Evidence map›Paper›PMID 37292889›Full record

ArticleResearch square2023

LinRace: single cell lineage reconstruction using paired lineage barcode and gene expression data.

Xinhai Pan, Hechen Li, Pranav Putta, Xiuwei Zhang

Open access · greenAbstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in Research square, 2023. 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, 0 citations in OpenAlex.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

4 authors at 1 institution in 1 country.

Xinhai PanSchool of Computational Science and Engineering, Georgia Institute of Technology, Atlanta GA 30332, USA.ORCID 0000-0002-3914-8489
Hechen LiSchool of Computational Science and Engineering, Georgia Institute of Technology, Atlanta GA 30332, USA.ORCID 0000-0003-4907-429X
Pranav PuttaSchool of Computational Science and Engineering, Georgia Institute of Technology, Atlanta GA 30332, USA.
Xiuwei ZhangSchool of Computational Science and Engineering, Georgia Institute of Technology, Atlanta GA 30332, USA.ORCID 0000-0002-1713-772X
Georgia Institute of Technology · US

Funding

Studying temporal dynamics and regulatory mechanisms of single cells with a unified framework and multi-omics dataR35GM143070 · NIGMS · GEORGIA INSTITUTE OF TECHNOLOGY · PI ZHANG, XIUWEI · 2021 to 2025
$1.8M
NIGMS NIH HHS R35 GM143070
6 · The paper itself

Abstract

Understanding how single cells divide and differentiate into different cell types in developed organs is one of the major tasks of developmental and stem cell biology. Recently, lineage tracing technology using CRISPR/Cas9 genome editing have enabled simultaneous readouts of gene expressions and lineage barcodes in single cells, which allows for the reconstruction of the cell division tree, and even the detection of cell types and differentiation trajectories at the whole organism level. While most state-of-the-art methods for lineage reconstruction utilize only the lineage barcode data, methods that incorporate gene expression data are emerging, aiming to improve the accuracy of lineage reconstruction. However, effectively incorporating the gene expression data requires a reasonable model on how gene expression data changes along generations of divisions. Here, we present LinRace (

Indexed as

CRISPR/Cas9 genome editingMaximum likelihoodNeighbor Joiningsingle cell lineage reconstruction

Identifiers

PMID37292889
PMCPMC10246273
OpenAlexW4377690788

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.