DIYA: a bacterial annotation pipeline for any genomics lab (2009)
Stewart, Andrew C., Osborne, Brian, Read, Timothy D.
Summary:DIYA (Do-It-Yourself Annotator) is a modular and configurable open source pipeline software, written in Perl, used for the rapid annotation of bacterial genome sequences. The software is...
Scaffolding and validation of bacterial genome assemblies using optical restriction maps (2008)
Nagarajan, Niranjan, Read, Timothy D., Pop, Mihai
Motivation: New, high-throughput sequencing technologies have made it feasible to cheaply generate vast amounts of sequence information from a genome of interest. The computational reconstruction of...
Sozhamannan, Shanmuga, Chute, Michael D, McAfee, Farrell D, Fouts, Derrick E, Akmal, Arya, Galloway, Darrell R, ...
Abstract Background Bacillus anthracis is considered to be a recently emerged clone within the Bacillus cereus sensu lato group. The B. anthracis genome sequence contains four putative lambdoid...
Shuffling bacterial metabolomes (2006)
Thomason, Brendan, Read, Timothy D
Abstract Horizontal gene transfer (HGT) has a far more significant role than gene duplication in bacterial evolution. This has recently been illustrated by work demonstrating the importance of HGT in...
Microarray-based resequencing of multiple Bacillus anthracisisolates (2004)
Zwick, Michael E, Mcafee, Farrell, Cutler, David J, Read, Timothy D, Ravel, Jacques, Bowman, Gregory R, ...
Abstract We used custom-designed resequencing arrays to generate 3.1 Mb of genomic sequence from a panel of 56 Bacillus anthracis strains. Sequence quality was shown to be very high by replication...
Rasko, David A., Ravel, Jacques, Økstad, Ole Andreas, Helgason, Erlendur, Cer, Regina Z., Jiang, Lingxia, ...
We sequenced the complete genome of Bacillus cereus ATCC 10987, a non‐lethal dairy isolate in the same genetic subgroup as Bacillus anthracis. Comparison of the chromosomes demonstrated that...
Microbial genome jambalaya (2003)
A report on the third American Society of Microbiology (ASM) and The Institute for Genomic Research (TIGR) Microbial Genomes Conference, New Orleans, USA, 29 January to I February 2003.
Read, Timothy D., Satola, Sarah W., Farley, Monica M.
Haemophilus influenzae pili are surface structures that promote attachment to human epithelial cells. The five genes that encode pili, hifABCDE, are found inserted in genomes either between pmbA and...
Copy Number of Pilus Gene Clusters in Haemophilus influenzae and Variation in the hifE Pilin Gene
Read, Timothy D., Satola, Sarah W., Opdyke, Jason A., Farley, Monica M.
Brazilian purpuric fever (BPF)-associated Haemophilus influenzae biogroup aegyptius strain F3031 contains two identical copies of a five gene cluster (hifA to hifE) encoding pili similar to...
Tettelin, Hervé, Masignani, Vega, Cieslewicz, Michael J., Eisen, Jonathan A., Peterson, Scott, Wessels, Michael R., ...
The 2,160,267 bp genome sequence of Streptococcus agalactiae, the leading cause of bacterial sepsis, pneumonia, and meningitis in neonates in the U.S. and Europe, is predicted to encode 2,175 genes....
Paulsen, Ian T., Seshadri, Rekha, Nelson, Karen E., Eisen, Jonathan A., Heidelberg, John F., Read, Timothy D., ...
The 3.31-Mb genome sequence of the intracellular pathogen and potential bioterrorism agent, Brucella suis, was determined. Comparison of B. suis with Brucella melitensis has defined a finite set of...
Weiner, Matthew A., Read, Timothy D., Hanna, Philip C.
We identified a tri-cistronic operon, gerH, in Bacillus anthracis that is important for endospore germination triggered by two distinct germination response pathways termed inosine-His and...
Molecular Analysis of the Multiple GroEL Proteins of Chlamydiae
Karunakaran, Karuna P., Noguchi, Yasuyuki, Read, Timothy D., Cherkasov, Artem, Kwee, Jeffrey, Shen, Caixia, ...
Genome sequencing revealed that all six chlamydiae genomes contain three groEL-like genes (groEL1, groEL2, and groEL3). Phylogenetic analysis of groEL1, groEL2, and groEL3 indicates that these genes...
Complete genome sequence of the Q-fever pathogen Coxiella burnetii
Seshadri, Rekha, Paulsen, Ian T., Eisen, Jonathan A., Read, Timothy D., Nelson, Karen E., Nelson, William C., ...
The 1,995,275-bp genome of Coxiella burnetii, Nine Mile phase I RSA493, a highly virulent zoonotic pathogen and category B bioterrorism agent, was sequenced by the random shotgun method. This...
A report on the third American Society of Microbiology (ASM) and The Institute for Genomic Research (TIGR) Microbial Genomes Conference, New Orleans, USA, 29 January to 1 February 2003.
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...
Rasko, David A., Ravel, Jacques, Økstad, Ole Andreas, Helgason, Erlendur, Cer, Regina Z., Jiang, Lingxia, ...
We sequenced the complete genome of Bacillus cereus ATCC 10987, a non-lethal dairy isolate in the same genetic subgroup as Bacillus anthracis. Comparison of the chromosomes demonstrated that B.cereus...
Horizontal Transfer of CS1 Pilin Genes of Enterotoxigenic Escherichia coli
Froehlich, Barbara, Holtzapple, Erik, Read, Timothy D., Scott, June R.
CS1 is one of a limited number of serologically distinct pili found in enterotoxigenic Escherichia coli (ETEC) strains associated with disease in people. The genes for the CS1 pilus are on a large...
Hoffmaster, Alex R., Ravel, Jacques, Rasko, David A., Chapman, Gail D., Chute, Michael D., Marston, Chung K., ...
Bacillus anthracis is the etiologic agent of anthrax, an acute fatal disease among mammals. It was thought to differ from Bacillus cereus, an opportunistic pathogen and cause of food poisoning, by...
Pearson, Talima, Busch, Joseph D., Ravel, Jacques, Read, Timothy D., Rhoton, Shane D., U'Ren, Jana M., ...
Phylogenetic reconstruction using molecular data is often subject to homoplasy, leading to inaccurate conclusions about phylogenetic relationships among operational taxonomic units. Compared with...
Økstad, Ole Andreas, Tourasse, Nicolas J., Stabell, Fredrik B., Sundfær, Cathrine K., Egge-Jacobsen, Wolfgang, Risøen, Per Arne, ...
Bacillus cereus strains ATCC 10987 and ATCC 14579 harbor a ∼155-bp repeated element, bcr1, which is conserved in B. cereus, B. anthracis, B. thuringiensis, and B. mycoides but not in B. subtilis...
Microarray-based resequencing of multiple Bacillus anthracis isolates
Zwick, Michael E, Mcafee, Farrell, Cutler, David J, Read, Timothy D, Ravel, Jacques, Bowman, Gregory R, ...
Custom-designed resequencing arrays were used to generate 3.1 Mb of genomic sequence from a panel of 56 Bacillus anthracis strains. Sequence quality was shown to be very high by replication and by...
Shuffling bacterial metabolomes
Thomason, Brendan, Read, Timothy D
Horizontal gene transfer (HGT) is more important than gene duplication in bacterial evolution, as has recently been illustrated by work demonstrating the role of HGT in the emergence of bacterial...
Sequencing Bacillus anthracis Typing Phages Gamma and Cherry Reveals a Common Ancestry
Fouts, Derrick E., Rasko, David A., Cer, Regina Z., Jiang, Lingxia, Fedorova, Nadia B., Shvartsbeyn, Alla, ...
The genetic relatedness of the Bacillus anthracis typing phages Gamma and Cherry was determined by nucleotide sequencing and comparative analysis. The genomes of these two phages were identical...
The Bacillus anthracis chromosome contains four conserved, excision-proficient, putative prophages
Sozhamannan, Shanmuga, Chute, Michael D, McAfee, Farrell D, Fouts, Derrick E, Akmal, Arya, Galloway, Darrell R, ...
Read, Timothy D., Satola, Sarah W., Farley, Monica M.
Haemophilus influenzae pili are surface structures that promote attachment to human epithelial cells. The five genes that encode pili, hifABCDE, are found inserted in genomes either between pmbA and...
Copy Number of Pilus Gene Clusters in Haemophilus influenzae and Variation in the hifE Pilin Gene
Read, Timothy D., Satola, Sarah W., Opdyke, Jason A., Farley, Monica M.
Brazilian purpuric fever (BPF)-associated Haemophilus influenzae biogroup aegyptius strain F3031 contains two identical copies of a five gene cluster (hifA to hifE) encoding pili similar to...
Tettelin, Hervé, Masignani, Vega, Cieslewicz, Michael J., Eisen, Jonathan A., Peterson, Scott, Wessels, Michael R., ...
The 2,160,267 bp genome sequence of Streptococcus agalactiae, the leading cause of bacterial sepsis, pneumonia, and meningitis in neonates in the U.S. and Europe, is predicted to encode 2,175 genes....
Paulsen, Ian T., Seshadri, Rekha, Nelson, Karen E., Eisen, Jonathan A., Heidelberg, John F., Read, Timothy D., ...
The 3.31-Mb genome sequence of the intracellular pathogen and potential bioterrorism agent, Brucella suis, was determined. Comparison of B. suis with Brucella melitensis has defined a finite set of...
Weiner, Matthew A., Read, Timothy D., Hanna, Philip C.
We identified a tri-cistronic operon, gerH, in Bacillus anthracis that is important for endospore germination triggered by two distinct germination response pathways termed inosine-His and...
Molecular Analysis of the Multiple GroEL Proteins of Chlamydiae
Karunakaran, Karuna P., Noguchi, Yasuyuki, Read, Timothy D., Cherkasov, Artem, Kwee, Jeffrey, Shen, Caixia, ...
Genome sequencing revealed that all six chlamydiae genomes contain three groEL-like genes (groEL1, groEL2, and groEL3). Phylogenetic analysis of groEL1, groEL2, and groEL3 indicates that these genes...
Complete genome sequence of the Q-fever pathogen Coxiella burnetii
Seshadri, Rekha, Paulsen, Ian T., Eisen, Jonathan A., Read, Timothy D., Nelson, Karen E., Nelson, William C., ...
The 1,995,275-bp genome of Coxiella burnetii, Nine Mile phase I RSA493, a highly virulent zoonotic pathogen and category B bioterrorism agent, was sequenced by the random shotgun method. This...
A report on the third American Society of Microbiology (ASM) and The Institute for Genomic Research (TIGR) Microbial Genomes Conference, New Orleans, USA, 29 January to 1 February 2003.
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...
Rasko, David A., Ravel, Jacques, Økstad, Ole Andreas, Helgason, Erlendur, Cer, Regina Z., Jiang, Lingxia, ...
We sequenced the complete genome of Bacillus cereus ATCC 10987, a non-lethal dairy isolate in the same genetic subgroup as Bacillus anthracis. Comparison of the chromosomes demonstrated that B.cereus...
Horizontal Transfer of CS1 Pilin Genes of Enterotoxigenic Escherichia coli
Froehlich, Barbara, Holtzapple, Erik, Read, Timothy D., Scott, June R.
CS1 is one of a limited number of serologically distinct pili found in enterotoxigenic Escherichia coli (ETEC) strains associated with disease in people. The genes for the CS1 pilus are on a large...
Hoffmaster, Alex R., Ravel, Jacques, Rasko, David A., Chapman, Gail D., Chute, Michael D., Marston, Chung K., ...
Bacillus anthracis is the etiologic agent of anthrax, an acute fatal disease among mammals. It was thought to differ from Bacillus cereus, an opportunistic pathogen and cause of food poisoning, by...
Pearson, Talima, Busch, Joseph D., Ravel, Jacques, Read, Timothy D., Rhoton, Shane D., U'Ren, Jana M., ...
Phylogenetic reconstruction using molecular data is often subject to homoplasy, leading to inaccurate conclusions about phylogenetic relationships among operational taxonomic units. Compared with...
Økstad, Ole Andreas, Tourasse, Nicolas J., Stabell, Fredrik B., Sundfær, Cathrine K., Egge-Jacobsen, Wolfgang, Risøen, Per Arne, ...
Bacillus cereus strains ATCC 10987 and ATCC 14579 harbor a ∼155-bp repeated element, bcr1, which is conserved in B. cereus, B. anthracis, B. thuringiensis, and B. mycoides but not in B. subtilis...
Microarray-based resequencing of multiple Bacillus anthracis isolates
Zwick, Michael E, Mcafee, Farrell, Cutler, David J, Read, Timothy D, Ravel, Jacques, Bowman, Gregory R, ...
Custom-designed resequencing arrays were used to generate 3.1 Mb of genomic sequence from a panel of 56 Bacillus anthracis strains. Sequence quality was shown to be very high by replication and by...
Shuffling bacterial metabolomes
Thomason, Brendan, Read, Timothy D
Horizontal gene transfer (HGT) is more important than gene duplication in bacterial evolution, as has recently been illustrated by work demonstrating the role of HGT in the emergence of bacterial...
Sequencing Bacillus anthracis Typing Phages Gamma and Cherry Reveals a Common Ancestry
Fouts, Derrick E., Rasko, David A., Cer, Regina Z., Jiang, Lingxia, Fedorova, Nadia B., Shvartsbeyn, Alla, ...
The genetic relatedness of the Bacillus anthracis typing phages Gamma and Cherry was determined by nucleotide sequencing and comparative analysis. The genomes of these two phages were identical...
The Bacillus anthracis chromosome contains four conserved, excision-proficient, putative prophages
Sozhamannan, Shanmuga, Chute, Michael D, McAfee, Farrell D, Fouts, Derrick E, Akmal, Arya, Galloway, Darrell R, ...
Genomic Plasticity of the rrn-nqrF Intergenic Segment in the Chlamydiaceae▿
Liu, Zhi, Rank, Roger, Kaltenboeck, Bernhard, Magnino, Simone, Dean, Deborah, Burall, Laurel, ...
In Chlamydiaceae, the nucleotide sequence between the 5S rRNA gene and the gene for subunit F of the Na+-translocating NADH-quinone reductase (nqrF or dmpP) has varied lengths and gene contents. We...
Scaffolding and validation of bacterial genome assemblies using optical restriction maps
Nagarajan, Niranjan, Read, Timothy D., Pop, Mihai
Motivation: New, high-throughput sequencing technologies have made it feasible to cheaply generate vast amounts of sequence information from a genome of interest. The computational reconstruction of...
Genotyping of Bacillus cereus Strains by Microarray-Based Resequencing
Zwick, Michael E., Kiley, Maureen P., Stewart, Andrew C., Mateczun, Alfred, Read, Timothy D.
The ability to distinguish microbial pathogens from closely related but nonpathogenic strains is key to understanding the population biology of these organisms. In this regard, Bacillus anthracis,...
Sozhamannan, Shanmuga, McKinstry, Michael, Lentz, Shannon M., Jalasvuori, Matti, McAfee, Farrell, Smith, Angela, ...
The genome sequence of a Bacillus anthracis-specific clear plaque mutant phage, AP50c, contains 31 open reading frames spanning 14,398 bp, has two mutations compared to wild-type AP50t, and has a...
Poly, Frédéric, Read, Timothy D., Chen, Yu-Han, Monteiro, Mario A., Serichantalergs, Oralak, Pootong, Piyarat, ...
The development of vaccines against Campylobacter jejuni would be facilitated by the ability to perform phase II challenge studies. However, molecular mimicry of the lipooligosaccharide (LOS) of most...
DIYA: a bacterial annotation pipeline for any genomics lab
Stewart, Andrew C., Osborne, Brian, Read, Timothy D.
Summary:DIYA (Do-It-Yourself Annotator) is a modular and configurable open source pipeline software, written in Perl, used for the rapid annotation of bacterial genome sequences. The software is...
The Complete Genome Sequence of Bacillus anthracis Ames “Ancestor”▿
Ravel, Jacques, Jiang, Lingxia, Stanley, Scott T., Wilson, Mark R., Decker, R. Scott, Read, Timothy D., ...
The pathogenic bacterium Bacillus anthracis has become the subject of intense study as a result of its use in a bioterrorism attack in the United States in September and October 2001. Previous...