Califano, Andrea

The Immune Landscape of Cancer

Thorsson, V., Gibbs, D. L., Brown, S. D., Wolf, D., Bortone, D. S., Ou Yang, T.-H., Porta-Pardo, E., Gao, G. F., Plaisier, C. L., Eddy, J. A., et al. (2018) · Immunity

Cancer Immunotherapy and BiomarkersImmune cells in cancer

Cited by 5,870

Cross-species single-cell analysis of pancreatic ductal adenocarcinoma reveals antigen-presenting cancer-associated fibroblasts

Elyada, E., Bolisetty, M., Laise, P., Flynn, W. F., Courtois, E. T., Burkhart, R. A., Teinor, J. A., Belleau, P., Biffi, G., Lucito, M. S., et al. (2019) · Cancer Discovery

Pancreatic and Hepatic Oncology ResearchPeptidase Inhibition and Analysis

Cited by 2,241

Functional characterization of somatic mutations in cancer using network-based inference of protein activity

Alvarez, M. J., Shen, Y., Giorgi, F. M., Lachmann, A., Ding, B. B., Ye, B. H., & Califano, A. (2016) · Nature Genetics

Bioinformatics and Genomic NetworksCancer Genomics and Diagnostics

Cited by 966

Structure-based prediction of protein–protein interactions on a genome-wide scale

Zhang, Q. C., Petrey, D., Deng, L., Qiang, L., Shi, Y., Thu, C. A., Bisikirska, B., Lefebvre, C., Accili, D., Hunter, T., et al. (2012) · Nature

Bioinformatics and Genomic NetworksProtein Structure and Dynamics

Cited by 723

A multi-organ chip with matured tissue niches linked by vascular flow

Ronaldson-Bouchard, K., Teles, D., Yeager, K., Tavakol, D. N., Zhao, Y., Chramiec, A., Tagore, S., Summers, M., Stylianos, S., Tamargo, M., et al. (2022) · Nature Biomedical Engineering

3D Printing in Biomedical ResearchTissue Engineering and Regenerative Medicine

Cited by 512

Promotion of cholangiocarcinoma growth by diverse cancer-associated fibroblast subpopulations

Affo, S., Nair, A., Brundu, F., Ravichandra, A., Bhattacharjee, S., Matsuda, M., Chin, L., Filliol, A., Wen, W., Song, X., et al. (2021) · Cancer Cell

Cholangiocarcinoma and Gallbladder Cancer StudiesLiver physiology and pathology

Cited by 416

Reverse engineering cellular networks

Margolin, A. A., Wang, K., Lim, W. K., Kustagi, M., Nemenman, I., & Califano, A. (2006) · Nature Protocols

Gene Regulatory Network AnalysisBioinformatics and Genomic Networks

Cited by 379

Elucidating Compound Mechanism of Action by Network Perturbation Analysis

Woo, J. H., Shimoni, Y., Yang, W. S., Subramaniam, P., Iyer, A., Nicoletti, P., Rodríguez Martínez, M., López, G., Mattioli, M., Realubit, R., et al. (2015) · Cell

Bioinformatics and Genomic NetworksComputational Drug Discovery Methods

Cited by 351

A community computational challenge to predict the activity of pairs of compounds

Community, N.-D., Bansal, M., Yang, J., Karan, C., Menden, M. P., Costello, J. C., Tang, H., Xiao, G., Li, Y., Allen, J., et al. (2014) · Nature Biotechnology

Computational Drug Discovery MethodsGene Regulatory Network Analysis

Cited by 321

Genomic and phenotypic characterization of a broad panel of patient-derived xenografts reflects the diversity of glioblastoma

Vaubel, R. A., Tian, S., Remonde, D., Schroeder, M. A., Mladek, A. C., Kitange, G. J., Caron, A., Kollmeyer, T. M., Grove, R., Peng, S., et al. (2020) · Clinical Cancer Research

Glioma Diagnosis and TreatmentCancer Genomics and Diagnostics

Cited by 227

Experimental microdissection enables functional harmonisation of pancreatic cancer subtypes

Maurer, C., Holmstrom, S. R., He, J., Laise, P., Su, T., Ahmed, A., Hibshoosh, H., Chabot, J. A., Oberstein, P. E., Sepulveda, A. R., et al. (2019) · Gut

Pancreatic and Hepatic Oncology ResearchGene expression and cancer classification

Cited by 216

An expanded universe of cancer targets

Hahn, W. C., Bader, J. S., Braun, T. P., Califano, A., Clemons, P. A., Druker, B. J., Ewald, A. J., Fu, H., Jagu, S., Kemp, C. J., et al. (2021) · Cell

Cancer Genomics and DiagnosticsChromatin Remodeling and Cancer

Cited by 213

A precision oncology approach to the pharmacological targeting of mechanistic dependencies in neuroendocrine tumors

Alvarez, M. J., Subramaniam, P. S., Tang, L. H., Grunn, A., Aburi, M., Rieckhof, G., Komissarova, E. V., Hagan, E. A., Bodei, L., Clemons, P. A., et al. (2018) · Nature Genetics

Neuroendocrine Tumor Research AdvancesNeuroblastoma Research and Treatments

Cited by 210

Tumour-selective activity of RAS-GTP inhibition in pancreatic cancer

Wasko, U. N., Jiang, J., Dalton, T. C., Curiel-Garcia, A., Edwards, A. C., Wang, Y., Lee, B., Orlen, M., Tian, S., Stalnecker, C. A., et al. (2024) · Nature

Pancreatic and Hepatic Oncology ResearchProtein Kinase Regulation and GTPase Signaling

Cited by 209

Identification of Causal Genetic Drivers of Human Disease through Systems-Level Analysis of Regulatory Networks

Chen, J. C., Alvarez, M. J., Talos, F., Dhruv, H., Rieckhof, G. E., Iyer, A., Diefes, K. L., Aldape, K., Berens, M., Shen, M. M., et al. (2014) · Cell

Bioinformatics and Genomic NetworksGlioma Diagnosis and Treatment

Cited by 188

Differentiation-state plasticity is a targetable resistance mechanism in basal-like breast cancer

Risom, T., Langer, E. M., Chapman, M. P., Rantala, J., Fields, A. J., Boniface, C., Alvarez, M. J., Kendsersky, N. D., Pelz, C. R., Johnson-Camacho, K., et al. (2018) · Nature Communications

Cancer Cells and MetastasisBreast Cancer Treatment Studies

Cited by 174

A CRISPR/Cas9-Engineered ARID1A -Deficient Human Gastric Cancer Organoid Model Reveals Essential and Nonessential Modes of Oncogenic Transformation

Lo, Y.-H., Kolahi, K. S., Du, Y., Chang, C.-Y., Krokhotin, A., Nair, A., Sobba, W. D., Karlsson, K., Jones, S. J., Longacre, T. A., et al. (2021) · Cancer Discovery

Chromatin Remodeling and CancerCRISPR and Genetic Engineering

Cited by 174

ZFHX4 Interacts with the NuRD Core Member CHD4 and Regulates the Glioblastoma Tumor-Initiating Cell State

Chudnovsky, Y., Kim, D., Zheng, S., Whyte, W. A., Bansal, M., Bray, M.-A., Gopal, S., Theisen, M. A., Bilodeau, S., Thiru, P., et al. (2014) · Cell Reports

Glioma Diagnosis and TreatmentCancer Cells and Metastasis

Cited by 136

Identification of neurodegenerative factors using translatome–regulatory network analysis

Brichta, L., Shin, W., Jackson-Lewis, V., Blesa, J., Yap, E.-L., Walker, Z., Zhang, J., Roussarie, J.-P., Alvarez, M. J., Califano, A., et al. (2015) · Nature Neuroscience

Parkinson's Disease Mechanisms and TreatmentsNuclear Receptors and Signaling

Cited by 118

Assembly and Interrogation of Alzheimer’s Disease Genetic Networks Reveal Novel Regulators of Progression

Aubry, S., Shin, W., Crary, J. F., Lefort, R., Qureshi, Y. H., Lefebvre, C., Califano, A., & Shelanski, M. L. (2015) · PLOS ONE

Alzheimer's disease research and treatmentsBioinformatics and Genomic Networks

Cited by 106

HER3 Is an Actionable Target in Advanced Prostate Cancer

Gil, V., Miranda, S., Riisnaes, R., Gurel, B., D’Ambrosio, M., Vasciaveo, A., Crespo, M., Ferreira, A., Brina, D., Troiani, M., et al. (2021) · Cancer Research

Prostate Cancer Treatment and ResearchHER2/EGFR in Cancer Research

Cited by 68

A community challenge for a pancancer drug mechanism of action inference from perturbational profile data

Douglass, E. F., Allaway, R. J., Szalai, B., Wang, W., Tian, T., Fernández-Torras, A., Realubit, R., Karan, C., Zheng, S., Pessia, A., et al. (2022) · Cell Reports Medicine

Computational Drug Discovery MethodsGene expression and cancer classification

Cited by 68

Systematic elucidation and pharmacological targeting of tumor-infiltrating regulatory T cell master regulators

Obradovic, A., Ager, C., Turunen, M., Nirschl, T., Khosravi-Maharlooei, M., Iuga, A., Jackson, C. M., Yegnasubramanian, S., Tomassoni, L., Fernandez, E. C., et al. (2023) · Cancer Cell

T-cell and B-cell ImmunologyCancer Immunotherapy and Biomarkers

Cited by 66

Regulation of extra-embryonic endoderm stem cell differentiation by Nodal and Cripto signaling

Julio, M. K.-D., Alvarez, M. J., Galli, A., Chu, J., Price, S. M., Califano, A., & Shen, M. M. (2011) · Development

Developmental Biology and Gene RegulationPluripotent Stem Cells Research

Cited by 62