deficient Strain of Escherichia coli K-12 by Anton, Brian P, Mongodin, Emmanuel F, Agrawal, Sonia, Fomenkov, Alexey, Byrd, Devon R, Roberts, Richard J, Raleigh, Elisabeth A

“…We report the complete sequence of ER2796, a laboratory strain of Escherichia coli K-12 that is completely defective in DNA methylation. Because of its lack of…”
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EcoBLMcrX, a classical modification-dependent restriction enzyme in Escherichia coli B: Characterization in vivo and in vitro with a new approach to cleavage site determination by Fomenkov, Alexey, Sun, Zhiyi, Dila, Deborah K, Anton, Brian P, Roberts, Richard J, Raleigh, Elisabeth A

“…Here we characterize the modification-dependent restriction enzyme (MDE) EcoBLMcrX in vivo, in vitro and in its genomic environment. MDE cleavage of modified…”
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RimO, a MiaB-like enzyme, methylthiolates the universally conserved Asp88 residue of ribosomal protein S12 in Escherichia coli by Anton, Brian P, Saleh, Lana, Benner, Jack S, Raleigh, Elisabeth A, Kasif, Simon, Roberts, Richard J

“…Ribosomal protein S12 undergoes a unique posttranslational modification, methylthiolation of residue D88, in Escherichia coli and several other bacteria. Using…”
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Comparative Methylome Analysis of the Occasional Ruminant Respiratory Pathogen Bibersteinia trehalosi by Anton, Brian P, Harhay, Gregory P, Smith, Timothy P L, Blom, Jochen, Roberts, Richard J

“…We examined and compared both the methylomes and the modification-related gene content of four sequenced strains of Bibersteinia trehalosi isolated from the…”
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Characterization of RimO, a New Member of the Methylthiotransferase Subclass of the Radical SAM Superfamily by Lee, Kyung-Hoon, Saleh, Lana, Anton, Brian P, Madinger, Catherine L, Benner, Jack S, Iwig, David F, Roberts, Richard J, Krebs, Carsten, Booker, Squire J

“…RimO, encoded by the yliG gene in Escherichia coli, has been recently identified in vivo as the enzyme responsible for the attachment of a methylthio group on…”
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Genomic Analysis of Haloarchaea from Diverse Environments, including Permian Halite, Reveals Diversity of Ultraviolet Radiation Survival and DNA Photolyase Gene Variants by Nag, Sagorika, DasSarma, Priya, Crowley, David J, Hamawi, Rafael, Tepper, Samantha, Anton, Brian P, Guzmán, Daniel, DasSarma, Shiladitya

“…Ultraviolet (UV) radiation responses of extremophilic and archaeal microorganisms are of interest from evolutionary, physiological, and astrobiological…”
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Beyond Restriction Modification: Epigenomic Roles of DNA Methylation in Prokaryotes by Anton, Brian P, Roberts, Richard J

“…The amount of bacterial and archaeal genome sequence and methylome data has greatly increased over the last decade, enabling new insights into the functional…”
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Functional characterization of the YmcB and YqeV tRNA methylthiotransferases of Bacillus subtilis by Anton, Brian P, Russell, Susan P, Vertrees, Jason, Kasif, Simon, Raleigh, Elisabeth A, Limbach, Patrick A, Roberts, Richard J

“…Methylthiotransferases (MTTases) are a closely related family of proteins that perform both radical-S-adenosylmethionine (SAM) mediated sulfur insertion and…”
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Objective: biochemical function by Anton, Brian P, Kasif, Simon, Roberts, Richard J, Steffen, Martin

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Thousands of missed genes found in bacterial genomes and their analysis with COMBREX by Wood, Derrick E, Lin, Henry, Levy-Moonshine, Ami, Swaminathan, Rajiswari, Chang, Yi-Chien, Anton, Brian P, Osmani, Lais, Steffen, Martin, Kasif, Simon, Salzberg, Steven L

“…The dramatic reduction in the cost of sequencing has allowed many researchers to join in the effort of sequencing and annotating prokaryotic genomes…”
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effect of carbon source on the secretome of Kluyveromyces lactis by Madinger, Catherine L, Sharma, Shamik S, Anton, Brian P, Fields, Lauren G, Cushing, Michelle L, Canovas, Julie, Taron, Christopher H, Benner, Jack S

“…A proteomic analysis was performed on spent fermentation medium following bioreactor propagation of a wild-type industrial strain to identify proteins…”
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The methylomes of six bacteria by Murray, Iain A, Clark, Tyson A, Morgan, Richard D, Boitano, Matthew, Anton, Brian P, Luong, Khai, Fomenkov, Alexey, Turner, Stephen W, Korlach, Jonas, Roberts, Richard J

“…Six bacterial genomes, Geobacter metallireducens GS-15, Chromohalobacter salexigens, Vibrio breoganii 1C-10, Bacillus cereus ATCC 10987, Campylobacter jejuni…”
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COMBREX-DB: an experiment centered database of protein function: knowledge, predictions and knowledge gaps by Chang, Yi-Chien, Hu, Zhenjun, Rachlin, John, Anton, Brian P, Kasif, Simon, Roberts, Richard J, Steffen, Martin

“…The COMBREX database (COMBREX-DB; combrex.bu.edu) is an online repository of information related to (i) experimentally determined protein function, (ii)…”
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