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Coutinho, D. F., Mundi, P. S., Marks, L. J., Burke, C., Ortiz, M. V., Diolaiti, D., Bird, L., Vallance, K., Ibáñez, G., You, D., et al. (2022) · Med · doi:10.1016/j.medj.2022.09.002 · Cited by 22 · see citing works

Developmental and MAPK-responsive transcription factors drive distinct malignant subtypes and genetic dependencies in pancreatic cancerPreprint

Laise, P., Turunen, M. M., Garcia, A. C., Tomassoni, L., Maurer, H. C., Elyada, E., Schmierer, B., Worley, J., Kesner, J. S., Tan, X., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.10.27.357269 · Cited by 21 · see citing works

Reply to ‘H-STS, L-STS and KRJ-I are not authentic GEPNET cell lines’

Alvarez, M. J., Yan, P., Alpaugh, M. L., Bowden, M., Sicińska, E., Zhou, C. W., Karan, C., Realubit, R. B., Mundi, P. S., Grunn, A., et al. (2019) · Nature Genetics · doi:10.1038/s41588-019-0509-5 · Cited by 16 · see citing works

Translational Strategies for Repotrectinib in Neuroblastoma

O’Donohue, T. J., Ibáñez, G., Coutinho, D. F., Mauguen, A., Siddiquee, A. H., Rosales, N., Calder, P., Ndengu, A. A., You, D., Long, M. M., et al. (2021) · Molecular Cancer Therapeutics · doi:10.1158/1535-7163.mct-21-0126 · Cited by 13 · see citing works

Successful liver transplantation for non‐resectable desmoplastic nested spindle cell tumor complicated by Cushing's syndrome

Tehseen, S., Rapkin, L. B., Schemankewitz, E., Magliocca, J. F., & Romero, R. (2017) · Pediatric Transplantation · doi:10.1111/petr.13000 · Cited by 11 · see citing works

Establishment of patient-derived xenografts from patients with gastrointestinal stromal tumors: analysis of clinicopathological characteristics related to engraftment success

Na, Y.-S., Ryu, M., Park, Y. S., Lee, C., Lee, J., Park, Y., Park, J. M., Ma, J., & Kang, Y. (2020) · Scientific Reports · doi:10.1038/s41598-020-64552-w · Cited by 11 · see citing works

Single-cell based elucidation of molecularly-distinct glioblastoma states and drug sensitivityPreprint

Ding, H., Burgenske, D. M., Zhao, W., Subramaniam, P. S., Bakken, K. K., He, L., Alvarez, M. J., Laise, P., Paull, E., Spinazzi, E. F., et al. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/675439 · Cited by 8 · see citing works

Osteosarcoma

Beird, H. C., Bielack, S. S., Flanagan, A. M., Gill, J., Heymann, D., Janeway, K. A., Livingston, J. A., Roberts, R. D., Strauss, S. J., & Gorlick, R. (2022) · Nature Reviews Disease Primers · doi:10.1038/s41572-022-00409-y · Cited by 660 · see citing works

NetBID2 provides comprehensive hidden driver analysis

Dong, X., Ding, L., Thrasher, A., Wang, X., Liu, J., Pan, Q., Rash, J., Dhungana, Y., Yang, X., Risch, I., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-38335-6 · Cited by 37 · see citing works

PDX models for functional precision oncology and discovery science

Blanchard, Z., Brown, E. A., Ghazaryan, A., & Welm, A. L. (2024) · Nature reviews. Cancer · doi:10.1038/s41568-024-00779-3 · Cited by 38 · see citing works

Network-based elucidation of colon cancer drug resistance mechanisms by phosphoproteomic time-series analysis

Rosenberger, G., Li, W., Turunen, M. M., He, J., Subramaniam, P. S., Pampou, S., Griffin, A. T., Karan, C., Kerwin, P., Murray, D., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-47957-3 · Cited by 21 · see citing works

Computational drug prediction in hepatoblastoma by integrating pan-cancer transcriptomics with pharmacological response

Failli, M., Demir, S., Río-Álvarez, Á. D., Carrillo-Reixach, J., Royo, L., Domingo-Sàbat, M., Childs, M., Maibach, R., Alaggio, R., Czauderna, P. S., et al. (2023) · Hepatology · doi:10.1097/hep.0000000000000601 · Cited by 16 · see citing works

The Hallmarks of Predictive Oncology

Singhal, A., Zhao, X., Wall, P., So, E., Calderini, G., Partin, A., Koussa, N. C., Vasanthakumari, P., Narykov, O., Zhu, Y., et al. (2025) · Cancer Discovery · doi:10.1158/2159-8290.cd-24-0760 · Cited by 17 · see citing works

Single-cell analysis reveals a longitudinal trajectory of meningioma evolution and heterogeneity

Lee, J. Y., Lee, E. J., Seo, B. Y., Kim, J., Song, Y., Lee, D., Moon, N., Koo, H., Park, C., Kim, M.-S., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-60653-0 · Cited by 12 · see citing works

Long-term survival and undetectable circulating tumor DNA following comprehensive involved site radiotherapy for oligometastases

Radigan, R., Kao, C. S., Krainock, M. R., Liu, M. C., Gupta, V., Alexander, L., Missios, S., Hsu, J., Sangal, A., Milano, M. T., et al. (2025) · Scientific Reports · doi:10.1038/s41598-025-88266-z · Cited by 11 · see citing works

Network-based approach elucidates critical genes in BRCA subtypes and chemotherapy response in triple negative breast cancer

Agrawal, P., Jain, N., Gopalan, V., Timon, A. J., Singh, A., Rajagopal, P., & Hannenhalli, S. (2024) · iScience · doi:10.1016/j.isci.2024.109752 · Cited by 7 · see citing works

Systems Biology of the Cancer Cell

Janes, K. A., & Lazzara, M. J. (2024) · Annual Review of Biomedical Engineering · doi:10.1146/annurev-bioeng-103122-030552 · Cited by 9 · see citing works

Differential analysis of testicular LncRNA in Kazakh horses of different ages

Zhao-Fa, L. U., Wen, M., Yao, X., Meng, J., Wang, J., Zeng, Y., Li, L., & Ren, W. (2025) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2025.146228 · Cited by 9 · see citing works

Subtype-selective prenylated isoflavonoids disrupt regulatory drivers of MYCN-amplified cancers

Stokes, M. E., Vasciaveo, A., Small, J. C., Zask, A., Reznik, E., Smith, N., Wang, Q., Daniels, J., Forouhar, F., Rajbhandari, P., et al. (2023) · Cell chemical biology · doi:10.1016/j.chembiol.2023.11.007 · Cited by 9 · see citing works

Real-World Outcomes of Molecular Tumor Board Treatment Recommendations

Nichetti, F., Brambilla, M., Duca, M., Piccolo, A., Miliziano, D., Cavalli, C., Marra, F., Ambrosini, P., Zanella, C., Vernieri, C., et al. (2025) · JCO Precision Oncology · doi:10.1200/po-24-00387 · Cited by 8 · see citing works

BRAF inhibitor resistance in melanoma: from resistance mechanisms to therapeutic innovations

Shang, Y., Cao, T., Li, J., Li, J., ZHANG, L., Ma, Q., Feng, L., & Zhao, H. (2026) · Molecular Biomedicine · doi:10.1186/s43556-026-00425-4 · Cited by 8 · see citing works

A model for network-based identification and pharmacological targeting of aberrant, replication-permissive transcriptional programs induced by viral infection

Laise, P., Stanifer, M. L., Bosker, G., Sun, X., Triana, S., Doldan, P., Manna, F. L., Menna, M. D., Realubit, R. B., Pampou, S., et al. (2022) · Communications Biology · doi:10.1038/s42003-022-03663-8 · Cited by 8 · see citing works

Ras-dependent activation of BMAL2 regulates hypoxic metabolism in pancreatic cancerPreprint

Curiel-Garcia, A., Holmstrom, S. R., Castillo, C., Palermo, C. F., Sastra, S. A., Andren, A. C., Tomassoni, L., Zhang, L., Large, T. Y. S. L., Sagalovskiy, I. R., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.03.19.533333 · Cited by 7 · see citing works

Epigenetic targeting of PGBD5-dependent DNA damage in SMARCB1-deficient sarcomas

Kazansky, Y., Mueller, H. S., Cameron, D., Demarest, P., Zaffaroni, N., Arrighetti, N., Zuco, V., Mundi, P. S., Kuwahara, Y., Somwar, R., et al. (2025) · Journal of Clinical Investigation · doi:10.1172/jci179282 · Cited by 7 · see citing works

A compendium of next-generation patient-derived models for diverse cancers

ElHarouni, D., Al‐Jazrawe, M., Choi, S., Dede, M., Hinoue, T., Misek, S. A., Noh, H., Zanella, L., Tseng, Y.-Y., Francies, H. E., et al. (2026) · Nature · doi:10.1038/s41586-026-10806-y · Cited by 8 · see citing works

Phenotypic maps for precision medicine: a promising systems biology tool for assessing therapy response and resistance at a personalized level

Bhattacharyya, S., Ehsan, S., & Karacosta, L. G. (2023) · Frontiers in Network Physiology · doi:10.3389/fnetp.2023.1256104 · Cited by 7 · see citing works

Systematic identification and targeting of master regulator checkpoints (MRC) governing tumor microenvironment-mediated immune evasion

Laise, P., Bosker, G., Babor, M., Sun, X., Andrews, S. J., Tomassoni, L., Califano, A., & Alvarez, M. J. (2025) · Journal for ImmunoTherapy of Cancer · doi:10.1136/jitc-2024-011355 · Cited by 5 · see citing works

A proteogenomic atlas of 1032 brain metastases identifies molecular subtypes, immune landscapes, and therapeutic vulnerabilities

Yang, Z., Wei, S., Duan, H., Wang, X., Zhang, D., Kiang, K. M. Y., Deng, Y., Yang, Y., Ku, Y., Hu, W., et al. (2026) · Nature Communications · doi:10.1038/s41467-026-68748-y · Cited by 7 · see citing works

Functional transcriptional signatures for tumor-type-agnostic phenotype predictionPreprint

Weistuch, C., Murgas, K. A., Zhu, J., Norton, L., Dill, K. A., Tannenbaum, A., & Deasy, J. O. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.04.12.536595 · Cited by 4 · see citing works

Elucidation and Pharmacologic Targeting of Master Regulator Dependencies in Coexisting Diffuse Midline Glioma SubpopulationsPreprint

Fernández, E. C., Tomassoni, L., Zhang, X., Wang, J., Obradović, A., Laise, P., Griffin, A. T., Vlahos, L. J., Minns, H. E., Morales, D. V., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.03.17.585370 · Cited by 4 · see citing works

Harnessing PDX and PDX 2.0: the next-generation paradigm for precision oncology and translational breakthroughs

Jian, C., Fu, H., Wu, W., Zhang, N., Liu, Z., Xia, Z., Luo, P., Zhang, H., & Cheng, Q. (2026) · Molecular Cancer · doi:10.1186/s12943-026-02594-w · Cited by 4 · see citing works

Molecular Oncodiagnostics in Precision Oncology: Integrating Tumor Transcriptomics, Patient Pharmacogenetics, and Ex Vivo Chemoresistance Testing to Improve Individual Chemotherapy Response

Rusciano, D. (2026) · Journal of Personalized Medicine · doi:10.3390/jpm16040176 · Cited by 3 · see citing works

Systematic design of combination therapy by targeting master regulators of coexisting diffuse midline glioma cell states

Fernández, E. C., Tomassoni, L., Zhang, X., Wang, J., Obradović, A., Laise, P., Griffin, A. T., Vlahos, L. J., Minns, H. E., Morales, D. V., et al. (2026) · Nature Genetics · doi:10.1038/s41588-026-02550-w · Cited by 8 · see citing works

A Patient‐to‐Model‐to‐Patient (PMP) Cancer Drug Discovery Protocol for Identifying and Validating Therapeutic Agents Targeting Tumor Regulatory Architecture

Laise, P., Bosker, G., Califano, A., & Alvarez, M. J. (2022) · Current Protocols · doi:10.1002/cpz1.544 · Cited by 3 · see citing works

A highly annotated drug combination resource for catalyzing precision combinatorial therapy

You, T., Wang, L., Wang, J., Xu, D., Xu, X., Li, N., Li, M. J., Wang, H., & Dong, X. (2025) · Scientific Data · doi:10.1038/s41597-025-05630-4 · Cited by 3 · see citing works

A Tumor-Agnostic, Topology-Informed Scoring Framework for Drug Repurposing: Application to CDK4/6 Inhibitor Resistance in HR+ Breast Cancer

Qian, K., Cai, Z., Liu, R., Wang, Y., Liu, J., Wu, M., Zhu, M., Wang, L., Gan, H., Yang, Z., et al. (2026) · Biomedicines · doi:10.3390/biomedicines14030592 · Cited by 2 · see citing works

Fifteen challenges for generative AI applications to cell biology

Dupire, L., Khan, A. A., Karaletsos, T., Kelley, S., Lundberg, E. K., Ma, J., Paull, E., Quake, S. R., Rabadán, R., Cassius, R., et al. (2026) · Cell · doi:10.1016/j.cell.2026.07.004 · Cited by 3 · see citing works

Organ-specific colonization and niche remodeling in a human tissue model of metastasis

Chramiec, A. G., Baldassarri, I., Öztürk, E., Tavakol, D. N., Wang, M. C., Summers, M., Yeager, K. J., Zhuang, R. Z., Srivastava, A., Tagore, S., et al. (2026) · Science Translational Medicine · doi:10.1126/scitranslmed.adv6871 · Cited by 2 · see citing works

Normal tissue transcriptional signatures for tumor-type-agnostic phenotype prediction

Weistuch, C., Murgas, K. A., Zhu, J., Norton, L., Dill, K. A., Tannenbaum, A., & Deasy, J. O. (2024) · Scientific Reports · doi:10.1038/s41598-024-76625-1 · Cited by 2 · see citing works

Road Map to Defeat Pancreatic Cancer

Ferguson, L. P., & Tuveson, D. A. (2025) · Annual Review of Cancer Biology · doi:10.1146/annurev-cancerbio-060624-044323 · Cited by 2 · see citing works

Identification and targeting of regulators of SARS-CoV-2–host interactions in the airway epithelium

Dirvin, B., Noh, H., Tomassoni, L., Cao, D., Zhou, Y., Ke, X., Qian, J., Jangra, S., Schotsaert, M., García‐Sastre, A., et al. (2025) · Science Advances · doi:10.1126/sciadv.adu2079 · Cited by 2 · see citing works

Feasibility trial of Darwin OncoTreat and OncoTarget precision medicine testing to improve outcomes for patients with limited metastatic disease that failed first-line systemic therapy

Radigan, R., Sangal, A., Zhang, D., Weber, J., Schmalzle, M., Finkelstein, A., Duggal, V., & Kao, J. (2025) · PLoS ONE · doi:10.1371/journal.pone.0325769 · Cited by 2 · see citing works

Case Study of Single-cell Protein Activity Based Drug Prediction for Precision Treatment of CholangiocarcinomaPreprint

Obradović, A., Tomassoni, L., Yu, D., Guillan, K. C., Souto, K., Fraser, E., Bates, S. E., Drake, C. G., Saenger, Y. M., Cruz, F. S. D., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.02.28.482410 · Cited by 2 · see citing works

Pan-cancer inference and validation of hypermorphic, hypomorphic and neomorphic mutations

Tagore, S., Tsang, S., Tangermann, C., Hu, L. Z., Diederichs, S., Mills, G. B., & Califano, A. (2026) · Nature Genetics · doi:10.1038/s41588-025-02482-x · Cited by 1 · see citing works

Single-cell protein activity analysis reveals aberrant myogenesis and IGF2-PI3K pathway dependencies in MYOD1 -mutant rhabdomyosarcoma

Dermawan, J. K., Vanoli, F., de Wardin, H. D. T., Levi, J. N., Sanchez, G. D. I., Siddiquee, A. H., Brosius, S., You, D., Tirode, F., Sung, P., et al. (2026) · Science Advances · doi:10.1126/sciadv.aea6453 · Cited by 1 · see citing works

Extracellular matrix-driven patient stratification and network modeling reveal distinct molecular grades with potential clinical implications

Dansık, A., Sarıca, S., Öztürk, E., & Tunçbağ, N. (2026) · npj Systems Biology and Applications · doi:10.1038/s41540-026-00697-0 · Cited by 1 · see citing works

Developmental and MAPK-responsive transcription factors regulate distinct malignant cell states and associated genetic dependencies in pancreatic cancer

Laise, P., Turunen, M., Curiel‐García, Á., Tomassoni, L., Maurer, H. C., Elyada, E., Schmierer, B., Worley, J., Kesner, J. S., Tan, X., et al. (2026) · Nature Genetics · doi:10.1038/s41588-026-02714-8 · Cited by 22 · see citing works

A forward genetic screen identifies Sirtuin1 as a driver of neuroendocrine prostate cancer

de Almeida, F. N., Vasciaveo, A., Giacobbe, A., Bernardo, M. D., Zou, M., Antao, A. M., de Brot, S., Rodríguez-Calero, A., Chui, A., Wang, A. L. E., et al. (2026) · The Journal of Experimental Medicine · doi:10.1084/jem.20241484 · Cited by 2 · see citing works

Compound Mechanism of Action and Polypharmacology can be Elucidated by Large-Scale Perturbational Profile AnalysisPreprint

Hu, L. Z., Hirschhorn, T., Goldstein, S. I., Murray, D., Trudeau, S. J., Turunen, M. M., Douglass, E. F., Pampou, S., Grunn, A., Dupire, L., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.10.08.561457 · Cited by 1 · see citing works

Identification and Pharmacological Targeting of Treatment-Resistant, Stem-like Breast Cancer Cells for Combination TherapyPreprint

Worley, J., Noh, H., You, D., Turunen, M. M., Ding, H., Paull, E., Griffin, A. T., Grunn, A., Zhang, M., Guillan, K. C., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.11.08.562798 · Cited by 1 · see citing works

Cancer Systems Biology

Califano, A., Bild, A., Sims, P. A., & Stolovitzky, G. A. (2022) · Elsevier eBooks · doi:10.1016/b978-0-12-821618-7.00260-1

Systematic Pan-cancer Functional Inference and Validation of Hyper, Hypo and Neomorphic MutationsPreprint

Tagore, S., Tsang, S., Mills, G. B., & Califano, A. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.04.29.538640

Network-based biomarker discovery for multiple sclerosis

Åkesson, J. (2023) · Linköping studies in science and technology. Dissertations · doi:10.3384/9789180753968

Optimizing transcriptome-based synthetic lethality predictions to improve targeted therapy / immunotherapy treatment prioritization in non-metastatic breast cancer: BC-SELECTPreprint

Kim, Y., Nagy, M. R., Pollard, R., & Rajagopal, P. S. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.08.15.608073

Single-Cell RNA Sequencing and Inferred Protein Activity Analysis Reveal a Distinct Tumor Phenotype in Early-Onset Colorectal Cancer PatientsPreprint

Cohen, D. A., Obradović, A., Jovanovic, L., Mitani, Y., Li, T., Lee, S., De, D., Bethancourt, C.-N. R., Shin, A. E., Dunbar, K. J., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.05.15.653154

Extracellular Matrix-Guided Tumor Stratification and Network Models Reveal Clinical Molecular GradesPreprint

Dansık, A., Sarıca, S., Öztürk, E., & Tunçbağ, N. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.08.29.672994

Systematic elucidation and pharmacologic targeting of non-oncogene dependencies in imatinib-resistant gastrointestinal stromal tumorPreprint

Mundi, P. S., Grunn, A., Kojadinovic, A., Pampou, S., Karan, C., Realubit, R. B., Caescu, C. I., Hibshoosh, H. H., Aburi, M., Alvarez, M. J., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.10.12.681609

Treatment options after tumor resistance: exploiting vulnerabilities from genome to tumor microenvironment

Li, J., Zhang, N., Piao, M., Zhao, J., Wang, Y., Li, C., Li, S., Huang, Z., Li, Y., Xun, Z., et al. (2026) · Cancer and Metastasis Reviews · doi:10.1007/s10555-026-10392-5

Abstract 849: Evaluation of a transcriptomics-based precision oncology platform for patient-therapy alignment in treatment resistant malignancies

Mundi, P. S., Cruz, F. S. D., Ortiz, M. V., Grunn, A., Diolaiti, D., Alvarez, M. J., Kung, A. L., & Califano, A. (2023) · Cancer Research · doi:10.1158/1538-7445.am2023-849

An RNA-Based Precision Oncology Platform for Patient-Therapy Alignment in a Diverse Set of Treatment Resistant MalignanciesPreprint

Mundi, P. S., Cruz, F. S. D., Grunn, A., Diolaiti, D., Mauguen, A., Rainey, A. R., Guillan, K. C., Siddiquee, A. H., You, D., Realubit, R. B., et al. (2022) · SSRN Electronic Journal · doi:10.2139/ssrn.4069033

Clinically oriented prediction of patient response to targeted and immunotherapies from the tumor transcriptome.

Aharonov, R., Dinstag, G., Shulman, E. D., Elis, E., Ben-Zvi, D. S., Tirosh, O., Maimon, E., Sinha, S., Nair, N. U., Apolo, A. B., et al. (2023) · Journal of Clinical Oncology · doi:10.1200/jco.2023.41.16_suppl.1553 · Cited by 2 · see citing works

Synthetic lethality-mediated precision oncology via the tumor transcriptome

Lee, J. S., Nair, N. U., Dinstag, G., Chapman, L. M., Chung, Y., Wang, K., Sinha, S., Cha, H., Kim, D., Schperberg, A. V., et al. (2021) · Cell · doi:10.1016/j.cell.2021.03.030 · Cited by 154 · see citing works

Abstract LBA015: Accelerating clinically-translatable discoveries using a network-and RNA-based precision-oncology framework

Vasciaveo, A., Zou, M., Arriaga, J. M., de Almeida, F. N., Douglass, E. F., Shen, M. M., Califano, A., & Abate-Shen, C. T. (2021) · Molecular Cancer Therapeutics · doi:10.1158/1535-7163.targ-21-lba015