Evidence map›Paper›PMID 39386640›Full record

ArticlebioRxiv : the preprint server for biology2024

SEISMICgraph: a web-based tool for RNA structure data visualization.

Federico Fuchs Wightman, Grant Yang, Yves J Martin des Taillades, Casper L'Esperance-Kerckhoff, Scott Grote, Matthew F Allan, Daniel Herschlag, Silvi Rouskin, Lauren D Hagler

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2024. 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

5 · Who and what money

Authors and funding

9 authors.

Federico Fuchs WightmanDepartment of Microbiology, Harvard School of Medicine, Boston, Massachusetts, 02115, United States.ORCID 0000-0003-3934-3628
Grant YangDepartment of Microbiology, Harvard School of Medicine, Boston, Massachusetts, 02115, United States.
Yves J Martin des TailladesDepartment of Biochemistry, Stanford University, Stanford, California, 94305, United States.
Casper L'Esperance-KerckhoffDepartment of Microbiology, Harvard School of Medicine, Boston, Massachusetts, 02115, United States.
Scott GroteDepartment of Microbiology, Harvard School of Medicine, Boston, Massachusetts, 02115, United States.
Matthew F AllanDepartment of Microbiology, Harvard School of Medicine, Boston, Massachusetts, 02115, United States.
Daniel HerschlagDepartment of Biochemistry, Stanford University, Stanford, California, 94305, United States.
Silvi RouskinDepartment of Microbiology, Harvard School of Medicine, Boston, Massachusetts, 02115, United States.
Lauren D HaglerDepartment of Biochemistry, Stanford University, Stanford, California, 94305, United States.

Funding

MOLECULAR BASIS OF VIRAL INFECTIVITYT32AI007245 · NIAID · HARVARD UNIVERSITY (MEDICAL SCHOOL) · PI Aaron Gregory Schmidt · 1985 to 2026
$11.3M
Constructing the nest - understanding the mechanisms of nidoviridae RNA genomes transcription and recombinationDP2AI175475 · NIAID · HARVARD MEDICAL SCHOOL · PI ROUSKIN, SILVIA · 2022 to 2022
$1.5M
NIAID NIH HHS DP2 AI175475NIAID NIH HHS T32 AI007245
6 · The paper itself

Abstract

In recent years, RNA has been increasingly recognized for its essential roles in biology, functioning not only as a carrier of genetic information but also as a dynamic regulator of gene expression through its interactions with other RNAs, proteins, and itself. Advances in chemical probing techniques have significantly enhanced our ability to identify RNA secondary structures and understand their regulatory roles. These developments, alongside improvements in experimental design and data processing, have greatly increased the resolution and throughput of structural analyses. Here, we introduce SEISMICgraph, a web-based tool designed to support RNA structure research by offering data visualization and analysis capabilities for a variety of chemical probing modalities. SEISMICgraph enables simultaneous comparison of data across different sequences and experimental conditions through a user-friendly interface that requires no programming expertise. We demonstrate its utility by investigating known and putative riboswitches and exploring how RNA modifications influence their structure and binding. SEISMICgraph's ability to rapidly visualize adenine-dependent structural changes and assess the impact of pseudouridylation on these transitions provides novel insights and establishes a roadmap for numerous future applications.

Identifiers

PMID39386640
PMCPMC11463429

What Socratic holds

Textmetadata
LicenceCC BY-NC-ND
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 Socratic graph.