Evidence map›Paper›PMID 24795371›Full record

ArticleApplied and environmental microbiology2014

Targeted and highly multiplexed detection of microorganisms by employing an ensemble of molecular probes.

Weihong Xu, Sujatha Krishnakumar, Molly Miranda, Michael A Jensen, Marilyn Fukushima, Curtis Palm, Eula Fung, Ronald W Davis, Robert P St Onge, Richard W Hyman

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Applied and environmental microbiology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

3 citing papers in PubMed.

  1. Article
  2. Article
  3. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

10 authors.

Weihong XuStanford Genome Technology Center, Palo Alto, California, USA.
Sujatha KrishnakumarStanford Genome Technology Center, Palo Alto, California, USA.
Molly MirandaStanford Genome Technology Center, Palo Alto, California, USA.
Michael A JensenStanford Genome Technology Center, Palo Alto, California, USA.
Marilyn FukushimaStanford Genome Technology Center, Palo Alto, California, USA.
Curtis PalmStanford Genome Technology Center, Palo Alto, California, USA.
Eula FungStanford Genome Technology Center, Palo Alto, California, USA.
Ronald W DavisStanford Genome Technology Center, Palo Alto, California, USA Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA Department of Genetics, Stanford University School of Medicine, Stanford, California, USA.
Robert P St OngeStanford Genome Technology Center, Palo Alto, California, USA Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA.
Richard W HymanStanford Genome Technology Center, Palo Alto, California, USA Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA rhyman@stanford.edu.

Funding

WHOLE YEAST GENOME TRANSCRIPTIONAL AND FUNCTIONAL GENE MAPS--A FEASIBILITY STUDYP01HG000205 · NHGRI · STANFORD UNIVERSITY · PI HOWE, ROGER THOMAS, JI, HANLEE P · 1990 to 2016
$120.9M
A NEW ES CELL DELETION RESOURCE AND WILLIAMS SYNDROMEF32HG000205 · NHGRI · JACKSON LABORATORY · PI GOODWIN, NEAL C · 1999 to 1999
–
NHGRI NIH HHS F32 HG000205NHGRI NIH HHS HG000205NHGRI NIH HHS P01 HG000205
6 · The paper itself

Abstract

The vast majority of microscopic life on earth consists of microbes that do not grow in laboratory culture. To profile the microbial diversity in environmental and clinical samples, we have devised and employed molecular probe technology, which detects and identifies bacteria that do and do not grow in culture. The only requirement is a short sequence of contiguous bases (currently 60 bases) unique to the genome of the organism of interest. The procedure is relatively fast, inexpensive, customizable, robust, and culture independent and uses commercially available reagents and instruments. In this communication, we report improving the specificity of the molecular probes substantially and increasing the complexity of the molecular probe set by over an order of magnitude (>1,200 probes) and introduce a new final readout method based upon Illumina sequencing. In addition, we employed molecular probes to identify the bacteria from vaginal swabs and demonstrate how a deliberate selection of molecular probes can identify less abundant bacteria even in the presence of much more abundant species.

Indexed as

BacteriaBacteriological TechniquesDNA, BacterialMolecular ProbesOligonucleotide Array Sequence AnalysisOligonucleotidesPolymerase Chain ReactionSensitivity and SpecificitySequence Analysis, DNADNA, BacterialMolecular ProbesOligonucleotides

Identifiers

PMID24795371
PMCPMC4068679

What OpenQuestion holds

Textmetadata
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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.