Evidence map›Paper›PMID 37162909›Full record

ArticlebioRxiv : the preprint server for biology2024

Structurally-informed human interactome reveals proteome-wide perturbations by disease mutations.

Dapeng Xiong, Yunguang Qiu, Junfei Zhao, Yadi Zhou, Dongjin Lee, Shobhita Gupta, Mateo Torres, Weiqiang Lu, Siqi Liang, Jin Joo Kang and 4 more

Open access · greenAbstract 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. 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, 4 citations in OpenAlex.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

14 authors at 5 institutions in 2 countries.

Dapeng XiongDepartment of Computational Biology, Cornell University, Ithaca, NY 14853, USA.
Yunguang QiuGenomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA.
Junfei ZhaoDepartment of Systems Biology, Herbert Irving Comprehensive Center, Columbia University, New York, NY 10032, USA.
Yadi ZhouGenomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA.
Dongjin LeeDepartment of Computational Biology, Cornell University, Ithaca, NY 14853, USA.
Shobhita GuptaWeill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA.
Mateo TorresDepartment of Computational Biology, Cornell University, Ithaca, NY 14853, USA.
Weiqiang LuShanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China.
Siqi LiangDepartment of Computational Biology, Cornell University, Ithaca, NY 14853, USA.
Jin Joo KangDepartment of Computational Biology, Cornell University, Ithaca, NY 14853, USA.
Charis EngGenomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA.
Joseph LoscalzoChanning Division of Network Medicine, Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
Feixiong ChengGenomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA.
Haiyuan YuDepartment of Computational Biology, Cornell University, Ithaca, NY 14853, USA.ORCID 0000-0001-7597-6049
Cornell University · USCleveland Clinic Lerner College of Medicine · USBrigham and Women's Hospital · USColumbia University · USEast China Normal University · CN

Funding

Boston Biomedical Innovation CenterU54HL119145 · NHLBI · BRIGHAM AND WOMEN'S HOSPITAL · PI GOLAN, DAVID E., LOSCALZO, JOSEPH · 2013 to 2021
$18.8M
Structure, Function, and Dynamics of Macro-molecular Complexes that Execute and Regulate Genome FunctionRM1GM139738 · NIGMS · CORNELL UNIVERSITY · PI Thomas George Wade Graham, Steven Zvi Josefowicz · 2021 to 2026
$14.4M
Endophenotype Network-based Approaches to Prediction and Population-based Validation of In Silico Drug Repurposing for Alzheimer's DiseaseR01AG066707 · NIA · CLEVELAND CLINIC LERNER COM-CWRU · PI Feixiong Cheng · 2020 to 2026
$4.9M
L-2-Hydroxyglutarate and Metabolic Remodeling in HypoxiaR01HL155107 · NHLBI · BRIGHAM AND WOMEN'S HOSPITAL · PI Joseph Loscalzo · 2021 to 2026
$4.1M
TREM2 Genotype-Informed Drug Repurposing and Combination Therapy Design for Alzheimer’s DiseaseR01AG076448 · NIA · CLEVELAND CLINIC LERNER COM-CWRU · PI Feixiong Cheng, Li Gan · 2022 to 2026
$4.0M
Alzheimer's MultiOme Data Repurposing: Artificial Intelligence, Network Medicine, and Therapeutics DiscoveryU01AG073323 · NIA · CLEVELAND CLINIC LERNER COM-CWRU · PI BEKRIS, LYNN, CHENG, FEIXIONG · 2021 to 2025
$4.0M
Integrated high-throughput functional assays to identify ulcerative colitis causal risk variantsR01DK115398 · NIDDK · CORNELL UNIVERSITY · PI KLEIN, ROBERT J., YU, HAIYUAN · 2018 to 2022
$3.3M
Interface-resolution domain-domain interactome map of the yeast complexomeR01GM130885 · NIGMS · DANA-FARBER CANCER INST · PI VIDAL, MARC · 2019 to 2022
$2.7M
Quantifying molecular consequences of human missense variants with large-scale interactome perturbation studiesR01GM125639 · NIGMS · CORNELL UNIVERSITY · PI ALEXOV, EMIL GEORGIEV, CLARK, ANDREW G · 2018 to 2021
$2.6M
Alzheimer's Disease and Related Dementia-like Sequelae of SARS-CoV-2 Infection: Virus-Host Interactome, Neuropathobiology, and Drug RepurposingRF1AG082211 · NIA · CLEVELAND CLINIC LERNER COM-CWRU · PI CHENG, FEIXIONG, PIEPER, ANDREW A · 2023 to 2023
$2.4M
Characterize neuronal and glial cell-specific vulnerability to proteinopathies in Alzheimer's disease using multimodal single-nuclei genomic and epigenomic approachesR01AG082118 · NIA · CLEVELAND CLINIC LERNER COM-CWRU · PI BONAKDARPOUR, BORNA, CHENG, FEIXIONG · 2023 to 2025
$2.4M
Dark GPCR signaling underlying the Microbiome-Gut-Brain Axis for Alzheimer's Disease and Related DementiaRF1NS133812 · NINDS · CLEVELAND CLINIC LERNER COM-CWRU · PI BROWN, JONATHAN MARK, CHENG, FEIXIONG · 2023 to 2023
$2.3M
American Heart Association-American Stroke Association 957729NHLBI NIH HHS R01 HL155096NHLBI NIH HHS R01 HL155107NHLBI NIH HHS U54 HL119145NIA NIH HHS R01 AG066707NIA NIH HHS R01 AG076448NIA NIH HHS R01 AG082118NIA NIH HHS R01 AG084250NIA NIH HHS R21 AG083003NIA NIH HHS R56 AG074001NIA NIH HHS RF1 AG082211NIA NIH HHS U01 AG073323NIDDK NIH HHS R01 DK115398NIGMS NIH HHS R01 GM124559NIGMS NIH HHS R01 GM125639NIGMS NIH HHS R01 GM130885NIGMS NIH HHS RM1 GM139738NINDS NIH HHS RF1 NS133812
6 · The paper itself

Abstract

Human genome sequencing studies have identified numerous loci associated with complex diseases. However, translating human genetic and genomic findings to disease pathobiology and therapeutic discovery remains a major challenge at multiscale interactome network levels. Here, we present a deep-learning-based ensemble framework, termed PIONEER (

Identifiers

PMID37162909
PMCPMC10168245
OpenAlexW4367053919

What Socratic 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 Socratic graph.