Evidence map›Paper›PMID 31745082›Full record

ArticleNature communications2019

A Bayesian machine learning approach for drug target identification using diverse data types.

Neel S Madhukar, Prashant K Khade, Linda Huang, Kaitlyn Gayvert, Giuseppe Galletti, Martin Stogniew, Joshua E Allen, Paraskevi Giannakakou, Olivier Elemento

Abstract read
In one paragraph

Article in Nature communications, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 110 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
110citing papers in PubMed, 1 pooled it
–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

110 citing papers in PubMed, 1 synthesis or guideline pooled it.

  1. Pooled it
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  7. Target identification and assessment in the era of AI.Nature reviews. Drug discovery · 2026
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50 more citing papers are in PubMed but not listed here.

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

9 authors.

Neel S MadhukarInstitute for Computational Biomedicine, Dept. of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, 10065, USA.ORCID http://orcid.org/0000-0002-2907-2062
Prashant K KhadeDivision of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medical College, New York, NY, 10065, USA.
Linda HuangInstitute for Computational Biomedicine, Dept. of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, 10065, USA.
Kaitlyn GayvertInstitute for Computational Biomedicine, Dept. of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, 10065, USA.ORCID http://orcid.org/0000-0001-9135-6501
Giuseppe GallettiDivision of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medical College, New York, NY, 10065, USA.
Martin StogniewOncoceutics, Inc., Philadelphia, PA, 19104, USA.
Joshua E AllenOncoceutics, Inc., Philadelphia, PA, 19104, USA. josh.allen@oncoceutics.com.
Paraskevi GiannakakouMeyer Cancer Center, Weill Cornell Medical College, New York, NY, 10065, USA. pag2015@med.cornell.edu.
Olivier ElementoInstitute for Computational Biomedicine, Dept. of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, 10065, USA. ole2001@med.cornell.edu.

Funding

Weill Cornell Medicine (WCM) SPORE in Prostate CancerP50CA211024 · NCI · WEILL MEDICAL COLL OF CORNELL UNIV · PI LODA, MASSIMO · 2017 to 2021
$10.9M
The joint WCM-NYGC Center for Functional and Clinical Interpretation of Tumor ProfilesU24CA210989 · NCI · WEILL MEDICAL COLL OF CORNELL UNIV · PI ELEMENTO, OLIVIER, ZODY, MICHAEL C · 2016 to 2020
$2.4M
Microtubule-Regulated RNA Translation: Implications for Taxane ChemotherapyR01CA177165 · NCI · WEILL MEDICAL COLL OF CORNELL UNIV · PI GIANNAKAKOU, PARASKEVI · 2014 to 2018
$1.8M
NCI NIH HHS R01 CA177165U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI) P50CA211024U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI) U24CA210989
6 · The paper itself

Abstract

Drug target identification is a crucial step in development, yet is also among the most complex. To address this, we develop BANDIT, a Bayesian machine-learning approach that integrates multiple data types to predict drug binding targets. Integrating public data, BANDIT benchmarked a ~90% accuracy on 2000+ small molecules. Applied to 14,000+ compounds without known targets, BANDIT generated ~4,000 previously unknown molecule-target predictions. From this set we validate 14 novel microtubule inhibitors, including 3 with activity on resistant cancer cells. We applied BANDIT to ONC201-an anti-cancer compound in clinical development whose target had remained elusive. We identified and validated DRD2 as ONC201's target, and this information is now being used for precise clinical trial design. Finally, BANDIT identifies connections between different drug classes, elucidating previously unexplained clinical observations and suggesting new drug repositioning opportunities. Overall, BANDIT represents an efficient and accurate platform to accelerate drug discovery and direct clinical application.

Indexed as

Bayes TheoremMachine LearningAntineoplastic AgentsDrug Delivery SystemsDrug DiscoveryDrug RepositioningHumansNeoplasmsAntineoplastic Agents

Identifiers

PMID31745082
PMCPMC6863850

What OpenQuestion holds

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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.