Evidence map›Paper›PMID 35398145›Full record

ArticleJournal of molecular biology2022

The Four mRNA Bases Have Quite Different (Un)folding Free Energies, Applications to RNA Splicing and Translation Initiation with BindOligoNet.

Julian M Hess, William K Jannen, Daniel P Aalberts

Open access · hybridAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Journal of molecular biology, 2022. 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
0.3field-weighted citation impact, top 46% of its field
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, 4 citations in OpenAlex.

  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

3 authors at 1 institution in 1 country.

Julian M HessWilliams College, Williamstown, MA 01267, USA.
William K JannenWilliams College, Williamstown, MA 01267, USA.
Daniel P AalbertsWilliams College, Williamstown, MA 01267, USA. Electronic address: aalberts@williams.edu.
Williams College · US

Funding

Binding and Splicing mRNAR15GM080690 · NIGMS · WILLIAMS COLLEGE · PI AALBERTS, DANIEL PAUL · 2007 to 2009
$300k
AREA: Optimizing gene expression with mRNA free energy modeling and algorithmsR15GM106372 · NIGMS · WILLIAMS COLLEGE · PI AALBERTS, DANIEL PAUL · 2014 to 2014
$255k
NIGMS NIH HHS R15 GM080690NIGMS NIH HHS R15 GM106372
6 · The paper itself

Abstract

Expression of mRNA is often regulated by the binding of a small RNA (miRNA, snoRNA, siRNA). While the pairing contribution to the net free energy is well parameterized and can be computed in O(N) time, the cost of removing pre-existing mRNA secondary structure has not received sufficient attention. Conventional methods for computing the unfolding free energy of a target mRNA are costly, scaling like the cube of the number of target bases O(N

Indexed as

Peptide Chain Initiation, TranslationalRNA, MessengerRNA SplicingAlgorithmsBinding SitesNucleic Acid ConformationNucleotidesRNA, Small NuclearSpliceosomesThermodynamicsNucleotidesRNA, MessengerRNA, Small NuclearU1 small nuclear RNAgene regulationmessenger RNAnucleic acidsribosome initiationSmall RNA

Identifiers

PMID35398145
PMCPMC12677014
OpenAlexW4223492051

What OpenQuestion holds

Textmetadata
LicenceTDM
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.