Evidence map›Paper›PMID 37961699›Full record

ArticlebioRxiv : the preprint server for biology2023

Yichen Si, ChangHee Lee, Yongha Hwang, Jeong H Yun, Weiqiu Cheng, Chun-Seok Cho, Miguel Quiros, Asma Nusrat, Weizhou Zhang, Goo Jun and 3 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 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.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

13 authors.

Yichen SiDepartment of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, 48109-2029, USA.
ChangHee LeeDepartment of Genetics, Harvard Medical School, Boston, MA 02115, USA.
Yongha HwangDepartment of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, Michigan, 48109-2200, USA.
Jeong H YunChanning Division of Network Medicine, and Division of Pulmonary and Critical Care, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA.ORCID 0000-0002-4361-8295
Weiqiu ChengDepartment of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, 48109-2029, USA.
Chun-Seok ChoDepartment of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, Michigan, 48109-2200, USA.
Miguel QuirosDepartment of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, 48109, USA.
Asma NusratDepartment of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, 48109, USA.
Weizhou ZhangDepartment of Pathology, Immunology, and Laboratory Medicine, University of Florida, College of Medicine, Gainesville, FL 32610-0275, USA.
Goo JunHuman Genetics Center, School of Public Health, University of Texas Health Science Center Houston, Houston, TX 77030, USA.ORCID 0000-0003-0891-0204
Sebastian ZöllnerDepartment of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, 48109-2029, USA.
Jun Hee LeeDepartment of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, Michigan, 48109-2200, USA.
Hyun Min KangDepartment of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, 48109-2029, USA.ORCID 0000-0002-3631-3979

Funding

The NRF2-FBP1 crossregulatory loop and the control of healthy and diseased liver metabolismR01DK133448 · NIDDK · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI Michael Karin, Jun Hee Lee · 2022 to 2026
$3.6M
Sestrins-mediated integration of leucine and exercise benefits for mitochondrial homeostasisR01AG079163 · NIA · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI Myungjin Kim, Jun Hee Lee · 2023 to 2026
$2.1M
Seq-Scope: Microscopic Examination of Spatial Single Cell Transcriptome in Cell and Tissue SenescenceUH3CA268091 · NCI · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI LEE, JUN HEE · 2023 to 2025
$1.7M
Leveraging long-range haplotypes in sequencing data to advance large scale genetic studiesR01HG011031 · NHGRI · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI ZOELLNER, SEBASTIAN · 2020 to 2023
$1.4M
Seq-Scope: Microscopic Examination of Spatial Single Cell Transcriptome in Cell and Tissue SenescenceUG3CA268091 · NCI · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI LEE, JUN HEE · 2021 to 2022
$1.1M
The role of COPD genetic risk factor HHIP on lymphocytic inflammationK08HL146972 · NHLBI · BRIGHAM AND WOMEN'S HOSPITAL · PI YUN, JEONG H · 2020 to 2024
$848k
NCI NIH HHS UG3 CA268091NCI NIH HHS UH3 CA268091NHGRI NIH HHS R01 HG011031NHLBI NIH HHS K08 HL146972NIA NIH HHS R01 AG079163NIDDK NIH HHS R01 DK133448
6 · The paper itself

Abstract

Spatial transcriptomics (ST) technologies have advanced to enable transcriptome-wide gene expression analysis at submicron resolution over large areas. Analysis of high-resolution ST data relies heavily on image-based cell segmentation or gridding, which often fails in complex tissues due to diversity and irregularity of cell size and shape. Existing segmentation-free analysis methods scale only to small regions and a small number of genes, limiting their utility in high-throughput studies. Here we present FICTURE, a segmentation-free spatial factorization method that can handle transcriptome-wide data labeled with billions of submicron resolution spatial coordinates. FICTURE is orders of magnitude more efficient than existing methods and it is compatible with both sequencing- and imaging-based ST data. FICTURE reveals the microscopic ST architecture for challenging tissues, such as vascular, fibrotic, muscular, and lipid-laden areas in real data where previous methods failed. FICTURE's cross-platform generality, scalability, and precision make it a powerful tool for exploring high-resolution ST.

Identifiers

PMID37961699
PMCPMC10635162

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.