Ondov, Brian D., Varadarajan, Anjana, Passalacqua, Karla D., Bergman, Nicholas H.
Summary: Here, we report the development of SOCS (short oligonucleotide color space), a program designed for efficient and flexible mapping of Applied Biosystems SOLiD sequence data onto a reference...
Operon Prediction for Sequenced Bacterial Genomes without Experimental Information � † (2006)
Nicholas H. Bergman, Karla D. Passalacqua, Philip C. Hanna, Zhaohui S. Qin
Various computational approaches have been proposed for operon prediction, but most algorithms rely on experimental or functional data that are only available for a small subset of sequenced genomes....
Nicholas H. Bergman, Karla D. Passalacqua, Philip C. Hanna, Zhaohui S. Qin, Nicholas H. Bergman, Ph. D
Various computational approaches have been proposed for operon prediction, but most algorithms rely on experimental or functional data that are only available for a small subset of sequenced genomes....
The three-dimensional architecture of the class I ligase ribozyme (2004)
BERGMAN, NICHOLAS H., LAU, NELSON C., LEHNERT, VALERIE, WESTHOF, ERIC, BARTEL, DAVID P.
The class I ligase ribozyme catalyzes a Mg++-dependent RNA-ligation reaction that is chemically analogous to a single step of RNA polymerization. Indeed, this ribozyme constitutes the catalytic...
Bergman, Nicholas H., Akerley, Brian J.
Bacteria exhibit extensive genetic heterogeneity within species. In many cases, these differences account for virulence properties unique to specific strains. Several such loci have been discovered...
Formation and Composition of the Bacillus anthracis Endospore†
Liu, Hongbin, Bergman, Nicholas H., Thomason, Brendan, Shallom, Shamira, Hazen, Alyson, Crossno, Joseph, ...
The endospores of Bacillus anthracis are the infectious particles of anthrax. Spores are dormant bacterial morphotypes able to withstand harsh environments for decades, which contributes to their...
Murine Macrophage Transcriptional Responses to Bacillus anthracis Infection and Intoxication
Bergman, Nicholas H., Passalacqua, Karla D., Gaspard, Renee, Shetron-Rama, Lynne M., Quackenbush, John, Hanna, Philip C.
Interactions between Bacillus anthracis and host macrophages represent critical early events in anthrax pathogenesis, but their details are not clearly understood. Here we report the first genomewide...
The three-dimensional architecture of the class I ligase ribozyme
BERGMAN, NICHOLAS H., LAU, NELSON C., LEHNERT, VALERIE, WESTHOF, ERIC, BARTEL, DAVID P.
The class I ligase ribozyme catalyzes a Mg++-dependent RNA-ligation reaction that is chemically analogous to a single step of RNA polymerization. Indeed, this ribozyme constitutes the catalytic...
Passalacqua, Karla D., Bergman, Nicholas H., Herring-Palmer, Amy, Hanna, Philip
The Bacillus anthracis chromosome encodes four unique, putative superoxide dismutase (sod) genes. During exponential growth and sporulation, sodA1, sodA2, and sodC are transcribed constitutively...
Bergman, Nicholas H., Akerley, Brian J.
Bacteria exhibit extensive genetic heterogeneity within species. In many cases, these differences account for virulence properties unique to specific strains. Several such loci have been discovered...
Formation and Composition of the Bacillus anthracis Endospore†
Liu, Hongbin, Bergman, Nicholas H., Thomason, Brendan, Shallom, Shamira, Hazen, Alyson, Crossno, Joseph, ...
The endospores of Bacillus anthracis are the infectious particles of anthrax. Spores are dormant bacterial morphotypes able to withstand harsh environments for decades, which contributes to their...
Murine Macrophage Transcriptional Responses to Bacillus anthracis Infection and Intoxication
Bergman, Nicholas H., Passalacqua, Karla D., Gaspard, Renee, Shetron-Rama, Lynne M., Quackenbush, John, Hanna, Philip C.
Interactions between Bacillus anthracis and host macrophages represent critical early events in anthrax pathogenesis, but their details are not clearly understood. Here we report the first genomewide...
The three-dimensional architecture of the class I ligase ribozyme
BERGMAN, NICHOLAS H., LAU, NELSON C., LEHNERT, VALERIE, WESTHOF, ERIC, BARTEL, DAVID P.
The class I ligase ribozyme catalyzes a Mg++-dependent RNA-ligation reaction that is chemically analogous to a single step of RNA polymerization. Indeed, this ribozyme constitutes the catalytic...
Passalacqua, Karla D., Bergman, Nicholas H., Herring-Palmer, Amy, Hanna, Philip
The Bacillus anthracis chromosome encodes four unique, putative superoxide dismutase (sod) genes. During exponential growth and sporulation, sodA1, sodA2, and sodC are transcribed constitutively...
Bergman, Nicholas H., Anderson, Erica C., Swenson, Ellen E., Niemeyer, Matthew M., Miyoshi, Amy D., Hanna, Philip C.
The life cycle of Bacillus anthracis includes both vegetative and endospore morphologies which alternate based on nutrient availability, and there is considerable evidence indicating that the ability...
Operon Prediction for Sequenced Bacterial Genomes without Experimental Information▿ †
Bergman, Nicholas H., Passalacqua, Karla D., Hanna, Philip C., Qin, Zhaohui S.
Various computational approaches have been proposed for operon prediction, but most algorithms rely on experimental or functional data that are only available for a small subset of sequenced genomes....
Biosynthetic Analysis of the Petrobactin Siderophore Pathway from Bacillus anthracis▿
Lee, Jung Yeop, Janes, Brian K., Passalacqua, Karla D., Pfleger, Brian F., Bergman, Nicholas H., Liu, Haichuan, ...
The asbABCDEF gene cluster from Bacillus anthracis is responsible for biosynthesis of petrobactin, a catecholate siderophore that functions in both iron acquisition and virulence in a murine model of...
Passalacqua, Karla D., Bergman, Nicholas H., Lee, Jung Yeop, Sherman, David H., Hanna, Philip C.
Microarray analyses were conducted to evaluate the paraquat-induced global transcriptional response of Bacillus anthracis Sterne (34F2) to varying levels of endogenous superoxide stress. Data...
Transcriptional Profiling of Bacillus anthracis during Infection of Host Macrophages▿ †
Bergman, Nicholas H., Anderson, Erica C., Swenson, Ellen E., Janes, Brian K., Fisher, Nathan, Niemeyer, Matthew M., ...
The interaction between Bacillus anthracis and the mammalian phagocyte is one of the central stages in the progression of inhalational anthrax, and it is commonly believed that the host cell plays a...
Ondov, Brian D., Varadarajan, Anjana, Passalacqua, Karla D., Bergman, Nicholas H.
Summary: Here, we report the development of SOCS (short oligonucleotide color space), a program designed for efficient and flexible mapping of Applied Biosystems SOLiD sequence data onto a reference...
Pfleger, Brian F., Kim, Youngchang, Nusca, Tyler D., Maltseva, Natalia, Lee, Jung Yeop, Rath, Christopher M., ...
Petrobactin, a virulence-associated siderophore produced by Bacillus anthracis, chelates ferric iron through the rare 3,4-isomer of dihydroxybenzoic acid (3,4-DHBA). Most catechol siderophores,...
Structure and Complexity of a Bacterial Transcriptome▿ †
Passalacqua, Karla D., Varadarajan, Anjana, Ondov, Brian D., Okou, David T., Zwick, Michael E., Bergman, Nicholas H.
Although gene expression has been studied in bacteria for decades, many aspects of the bacterial transcriptome remain poorly understood. Transcript structure, operon linkages, and information on...