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Efficient Normalized Conformal Prediction and Uncertainty Quantification for Anti-Cancer Drug Sensitivity Prediction with Deep Regression Forests

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Integrative analysis of pharmacogenomics in major cancer cell line databases using CellMinerCDBPreprint

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Cancer Dependency Map: Past and Present

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Age-related aberrant alternative splicing as a prognostic tool in older breast cancer patients

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Effective delivery of genome editor to cervical cancer targeting Mcl1 for cancer therapy

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TiRank prioritizes phenotypic niches in tumor microenvironment for clinical biomarker discovery

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Identification of Prognostic Biomarker Candidates Associated With Melanoma Using High-Dimensional Genomic Data

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Ether‐Linked Glycerophospholipids Are Potential Chemo‐Desensitisers and Are Associated With Overall Survival in Carcinoma Patients

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Integrative Genomic and Immune Profiling to Identify and Characterize High-Risk Subgroups in Acute Myeloid Leukemia: Development of a 20-Gene Predictive Signature and Its Clinical Implications

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Preclinical Solid Tumor Models to Study Novel Therapeutics in Brain Metastases

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Network Control Models With Personalized Genomics Data for Understanding Tumor Heterogeneity in Cancer

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Nonlinear mixed effects dose response modeling in high throughput drug screens: application to melanoma cell line analysis

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A novel model-checking approach for dose-response relationships

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SEMCM: A Self-Expressive Matrix Completion Model for Anti-cancer Drug Sensitivity Prediction

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Machine learning model for breast anticancer drug sensitivity prediction from gene expression

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Link clustering explains non-central and contextually essential genes in protein interaction networks

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Machine Learning and Systems Biology Approaches to Characterize Dosage-Based Gene Dependencies in Cancer Cells

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Reassessing pharmacogenomic cell sensitivity with multilevel statistical models

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PitViper: a software for comparative meta-analysis and annotation of functional screening data

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Immune-related gene signature improves prognosis prediction in patients with breast cancer and associates it with tumor immunity and inflammatory response

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Optimizing Drug-Target Interaction Predictions for Anti-Cancer Agents Using Machine Learning

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Long non-coding RNAs as a biomarker for homologous recombination deficiency and parp inhibitor sensitivity in high-grade serous ovarian cancers

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Molecular and Cell Biological Characterization of Patient‐Derived Head and Neck Squamous Carcinoma Cell Lines

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Graph-Based Framework for Anti-Cancer Drug-Target Interaction Prediction using Proteomics, Chemical Space and Genomic Features

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Single-cell multimodal profiling of pan-cancer cell lines uncovers gene regulatory principles underlying intrinsic cell states and environmental features

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Differential Splicing of Skipped Exons Predicts Drug Response in Cancer Cell Lines

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The IC-50-time evolution is a new model to improve drug responses consistency of large scale studies

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Advances in computational methods for identifying cancer driver genes

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Deciphering glycosylation-driven prognostic insights and therapeutic prospects in glioblastoma through a comprehensive regulatory model

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Clinical and pathological predictors of engraftment for patient-derived xenografts in lung adenocarcinoma

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DPH2 is a biomarker associated with cell death, immunity and prognosis based on pan-cancer analysis

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Inhibition of replication origins and ATR synergistically activates the innate immune system in cancer cells

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DruID: Personalized Dru g Recommendations by I ntegrating Multiple Biomedical D atabases for CancerPreprint

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Detection of circular RNAs and their potential as biomarkers predictive of drug responsePreprint

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Post-EMT: Cadherin-11 mediates cancer hijacking fibroblastsPreprint

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Reliable Anti-Cancer Drug Sensitivity Prediction and PrioritizationPreprint

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Reliable Anti-Cancer Drug Sensitivity Prediction and PrioritizationPreprint

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Age-related host factors regulate lung cancer progression.

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Karyotypic divergence confounds cellular phenotypes in large pharmacogenomic studiesPreprint

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iEDGE: integration of Epi-DNA and Gene Expression and applications to the discovery of somatic copy number-associated drivers in cancerPreprint

Li, A., Chapuy, B., Varelas, X., Paola Sebastiani, B., & Monti, S. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/573824

PharmacoDB: an integrative database for mining in vitro drug screening studiesPreprint

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Applications of Microarray in Cancer Cell Signaling Pathways

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Bimodality of gene expression in cancer patient tumors as interpretable biomarkers for drug sensitivityPreprint

Ba-Alawi, W., Nair, S. K., Li, B., Mammoliti, A., Smirnov, P., Mer, A. S., Penn, L. Z., & Haibe‐Kains, B. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.09.08.288688

Merkel Cell Polyomavirus Oncogenes Generate Targetable Synthetic Lethality

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Bioinformatic and Experimental Analysis Reveals Knockdown of KIF15 Promotes Cell Apoptosis via Activating Crosstalk of Multi-Pathways in Ovarian CancerPreprint

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Widespread multi-targeted therapy resistance via drug-induced secretome fucosylationPreprint

Aldonza, M. B. D., Cha, J., Yong, I., Ku, J., Lee, D., Sinitcyn, P. G., Cho, R.-E., Reyes, R. D., Kim, D., Sung, H.-J., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.04.21.440719

Utilizing proteomics and phosphoproteomics to predict ex vivo drug sensitivity across genetically diverse AML patientsPreprint

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Avaliação do papel do gene HOXC13 na regulação da proliferação e migração celular em câncer de cabeça e pescoço

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GNisi: A graph network for reconstructing Ising models from multivariate binarized dataPreprint

Slade, E., Kiselgof, S., Granovsky, L., & England, J. L. (2021) · arXiv (Cornell University) · doi:10.48550/arxiv.2109.04257

Therapeutic applications of three-dimensional organoid models in lung cancer

Yeo, C. D., Yun, Y.-P., Ahn, D. H., Hwang, Y., Yang, S. H., Won, H., Cho, H. J., Park, C. K., Kim, S. J., & Park, J. Y. (2021) · Organoid · doi:10.51335/organoid.2021.1.e6

Computational-driven understanding of the regulatory mechanisms of the breast cancer transcriptome and its implications for drug treatment

Huang, S. (2021) · Mspace (University of Manitoba)

Looking back at the first twenty years of genomics

Quackenbush, J. F. (2021) · Quantitative Biology · doi:10.15302/j-qb-021-0286

Data from Predictive and Therapeutic Implications of a Novel PLCγ1/SHP2-Driven Mechanism of Cetuximab Resistance in Metastatic Colorectal Cancer

Cruz-Duarte, R., de Almeida, C. R., Negrão, M., Fernandes, A., Borralho, P., Sobral, D., Gallego-Paez, L. M., Machado, D., Gramaça, J., Vı́lchez, J. M., et al. (2023) · doi:10.1158/1078-0432.c.6531303

Data from Predictive and Therapeutic Implications of a Novel PLCγ1/SHP2-Driven Mechanism of Cetuximab Resistance in Metastatic Colorectal Cancer

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Supplementary Material from A Pan-cancer Landscape of Interactions between Solid Tumors and Infiltrating Immune Cell Populations

Tamborero, D., Rubio-Pérez, C., Muiños, F., Sabarinathan, R., Piulats, J. M., Muntasell, A., Dienstmann, R., López-Bigas, N., & González-Pérez, A. (2023) · doi:10.1158/1078-0432.22470440.v1

Machine learning algorithm integrates bulk and single-cell transcriptome sequencing to reveal immune-related personalized therapy prediction features for pancreatic cancerPreprint

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Computational precision therapeutics and drug repositioning

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Anti-cancer effects of renieramycin T on human non-small cell lung cancer cells

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Post-EMT: Cadherin-11 mediates cancer hijacking fibroblastsPreprint

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StringFix: an annotation-guided transcriptome assembler improves the recovery of amino acid sequences from RNA-Seq reads

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DEVELOPMENT OF TARGETED DRUG COMBINATIONS BLOCKING MULTI-DRIVER ONCOGENESIS

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Ether-linked phosphatidylethanolamine is a chemo-desensitizer of human carcinomas and epithelial ovarian cancer cellsPreprint

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Reliable Anti-Cancer Drug Sensitivity Prediction and PrioritizationPreprint

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GAS-Luc2 Reporter Cell Lines for Immune Checkpoint Drug Screening in Solid Tumors

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Additional file 2 of Association of expression of epigenetic molecular factors with DNA methylation and sensitivity to chemotherapeutic agents in cancer cell lines

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Additional file 2 of Prevalence, causes and impact of TP53-loss phenocopying events in human tumors

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Additional file 21 of Association of expression of epigenetic molecular factors with DNA methylation and sensitivity to chemotherapeutic agents in cancer cell lines

Vural, S., Palmisano, A., Reinhold, W. C., Pommier, Y., Teicher, B. A., & Krushkal, J. (2021) · Figshare · doi:10.6084/m9.figshare.14176024

Additional file 4 of Prevalence, causes and impact of TP53-loss phenocopying events in human tumors

Fito-Lopez, B., Salvadores, M., Alvarez, M.-M., & Supek, F. (2024) · Figshare · doi:10.6084/m9.figshare.26584575

Additional file 3 of Prevalence, causes and impact of TP53-loss phenocopying events in human tumors

Fito-Lopez, B., Salvadores, M., Alvarez, M.-M., & Supek, F. (2024) · Figshare · doi:10.6084/m9.figshare.26584572

Additional file 1 of Association of expression of epigenetic molecular factors with DNA methylation and sensitivity to chemotherapeutic agents in cancer cell lines

Vural, S., Palmisano, A., Reinhold, W. C., Pommier, Y., Teicher, B. A., & Krushkal, J. (2021) · Figshare · doi:10.6084/m9.figshare.14176018

Additional file 1 of QSAR-derived affinity fingerprints (part 2): modeling performance for potency prediction

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Additional file 16 of Association of expression of epigenetic molecular factors with DNA methylation and sensitivity to chemotherapeutic agents in cancer cell lines

Vural, S., Palmisano, A., Reinhold, W. C., Pommier, Y., Teicher, B. A., & Krushkal, J. (2021) · Figshare · doi:10.6084/m9.figshare.14176006

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