Evidence map›Paper›PMID 38078749›Full record

ArticlemSystems2024

A bacterial sensor taxonomy across earth ecosystems for machine learning applications.

Helen Park, Marcin P Joachimiak, Sean P Jungbluth, Ziming Yang, William J Riehl, R Shane Canon, Adam P Arkin, Paramvir S Dehal

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in mSystems, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing 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

2 citing papers in PubMed.

  1. Article
  2. 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

8 authors.

Helen ParkCenter for Synthetic and Systems Biology, School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China.ORCID 0000-0003-0978-2179
Marcin P JoachimiakEnvironmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Sean P JungbluthEnvironmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Ziming YangComputational Science Initiative, Brookhaven National Laboratory, Upton, New York, USA.
William J RiehlEnvironmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
R Shane CanonEnvironmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Adam P ArkinEnvironmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.ORCID 0000-0002-4999-2931
Paramvir S DehalEnvironmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.ORCID 0000-0001-5810-2497

Funding

DOE | NNSA | LDRD | Lawrence Berkeley National Laboratory (LBNL)
6 · The paper itself

Abstract

Microbial communities have evolved to colonize all ecosystems of the planet, from the deep sea to the human gut. Microbes survive by sensing, responding, and adapting to immediate environmental cues. This process is driven by signal transduction proteins such as histidine kinases, which use their sensing domains to bind or otherwise detect environmental cues and "transduce" signals to adjust internal processes. We hypothesized that an ecosystem's unique stimuli leave a sensor "fingerprint," able to identify and shed insight on ecosystem conditions. To test this, we collected 20,712 publicly available metagenomes from

Indexed as

MetagenomicsMicrobiotaEarth, PlanetHumansMachine LearningMetagenomefeature importancehistidine kinasehuman microbiomemachine learningmetagenomicssensory transduction processes

Identifiers

PMID38078749
PMCPMC10804942

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

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.