Evidence map›Paper›PMID 40817189›Full record

ArticleNature nanotechnology2025

Designing lipid nanoparticles using a transformer-based neural network.

Alvin Chan, Ameya R Kirtane, Qing Rui Qu, Xisha Huang, Jonathan Woo, Deepak A Subramanian, Rajib Dey, Rika Semalty, Joshua D Bernstock, Taksim Ahmed and 14 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature nanotechnology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.

0numbers the graph read from it
0cells of the map it votes in
22citing 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

22 citing papers in PubMed.

  1. Review
  2. Dual pKa Lipid Nanoparticles for Lung-tropic mRNA Delivery and pH-Programmed Endosomal Escape.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026
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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

24 authors.

Alvin Chan *Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA. guoweialvin.chan@ntu.edu.sg.ORCID http://orcid.org/0000-0002-1041-3891
Ameya R Kirtane *Division of Gastroenterology, Hepatology and Endoscopy, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA. kirta001@umn.edu.ORCID http://orcid.org/0000-0002-3779-0363
Qing Rui QuDivision of Gastroenterology, Hepatology and Endoscopy, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.ORCID http://orcid.org/0009-0008-4938-5745
Xisha HuangDivision of Gastroenterology, Hepatology and Endoscopy, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
Jonathan WooDivision of Gastroenterology, Hepatology and Endoscopy, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.ORCID http://orcid.org/0009-0001-6950-0041
Deepak A SubramanianDavid H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.ORCID http://orcid.org/0000-0001-6224-7533
Rajib DeyDepartment of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.ORCID http://orcid.org/0009-0002-4844-368X
Rika SemaltyDivision of Gastroenterology, Hepatology and Endoscopy, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.ORCID http://orcid.org/0009-0004-1884-6706
Joshua D BernstockDavid H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
Taksim AhmedDivision of Gastroenterology, Hepatology and Endoscopy, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.ORCID http://orcid.org/0000-0001-7143-4621
Rowan HoneywellDivision of Gastroenterology, Hepatology and Endoscopy, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
Charles HanhurstDivision of Gastroenterology, Hepatology and Endoscopy, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.ORCID http://orcid.org/0009-0006-4049-4852
Isaac Diaz BecdachDavid H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.ORCID http://orcid.org/0009-0001-1890-6885
Leah S PrizantDavid H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.ORCID http://orcid.org/0009-0006-6866-9853
Ashley K BrownDivision of Gastroenterology, Hepatology and Endoscopy, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.ORCID http://orcid.org/0009-0005-2022-1534
Hao SongDavid H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.ORCID http://orcid.org/0000-0002-6383-0605
Justin Law CobbDivision of Gastroenterology, Hepatology and Endoscopy, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
Louis B DeRidderDivision of Gastroenterology, Hepatology and Endoscopy, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.ORCID http://orcid.org/0000-0001-7390-1481
Bruna SantosDivision of Gastroenterology, Hepatology and Endoscopy, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
Miguel JimenezDepartment of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.ORCID http://orcid.org/0000-0003-4211-1852
Michelle SunDivision of Gastroenterology, Hepatology and Endoscopy, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
Yuebin HuangDavid H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.ORCID http://orcid.org/0009-0009-0031-3617
Ceara ByrneDivision of Gastroenterology, Hepatology and Endoscopy, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
Giovanni TraversoDepartment of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA. cgt20@mit.edu.ORCID http://orcid.org/0000-0001-7851-4077

Funding

VIRUS PRODUCTION COREP30CA014051 · NCI · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI Jacqueline A. Lees · 1985 to 2026
$93.9M
NCI NIH HHS P30 CA014051
6 · The paper itself

Abstract

The RNA medicine revolution has been spurred by lipid nanoparticles (LNPs). The effectiveness of an LNP is determined by its lipid components and their ratios; however, experimental optimization is laborious and does not explore the full design space. Computational approaches such as deep learning can be greatly beneficial, but the composite nature of LNPs limits the effectiveness of existing single molecule-based algorithms to LNPs. Addressing this, our approach integrates the multi-component and multimodal features of composite formulations such as LNPs to predict their performance in an end-to-end manner. Here we generate one of the largest LNP datasets (LANCE) by varying LNP formulations to train our deep learning model, COMET. This transformer-based neural network not only accurately predicts the efficacy of LNPs but is adaptable to non-canonical LNP formulations such as those with two ionizable lipids and polymeric materials. Furthermore, COMET can predict LNP performance in a cell line outside of LANCE and predict LNP stability during lyophilization using only small training datasets. Experimental validation showed that our approach can identify LNPs that exhibit strong protein expression in vitro and in vivo, promising accelerated development of nucleic acid therapies with extensive potential across therapeutic and manufacturing applications.

Indexed as

LipidsNanoparticlesNeural Networks, ComputerAnimalsDeep LearningHumansLiposomesMiceLipid NanoparticlesLipidsLiposomes

Identifiers

PMID40817189
PMCPMC12534189

What OpenQuestion holds

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LicenceCC BY
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Registered trials

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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.