Evidence map›Paper›PMID 38826472›Full record

ArticlebioRxiv : the preprint server for biology2024

A reference-free algorithm discovers regulation in the plant transcriptome.

Elisabeth Meyer, Evan V Saldivar, Marek Kokot, Bo Xue, Sebastian Deorowicz, Seung Y Rhee, Julia Salzman

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

7 authors.

Elisabeth MeyerDepartment of Biochemistry, Stanford University, Stanford, CA, 94305, USA.ORCID 0000-0002-3108-6017
Evan V SaldivarDepartment of Biology, Stanford University, Stanford, CA, 94305, USA.ORCID 0000-0002-4383-3550
Marek KokotDepartment of Algorithmics and Software, Silesian University of Technology, Gliwice, Poland.ORCID 0000-0002-6420-1587
Bo XueDepartment of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA.ORCID 0000-0002-7957-3033
Sebastian DeorowiczDepartment of Algorithmics and Software, Silesian University of Technology, Gliwice, Poland.ORCID 0000-0002-9496-733X
Seung Y RheeDepartment of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA.ORCID 0000-0002-7572-4762
Julia SalzmanDepartment of Biochemistry, Stanford University, Stanford, CA, 94305, USA.

Funding

Supplement to Enhance Wellness and Resiliency in the Graduate EnvironmentT32GM007276 · NIGMS · STANFORD UNIVERSITY · PI MORRISON, ASHBY J. · 1985 to 2023
$32.9M
Computational- and experimental- driven discovery of splicing regulation and circRNA functionR35GM139517 · NIGMS · STANFORD UNIVERSITY · PI Julia Salzman · 2021 to 2026
$2.9M
NIGMS NIH HHS R35 GM139517NIGMS NIH HHS T32 GM007276
6 · The paper itself

Abstract

Most plant genomes and their regulation remain unknown. We used SPLASH - a new, reference-genome free sequence variation detection algorithm - to analyze transcriptional and post-transcriptional regulation from RNA-seq data. We discovered differential homolog expression during maize pollen development, and imbibition-dependent cryptic splicing in Arabidopsis seeds. SPLASH enables discovery of novel regulatory mechanisms, including differential regulation of genes from hybrid parental haplotypes, without the use of alignment to a reference genome.

Identifiers

PMID38826472
PMCPMC11142198

What OpenQuestion holds

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Registered trials

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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.