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Paper · 25947005

An empirical strategy to detect bacterial transcript structure from directional RNA-seq transcriptome data.

Wang Y and 2 others. BMC Genomics, 2015. Cited by 10 papers, by iCite.

11 sourcespapers-2026-11-12-0.1.0

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ConductScience Library. An empirical strategy to detect bacterial transcript structure from directional RNA-seq transcriptome data. Papers, record 25947005. Release papers-2026-11-12-0.1.0, 12 Nov 2026. https://conductscience.org/library/papers/25947005

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Paper

PubMed's record of the paper, with iCite's citation figures. No abstract is shown.

Title
An empirical strategy to detect bacterial transcript structure from directional RNA-seq transcriptome data.
PubMed
Journal
BMC Genomics
PubMed
Year
2015
PubMed
Publication types
Journal Article, Research Support, Non-U.S. Gov't
PubMed
Citations, by iCite
10
iCite
Relative citation ratio, by iCite
0.33
iCite
Revised in PubMed
2018-11-13
PubMed

Authors3

The authors in the order PubMed's record lists them, with the ORCID iDs it states.

OrderAuthorForenameKindORCID iD
1Wang YYejun
2MacKenzie KDKeith D
3White APAaron P

Source PubMed

Topics13

NLM's MeSH indexing of the paper, its major topics first.

MeSH termMajor
Salmonella typhimuriumMajor topic
Transcription, GeneticMajor topic
Bacterial Proteins
Base Sequence
DNA-Directed RNA Polymerases
Gene Library
Operon
Promoter Regions, Genetic
RNA, Messenger
Sigma Factor
Terminator Regions, Genetic
Transcription Initiation Site
Transcriptome

Source PubMed

Grants0

Each grant PubMed's record writes, matched to the NIH project NIH's grant and paper links name for this paper, and each of those links the record does not write.

None in this release.

Trials0

The trials whose ClinicalTrials.gov record lists the paper, and the trial numbers the paper's PubMed record names.

None in this release.

Comments and corrections0

PubMed's comments and corrections, NLM's own indexing: retractions first, then expressions of concern, errata and updates, and comments last.

None in this release.

References40

The papers the reference list in PubMed's record names, those in our copy of PubMed, in the list's order.

OrderPMIDTitleJournalYearIn PapersSource
110,823,905Operons in Escherichia coli: genomic analyses and predictions.Proc Natl Acad Sci U S A2000https://conductscience.org/library/papers/10823905PubMed
211,375,988Sigma38 (rpoS) RNA polymerase promoter engagement via -10 region nucleotides.J Biol Chem2001https://conductscience.org/library/papers/11375988PubMed
315,173,120WebLogo: a sequence logo generator.Genome Res2004https://conductscience.org/library/papers/15173120PubMed
4922,889Sizing and mapping of early adenovirus mRNAs by gel electrophoresis of S1 endonuclease-digested hybrids.Cell1977https://conductscience.org/library/papers/922889PubMed
590,173Characterization of the 5'-terminal structure of simian virus 40 early mRNA's.J Virol1979https://conductscience.org/library/papers/90173PubMed
62,461,560Rapid production of full-length cDNAs from rare transcripts: amplification using a single gene-specific oligonucleotide primer.Proc Natl Acad Sci U S A1988https://conductscience.org/library/papers/2461560PubMed
77,573,945Revolutions in rapid amplification of cDNA ends: new strategies for polymerase chain reaction cloning of full-length cDNA ends.Anal Biochem1995https://conductscience.org/library/papers/7573945PubMed
815,558,318Microarray analysis of RpoS-mediated gene expression in Escherichia coli K-12.Mol Genet Genomics2004https://conductscience.org/library/papers/15558318PubMed
916,287,942Improved prediction of bacterial transcription start sites.Bioinformatics2006https://conductscience.org/library/papers/16287942PubMed
1016,621,814Thin aggregative fimbriae and cellulose enhance long-term survival and persistence of Salmonella.J Bacteriol2006https://conductscience.org/library/papers/16621814PubMed

1 to 10 of 40

See all 40 references

Cited by6

The papers in our copy of PubMed whose reference list names this one, newest first. iCite, which reads more sources, counts 10 citations.

PMIDTitleJournalYearIn PapersSource
42,254,512A transcription unit based systems biology study on Salmonella typhimurium gene organization, evolution, co-expression, and regulation.Front Microbiol2026https://conductscience.org/library/papers/42254512PubMed
32,694,125Genome-Scale Transcription-Translation Mapping Reveals Features of Zymomonas mobilis Transcription Units and Promoters.mSystems2020https://conductscience.org/library/papers/32694125PubMed
32,332,138Transcriptome Analysis Reveals IsiA-Regulatory Mechanisms Underlying Iron Depletion and Oxidative-Stress Acclimation in Synechocystis sp. Strain PCC 6803.Appl Environ Microbiol2020https://conductscience.org/library/papers/32332138PubMed
27,706,236RNA-Seq of Borrelia burgdorferi in Multiple Phases of Growth Reveals Insights into the Dynamics of Gene Expression, Transcriptome Architecture, and Noncoding RNAs.PLoS One2016https://conductscience.org/library/papers/27706236PubMed
27,217,422Distribution and Evolution of Yersinia Leucine-Rich Repeat Proteins.Infect Immun2016https://conductscience.org/library/papers/27217422PubMed
25,824,832Bistable expression of CsgD in Salmonella enterica serovar Typhimurium connects virulence to persistence.Infect Immun2015https://conductscience.org/library/papers/25824832PubMed

Genes0

The genes the Gene search release ties to the paper: Swiss-Prot's references first, then PubTator's text mining.

None in this release.

Drugs0

The drugs whose trials, in the Pipelines release, list the paper.

None in this release.

Data0

The data bank entries PubMed's record names. Trial numbers are under Trials.

None in this release.

Data dates

The date of each source this release read.

PubMed
2026-11-06
PubMed
iCite
2026-11-05
iCite
PMC's ID file
2026-11-05
PMC's ID file
NIH RePORTER's grant and paper links
2026-11-01
NIH RePORTER's grant and paper links
Trials
2026-11-12
Gene search
2026-11-11
Pipelines
2026-09-18

Sources 11

  • ChEMBL, through Open TargetsCC BY-SA 3.0
  • ClinicalTrials.govNo license stated
  • HGNCCC0
  • iCiteCC BY 4.0
  • NCBI GenePublic domain (US government)
  • NIH RePORTER's grant and paper linksPublic domain
  • Open TargetsCC0 1.0
  • PMC's ID filePublic domain (US government)
  • PubMedNLM's terms
  • PubTator 3Public domain
  • UniProtCC BY 4.0
Each source's terms
  • ChEMBL, through Open TargetsCC BY-SA 3.0, for the parts from ChEMBL. Read on 8 Nov 2026 at https://platform-docs.opentargets.org/licence
  • ClinicalTrials.govnone stated
  • HGNCCC0: https://www.genenames.org/about/license/
  • iCiteCC BY 4.0
  • NCBI GeneNone named for the file. NCBI says information created by or for the US government on its site is in the public domain, and asks that NLM be acknowledged: https://www.ncbi.nlm.nih.gov/home/about/policies/
  • NIH RePORTER's grant and paper linksPublic domain (NIH RePORTER)
  • Open TargetsCC0 1.0. Open Targets asks that users cite its latest paper: Buniello et al. 2025, Open Targets Platform: facilitating therapeutic hypotheses building in drug discovery, Nucleic Acids Research 53(D1):D1467, PMID 39657122. Read on 8 Nov 2026 at https://platform-docs.opentargets.org/licence
  • PMC's ID fileNone named for the file. NCBI says information created by or for the US government on its site is in the public domain, and asks that NLM be acknowledged: https://www.ncbi.nlm.nih.gov/home/about/policies/
  • PubMedNLM's terms
  • PubTator 3Public domain
  • UniProtCC BY 4.0. UniProt's licence file: "All databases and documents in the UniProt FTP directory may be copied and redistributed freely, without advance permission, provided that this copyright statement is reproduced with each copy." UniProt asks that users cite its latest paper: The UniProt Consortium, UniProt: the Universal Protein Knowledgebase in 2025, Nucleic Acids Research 53:D609-D617, https://doi.org/10.1093/nar/gkae1010. Read on 9 Nov 2026 at https://www.uniprot.org/help/license

ClinicalTrials.gov's data carry an international copyright outside the United States: https://clinicaltrials.gov/about-site/terms-conditions.

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