Evidence map›Paper›PMID 36993652›Full record

ArticlebioRxiv : the preprint server for biology2023

Benchmarking of deep neural networks for predicting personal gene expression from DNA sequence highlights shortcomings.

Alexander Sasse, Bernard Ng, Anna E Spiro, Shinya Tasaki, David A Bennett, Christopher Gaiteri, Philip L De Jager, Maria Chikina, Sara Mostafavi

Abstract readPreprint
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

9 authors.

Alexander SassePaul G. Allen School of Computer Science and Engineering, University of Washington, WA, USA, 98195.
Bernard NgRush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois, USA, 60612.
Anna E SpiroPaul G. Allen School of Computer Science and Engineering, University of Washington, WA, USA, 98195.
Shinya TasakiRush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois, USA, 60612.
David A BennettRush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois, USA, 60612.
Christopher GaiteriRush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois, USA, 60612.
Philip L De JagerCenter for Translational & Computational Neuroimmunology, Department of Neurology, and the Taub Institute for the Study of Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA, 10032.
Maria ChikinaDepartment of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA, 15260.
Sara MostafaviPaul G. Allen School of Computer Science and Engineering, University of Washington, WA, USA, 98195.

Funding

SUPPLEMENT TO RUSH ALZHEIMERS DISEASE CENTER COREP30AG010161 · NIA · RUSH UNIVERSITY MEDICAL CENTER · PI LEURGANS, SUE E. · 1991 to 2020
$49.1M
EPIDEMIOLOGY OF NEURAL RESERVE AND NEUROBIOLOGY IN AGINGR01AG017917 · NIA · RUSH UNIVERSITY MEDICAL CENTER · PI BENNETT, DAVID ALAN · 2001 to 2023
$43.3M
Rush Alzheimer's Disease Research CenterP30AG072975 · NIA · RUSH UNIVERSITY MEDICAL CENTER · PI Lisa L Barnes, Julie A. Schneider · 2021 to 2026
$24.7M
RISK FACTORS, PATHOLOGY, AND CLINICAL EXPRESSIONS OF ADR01AG015819 · NIA · RUSH UNIVERSITY MEDICAL CENTER · PI BENNETT, DAVID ALAN · 1998 to 2024
$21.4M
Multi-omic network-directed proteoform discovery, dissection and functional validation to prioritize novel AD therapeutic targetsU01AG061356 · NIA · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI BENNETT, DAVID ALAN, DE JAGER, PHILIP L · 2018 to 2022
$13.7M
Pathway discovery, validation and compound identification for Alzheimer's disease - SupplementU01AG046152 · NIA · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI BENNETT, DAVID ALAN, DE JAGER, PHILIP L · 2013 to 2017
$13.6M
Identifying the molecular systems, networks, and key molecules that underlie cognitive resilienceR01AG057911 · NIA · UPSTATE MEDICAL UNIVERSITY · PI GAITERI, CHRISTOPHER A. · 2017 to 2021
$3.8M
Exploring the Role of the Brain Transcriptome in Cognitive DeclineR01AG036836 · NIA · BRIGHAM AND WOMEN'S HOSPITAL · PI DE JAGER, PHILIP L · 2011 to 2014
$2.9M
NIA NIH HHS P30 AG010161NIA NIH HHS P30 AG072975NIA NIH HHS R01 AG015819NIA NIH HHS R01 AG017917NIA NIH HHS R01 AG036836NIA NIH HHS R01 AG057911NIA NIH HHS U01 AG046152NIA NIH HHS U01 AG061356
6 · The paper itself

Abstract

Deep learning methods have recently become the state-of-the-art in a variety of regulatory genomic tasks

Identifiers

PMID36993652
PMCPMC10055057

What OpenQuestion holds

Textmetadata
LicenceCC BY-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.