Evidence map›Paper›PMID 39149271›Full record

ArticlebioRxiv : the preprint server for biology2024

Optics-free reconstruction of 2D images via DNA barcode proximity graphs.

Hanna Liao, Sanjay Kottapalli, Yuqi Huang, Matthew Chaw, Jase Gehring, Olivia Waltner, Melissa Phung-Rojas, Riza M Daza, Frederick A Matsen, Cole Trapnell and 2 more

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. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. Review
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

12 authors.

Hanna LiaoDepartment of Genome Sciences, University of Washington, Seattle, WA, USA.
Sanjay KottapalliDepartment of Genome Sciences, University of Washington, Seattle, WA, USA.
Yuqi HuangBasic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
Matthew ChawDepartment of Genome Sciences, University of Washington, Seattle, WA, USA.
Jase GehringDepartment of Genome Sciences, University of Washington, Seattle, WA, USA.
Olivia WaltnerDepartment of Genome Sciences, University of Washington, Seattle, WA, USA.
Melissa Phung-RojasBasic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
Riza M DazaDepartment of Genome Sciences, University of Washington, Seattle, WA, USA.
Frederick A MatsenBasic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
Cole TrapnellDepartment of Genome Sciences, University of Washington, Seattle, WA, USA.
Jay ShendureDepartment of Genome Sciences, University of Washington, Seattle, WA, USA.
Sanjay SrivatsanDepartment of Genome Sciences, University of Washington, Seattle, WA, USA.

Funding

Versatile, exponentially scalable methods for single cell molecular profilingR01HG010632 · NHGRI · UNIVERSITY OF WASHINGTON · PI Jay Ashok Shendure, Bruce Colston Trapnell · 2019 to 2026
$5.9M
Blending deep learning with probabilistic mechanistic models to predict and understand the evolution and function of adaptive immune receptorsR01AI146028 · NIAID · FRED HUTCHINSON CANCER RESEARCH CENTER · PI MATSEN, FREDERICK ALBERT · 2019 to 2024
$3.4M
NHGRI NIH HHS R01 HG010632NIAID NIH HHS R01 AI146028
6 · The paper itself

Abstract

Spatial genomic technologies include imaging- and sequencing-based methods (1-3). An emerging subcategory of sequencing-based methods relies on a surface coated with coordinate-associated DNA barcodes, which are leveraged to tag endogenous nucleic acids or cells in an overlaid tissue section (4-7). However, the physical registration of DNA barcodes to spatial coordinates is challenging, necessitating either high density printing of coordinate-specific oligonucleotides or

Identifiers

PMID39149271
PMCPMC11326233

What OpenQuestion 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 OpenQuestion graph.