Evidence map›Paper›PMID 28572834›Full record

ArticleAlgorithms for molecular biology : AMB2017

StreAM-[Formula: see text]: algorithms for analyzing coarse grained RNA dynamics based on Markov models of connectivity-graphs.

Sven Jager, Benjamin Schiller, Philipp Babel, Malte Blumenroth, Thorsten Strufe, Kay Hamacher

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

Article in Algorithms for molecular biology : AMB, 2017. 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
0.6field-weighted citation impact, top 34% 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

3 citing papers in PubMed, 7 citations in OpenAlex.

  1. Article
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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

6 authors at 2 institutions in 1 country.

Sven JagerDepartment of Biology, TU Darmstadt, Schnittspahnstr. 2, 64283 Darmstadt, Germany.ORCID 0000-0003-1410-9114
Benjamin SchillerDepartment of Computer Science, TU Dresden, Nöthnitzer Str. 46, 01187 Dresden, Germany.
Philipp BabelDepartment of Biology, TU Darmstadt, Schnittspahnstr. 2, 64283 Darmstadt, Germany.
Malte BlumenrothDepartment of Biology, TU Darmstadt, Schnittspahnstr. 2, 64283 Darmstadt, Germany.
Thorsten StrufeDepartment of Computer Science, TU Dresden, Nöthnitzer Str. 46, 01187 Dresden, Germany.
Kay HamacherDepartment of Biology, Department of Computer Science, Department of Physics, TU Darmstadt, Schnittspahnstr. 2, 64283 Darmstadt, Germany.
Technische Universität Darmstadt · DETechnische Universität Dresden · DE

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

backgroundIn this work, we present a new coarse grained representation of RNA dynamics. It is based on adjacency matrices and their interactions patterns obtained from molecular dynamics simulations. RNA molecules are well-suited for this representation due to their composition which is mainly modular and assessable by the secondary structure alone. These interactions can be represented as adjacency matrices of

resultsWe benchmark

conclusionsThe proposed algorithm performs well on large simulated as well as real world dynamic graphs. Additionally,

Indexed as

Coarse grainingDynamic graphsMarkovian dynamicsMolecular dynamicsRNASynthetic biology

Identifiers

PMID28572834
PMCPMC5450175
OpenAlexW2616999455

What OpenQuestion holds

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LicenceCC BY
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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.