Evidence map›Paper›PMID 40261968›Full record

ReviewCancer research2025

Illuminating the Noncoding Genome in Cancer Using Artificial Intelligence.

Maria Del Mar Alvarez-Torres, Xi Fu, Raul Rabadan

Abstract readReview
In one paragraph

Review in Cancer research, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing 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

4 citing papers in PubMed.

  1. Review
  2. Review
  3. Review
  4. Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

3 authors.

Maria Del Mar Alvarez-TorresProgram for Mathematical Genomics, Department of Systems Biology, Columbia University, New York, New York.ORCID 0009-0006-6157-4800
Xi FuProgram for Mathematical Genomics, Department of Systems Biology, Columbia University, New York, New York.ORCID 0000-0001-9835-5018
Raul RabadanProgram for Mathematical Genomics, Department of Systems Biology, Columbia University, New York, New York.ORCID 0000-0001-7946-9255

Funding

The Role of CTIP in Lymphocyte Development and LymphomagenesisP01CA174653 · NCI · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI GAUTIER, JEAN · 2014 to 2024
$17.6M
Towards a quantitative understanding of tumor evolutionR35CA253126 · NCI · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI Raul Rabadan · 2021 to 2026
$5.6M
Single-cell characterization of tumor and microenvironment co-evolution in Peripheral T-cell LymphomasU01CA243073 · NCI · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI PALOMERO, TERESA, RABADAN, RAUL · 2019 to 2023
$3.0M
Genetic characterization of osteoblast-induced leukemiasR01HL130937 · NHLBI · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI KOUSTENI, STAVROULA, RABADAN, RAUL · 2016 to 2019
$2.0M
National Institutes of Health (NIH) R01 HL159377NCI NIH HHS P01 CA174653NCI NIH HHS R35 CA253126NCI NIH HHS U01 CA243073NHLBI NIH HHS R01 HL130937Stand Up To Cancer (SU2C) SU2C Convergence 3.14
6 · The paper itself

Abstract

Understanding the vast noncoding cancer genome requires cutting-edge, high-resolution, and accessible strategies. Artificial intelligence is revolutionizing cancer research, enabling advanced models to analyze genome regulation. This review examines illustrative examples of noncoding mutations in cancer, focusing on both key regulatory elements and risk-associated variants that remain poorly understood, and compares key artificial intelligence models developed over the last decade for identifying functional noncoding variants, predicting gene expression impacts, and uncovering cancer-associated mutations. The discussion of the goals, data requirements, features, and outcomes of the models offers practical insights to help cancer researchers integrate these technologies into their work, regardless of computational expertise. This article is part of a special series: Driving Cancer Discoveries with Computational Research, Data Science, and Machine Learning/AI.

Indexed as

Artificial IntelligenceGenome, HumanNeoplasmsComputational BiologyGene Expression Regulation, NeoplasticGenomicsHumansMutation

Identifiers

PMID40261968
PMCPMC12214880

What OpenQuestion holds

Textmetadata
LicenceTDM
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.