
Andrew StewartJohns Hopkins University | JHU · Whiting School of Engineering
Andrew Stewart
Master of Science
About
40
Publications
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431
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Introduction
Education
September 2011 - June 2015
September 2001 - June 2006
Publications
Publications (40)
Thyroid carcinomas are known to harbor oncogenic driver mutations and advances in sequencing technology now allow the detection of these in fine needle aspiration biopsies (FNA). Recent work by The Cancer Genome Atlas (TCGA) Research Network has expanded the number of genetic alterations detected in papillary thyroid carcinomas (PTC). We sought to...
The key genes required for Bacillus anthracis to cause anthrax have been acquired recently by horizontal gene transfer. To understand the genetic background for the evolution of B. anthracis virulence, we obtained high-redundancy genome sequences of 45 strains of the Bacillus cereus sensu lato (s.l.) species that were chosen for their genetic diver...
Location of true positive variants in the genome of the parent strains compared to the reference genomes.
(0.09 MB DOC)
Background:
The anthrax letter attacks of 2001 highlighted the need for rapid identification of biothreat agents not only for epidemiological surveillance of the intentional outbreak but also for implementing appropriate countermeasures, such as antibiotic treatment, in a timely manner to prevent further casualties. It is clear from the 2001 cases...
Results of amosvalidate [37] analysis on the eight genomes of this study.
Y. pestis CO92 signatures longer than 100 bp computed by the Insignia [44] pipeline.
Y. enterocolitica signatures longer than 100 bp computed by the Insignia pipeline.
An E. coli strain with known plasmids was a positive control.
Sequences of the new genomes that match (that is, invalidate) the Y. enterocolitica signatures.
Y. pestis genome with the Insiginia-indentified repeats and genome islands identified using IslandViewer [45] plotted. The figure was created using DNAPlotter [106].
The eight genomes sequenced in this study are represented as pseudocontigs, ordered by a combination of optical mapping and alignment to the closest completed reference genome.
Whole genome multiple alignment produced by MAUVE of the 11 Yersinia genomes in XMFA format [106].
Estimates for genome sizes (in Mbp) based on optical map data.
Sequences of the detected repeat families.
Statistics from running DIYA [89] and frameshift detection programs on the eight genomes sequenced in this study and various other enterobacterial genomes downloaded from NCBI.
These consist of ISfinder [40], RepeatScout [41]and amosvalidate [37] results (GFF format); repeats found by RepeatScout in fasta format, scaffold files (NCBI AGP format); and information about length of contigs, read count, estimated repeat number, count in scaffold and whether or not the contig was placed by SOMA [39].
Sequences of the new genomes that match (that is, invalidate) the Y. pestis CO92 signatures listed in Additional file 7.
The top level directory consists of a directory called Additional_cluster_files and 5010 directories, one for each multi-protein cluster family. (This top level directory has been split into three data files for uploading purposes (Additional files 15, 16, 17.) Within the directory are the following files: PGL1_unique_Yersinia_unclustered.out - lis...
Complete protein sets for the 11 species of Yersinia.
Putative antibiotic resistance genes in the Yersinia genus determined using the Antibiotic Resistance Genes Database [45].
Y. enterocolitica genome with the Insiginia-indentified repeats and genome islands identified using IslandViewer [45] plotted. The figure was created using DNAPlotter [106].
The top level directory consists of a directory called Additional_cluster_files and 5010 directories, one for each multi-protein cluster family. (This top level directory has been split into three data files for uploading purposes (Additional files 15, 16, 17.) Within the directory are the following files: PGL1_unique_Yersinia_unclustered.out - lis...
Phylogeny of TTSS component YscN in Yersinia and other enterobacteria species.
The top level directory consists of a directory called Additional_cluster_files and 5010 directories, one for each multi-protein cluster family. (This top level directory has been split into three data files for uploading purposes (Additional files 15, 16, 17).) Within the directory are the following files: PGL1_unique_Yersinia_unclustered.out - li...
To evaluate node support, a majority rule-consensus tree of 1,000 bootstrap replicates was computed. E. coli was used as an outgroup species.
To evaluate node support, a majority rule-consensus tree of 1,000 bootstrap replicates was computed. E. coli was used as an outgroup species.
A curve showing the rate of decline in number of this set as more non-pathogen genomes are added is also included.
Calculations for the estimation of Π from aligned Yersinia core genomes.
New DNA sequencing technologies have enabled detailed comparative genomic analyses of entire genera of bacterial pathogens. Prior to this study, three species of the enterobacterial genus Yersinia that cause invasive human diseases (Yersinia pestis, Yersinia pseudotuberculosis, and Yersinia enterocolitica) had been sequenced. However, there were no...
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 currently used to take DNA contigs as input, either in the form of complete genomes or the result of shotgun sequencing, and produce an annotated sequence in Genba...
We sought to identify proteins in the Bacillus anthracis spore, conserved in other strains of the closely related Bacillus cereus group, that elicit an immune response in mammals. Two high throughput approaches were used. First, an in silico screening identified 200 conserved putative B. anthracis spore components. A total of 192 of those candidate...
BDRD-01 resequencing array (RA) reference sequence information.
(0.02 MB PDF)
Reference genomic sequence used to design the BDRD-01 resequencing array (RA).
(0.03 MB PDF)
Phylogenetic tree inferred for 36-strains with MLST data. Neighbor-joining phylogenetic tree inferred using multilocus sequence typing (MLST) data for a subsample of 36 B. cereus strains. Bootstrap values for nodes with greater than 99% support (1000 replicates total) are shown.
(0.97 MB TIF)
B. anthracis strains resequenced in Zwick, M. E. et al. (2005)
(0.06 MB PDF)
Phylogenetic tree inferred for 36-strains with RA data. Neighbor-joining phylogenetic tree inferred using resequencing array (RA) data with a quality score threshold of 30 for a subsample of 36 B. cereus strains. Bootstrap values for nodes with greater than 99% support (1000 replicates total) are shown. The purple box marks a clade of Bacillus stra...
Proportion bases called (QS 30) for each B. anthracis molecule
(0.04 MB PDF)
Bacillus resequencing results.
(0.05 MB PDF)
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, the bacterium that causes inhalational anthrax, is of interest because it is closely related and often difficult to distinguish from other members of the...