Evidence map›Paper›PMID 40065155›Full record

ReviewNature reviews. Genetics2025

Adapting systems biology to address the complexity of human disease in the single-cell era.

David S Fischer, Martin A Villanueva, Peter S Winter, Alex K Shalek

Abstract readReview
In one paragraph

Review in Nature reviews. Genetics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.

0numbers the graph read from it
0cells of the map it votes in
15citing 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

15 citing papers in PubMed.

  1. Article
  2. Review
  3. Review
  4. Review
  5. Article
  6. Review
  7. Article
  8. Review
  9. Spatial architecture of development and disease.Nature reviews. Genetics · 2026
    Review
  10. Challenges and potential applications of AI in systems biology.Nature reviews. Molecular cell biology · 2026
    Article
  11. Special Issue "Molecular Progression in Genome-Related Diseases".International journal of molecular sciences · 2026
    Article
  12. Article
  13. Article
  14. Review
  15. 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

4 authors.

David S FischerEric and Wendy Schmidt Center, Broad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID http://orcid.org/0000-0002-1293-7656
Martin A VillanuevaInstitute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA.ORCID http://orcid.org/0000-0002-7630-1403
Peter S Winter *Broad Institute of MIT and Harvard, Cambridge, MA, USA. pwinter@broadinstitute.org.ORCID http://orcid.org/0000-0002-6557-3219
Alex K Shalek *Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA. shalek@mit.edu.ORCID http://orcid.org/0000-0001-5670-8778

Funding

IMMUNE MECHANISMS OF PROTECTION AGAINST MYCOBACTERIUM TUBERCULOSIS CENTER (IMPAC-TB)75N93019C00071 · NIAID · HARVARD UNIVERSITY D/B/A HARVARD SCHOOL OF PUBLIC HEALTH · PI FORTUNE, SARAH · 2019 to 2025
$57.3M
I4C 2.0: Immunotherapy for CureUM1AI164556 · NIAID · BETH ISRAEL DEACONESS MEDICAL CENTER · PI Dan H. Barouch, John W Mellors · 2021 to 2026
$28.0M
NHP CoreP01AI177687 · NIAID · BETH ISRAEL DEACONESS MEDICAL CENTER · PI Boris Dominik Juelg · 2023 to 2026
$7.4M
Defining the impact of drug use on immune function and fitness against HIV-1DP1DA053731 · NIDA · MASSACHUSETTS GENERAL HOSPITAL · PI SHALEK, ALEX K · 2021 to 2025
$5.9M
Single-Cell Analysis of the HIV/SIV ReservoirR01AI149670 · NIAID · BETH ISRAEL DEACONESS MEDICAL CENTER · PI BAROUCH, DAN H., SHALEK, ALEX K · 2020 to 2024
$4.6M
Bill & Melinda Gates Foundation INV-027498NIAID NIH HHS P01 AI177687NIAID NIH HHS R01 AI149670NIAID NIH HHS UM1 AI164556NIDA NIH HHS DP1 DA053731NIH HHS 75N93019C00071Wellcome Trust
6 · The paper itself

Abstract

Systems biology aims to achieve holistic insights into the molecular workings of cellular systems through iterative loops of measurement, analysis and perturbation. This framework has had remarkable success in unicellular model organisms, and recent experimental and computational advances - from single-cell and spatial profiling to CRISPR genome editing and machine learning - have raised the exciting possibility of leveraging such strategies to prevent, diagnose and treat human diseases. However, adapting systems-inspired approaches to dissect human disease complexity is challenging, given that discrepancies between the biological features of human tissues and the experimental models typically used to probe function (which we term 'translational distance') can confound insight. Here we review how samples, measurements and analyses can be contextualized within overall multiscale human disease processes to mitigate data and representation gaps. We then examine ways to bridge the translational distance between systems-inspired human discovery loops and model system validation loops to empower precision interventions in the era of single-cell genomics.

Indexed as

Single-Cell AnalysisSystems BiologyGene EditingGenomicsHumansMachine Learning

Identifiers

PMID40065155
PMCPMC13552703

What OpenQuestion holds

Textmetadata
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.