Evidence map›Paper›PMID 41091803›Full record

ReviewCancer research2025

A Roadmap for the Future of Systems Biology in Cancer Research.

H Steven Wiley, Carlos F Lopez, Andrei S Rodin, Russell C Rockne, Thomas E Yankeelov, Herbert M Sauro, Ghmkin Hassan, Sandhya Prabhakaran, Emek Demir, Mengzhou Hu and 18 more

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. Article
  2. Article
  3. Article
  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

28 authors.

H Steven WileyEnvironmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington.ORCID 0000-0003-0232-6867
Carlos F LopezMultiscale Modeling Group, Institute of Technology, Altos Labs, Redwood City, California.ORCID 0000-0003-3668-7468
Andrei S RodinDepartment of Computational and Quantitative Medicine, Beckman Research Institute, City of Hope National Medical Center, Duarte, California.ORCID 0000-0002-2570-0332
Russell C RockneDepartment of Computational and Quantitative Medicine, Beckman Research Institute, City of Hope National Medical Center, Duarte, California.ORCID 0000-0002-1557-159X
Thomas E YankeelovOden Institute for Computational Engineering and Sciences, Livestrong Cancer Institutes, Austin, Texas.ORCID 0000-0001-6201-3913
Herbert M SauroDepartment of Bioengineering, University of Washington, Seattle, Washington.ORCID 0000-0002-3659-6817
Ghmkin HassanDepartment of Surgery, Center for Bioengineering and Tissue Regeneration, University of California, San Francisco, San Francisco, California.ORCID 0000-0002-2725-7899
Sandhya PrabhakaranIntegrated Mathematical Oncology Department, Moffitt Cancer Center, Tampa, Florida.ORCID 0000-0002-9537-507X
Emek DemirMolecular and Medical Genetics, OHSU Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon.ORCID 0000-0002-3663-7113
Mengzhou HuDepartment of Medicine, University of California San Diego, San Diego, California.ORCID 0000-0002-1571-8029
Juan Fuxman BassBiology Department, Boston University, Boston, Massachusetts.ORCID 0000-0001-9457-1207
Kimberly A LuddyCancer Biology and Evolution Program, Moffitt Cancer Center, Tampa, Florida.ORCID 0000-0002-5172-221X
Hannah NewmanCancer Biology and Evolution Program, Moffitt Cancer Center, Tampa, Florida.ORCID 0000-0002-7007-5361
Jonathan P MochelPrecision One Health Initiative, Department of Pathology, University of Georgia College of Veterinary Medicine, Athens, Georgia.ORCID 0000-0002-0997-3111
James C CostelloDepartment of Pharmacology, University of Colorado Cancer Center, University of Colorado Anschutz Medical Campus, Aurora, Colorado.ORCID 0000-0003-3158-9682
Jianhua XingDepartment of Computational and Systems Biology, UPCI Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania.ORCID 0000-0002-3700-8765
Said M AfifyDepartment of Oncology, Lombardi Comprehensive Cancer Centre, Georgetown University, Washington, District of Columbia.ORCID 0000-0003-4026-1400
Ahmet AcarDepartment of Biological Sciences, Middle East Technical University, Ankara, Turkiye.ORCID 0000-0002-2478-8029
Melanie Haden GephartDepartment of Neurosurgery, Stanford Medical School, Stanford, California.ORCID 0000-0003-2965-9231
Song FengBiological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington.ORCID 0000-0003-3983-9009
Orion BanksSage Bionetworks, Seattle, Washington.ORCID 0000-0001-6482-0030
Jineta BanerjeeSage Bionetworks, Seattle, Washington.ORCID 0000-0002-1775-3645
Ashley ClaytonSage Bionetworks, Seattle, Washington.ORCID 0000-0002-4570-2706
David E HillCenter for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, Massachusetts.ORCID 0000-0001-5192-0921
Randy F SweisSection of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, Illinois.ORCID 0000-0002-0497-9637
Maxine C Umeh-GarciaDepartment of Neurosurgery, Stanford University, Stanford, California.ORCID 0000-0003-4087-3482
Yapeng SuHerbold Computational Biology Program, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.ORCID 0000-0002-6305-8467
Aaron S MeyerDepartment of Bioengineering, University of California, Los Angeles, Los Angeles, California.ORCID 0000-0003-4513-1840

Funding

Transgenic Mouse FacilityP30CA033572 · NCI · CITY OF HOPE/BECKMAN RESEARCH INSTITUTE · PI STANLEY R. HAMILTON · 1985 to 2026
$86.3M
Bridge2AI: Cell Maps for AI (CM4AI) Data Generation ProjectOT2OD032742 · OD · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI Jean-Christophe Bélisle-Pipon, TIMOTHY W CLARK · 2022 to 2026
$21.5M
The Cancer Cell Map Initiative v2.0U54CA274502 · NCI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Trey Ideker, Nevan J Krogan · 2022 to 2026
$14.2M
Spatial Transcriptomics Explorer (STE): An open-source resource for visualizing spatial gene expression dataU24CA274494 · NCI · SAGE BIONETWORKS · PI Jineta Banerjee, Susheel Varma · 2022 to 2026
$10.1M
Rewiring of regulatory networks in breast cancer by transcription factor isoformsU01CA232161 · NCI · DANA-FARBER CANCER INST · PI BULYK, MARTHA L, FUXMAN BASS, JUAN IGNACIO · 2018 to 2022
$4.1M
A physical sciences approach to investigate the role of exosomes in metastatic progressionU01CA250044 · NCI · UNIVERSITY OF PENNSYLVANIA · PI GUO, WEI, RADHAKRISHNAN, RAVI · 2021 to 2025
$3.9M
Information flow and state transitions at the system and multi-dimensional scales in leukemia progressionU01CA250046 · NCI · BECKMAN RESEARCH INSTITUTE/CITY OF HOPE · PI KUO, YA-HUEI, MARCUCCI, GUIDO · 2020 to 2024
$3.6M
Systems analysis of aggressive prostate cancer pathologyU01CA231978 · NCI · UNIVERSITY OF COLORADO DENVER · PI COSTELLO, JAMES CHRISTOPHER, CRAMER, SCOTT D · 2019 to 2023
$3.4M
Reverse Sensitivity Analysis for Identifying Predictive Proteomics Signatures of CancerU01CA227544 · NCI · BATTELLE PACIFIC NORTHWEST LABORATORIES · PI QIAN, WEI-JUN, SAURO, HERBERT M. · 2019 to 2023
$3.1M
Experimental-Computational Synthesis of Altered Immune Signaling in Breast CancerU01CA232216 · NCI · BECKMAN RESEARCH INSTITUTE/CITY OF HOPE · PI LEE, PETER POON-HANG, ROCKNE, RUSSELL CHRISTIAN · 2019 to 2023
$3.0M
Multiscale Computational Models Guided By Emerging Cellular Dynamics Quantification For Predicting Optimum Immune Checkpoint And Targeted Therapy SchedulesU01CA243075 · NCI · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI JACKSON, TRACHETTE · 2020 to 2024
$2.6M
Using label-free Raman microscopy to predict therapeutic resistance of TNBC cellsU01CA253540 · NCI · UNIVERSITY OF TEXAS AT AUSTIN · PI BROCK, AMY, YANKEELOV, THOMAS E · 2020 to 2024
$2.1M
Japan Society for the Promotion of Science (JSPS) 23K15972Mark Foundation For Cancer Research (The Mark Foundation for Cancer Research) Emerging Leader AwardNational Cancer Institute (NCI) OT2OD032742National Cancer Institute (NCI) R01GM148525National Cancer Institute (NCI) R01LM013138National Cancer Institute (NCI) U01CA227544National Cancer Institute (NCI) U01CA231978National Cancer Institute (NCI) U01CA232161National Cancer Institute (NCI) U01CA232216National Cancer Institute (NCI) U01CA243075National Cancer Institute (NCI) U01CA250044National Cancer Institute (NCI) U01CA250046National Cancer Institute (NCI) U01CA253540National Cancer Institute (NCI) U24CA274494National Cancer Institute (NCI) U54CA274502NCI NIH HHS P30 CA033572NCI NIH HHS R33 CA256086NCI NIH HHS U01 CA227544NCI NIH HHS U01 CA231978NCI NIH HHS U01 CA232161NCI NIH HHS U01 CA232216NCI NIH HHS U01 CA243075NCI NIH HHS U01 CA250044NCI NIH HHS U01 CA250046NCI NIH HHS U01 CA253540NCI NIH HHS U24 CA274494NCI NIH HHS U54 CA274502NIGMS NIH HHS R01 GM148525NIH HHS OT2 OD032742NLM NIH HHS R01 LM013138
6 · The paper itself

Abstract

Cancer systems biology seeks to understand how cancer arises as a system of interconnected molecules, cells, and tissues, with the goal of understanding, predicting, and controlling the disease. In the last decade, the field has rapidly grown as advances in experimental, computational, and analytic technologies have improved our ability to capture and recapitulate the complexities of cancer at multiple scales. However, the field's promise to understand how specific molecular changes give rise to altered cancer outcomes remains incompletely fulfilled. Fortunately, an opportunity exists to accelerate progress by better coordinating modeling and data-gathering efforts across the cancer systems biology community. This will create the foundation for building accurate, multiscale cancer models that can better predict and identify improved therapeutic interventions. Here, we outline some of the current challenges in cancer systems biology research, how they can be addressed, and actions that the community can take to accelerate progress in the field. This article is part of a special series: Driving Cancer Discoveries with Computational Research, Data Science, and Machine Learning/AI .

Indexed as

Biomedical ResearchNeoplasmsSystems BiologyComputational BiologyHumansMachine Learning

Identifiers

PMID41091803
PMCPMC12893804

What OpenQuestion holds

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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.