Datasets:
vgainullin
/
xciting_data

Dataset card Data Studio Files
xet
 Community
1
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3
INTRODUCTION
1
10
[ "B10", "B5", "B11 B12 B13", "B14", "B15", "B16" ]
17,392,345
pmid-11248028|pmid-11101533|pmid-12457560|pmid-15340139|pmid-15564671|pmid-11593008|pmid-12677067|NA
This location makes a concomitant binding of S1 to the stalled ribosome and to tmRNA during initial loading very unlikely.
[ "10", "5", "11–13", "14", "15", "16" ]
122
8,300
0
false
This location makes a concomitant binding of S1 to the stalled ribosome and to tmRNA during initial loading very unlikely.
[]
This location makes a concomitant binding of S1 to the stalled ribosome and to tmRNA during initial loading very unlikely.
true
true
true
true
true
1,341
3
INTRODUCTION
1
10
[ "B10", "B5", "B11 B12 B13", "B14", "B15", "B16" ]
17,392,345
pmid-11248028|pmid-11101533|pmid-12457560|pmid-15340139|pmid-15564671|pmid-11593008|pmid-12677067|NA
Moreover, recent cryo-EM data indicate that tmRNA enters stalled ribosomes in the absence of S1 (15,16), arguing for a role of S1 in trans-translation in solution and not when bound to the ribosomes.
[ "10", "5", "11–13", "14", "15", "16" ]
199
8,301
0
false
Moreover, recent cryo-EM data indicate that tmRNA enters stalled ribosomes in the absence of S1, arguing for a role of S1 in trans-translation in solution and not when bound to the ribosomes.
[ "15,16" ]
Moreover, recent cryo-EM data indicate that tmRNA enters stalled ribosomes in the absence of S1, arguing for a role of S1 in trans-translation in solution and not when bound to the ribosomes.
true
true
true
true
true
1,341
4
INTRODUCTION
1
17
[ "B17", "B18", "B19", "B20" ]
17,392,345
pmid-6212755|pmid-2120211|pmid-11479568|pmid-11453691
Protein S1 is essential for cell viability (17) and autoregulates its own synthesis (18), so that its concentration cannot be easily manipulated in vivo (see subsequently).
[ "17", "18", "19", "20" ]
172
8,302
1
false
Protein S1 is essential for cell viability and autoregulates its own synthesis, so that its concentration cannot be easily manipulated in vivo (see subsequently).
[ "17", "18" ]
Protein S1 is essential for cell viability and autoregulates its own synthesis, so that its concentration cannot be easily manipulated in vivo (see subsequently).
true
true
true
true
true
1,342
4
INTRODUCTION
1
17
[ "B17", "B18", "B19", "B20" ]
17,392,345
pmid-6212755|pmid-2120211|pmid-11479568|pmid-11453691
We therefore developed an in vitro method to assess precisely its role in trans-translation.
[ "17", "18", "19", "20" ]
92
8,303
0
false
We therefore developed an in vitro method to assess precisely its role in trans-translation.
[]
We therefore developed an in vitro method to assess precisely its role in trans-translation.
true
true
true
true
true
1,342
4
INTRODUCTION
1
19
[ "B17", "B18", "B19", "B20" ]
17,392,345
pmid-6212755|pmid-2120211|pmid-11479568|pmid-11453691
Assays were set up with purified recombinant proteins (19) and ribosomes depleted from protein S1 (20).
[ "17", "18", "19", "20" ]
103
8,304
1
false
Assays were set up with purified recombinant proteins and ribosomes depleted from protein S1.
[ "19", "20" ]
Assays were set up with purified recombinant proteins and ribosomes depleted from protein S1.
true
true
true
true
true
1,342
4
INTRODUCTION
1
17
[ "B17", "B18", "B19", "B20" ]
17,392,345
pmid-6212755|pmid-2120211|pmid-11479568|pmid-11453691
We took advantage of the fact that polyU genuinely lacks a termination codon, so that its translation in the presence of Phe-tRNAPhe yields stalled ribosomes, wherever translation initiates on the polyU RNAs.
[ "17", "18", "19", "20" ]
208
8,305
0
false
We took advantage of the fact that polyU genuinely lacks a termination codon, so that its translation in the presence of Phe-tRNAPhe yields stalled ribosomes, wherever translation initiates on the polyU RNAs.
[]
We took advantage of the fact that polyU genuinely lacks a termination codon, so that its translation in the presence of Phe-tRNAPhe yields stalled ribosomes, wherever translation initiates on the polyU RNAs.
true
true
true
true
true
1,342
4
INTRODUCTION
1
17
[ "B17", "B18", "B19", "B20" ]
17,392,345
pmid-6212755|pmid-2120211|pmid-11479568|pmid-11453691
We found that S1 is dispensable for the codon-independent transfer of the stalled nascent peptide chain to the alanine from alanylated-tmRNAAla but is required for the translation of tmRNA internal ORF.
[ "17", "18", "19", "20" ]
202
8,306
0
false
We found that S1 is dispensable for the codon-independent transfer of the stalled nascent peptide chain to the alanine from alanylated-tmRNAAla but is required for the translation of tmRNA internal ORF.
[]
We found that S1 is dispensable for the codon-independent transfer of the stalled nascent peptide chain to the alanine from alanylated-tmRNAAla but is required for the translation of tmRNA internal ORF.
true
true
true
true
true
1,342
4
INTRODUCTION
1
17
[ "B17", "B18", "B19", "B20" ]
17,392,345
pmid-6212755|pmid-2120211|pmid-11479568|pmid-11453691
The N-terminal domain of the protein that is required for ribosome binding is dispensable for trans-translation, indicating that the role of S1 during tmRNA-mediated protein tagging takes place outside from the ribosome, presumably when in complex with soluble tmRNA.
[ "17", "18", "19", "20" ]
267
8,307
0
false
The N-terminal domain of the protein that is required for ribosome binding is dispensable for trans-translation, indicating that the role of S1 during tmRNA-mediated protein tagging takes place outside from the ribosome, presumably when in complex with soluble tmRNA.
[]
The N-terminal domain of the protein that is required for ribosome binding is dispensable for trans-translation, indicating that the role of S1 during tmRNA-mediated protein tagging takes place outside from the ribosome, presumably when in complex with soluble tmRNA.
true
true
true
true
true
1,342
4
INTRODUCTION
1
17
[ "B17", "B18", "B19", "B20" ]
17,392,345
pmid-6212755|pmid-2120211|pmid-11479568|pmid-11453691
Also, tmRNA-mediated protein tagging is reduced in vivo when the expression levels of protein S1 are either reduced or increased, compared to wild-type cells.
[ "17", "18", "19", "20" ]
158
8,308
0
false
Also, tmRNA-mediated protein tagging is reduced in vivo when the expression levels of protein S1 are either reduced or increased, compared to wild-type cells.
[]
Also, tmRNA-mediated protein tagging is reduced in vivo when the expression levels of protein S1 are either reduced or increased, compared to wild-type cells.
true
true
true
true
true
1,342
4
INTRODUCTION
1
17
[ "B17", "B18", "B19", "B20" ]
17,392,345
pmid-6212755|pmid-2120211|pmid-11479568|pmid-11453691
Altogether, these results indicate that S1 plays an important role during trans-translation that is distinct from its documented role during protein synthesis.
[ "17", "18", "19", "20" ]
159
8,309
0
false
Altogether, these results indicate that S1 plays an important role during trans-translation that is distinct from its documented role during protein synthesis.
[]
Altogether, these results indicate that S1 plays an important role during trans-translation that is distinct from its documented role during protein synthesis.
true
true
true
true
true
1,342
0
INTRODUCTION
1
1
[ "b1", "b3", "b4" ]
17,012,284
pmid-8905084|pmid-15365022|pmid-12791858
For both surveillance and diagnostic applications, fine-scale pathogen identification and near-neighbor discrimination is important; therefore, an assay that monitors at this very specific level is desirable for many types of samples such as clinical and environmental (1–3).
[ "1", "3", "4" ]
275
8,310
0
false
For both surveillance and diagnostic applications, fine-scale pathogen identification and near-neighbor discrimination is important; therefore, an assay that monitors at this very specific level is desirable for many types of samples such as clinical and environmental.
[ "1–3" ]
For both surveillance and diagnostic applications, fine-scale pathogen identification and near-neighbor discrimination is important; therefore, an assay that monitors at this very specific level is desirable for many types of samples such as clinical and environmental.
true
true
true
true
true
1,343
0
INTRODUCTION
1
1
[ "b1", "b3", "b4" ]
17,012,284
pmid-8905084|pmid-15365022|pmid-12791858
To successfully use any method based on DNA or RNA detection, these assays must be coupled with large databases of nucleic acid sequence information for assay design to ensure that the desired information is provided and for the interpretation of raw data.
[ "1", "3", "4" ]
256
8,311
0
false
To successfully use any method based on DNA or RNA detection, these assays must be coupled with large databases of nucleic acid sequence information for assay design to ensure that the desired information is provided and for the interpretation of raw data.
[]
To successfully use any method based on DNA or RNA detection, these assays must be coupled with large databases of nucleic acid sequence information for assay design to ensure that the desired information is provided and for the interpretation of raw data.
true
true
true
true
true
1,343
0
INTRODUCTION
1
4
[ "b1", "b3", "b4" ]
17,012,284
pmid-8905084|pmid-15365022|pmid-12791858
Several well-established techniques use PCR to amplify individual target pieces of sequenced genomes to provide detection of organisms (4).
[ "1", "3", "4" ]
139
8,312
1
false
Several well-established techniques use PCR to amplify individual target pieces of sequenced genomes to provide detection of organisms.
[ "4" ]
Several well-established techniques use PCR to amplify individual target pieces of sequenced genomes to provide detection of organisms.
true
true
true
true
true
1,343
0
INTRODUCTION
1
1
[ "b1", "b3", "b4" ]
17,012,284
pmid-8905084|pmid-15365022|pmid-12791858
These methods can roughly be divided into approaches that target individual short sequence lengths or probes (<40 bp) and methods that examine longer probes.
[ "1", "3", "4" ]
157
8,313
0
false
These methods can roughly be divided into approaches that target individual short sequence lengths or probes and methods that examine longer probes.
[ "<40 bp" ]
These methods can roughly be divided into approaches that target individual short sequence lengths or probes and methods that examine longer probes.
true
true
true
true
true
1,343
0
INTRODUCTION
1
1
[ "b1", "b3", "b4" ]
17,012,284
pmid-8905084|pmid-15365022|pmid-12791858
The advantage of using short probes is that when the uniqueness of the probe has been assured and unique primers are also selected, this method gives good specificity.
[ "1", "3", "4" ]
167
8,314
0
false
The advantage of using short probes is that when the uniqueness of the probe has been assured and unique primers are also selected, this method gives good specificity.
[]
The advantage of using short probes is that when the uniqueness of the probe has been assured and unique primers are also selected, this method gives good specificity.
true
true
true
true
true
1,343
0
INTRODUCTION
1
1
[ "b1", "b3", "b4" ]
17,012,284
pmid-8905084|pmid-15365022|pmid-12791858
This approach is capable of providing fine-scale identification of several genetically close organisms by selecting a sufficient number of probes.
[ "1", "3", "4" ]
146
8,315
0
false
This approach is capable of providing fine-scale identification of several genetically close organisms by selecting a sufficient number of probes.
[]
This approach is capable of providing fine-scale identification of several genetically close organisms by selecting a sufficient number of probes.
true
true
true
true
true
1,343
0
INTRODUCTION
1
1
[ "b1", "b3", "b4" ]
17,012,284
pmid-8905084|pmid-15365022|pmid-12791858
However, this can rapidly lead to a very large number of total probes being required to detect all organisms of interest.
[ "1", "3", "4" ]
121
8,316
0
false
However, this can rapidly lead to a very large number of total probes being required to detect all organisms of interest.
[]
However, this can rapidly lead to a very large number of total probes being required to detect all organisms of interest.
true
true
true
true
true
1,343
0
INTRODUCTION
1
1
[ "b1", "b3", "b4" ]
17,012,284
pmid-8905084|pmid-15365022|pmid-12791858
In addition these selected probes, which in the initial selection process were determined to be unique, are often later found to be less specific as more organisms are sequenced or are less specific under conditions that differ from the original conditions.
[ "1", "3", "4" ]
257
8,317
0
false
In addition these selected probes, which in the initial selection process were determined to be unique, are often later found to be less specific as more organisms are sequenced or are less specific under conditions that differ from the original conditions.
[]
In addition these selected probes, which in the initial selection process were determined to be unique, are often later found to be less specific as more organisms are sequenced or are less specific under conditions that differ from the original conditions.
true
true
true
true
true
1,343
0
INTRODUCTION
1
1
[ "b1", "b3", "b4" ]
17,012,284
pmid-8905084|pmid-15365022|pmid-12791858
This is particularly a problem for organisms belonging to a family with a high mutation rate and also for pathogens that have relatively few neighboring pathogens sequenced.
[ "1", "3", "4" ]
173
8,318
0
false
This is particularly a problem for organisms belonging to a family with a high mutation rate and also for pathogens that have relatively few neighboring pathogens sequenced.
[]
This is particularly a problem for organisms belonging to a family with a high mutation rate and also for pathogens that have relatively few neighboring pathogens sequenced.
true
true
true
true
true
1,343
0
INTRODUCTION
1
1
[ "b1", "b3", "b4" ]
17,012,284
pmid-8905084|pmid-15365022|pmid-12791858
In addition, PCR approaches focused on short unique probes are not capable of detecting the presence of new significant mutations nor can they easily resolve base sequence details.
[ "1", "3", "4" ]
180
8,319
0
false
In addition, PCR approaches focused on short unique probes are not capable of detecting the presence of new significant mutations nor can they easily resolve base sequence details.
[]
In addition, PCR approaches focused on short unique probes are not capable of detecting the presence of new significant mutations nor can they easily resolve base sequence details.
true
true
true
true
true
1,343
0
INTRODUCTION
1
1
[ "b1", "b3", "b4" ]
17,012,284
pmid-8905084|pmid-15365022|pmid-12791858
Approaches that use longer individual probes avoid many of these issues at the cost of being less specific.
[ "1", "3", "4" ]
107
8,320
0
false
Approaches that use longer individual probes avoid many of these issues at the cost of being less specific.
[]
Approaches that use longer individual probes avoid many of these issues at the cost of being less specific.
true
true
true
true
true
1,343
0
INTRODUCTION
1
1
[ "b1", "b3", "b4" ]
17,012,284
pmid-8905084|pmid-15365022|pmid-12791858
This issue means most of these approaches are not suitable for providing the information desired, providing impetus to this work.
[ "1", "3", "4" ]
129
8,321
0
false
This issue means most of these approaches are not suitable for providing the information desired, providing impetus to this work.
[]
This issue means most of these approaches are not suitable for providing the information desired, providing impetus to this work.
true
true
true
true
true
1,343
1
INTRODUCTION
1
5
[ "b5", "b12", "b6", "b9", "b10", "b13", "b14", "b15", "b16", "b17", "b15", "b16" ]
17,012,284
pmid-11691856|pmid-15123581|pmid-9582189|pmid-12030762|pmid-11976131|pmid-14993206|pmid-16391044|pmid-16704813|pmid-16481660|pmid-2231712|pmid-16704813|pmid-16481660
High-density resequencing microarrays produce variable length segments, 102–105 bp, of direct sequence information.
[ "5", "12", "6", "9", "10", "13", "14", "15", "16", "17", "15", "16" ]
115
8,322
0
false
High-density resequencing microarrays produce variable length segments, 102–105 bp, of direct sequence information.
[]
High-density resequencing microarrays produce variable length segments, 102–105 bp, of direct sequence information.
true
true
true
true
true
1,344
1
INTRODUCTION
1
5
[ "b5", "b12", "b6", "b9", "b10", "b13", "b14", "b15", "b16", "b17", "b15", "b16" ]
17,012,284
pmid-11691856|pmid-15123581|pmid-9582189|pmid-12030762|pmid-11976131|pmid-14993206|pmid-16391044|pmid-16704813|pmid-16481660|pmid-2231712|pmid-16704813|pmid-16481660
This target sequence falls in the longer target regime of PCR approaches but rather than being hybridized to a longer less-specific probe on the microarray, many shorter specific probes are placed on the microarray to allow more detailed determinations from the entire PCR amplicon.
[ "5", "12", "6", "9", "10", "13", "14", "15", "16", "17", "15", "16" ]
282
8,323
0
false
This target sequence falls in the longer target regime of PCR approaches but rather than being hybridized to a longer less-specific probe on the microarray, many shorter specific probes are placed on the microarray to allow more detailed determinations from the entire PCR amplicon.
[]
This target sequence falls in the longer target regime of PCR approaches but rather than being hybridized to a longer less-specific probe on the microarray, many shorter specific probes are placed on the microarray to allow more detailed determinations from the entire PCR amplicon.
true
true
true
true
true
1,344
1
INTRODUCTION
1
5
[ "b5", "b12", "b6", "b9", "b10", "b13", "b14", "b15", "b16", "b17", "b15", "b16" ]
17,012,284
pmid-11691856|pmid-15123581|pmid-9582189|pmid-12030762|pmid-11976131|pmid-14993206|pmid-16391044|pmid-16704813|pmid-16481660|pmid-2231712|pmid-16704813|pmid-16481660
This also means that the specificity of the primers used can be relaxed.
[ "5", "12", "6", "9", "10", "13", "14", "15", "16", "17", "15", "16" ]
72
8,324
0
false
This also means that the specificity of the primers used can be relaxed.
[]
This also means that the specificity of the primers used can be relaxed.
true
true
true
true
true
1,344
1
INTRODUCTION
1
5
[ "b5", "b12", "b6", "b9", "b10", "b13", "b14", "b15", "b16", "b17", "b15", "b16" ]
17,012,284
pmid-11691856|pmid-15123581|pmid-9582189|pmid-12030762|pmid-11976131|pmid-14993206|pmid-16391044|pmid-16704813|pmid-16481660|pmid-2231712|pmid-16704813|pmid-16481660
They have been successfully used to detect single nucleotide polymorphism (SNP) and genetic variants from viral, bacterial and eukaryotic genomes (5–12).
[ "5", "12", "6", "9", "10", "13", "14", "15", "16", "17", "15", "16" ]
153
8,325
0
false
They have been successfully used to detect single nucleotide polymorphism (SNP) and genetic variants from viral, bacterial and eukaryotic genomes.
[ "5–12" ]
They have been successfully used to detect single nucleotide polymorphism (SNP) and genetic variants from viral, bacterial and eukaryotic genomes.
true
true
true
true
true
1,344
1
INTRODUCTION
1
5
[ "b5", "b12", "b6", "b9", "b10", "b13", "b14", "b15", "b16", "b17", "b15", "b16" ]
17,012,284
pmid-11691856|pmid-15123581|pmid-9582189|pmid-12030762|pmid-11976131|pmid-14993206|pmid-16391044|pmid-16704813|pmid-16481660|pmid-2231712|pmid-16704813|pmid-16481660
Their use for SNP detection has clearly established their ability to provide reliable quality sequence information.
[ "5", "12", "6", "9", "10", "13", "14", "15", "16", "17", "15", "16" ]
115
8,326
0
false
Their use for SNP detection has clearly established their ability to provide reliable quality sequence information.
[]
Their use for SNP detection has clearly established their ability to provide reliable quality sequence information.
true
true
true
true
true
1,344
1
INTRODUCTION
1
5
[ "b5", "b12", "b6", "b9", "b10", "b13", "b14", "b15", "b16", "b17", "b15", "b16" ]
17,012,284
pmid-11691856|pmid-15123581|pmid-9582189|pmid-12030762|pmid-11976131|pmid-14993206|pmid-16391044|pmid-16704813|pmid-16481660|pmid-2231712|pmid-16704813|pmid-16481660
In most cases, the microarrays were designed to study a limited number of genetically similar target pathogens and for many cases, the detection methods relied only on recognizing hybridization patterns for identification (6,9,10,13,14).
[ "5", "12", "6", "9", "10", "13", "14", "15", "16", "17", "15", "16" ]
237
8,327
0
false
In most cases, the microarrays were designed to study a limited number of genetically similar target pathogens and for many cases, the detection methods relied only on recognizing hybridization patterns for identification.
[ "6,9,10,13,14" ]
In most cases, the microarrays were designed to study a limited number of genetically similar target pathogens and for many cases, the detection methods relied only on recognizing hybridization patterns for identification.
true
true
true
true
true
1,344
1
INTRODUCTION
1
5
[ "b5", "b12", "b6", "b9", "b10", "b13", "b14", "b15", "b16", "b17", "b15", "b16" ]
17,012,284
pmid-11691856|pmid-15123581|pmid-9582189|pmid-12030762|pmid-11976131|pmid-14993206|pmid-16391044|pmid-16704813|pmid-16481660|pmid-2231712|pmid-16704813|pmid-16481660
Taking advantage of the sequential base resolution capability of resequencing microarrays that is required for SNP detection, resequencing has recently been successfully adapted recently using a different approach for organism identification of multiple bacterial and viral pathogens while allowing for fine detailed dis...
[ "5", "12", "6", "9", "10", "13", "14", "15", "16", "17", "15", "16" ]
421
8,328
0
false
Taking advantage of the sequential base resolution capability of resequencing microarrays that is required for SNP detection, resequencing has recently been successfully adapted recently using a different approach for organism identification of multiple bacterial and viral pathogens while allowing for fine detailed dis...
[ "15–16" ]
Taking advantage of the sequential base resolution capability of resequencing microarrays that is required for SNP detection, resequencing has recently been successfully adapted recently using a different approach for organism identification of multiple bacterial and viral pathogens while allowing for fine detailed dis...
true
true
true
true
true
1,344
1
INTRODUCTION
1
5
[ "b5", "b12", "b6", "b9", "b10", "b13", "b14", "b15", "b16", "b17", "b15", "b16" ]
17,012,284
pmid-11691856|pmid-15123581|pmid-9582189|pmid-12030762|pmid-11976131|pmid-14993206|pmid-16391044|pmid-16704813|pmid-16481660|pmid-2231712|pmid-16704813|pmid-16481660
The new methodology differed from earlier work by using the resolved bases as the query of a similarity search of DNA databases to identify the most likely species and variants that match the base calls from the hybridization observed.
[ "5", "12", "6", "9", "10", "13", "14", "15", "16", "17", "15", "16" ]
235
8,329
0
false
The new methodology differed from earlier work by using the resolved bases as the query of a similarity search of DNA databases to identify the most likely species and variants that match the base calls from the hybridization observed.
[]
The new methodology differed from earlier work by using the resolved bases as the query of a similarity search of DNA databases to identify the most likely species and variants that match the base calls from the hybridization observed.
true
true
true
true
true
1,344
1
INTRODUCTION
1
5
[ "b5", "b12", "b6", "b9", "b10", "b13", "b14", "b15", "b16", "b17", "b15", "b16" ]
17,012,284
pmid-11691856|pmid-15123581|pmid-9582189|pmid-12030762|pmid-11976131|pmid-14993206|pmid-16391044|pmid-16704813|pmid-16481660|pmid-2231712|pmid-16704813|pmid-16481660
The system was capable of testing for 26 pathogens simultaneously and could detect the presence of multiple pathogens.
[ "5", "12", "6", "9", "10", "13", "14", "15", "16", "17", "15", "16" ]
118
8,330
0
false
The system was capable of testing for 26 pathogens simultaneously and could detect the presence of multiple pathogens.
[]
The system was capable of testing for 26 pathogens simultaneously and could detect the presence of multiple pathogens.
true
true
true
true
true
1,344
1
INTRODUCTION
1
17
[ "b5", "b12", "b6", "b9", "b10", "b13", "b14", "b15", "b16", "b17", "b15", "b16" ]
17,012,284
pmid-11691856|pmid-15123581|pmid-9582189|pmid-12030762|pmid-11976131|pmid-14993206|pmid-16391044|pmid-16704813|pmid-16481660|pmid-2231712|pmid-16704813|pmid-16481660
A software program, resequencing pathogen identifier (REPI), was used to simplify data analysis by performing similarity searches of a genetic database using basic local alignment search tool (BLAST) (17).
[ "5", "12", "6", "9", "10", "13", "14", "15", "16", "17", "15", "16" ]
205
8,331
1
false
A software program, resequencing pathogen identifier (REPI), was used to simplify data analysis by performing similarity searches of a genetic database using basic local alignment search tool (BLAST).
[ "17" ]
A software program, resequencing pathogen identifier (REPI), was used to simplify data analysis by performing similarity searches of a genetic database using basic local alignment search tool (BLAST).
true
true
true
true
true
1,344
1
INTRODUCTION
1
5
[ "b5", "b12", "b6", "b9", "b10", "b13", "b14", "b15", "b16", "b17", "b15", "b16" ]
17,012,284
pmid-11691856|pmid-15123581|pmid-9582189|pmid-12030762|pmid-11976131|pmid-14993206|pmid-16391044|pmid-16704813|pmid-16481660|pmid-2231712|pmid-16704813|pmid-16481660
The REPI program used BLAST default settings and would only return sequences that might represent the hybridization if the expect value, a quantity calculated by the BLAST program that indicates the likelihood that the sequence match found would have occurred by random chance in the database, was <10−9.
[ "5", "12", "6", "9", "10", "13", "14", "15", "16", "17", "15", "16" ]
304
8,332
0
false
The REPI program used BLAST default settings and would only return sequences that might represent the hybridization if the expect value, a quantity calculated by the BLAST program that indicates the likelihood that the sequence match found would have occurred by random chance in the database, was <10−9.
[]
The REPI program used BLAST default settings and would only return sequences that might represent the hybridization if the expect value, a quantity calculated by the BLAST program that indicates the likelihood that the sequence match found would have occurred by random chance in the database, was <10−9.
true
true
true
true
true
1,344
1
INTRODUCTION
1
5
[ "b5", "b12", "b6", "b9", "b10", "b13", "b14", "b15", "b16", "b17", "b15", "b16" ]
17,012,284
pmid-11691856|pmid-15123581|pmid-9582189|pmid-12030762|pmid-11976131|pmid-14993206|pmid-16391044|pmid-16704813|pmid-16481660|pmid-2231712|pmid-16704813|pmid-16481660
This screened out all cases that had insufficient signal; however, the final determination of what pathogen(s) was detected and to what degree discrimination was possible required manual examination of the returned results.
[ "5", "12", "6", "9", "10", "13", "14", "15", "16", "17", "15", "16" ]
223
8,333
0
false
This screened out all cases that had insufficient signal; however, the final determination of what pathogen(s) was detected and to what degree discrimination was possible required manual examination of the returned results.
[]
This screened out all cases that had insufficient signal; however, the final determination of what pathogen(s) was detected and to what degree discrimination was possible required manual examination of the returned results.
true
true
true
true
true
1,344
1
INTRODUCTION
1
5
[ "b5", "b12", "b6", "b9", "b10", "b13", "b14", "b15", "b16", "b17", "b15", "b16" ]
17,012,284
pmid-11691856|pmid-15123581|pmid-9582189|pmid-12030762|pmid-11976131|pmid-14993206|pmid-16391044|pmid-16704813|pmid-16481660|pmid-2231712|pmid-16704813|pmid-16481660
This method successfully allowed fine discrimination of various adenoviruses and strain identifications of Flu A and B samples in agreement with conventional sampling results (15,16).
[ "5", "12", "6", "9", "10", "13", "14", "15", "16", "17", "15", "16" ]
183
8,334
0
false
This method successfully allowed fine discrimination of various adenoviruses and strain identifications of Flu A and B samples in agreement with conventional sampling results.
[ "15,16" ]
This method successfully allowed fine discrimination of various adenoviruses and strain identifications of Flu A and B samples in agreement with conventional sampling results.
true
true
true
true
true
1,344
1
INTRODUCTION
1
5
[ "b5", "b12", "b6", "b9", "b10", "b13", "b14", "b15", "b16", "b17", "b15", "b16" ]
17,012,284
pmid-11691856|pmid-15123581|pmid-9582189|pmid-12030762|pmid-11976131|pmid-14993206|pmid-16391044|pmid-16704813|pmid-16481660|pmid-2231712|pmid-16704813|pmid-16481660
Two important advantages of this approach were that the information was always recovered at the most detailed level possible and that it was capable of still recognizing organisms with recent mutations.
[ "5", "12", "6", "9", "10", "13", "14", "15", "16", "17", "15", "16" ]
202
8,335
0
false
Two important advantages of this approach were that the information was always recovered at the most detailed level possible and that it was capable of still recognizing organisms with recent mutations.
[]
Two important advantages of this approach were that the information was always recovered at the most detailed level possible and that it was capable of still recognizing organisms with recent mutations.
true
true
true
true
true
1,344
1
INTRODUCTION
1
5
[ "b5", "b12", "b6", "b9", "b10", "b13", "b14", "b15", "b16", "b17", "b15", "b16" ]
17,012,284
pmid-11691856|pmid-15123581|pmid-9582189|pmid-12030762|pmid-11976131|pmid-14993206|pmid-16391044|pmid-16704813|pmid-16481660|pmid-2231712|pmid-16704813|pmid-16481660
This approach also maintained specificity well, as it was not dependent on the uniqueness of a few individual short probes.
[ "5", "12", "6", "9", "10", "13", "14", "15", "16", "17", "15", "16" ]
123
8,336
0
false
This approach also maintained specificity well, as it was not dependent on the uniqueness of a few individual short probes.
[]
This approach also maintained specificity well, as it was not dependent on the uniqueness of a few individual short probes.
true
true
true
true
true
1,344
2
INTRODUCTION
0
null
null
17,012,284
null
Although this analysis method has utility, there are several shortcomings: it is time consuming, not optimized to maximize sensitivity, has complicated results, is suitable only for an expert, and contains redundant or duplicate information.
null
241
8,337
0
false
null
null
Although this analysis method has utility, there are several shortcomings: it is time consuming, not optimized to maximize sensitivity, has complicated results, is suitable only for an expert, and contains redundant or duplicate information.
true
true
true
true
true
1,345
2
INTRODUCTION
0
null
null
17,012,284
null
The process was time consuming because only the initial screening was handled automatically while the remaining steps required manual interpretation before the detection analysis was complete.
null
192
8,338
0
false
null
null
The process was time consuming because only the initial screening was handled automatically while the remaining steps required manual interpretation before the detection analysis was complete.
true
true
true
true
true
1,345
2
INTRODUCTION
0
null
null
17,012,284
null
Because a simple criterion (expect value cutoff of 10−9) and non-optimized BLAST parameters were used to consider a pathogen detected, the REPI algorithm provided a list of candidate organisms but did not make a final simple conclusion or relate the results of one prototype sequence to another.
null
295
8,339
0
false
null
null
Because a simple criterion (expect value cutoff of 10−9) and non-optimized BLAST parameters were used to consider a pathogen detected, the REPI algorithm provided a list of candidate organisms but did not make a final simple conclusion or relate the results of one prototype sequence to another.
true
true
true
true
true
1,345
2
INTRODUCTION
0
null
null
17,012,284
null
Instead a manual process was used to make the final determination, but because the REPI program provided all similar results and the use of public nucleic acid databases containing redundant entries, a large amount of data was presented to a user that was not useful.
null
267
8,340
0
false
null
null
Instead a manual process was used to make the final determination, but because the REPI program provided all similar results and the use of public nucleic acid databases containing redundant entries, a large amount of data was presented to a user that was not useful.
true
true
true
true
true
1,345
2
INTRODUCTION
0
null
null
17,012,284
null
In addition, with a manual process it was not possible to establish that the algorithm developed was generally applicable for any organism where nucleic acid base resolved sequence information has been provided.
null
211
8,341
0
false
null
null
In addition, with a manual process it was not possible to establish that the algorithm developed was generally applicable for any organism where nucleic acid base resolved sequence information has been provided.
true
true
true
true
true
1,345
3
INTRODUCTION
0
null
null
17,012,284
null
In this paper, we describe a new software expert system, Computer-Implemented Biological Sequence Identifier system 2.0 (CIBSI 2.0), that successfully uses resolved base sequence information from custom designed Affymetrix resequencing microarrays to provide a simple list of organisms that are detected.
null
304
8,342
0
false
null
null
In this paper, we describe a new software expert system, Computer-Implemented Biological Sequence Identifier system 2.0 (CIBSI 2.0), that successfully uses resolved base sequence information from custom designed Affymetrix resequencing microarrays to provide a simple list of organisms that are detected.
true
true
true
true
true
1,346
3
INTRODUCTION
0
null
null
17,012,284
null
This algorithm addresses the most important shortcoming of previous methods by incorporating new features to completely automate pathogen identification.
null
153
8,343
0
false
null
null
This algorithm addresses the most important shortcoming of previous methods by incorporating new features to completely automate pathogen identification.
true
true
true
true
true
1,346
3
INTRODUCTION
0
null
null
17,012,284
null
We have demonstrated the effectiveness of this algorithm for identification via several examples.
null
97
8,344
0
false
null
null
We have demonstrated the effectiveness of this algorithm for identification via several examples.
true
true
true
true
true
1,346
3
INTRODUCTION
0
null
null
17,012,284
null
The single program is capable of making correct decisions for all 26 pathogens contained on the Respiratory Pathogen Microarray v.1 (RPM v.1), whether detected alone or in combinations, with improved sensitivity.
null
212
8,345
0
false
null
null
The single program is capable of making correct decisions for all 26 pathogens contained on the Respiratory Pathogen Microarray v.1 (RPM v.1), whether detected alone or in combinations, with improved sensitivity.
true
true
true
true
true
1,346
3
INTRODUCTION
0
null
null
17,012,284
null
Although the program is currently applied to resequencing microarrays, the methodologies developed remain generally applicable.
null
127
8,346
0
false
null
null
Although the program is currently applied to resequencing microarrays, the methodologies developed remain generally applicable.
true
true
true
true
true
1,346
3
INTRODUCTION
0
null
null
17,012,284
null
Only the first portion of the algorithm handles issues specific to microarrays while the remainder deals with sequences that are suitable for use as a query by the BLAST algorithm.
null
180
8,347
0
false
null
null
Only the first portion of the algorithm handles issues specific to microarrays while the remainder deals with sequences that are suitable for use as a query by the BLAST algorithm.
true
true
true
true
true
1,346
3
INTRODUCTION
0
null
null
17,012,284
null
In developing the general identification algorithm, we have identified and resolved issues specific to resequencing microarrays that complicate their use.
null
154
8,348
0
false
null
null
In developing the general identification algorithm, we have identified and resolved issues specific to resequencing microarrays that complicate their use.
true
true
true
true
true
1,346
3
INTRODUCTION
0
null
null
17,012,284
null
Because the entire decision process for what is detected has been automated, it is straightforward to test whether the rules used to make identifications are rigorous and applicable to any pathogen.
null
198
8,349
0
false
null
null
Because the entire decision process for what is detected has been automated, it is straightforward to test whether the rules used to make identifications are rigorous and applicable to any pathogen.
true
true
true
true
true
1,346
3
INTRODUCTION
0
null
null
17,012,284
null
With this efficient program, resequencing based assays can provide a competitive method to test simultaneously for many possible pathogens, providing output that can be interpreted by a non-expert.
null
197
8,350
0
false
null
null
With this efficient program, resequencing based assays can provide a competitive method to test simultaneously for many possible pathogens, providing output that can be interpreted by a non-expert.
true
true
true
true
true
1,346
0
DISCUSSION
0
null
null
17,012,284
pmid-8905084|pmid-15365022|pmid-12791858
The algorithm we have developed successfully provided pathogen identification to the maximum level of detail possible (species or strain) depending on the quality of each ProSeq.
null
178
8,351
0
false
null
null
The algorithm we have developed successfully provided pathogen identification to the maximum level of detail possible (species or strain) depending on the quality of each ProSeq.
true
true
true
true
true
1,347
0
DISCUSSION
0
null
null
17,012,284
pmid-8905084|pmid-15365022|pmid-12791858
This identification capability requires minimal input on the identity of the pathogens, making non-expert use feasible.
null
119
8,352
0
false
null
null
This identification capability requires minimal input on the identity of the pathogens, making non-expert use feasible.
true
true
true
true
true
1,347
0
DISCUSSION
0
null
null
17,012,284
pmid-8905084|pmid-15365022|pmid-12791858
The crucial feature incorporated that allowed complete automation was the use of taxonomic databases, which classify organisms into ordered groups and provide relationships between organism entries, allowing removal of redundancies, comparison of different related prototype sequences and simplification of data presenta...
null
325
8,353
0
false
null
null
The crucial feature incorporated that allowed complete automation was the use of taxonomic databases, which classify organisms into ordered groups and provide relationships between organism entries, allowing removal of redundancies, comparison of different related prototype sequences and simplification of data presenta...
true
true
true
true
true
1,347
0
DISCUSSION
0
null
null
17,012,284
pmid-8905084|pmid-15365022|pmid-12791858
This allows databases, i.e.
null
27
8,354
0
false
null
null
This allows databases, i.e.
true
true
true
true
true
1,347
0
DISCUSSION
0
null
null
17,012,284
pmid-8905084|pmid-15365022|pmid-12791858
NCBI, that are redundant and subject to minimal curation but which constantly receive updated and new sequence information to be used with great success.
null
153
8,355
0
false
null
null
NCBI, that are redundant and subject to minimal curation but which constantly receive updated and new sequence information to be used with great success.
true
true
true
true
true
1,347
0
DISCUSSION
0
null
null
17,012,284
pmid-8905084|pmid-15365022|pmid-12791858
Although we have demonstrated this using only the NCBI databases, other databases or custom made ones could have easily been used, which might improve performance.
null
163
8,356
0
false
null
null
Although we have demonstrated this using only the NCBI databases, other databases or custom made ones could have easily been used, which might improve performance.
true
true
true
true
true
1,347
0
DISCUSSION
0
null
null
17,012,284
pmid-8905084|pmid-15365022|pmid-12791858
The algorithm is capable of providing accurate identifications at all analysis levels for pathogens that are less variable or are represented by highly conserved ProSeqs.
null
170
8,357
0
false
null
null
The algorithm is capable of providing accurate identifications at all analysis levels for pathogens that are less variable or are represented by highly conserved ProSeqs.
true
true
true
true
true
1,347
0
DISCUSSION
0
null
null
17,012,284
pmid-8905084|pmid-15365022|pmid-12791858
For more variable or rapidly mutating pathogens, e.g.
null
53
8,358
0
false
null
null
For more variable or rapidly mutating pathogens, e.g.
true
true
true
true
true
1,347
0
DISCUSSION
0
null
null
17,012,284
pmid-8905084|pmid-15365022|pmid-12791858
Influenza A virus, ProSeq identification Task(I) and ProSeq grouping Task(II) still provided accurate detailed identifications, but the pathogen determination Task(III) was unable to report fine scale discrimination.
null
216
8,359
0
false
null
null
Influenza A virus, ProSeq identification Task(I) and ProSeq grouping Task(II) still provided accurate detailed identifications, but the pathogen determination Task(III) was unable to report fine scale discrimination.
true
true
true
true
true
1,347
0
DISCUSSION
0
null
null
17,012,284
pmid-8905084|pmid-15365022|pmid-12791858
The comparison of the conventionally sequenced Influenza virus gene sequences illustrated that the algorithm is capable of automatically adjusting for updates in databases.
null
172
8,360
0
false
null
null
The comparison of the conventionally sequenced Influenza virus gene sequences illustrated that the algorithm is capable of automatically adjusting for updates in databases.
true
true
true
true
true
1,347
0
DISCUSSION
0
null
null
17,012,284
pmid-8905084|pmid-15365022|pmid-12791858
The algorithm demonstrated its capability to properly distinguish hybridizations on a ProSeq caused by the specified pathogen from those caused by genetically close (near neighbor) strains and did not make incorrect identifications, eliminating one potential cause of false positives.
null
284
8,361
0
false
null
null
The algorithm demonstrated its capability to properly distinguish hybridizations on a ProSeq caused by the specified pathogen from those caused by genetically close (near neighbor) strains and did not make incorrect identifications, eliminating one potential cause of false positives.
true
true
true
true
true
1,347
0
DISCUSSION
0
null
null
17,012,284
pmid-8905084|pmid-15365022|pmid-12791858
Filtering the raw hybridization results served to reduce the computation time, accounted for potential primer interference and more importantly reduced potential biasing.
null
170
8,362
0
false
null
null
Filtering the raw hybridization results served to reduce the computation time, accounted for potential primer interference and more importantly reduced potential biasing.
true
true
true
true
true
1,347
0
DISCUSSION
0
null
null
17,012,284
pmid-8905084|pmid-15365022|pmid-12791858
This simple integrated algorithm provided sufficient and accurate identification, so that immediate use of the RPM v.1 or similar resequencing arrays and assay is possible.
null
172
8,363
0
false
null
null
This simple integrated algorithm provided sufficient and accurate identification, so that immediate use of the RPM v.1 or similar resequencing arrays and assay is possible.
true
true
true
true
true
1,347
0
DISCUSSION
0
null
null
17,012,284
pmid-8905084|pmid-15365022|pmid-12791858
Although not discussed in this paper, the algorithm has successfully detected the presence of simulated multi-infections (Lin et al., submitted for publication).
null
161
8,364
0
false
null
null
Although not discussed in this paper, the algorithm has successfully detected the presence of simulated multi-infections (Lin et al., submitted for publication).
true
true
true
true
true
1,347
0
DISCUSSION
0
null
null
17,012,284
pmid-8905084|pmid-15365022|pmid-12791858
The algorithm as currently developed will detect mixtures when the organisms have sufficient variation; however, detection of a mixture of an organism and its mutation strain in a sample is uncertain in its present phase.
null
221
8,365
0
false
null
null
The algorithm as currently developed will detect mixtures when the organisms have sufficient variation; however, detection of a mixture of an organism and its mutation strain in a sample is uncertain in its present phase.
true
true
true
true
true
1,347
0
DISCUSSION
0
null
null
17,012,284
pmid-8905084|pmid-15365022|pmid-12791858
In principle it may be possible to detect such mixtures as the resequencing microarray can detect and sequence diploid organisms.
null
129
8,366
0
false
null
null
In principle it may be possible to detect such mixtures as the resequencing microarray can detect and sequence diploid organisms.
true
true
true
true
true
1,347
1
DISCUSSION
0
null
null
17,012,284
pmid-11691856|pmid-15123581|pmid-9582189|pmid-12030762|pmid-11976131|pmid-14993206|pmid-16391044|pmid-16704813|pmid-16481660|pmid-2231712|pmid-16704813|pmid-16481660
Besides demonstrating the success of the CIBSI 2.0 program, the work involved in developing the algorithm allowed insight into the importance of proper ProSeq selection.
null
169
8,367
0
false
null
null
Besides demonstrating the success of the CIBSI 2.0 program, the work involved in developing the algorithm allowed insight into the importance of proper ProSeq selection.
true
true
true
true
true
1,348
1
DISCUSSION
0
null
null
17,012,284
pmid-11691856|pmid-15123581|pmid-9582189|pmid-12030762|pmid-11976131|pmid-14993206|pmid-16391044|pmid-16704813|pmid-16481660|pmid-2231712|pmid-16704813|pmid-16481660
The RPM v.1 was the first resequencing array designed specifically for multiple pathogen detection using database similarity searching and served as a prototype for this application.
null
182
8,368
0
false
null
null
The RPM v.1 was the first resequencing array designed specifically for multiple pathogen detection using database similarity searching and served as a prototype for this application.
true
true
true
true
true
1,348
1
DISCUSSION
0
null
null
17,012,284
pmid-11691856|pmid-15123581|pmid-9582189|pmid-12030762|pmid-11976131|pmid-14993206|pmid-16391044|pmid-16704813|pmid-16481660|pmid-2231712|pmid-16704813|pmid-16481660
We have demonstrated that a single ProSeq with as few as 100 bp, when designed correctly, can be sufficient to unambiguously identify an organism.
null
146
8,369
0
false
null
null
We have demonstrated that a single ProSeq with as few as 100 bp, when designed correctly, can be sufficient to unambiguously identify an organism.
true
true
true
true
true
1,348
1
DISCUSSION
0
null
null
17,012,284
pmid-11691856|pmid-15123581|pmid-9582189|pmid-12030762|pmid-11976131|pmid-14993206|pmid-16391044|pmid-16704813|pmid-16481660|pmid-2231712|pmid-16704813|pmid-16481660
However, it is clearly indicated that several longer ProSeqs provide better confirmation and more detailed information of a pathogen.
null
133
8,370
0
false
null
null
However, it is clearly indicated that several longer ProSeqs provide better confirmation and more detailed information of a pathogen.
true
true
true
true
true
1,348
1
DISCUSSION
0
null
null
17,012,284
pmid-11691856|pmid-15123581|pmid-9582189|pmid-12030762|pmid-11976131|pmid-14993206|pmid-16391044|pmid-16704813|pmid-16481660|pmid-2231712|pmid-16704813|pmid-16481660
Although the algorithm provides accuracy equivalent to manual analysis for determinations of individual ProSeqs, the current algorithm is only partially successful in integrating information from multiple ProSeqs.
null
213
8,371
0
false
null
null
Although the algorithm provides accuracy equivalent to manual analysis for determinations of individual ProSeqs, the current algorithm is only partially successful in integrating information from multiple ProSeqs.
true
true
true
true
true
1,348
1
DISCUSSION
0
null
null
17,012,284
pmid-11691856|pmid-15123581|pmid-9582189|pmid-12030762|pmid-11976131|pmid-14993206|pmid-16391044|pmid-16704813|pmid-16481660|pmid-2231712|pmid-16704813|pmid-16481660
The emphasis of the design to this point has been on capabilities that are generally applicable to any pathogen.
null
112
8,372
0
false
null
null
The emphasis of the design to this point has been on capabilities that are generally applicable to any pathogen.
true
true
true
true
true
1,348
1
DISCUSSION
0
null
null
17,012,284
pmid-11691856|pmid-15123581|pmid-9582189|pmid-12030762|pmid-11976131|pmid-14993206|pmid-16391044|pmid-16704813|pmid-16481660|pmid-2231712|pmid-16704813|pmid-16481660
We are incorporating these insights in our newer more comprehensive resequencing array designs.
null
95
8,373
0
false
null
null
We are incorporating these insights in our newer more comprehensive resequencing array designs.
true
true
true
true
true
1,348
1
DISCUSSION
0
null
null
17,012,284
pmid-11691856|pmid-15123581|pmid-9582189|pmid-12030762|pmid-11976131|pmid-14993206|pmid-16391044|pmid-16704813|pmid-16481660|pmid-2231712|pmid-16704813|pmid-16481660
Improving on level of detail reported in pathogen determination Task(III) will require more information about an individual pathogen and may have to be developed for each specific pathogen or class of pathogens.
null
211
8,374
0
false
null
null
Improving on level of detail reported in pathogen determination Task(III) will require more information about an individual pathogen and may have to be developed for each specific pathogen or class of pathogens.
true
true
true
true
true
1,348
1
DISCUSSION
0
null
null
17,012,284
pmid-11691856|pmid-15123581|pmid-9582189|pmid-12030762|pmid-11976131|pmid-14993206|pmid-16391044|pmid-16704813|pmid-16481660|pmid-2231712|pmid-16704813|pmid-16481660
This information is also required for the algorithm to identify which differences between a sample and database entries represent significant mutations.
null
152
8,375
0
false
null
null
This information is also required for the algorithm to identify which differences between a sample and database entries represent significant mutations.
true
true
true
true
true
1,348
1
DISCUSSION
0
null
null
17,012,284
pmid-11691856|pmid-15123581|pmid-9582189|pmid-12030762|pmid-11976131|pmid-14993206|pmid-16391044|pmid-16704813|pmid-16481660|pmid-2231712|pmid-16704813|pmid-16481660
Future work will involve improving the use of the current taxonomic database or potentially developing a new relational database that is specific to our needs and then incorporating more specific information of target pathogens.
null
228
8,376
0
false
null
null
Future work will involve improving the use of the current taxonomic database or potentially developing a new relational database that is specific to our needs and then incorporating more specific information of target pathogens.
true
true
true
true
true
1,348
1
DISCUSSION
0
null
null
17,012,284
pmid-11691856|pmid-15123581|pmid-9582189|pmid-12030762|pmid-11976131|pmid-14993206|pmid-16391044|pmid-16704813|pmid-16481660|pmid-2231712|pmid-16704813|pmid-16481660
The hierarchal design of the data analysis makes it easy to incorporate analysis that build upon the analysis already performed.
null
128
8,377
0
false
null
null
The hierarchal design of the data analysis makes it easy to incorporate analysis that build upon the analysis already performed.
true
true
true
true
true
1,348
2
DISCUSSION
0
null
null
17,012,284
null
We have met with some success in the current version but want to have increased automated discrimination.
null
105
8,378
0
false
null
null
We have met with some success in the current version but want to have increased automated discrimination.
true
true
true
true
true
1,349
2
DISCUSSION
0
null
null
17,012,284
null
We have a well-defined path to completing this aim.
null
51
8,379
0
false
null
null
We have a well-defined path to completing this aim.
true
true
true
true
true
1,349
2
DISCUSSION
0
null
null
17,012,284
null
The use of properly designed resequencing microarrays and this automated detection algorithm provides a way forward to developing assays that can test for multiple organisms simultaneously while providing fine strain level discrimination giving access to information about detailed strain recognition, antibiotic resista...
null
350
8,380
0
false
null
null
The use of properly designed resequencing microarrays and this automated detection algorithm provides a way forward to developing assays that can test for multiple organisms simultaneously while providing fine strain level discrimination giving access to information about detailed strain recognition, antibiotic resista...
true
true
true
true
true
1,349
2
DISCUSSION
0
null
null
17,012,284
null
This is a capability that other approaches cannot currently provide.
null
68
8,381
0
false
null
null
This is a capability that other approaches cannot currently provide.
true
true
true
true
true
1,349
2
DISCUSSION
0
null
null
17,012,284
null
In addition, since the design of the original 30 kb RPM microarray, the possible sequence content of the current array has increased 10-fold to 300 kb and further increases in array density are still attainable.
null
211
8,382
0
false
null
null
In addition, since the design of the original 30 kb RPM microarray, the possible sequence content of the current array has increased 10-fold to 300 kb and further increases in array density are still attainable.
true
true
true
true
true
1,349
2
DISCUSSION
0
null
null
17,012,284
null
This, coupled with our identification algorithms, will allow the analysis of partial sequence information from even more organisms for applications such as differential diagnostics for illnesses with multiple potential causes (i.e.
null
231
8,383
0
false
null
null
This, coupled with our identification algorithms, will allow the analysis of partial sequence information from even more organisms for applications such as differential diagnostics for illnesses with multiple potential causes (i.e.
true
true
true
true
true
1,349
2
DISCUSSION
0
null
null
17,012,284
null
febrile respiratory illness), tracking of emergent pathogens, distinction of biological threats from harmless near genetic neighbors in surveillance applications and for tracking the impact of co-infections or super infections.
null
227
8,384
0
false
null
null
febrile respiratory illness), tracking of emergent pathogens, distinction of biological threats from harmless near genetic neighbors in surveillance applications and for tracking the impact of co-infections or super infections.
false
true
true
true
false
1,349
2
DISCUSSION
0
null
null
17,012,284
null
The concept of categorizing and reporting different degrees of identification depending on the quality of samples and set of target sequences is not limited to resequencing microarrays but is more generally applicable to any platform that is capable of returning sequence level calls that can be used to query a referenc...
null
335
8,385
0
false
null
null
The concept of categorizing and reporting different degrees of identification depending on the quality of samples and set of target sequences is not limited to resequencing microarrays but is more generally applicable to any platform that is capable of returning sequence level calls that can be used to query a referenc...
true
true
true
true
true
1,349
2
DISCUSSION
0
null
null
17,012,284
null
As the trend for assays that test for multiple pathogens increases, automated analysis tools, such as this one, become more crucial for rapid identification in simple formats useful to the non-expert on a day to day basis.
null
222
8,386
0
false
null
null
As the trend for assays that test for multiple pathogens increases, automated analysis tools, such as this one, become more crucial for rapid identification in simple formats useful to the non-expert on a day to day basis.
true
true
true
true
true
1,349
2
DISCUSSION
0
null
null
17,012,284
null
The remaining hurdle to using resequencing microarrays as a routine assay method is now clearly the sample processing methods.
null
126
8,387
0
false
null
null
The remaining hurdle to using resequencing microarrays as a routine assay method is now clearly the sample processing methods.
true
true
true
true
true
1,349
2
DISCUSSION
0
null
null
17,012,284
null
Further automating these steps is an important area of future research and development.
null
87
8,388
0
false
null
null
Further automating these steps is an important area of future research and development.
true
true
true
true
true
1,349
3
DISCUSSION
0
null
null
17,012,284
null
The program can be obtained free of charge for research purposes by contacting the authors.
null
91
8,389
0
false
null
null
The program can be obtained free of charge for research purposes by contacting the authors.
true
true
true
true
true
1,350
0
INTRODUCTION
1
1
[ "B1", "B2", "B3 B4 B5", "B6", "B7", "B8", "B9", "B10", "B11" ]
17,395,638
pmid-3521892|pmid-1280335|pmid-14654705|pmid-11390393|pmid-7526223|pmid-9707438|pmid-12055299|pmid-2583104|pmid-11741337|pmid-16452296|pmid-8670815|pmid-11867541|pmid-11871663|pmid-12169588|pmid-10047480|pmid-17040898
It is well established now that mRNA decay has an integral role in the control of gene expression.
[ "1", "2", "3–5", "6", "7", "8", "9", "10", "11" ]
98
8,390
0
false
It is well established now that mRNA decay has an integral role in the control of gene expression.
[]
It is well established now that mRNA decay has an integral role in the control of gene expression.
true
true
true
true
true
1,351
0
INTRODUCTION
1
1
[ "B1", "B2", "B3 B4 B5", "B6", "B7", "B8", "B9", "B10", "B11" ]
17,395,638
pmid-3521892|pmid-1280335|pmid-14654705|pmid-11390393|pmid-7526223|pmid-9707438|pmid-12055299|pmid-2583104|pmid-11741337|pmid-16452296|pmid-8670815|pmid-11867541|pmid-11871663|pmid-12169588|pmid-10047480|pmid-17040898
mRNAs can be degraded by a number of mechanisms that act independently, in parallel or sequentially.
[ "1", "2", "3–5", "6", "7", "8", "9", "10", "11" ]
100
8,391
0
false
mRNAs can be degraded by a number of mechanisms that act independently, in parallel or sequentially.
[]
mRNAs can be degraded by a number of mechanisms that act independently, in parallel or sequentially.
false
true
true
true
false
1,351
0
INTRODUCTION
1
3–5
[ "B1", "B2", "B3 B4 B5", "B6", "B7", "B8", "B9", "B10", "B11" ]
17,395,638
pmid-3521892|pmid-1280335|pmid-14654705|pmid-11390393|pmid-7526223|pmid-9707438|pmid-12055299|pmid-2583104|pmid-11741337|pmid-16452296|pmid-8670815|pmid-11867541|pmid-11871663|pmid-12169588|pmid-10047480|pmid-17040898
Several cis- and trans-acting factors including higher order RNA structures (1,2), RNA-binding proteins (3–5) and translating ribosomes (6,7) control the sensitivity of an mRNA molecule to degradation.
[ "1", "2", "3–5", "6", "7", "8", "9", "10", "11" ]
201
8,392
1
false
Several cis- and trans-acting factors including higher order RNA structures, RNA-binding proteins and translating ribosomes control the sensitivity of an mRNA molecule to degradation.
[ "1,2", "3–5", "6,7" ]
Several cis- and trans-acting factors including higher order RNA structures, RNA-binding proteins and translating ribosomes control the sensitivity of an mRNA molecule to degradation.
true
true
true
true
true
1,351
0
INTRODUCTION
1
1
[ "B1", "B2", "B3 B4 B5", "B6", "B7", "B8", "B9", "B10", "B11" ]
17,395,638
pmid-3521892|pmid-1280335|pmid-14654705|pmid-11390393|pmid-7526223|pmid-9707438|pmid-12055299|pmid-2583104|pmid-11741337|pmid-16452296|pmid-8670815|pmid-11867541|pmid-11871663|pmid-12169588|pmid-10047480|pmid-17040898
Hairpin structures located at the 3′ end of operons or in intercistronic regions protect mRNA molecules from digestion by 3′–5′ exoribonucleases.
[ "1", "2", "3–5", "6", "7", "8", "9", "10", "11" ]
145
8,393
0
false
Hairpin structures located at the 3′ end of operons or in intercistronic regions protect mRNA molecules from digestion by 3′–5′ exoribonucleases.
[]
Hairpin structures located at the 3′ end of operons or in intercistronic regions protect mRNA molecules from digestion by 3′–5′ exoribonucleases.
true
true
true
true
true
1,351
0
INTRODUCTION
1
1
[ "B1", "B2", "B3 B4 B5", "B6", "B7", "B8", "B9", "B10", "B11" ]
17,395,638
pmid-3521892|pmid-1280335|pmid-14654705|pmid-11390393|pmid-7526223|pmid-9707438|pmid-12055299|pmid-2583104|pmid-11741337|pmid-16452296|pmid-8670815|pmid-11867541|pmid-11871663|pmid-12169588|pmid-10047480|pmid-17040898
To overcome these barriers, bacteria initiate RNA degradation by endoribonucleolytic cleavages mostly carried out by RNase E in E.coli.
[ "1", "2", "3–5", "6", "7", "8", "9", "10", "11" ]
135
8,394
0
false
To overcome these barriers, bacteria initiate RNA degradation by endoribonucleolytic cleavages mostly carried out by RNase E in E.coli.
[]
To overcome these barriers, bacteria initiate RNA degradation by endoribonucleolytic cleavages mostly carried out by RNase E in E.coli.
true
true
true
true
true
1,351
0
INTRODUCTION
1
1
[ "B1", "B2", "B3 B4 B5", "B6", "B7", "B8", "B9", "B10", "B11" ]
17,395,638
pmid-3521892|pmid-1280335|pmid-14654705|pmid-11390393|pmid-7526223|pmid-9707438|pmid-12055299|pmid-2583104|pmid-11741337|pmid-16452296|pmid-8670815|pmid-11867541|pmid-11871663|pmid-12169588|pmid-10047480|pmid-17040898
RNase III and RNase G have also been found to initiate RNA decay in certain cases (8,9).
[ "1", "2", "3–5", "6", "7", "8", "9", "10", "11" ]
88
8,395
0
false
RNase III and RNase G have also been found to initiate RNA decay in certain cases.
[ "8,9" ]
RNase III and RNase G have also been found to initiate RNA decay in certain cases.
true
true
true
true
true
1,351
0
INTRODUCTION
1
1
[ "B1", "B2", "B3 B4 B5", "B6", "B7", "B8", "B9", "B10", "B11" ]
17,395,638
pmid-3521892|pmid-1280335|pmid-14654705|pmid-11390393|pmid-7526223|pmid-9707438|pmid-12055299|pmid-2583104|pmid-11741337|pmid-16452296|pmid-8670815|pmid-11867541|pmid-11871663|pmid-12169588|pmid-10047480|pmid-17040898
RNA fragments resulting from endonucleolytic cleavages can be either further degraded endonucleolytically or by the 3′–5′ exonucleases, polynucleotide phosphorylase (PNPase), RNase II and RNase R [reviewed in (10)].
[ "1", "2", "3–5", "6", "7", "8", "9", "10", "11" ]
215
8,396
0
false
RNA fragments resulting from endonucleolytic cleavages can be either further degraded endonucleolytically or by the 3′–5′ exonucleases, polynucleotide phosphorylase (PNPase), RNase II and RNase R.
[ "reviewed in (10)" ]
RNA fragments resulting from endonucleolytic cleavages can be either further degraded endonucleolytically or by the 3′–5′ exonucleases, polynucleotide phosphorylase (PNPase), RNase II and RNase R.
true
true
true
true
true
1,351
0
INTRODUCTION
1
11
[ "B1", "B2", "B3 B4 B5", "B6", "B7", "B8", "B9", "B10", "B11" ]
17,395,638
pmid-3521892|pmid-1280335|pmid-14654705|pmid-11390393|pmid-7526223|pmid-9707438|pmid-12055299|pmid-2583104|pmid-11741337|pmid-16452296|pmid-8670815|pmid-11867541|pmid-11871663|pmid-12169588|pmid-10047480|pmid-17040898
Oligo(A) tails can be added to RNA fragments resulting from endo- or exonucleolytic cleavages and promote their exonucleolytic degradation (11).
[ "1", "2", "3–5", "6", "7", "8", "9", "10", "11" ]
144
8,397
1
false
Oligo(A) tails can be added to RNA fragments resulting from endo- or exonucleolytic cleavages and promote their exonucleolytic degradation.
[ "11" ]
Oligo(A) tails can be added to RNA fragments resulting from endo- or exonucleolytic cleavages and promote their exonucleolytic degradation.
true
true
true
true
true
1,351
1
INTRODUCTION
1
12
[ "B12", "B13", "B14", "B15", "B16", "B17", "B17 B18 B19", "B20", "B21", "B22", "B23", "B24", "B25 B26 B27", "B24" ]
17,395,638
pmid-12464173|pmid-15145579|pmid-10786850|pmid-16111937|pmid-16455498|pmid-1380161|pmid-1380161|pmid-7523833|pmid-7688127|pmid-12941949|pmid-15145828|pmid-7533264|pmid-10594833|pmid-15743942|pmid-7732015|pmid-7534403|pmid-14622415|pmid-15743942|pmid-12526800|pmid-12787364|NA|pmid-16020788
As opposed to their predominant role in eukaryotes, poly(A) tails act as RNA-destabilizing elements in bacteria (12).
[ "12", "13", "14", "15", "16", "17", "17–19", "20", "21", "22", "23", "24", "25–27", "24" ]
117
8,398
1
false
As opposed to their predominant role in eukaryotes, poly(A) tails act as RNA-destabilizing elements in bacteria.
[ "12" ]
As opposed to their predominant role in eukaryotes, poly(A) tails act as RNA-destabilizing elements in bacteria.
true
true
true
true
true
1,352
1
INTRODUCTION
1
13
[ "B12", "B13", "B14", "B15", "B16", "B17", "B17 B18 B19", "B20", "B21", "B22", "B23", "B24", "B25 B26 B27", "B24" ]
17,395,638
pmid-12464173|pmid-15145579|pmid-10786850|pmid-16111937|pmid-16455498|pmid-1380161|pmid-1380161|pmid-7523833|pmid-7688127|pmid-12941949|pmid-15145828|pmid-7533264|pmid-10594833|pmid-15743942|pmid-7732015|pmid-7534403|pmid-14622415|pmid-15743942|pmid-12526800|pmid-12787364|NA|pmid-16020788
A destabilizing function for poly(A) tails has also been subsequently reported in mitochondria of higher plants (13), chloroplasts (14), and the nucleus of yeast and humans [reviewed in (15,16)].
[ "12", "13", "14", "15", "16", "17", "17–19", "20", "21", "22", "23", "24", "25–27", "24" ]
195
8,399
1
false
A destabilizing function for poly(A) tails has also been subsequently reported in mitochondria of higher plants, chloroplasts, and the nucleus of yeast and humans.
[ "13", "14", "reviewed in (15,16)" ]
A destabilizing function for poly(A) tails has also been subsequently reported in mitochondria of higher plants, chloroplasts, and the nucleus of yeast and humans.
true
true
true
true
true
1,352