Evidence map›Paper›PMID 42818572›Full record

ArticlebioRxiv : the preprint server for biology2026

Nearest Neighbor Parameters for Estimating RNA Folding Stability with

Olivia M Hiltke, Elzbieta Kierzek, Martina Prochota, Marta Rachwalak, Megan Miaro, Thandolwethu Shabangu, Sylwia Gorczynska, Ryszard Kierzek, David H Mathews

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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

0 citing papers in PubMed.

No citing paper in PubMed yet.

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

9 authors.

Olivia M HiltkeDepartment of Biochemistry & Biophysics and Center for RNA Biology, University of Rochester Medical Center, Rochester, New York 14526, USA.
Elzbieta KierzekInstitute of Bioorganic Chemistry Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
Martina ProchotaInstitute of Bioorganic Chemistry Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
Marta RachwalakInstitute of Bioorganic Chemistry Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
Megan MiaroDepartment of Biochemistry & Biophysics and Center for RNA Biology, University of Rochester Medical Center, Rochester, New York 14526, USA.
Thandolwethu ShabanguDepartment of Biochemistry & Biophysics and Center for RNA Biology, University of Rochester Medical Center, Rochester, New York 14526, USA.
Sylwia GorczynskaInstitute of Bioorganic Chemistry Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
Ryszard KierzekInstitute of Bioorganic Chemistry Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
David H MathewsDepartment of Biochemistry & Biophysics and Center for RNA Biology, University of Rochester Medical Center, Rochester, New York 14526, USA.ORCID 0000-0002-2907-6557

Funding

Training in Wellness and Resiliency at the University of Rochester Medical Center and College of Arts, Sciences & EngineeringT32GM135134 · NIGMS · UNIVERSITY OF ROCHESTER · PI Jeffrey J Hayes, Lynne E Maquat · 2020 to 2026
$2.9M
RNA Structure Modeling Using Physics and Sequence ComparisonR35GM145283 · NIGMS · UNIVERSITY OF ROCHESTER · PI DAVID H. MATHEWS · 2022 to 2026
$2.7M
NIGMS NIH HHS R35 GM145283NIGMS NIH HHS T32 GM135134
6 · The paper itself

Abstract

RNAs regulate gene expression and cellular processes, often relying on specific conformations for function. RNA folding is hierarchical and sequence-dependent, with nearest-neighbor thermodynamic models commonly used to predict secondary structure. Current models were developed using optical melting experiments in 1 M NaCl, which does not represent the cellular environment. To address this, we developed a new model in Advanced Dulbecco's Modified Eagle Medium (Adv. DMEM), which mimics mammalian extracellular ionic composition. This

Identifiers

PMID42818572
PMCPMC13622511

What OpenQuestion holds

Textmetadata
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.