Evidence map›Paper›PMID 42259811›Full record

ArticleNature communications2026

Gene dependency-informed inference of response to targeted cancer therapies.

Nilabja Bhattacharjee, Sreeram Chandra Murthy Peela, Abhishek Halder, Bernadette Mathew, Swarnava Samanta, Sakshi Gujral, Stuti Kumari, Smruti Panda, Ritwik Ganguly, Gaurav Ahuja and 3 more

Abstract read
In one paragraph

Article in Nature communications, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. HuRInterDB: A Database Exploring the Landscape of lncRNA-Protein Interactions.Computational and structural biotechnology journal · 2026
    Article
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

13 authors.

Nilabja Bhattacharjee *Department of Computational Biology, Indraprastha Institute of Information Technology - Delhi (IIITD), New Delhi, India.ORCID http://orcid.org/0009-0007-7752-6990
Sreeram Chandra Murthy Peela *Department of Computational Biology, Indraprastha Institute of Information Technology - Delhi (IIITD), New Delhi, India. srirambds.murthy@gmail.com.ORCID http://orcid.org/0000-0003-3379-6263
Abhishek HalderDepartment of Computer Sciences and Engineering, Indraprastha Institute of Information Technology - Delhi (IIITD), New Delhi, India.ORCID http://orcid.org/0000-0003-0005-0254
Bernadette MathewDepartment of Computational Biology, Indraprastha Institute of Information Technology - Delhi (IIITD), New Delhi, India.ORCID http://orcid.org/0009-0005-8033-2965
Swarnava SamantaDepartment of Computational Biology, Indraprastha Institute of Information Technology - Delhi (IIITD), New Delhi, India.
Sakshi GujralDepartment of Computer Sciences and Engineering, Indraprastha Institute of Information Technology - Delhi (IIITD), New Delhi, India.
Stuti KumariDepartment of Computer Sciences and Engineering, Indraprastha Institute of Information Technology - Delhi (IIITD), New Delhi, India.
Smruti PandaDepartment of Computational Biology, Indraprastha Institute of Information Technology - Delhi (IIITD), New Delhi, India.
Ritwik GangulyDepartment of Computational Biology, Indraprastha Institute of Information Technology - Delhi (IIITD), New Delhi, India.
Gaurav AhujaDepartment of Computational Biology, Indraprastha Institute of Information Technology - Delhi (IIITD), New Delhi, India.ORCID http://orcid.org/0000-0002-2837-9361
Subhajyoti DeRutgers Cancer Institute, Rutgers, New Brunswick, NJ, USA.
Angshul MajumdarDepartment of Electronics and Communications Engineering, Indraprastha Institute of Information Technology - Delhi (IIITD), New Delhi, India.
Debarka SenguptaDepartment of Computational Biology, Indraprastha Institute of Information Technology - Delhi (IIITD), New Delhi, India. debarka@iiitd.ac.in.ORCID http://orcid.org/0000-0002-6353-5411

Funding

Computational genomic analysis of genomic variations in human tissuesR35GM149224 · NIGMS · RUTGERS BIOMEDICAL AND HEALTH SCIENCES · PI Subhajyoti De · 2023 to 2026
$1.4M
Department of Biotechnology, Ministry of Science and Technology (DBT) DBTHRDPMU/JRF/BET- 24/I/2024-25/306Department of Biotechnology, Ministry of Science and Technology (DBT) IC-12044(12)/4/2022-ICD-DBT)DST | Science and Engineering Research Board (SERB) CRG/2022/007706Indian Council of Medical Research (ICMR) EMDR/IG/16/2024-01-01321NIGMS NIH HHS R35 GM149224U.S. Department of Health & Human Services | National Institutes of Health (NIH) 35GM149224
6 · The paper itself

Abstract

Targeted therapies such as small-molecule inhibitors act by blocking proteins essential for cancer cell survival, yet omics-based modeling of drug sensitivity often lacks mechanistic grounding. We present FORGE (Factorization Of Response and Gene Essentiality), a joint matrix factorization framework that co-models drug response and target gene dependency to enable biologically informed stratification of treatment groups. FORGE derives a Benefit Score from basal gene expression to estimate therapeutic potential. In unseen cell lines treated with erlotinib, FORGE achieves high concordance for dependency (0.69) and IC

Indexed as

Antineoplastic AgentsMolecular Targeted TherapyNeoplasmsAnimalsCell Line, TumorErlotinib HydrochlorideGene Expression Regulation, NeoplasticHumansMiceXenograft Model Antitumor AssaysAntineoplastic AgentsErlotinib Hydrochloride

Identifiers

PMID42259811
PMCPMC13396380

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.