Evidence map›Paper›PMID 37864197›Full record

ArticleGenome biology2023

DIVE: a reference-free statistical approach to diversity-generating and mobile genetic element discovery.

Jordi Abante, Peter L Wang, Julia Salzman

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Genome biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing 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

5 citing papers in PubMed.

  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

3 authors.

Jordi AbanteBiomedical Data Science, Stanford University, 1265 Welch Rd, Palo Alto, 94305, CA, USA.
Peter L WangBiomedical Data Science, Stanford University, 1265 Welch Rd, Palo Alto, 94305, CA, USA.
Julia SalzmanBiomedical Data Science, Stanford University, 1265 Welch Rd, Palo Alto, 94305, CA, USA. julia.salzman@stanford.edu.

Funding

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 GM139517
6 · The paper itself

Abstract

Diversity-generating and mobile genetic elements are key to microbial and viral evolution and can result in evolutionary leaps. State-of-the-art algorithms to detect these elements have limitations. Here, we introduce DIVE, a new reference-free approach to overcome these limitations using information contained in sequencing reads alone. We show that DIVE has improved detection power compared to existing reference-based methods using simulations and real data. We use DIVE to rediscover and characterize the activity of known and novel elements and generate new biological hypotheses about the mobilome. Building on DIVE, we develop a reference-free framework capable of de novo discovery of mobile genetic elements.

Indexed as

Gene Transfer, HorizontalInterspersed Repetitive SequencesDNA Transposable ElementsDNA Transposable ElementsCRISPRDiversity-generating mechanismsHorizontal gene transferIntegrative and conjugative elementsMobile genetic elementsNon-coding RNATransposable elements

Identifiers

PMID37864197
PMCPMC10589994

What OpenQuestion holds

Textmetadata
LicenceCC BY
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.