Evidence map›Paper›PMID 40631230›Full record

ArticlebioRxiv : the preprint server for biology2025

spRefine Denoises and Imputes Spatial Transcriptomics with a Reference-Free Framework Powered by Genomic Language Model.

Tianyu Liu, Tinglin Huang, Wengong Jin, Tinyi Chu, Rex Ying, Hongyu Zhao

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2025. 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

6 authors.

Tianyu LiuInterdepartmental Program in Computational Biology & Bioinformatics, Yale University, New Haven, 06511, CT, USA.
Tinglin HuangDepartment of Computer Science, Yale University, New Haven, 06511, CT, USA.
Wengong JinDepartment of Computer Science, Northeastern University, Boston, 02115, MA, USA.
Tinyi ChuDepartment of Biostatistics, Yale University, New Haven, 06511, CT, USA.
Rex YingDepartment of Computer Science, Yale University, New Haven, 06511, CT, USA.
Hongyu ZhaoInterdepartmental Program in Computational Biology & Bioinformatics, Yale University, New Haven, 06511, CT, USA.ORCID 0000-0003-1195-9607

Funding

Laboratory, Data Analysis, and Coordinating Center (LDACC) for the Developmental Human Genotype-Tissue Expression ProjectU24HG012108 · NHGRI · YALE UNIVERSITY · PI GERSTEIN, MARK BENDER, HUTTNER, ANITA JULIANE · 2021 to 2025
$8.7M
Computational and Statistical Methods to determine variant effect across cell types and development stagesU01HG013840 · NHGRI · YALE UNIVERSITY · PI GERSTEIN, MARK BENDER, ZHAO, HONGYU · 2024 to 2024
$1.9M
Computational Modeling of the Interplay between External Signaling and Transcription Rewiring using Spatial Transcriptomics and Single Cell Multiome DataK99HG013429 · NHGRI · YALE UNIVERSITY · PI CHU, TIN YI · 2024 to 2025
$284k
NHGRI NIH HHS K99 HG013429NHGRI NIH HHS U01 HG013840NHGRI NIH HHS U24 HG012108
6 · The paper itself

Abstract

The analysis of spatial transcriptomics is hindered by high noise levels and missing gene measurements, challenges that are further compounded by the higher cost of spatial data compared to traditional single-cell data. To overcome this challenge, we introduce

Indexed as

AgeingData DenoisingData ImputationFoundation ModelSpatial TranscriptomicsSurvival Analysis

Identifiers

PMID40631230
PMCPMC12236840

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC
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.