A Next Generation Connectivity Map: L1000 Platform and the First 1,000,000 Profiles

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6. Artificial Intelligence-Based Methods for Drug Repurposing and Development in Cancer
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8. An integrated transcriptomic analysis of autism spectrum disorder
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9. Interpreting molecular similarity between patients as a determinant of disease comorbidity relationships
   Jon Sánchez-Valle, Héctor Tejero, José M. Fernández, David Juan, Beatriz Urda-García, Salvador Capella-Gutiérrez, Fátima Al‐Shahrour, Rafael Tabarés‐Seisdedos, Anaı̈s Baudot, Véra Pancaldi et al. · 2020 · Nature Communications
10. Up-regulation of hypoxia-inducible factor antisense as a novel approach to treat ovarian cancer
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11. Integration of genetic variants and gene network for drug repurposing in colorectal cancer
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13. Identification of Prognostic Model and Biomarkers for Cancer Stem Cell Characteristics in Glioblastoma by Network Analysis of Multi-Omics Data and Stemness Indices
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14. Drivers of and Obstacles to the Adoption of Toxicogenomics for Chemical Risk Assessment: Insights from Social Science Perspectives
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15. MHC-II Signature Correlates With Anti-Tumor Immunity and Predicts anti-PD-L1 Response of Bladder Cancer
    Yi, Ruibin, Hong, Shuo, Zhang, Yueming, Lin, Anqi, Ying, Haoxuan, Zou, Weidong, Wang, Qiongyao, Wei, Ting, Cheng, Quan, Zhu, Weiliang et al. · 2022 · Frontiers in Cell and Developmental Biology
16. Anti-Epileptic Drug Target Perturbation and Intracranial Aneurysm Risk: Mendelian Randomization and Colocalization Study
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17. Construction of a novel choline metabolism-related signature to predict prognosis, immune landscape, and chemotherapy response in colon adenocarcinoma
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18. Drug repurposing in autosomal dominant polycystic kidney disease
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19. Identification of metastasis-related genes for predicting prostate cancer diagnosis, metastasis and immunotherapy drug candidates using machine learning approaches
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20. Benchmarking machine learning methods for synthetic lethality prediction in cancer
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21. A multiomic atlas identifies a treatment-resistant, bone marrow progenitor-like cell population in T cell acute lymphoblastic leukemia
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22. Evaluating current status of network pharmacology for herbal medicine focusing on identifying mechanisms and therapeutic effects
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23. Utilization of precision medicine digital twins for drug discovery in Alzheimer's disease
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24. Using Drug Expression Profiles and Machine Learning Approach for Drug Repurposing
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25. Comparison of Target Features for Predicting Drug-Target Interactions by Deep Neural Network Based on Large-Scale Drug-Induced Transcriptome Data
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26. Progress in data interoperability to support computational toxicology and chemical safety evaluation
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27. Identification of C3 as a therapeutic target for diabetic nephropathy by bioinformatics analysis
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28. Reconciling multiple connectivity scores for drug repurposing
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29. SARS-CoV-2 early infection signature identified potential key infection mechanisms and drug targets
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30. A radiogenomics application for prognostic profiling of endometrial cancer
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31. Scaling Large Language Models for Next-Generation Single-Cell Analysis
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32. Benchmarking algorithms for generalizable single-cell perturbation response prediction
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33. A systematic evaluation of deep learning methods for the prediction of drug synergy in cancer
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34. A Systematic Review of Deep Learning Methodologies Used in the Drug Discovery Process with Emphasis on In Vivo Validation
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35. 5-aminosalicylic acid suppresses osteoarthritis through the OSCAR-PPARγ axis
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36. Integration of 3D bioprinting and multi-algorithm machine learning identified glioma susceptibilities and microenvironment characteristics
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37. Building a translational cancer dependency map for The Cancer Genome Atlas
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38. Drug-Induced Rhabdomyolysis Atlas (DIRA) for idiosyncratic adverse drug reaction management
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39. Prioritization of novel ADPKD drug candidates from disease-stage specific gene expression profiles
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40. On the Role of Artificial Intelligence in Genomics to Enhance Precision Medicine
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41. Oxytocin’s anti-inflammatory and proimmune functions in COVID-19: a transcriptomic signature-based approach
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42. Network-Based Analysis of Fatal Comorbidities of COVID-19 and Potential Therapeutics
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43. Molecular Signature Predictive of Long-Term Liver Fibrosis Progression to Inform Antifibrotic Drug Development
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44. Prediction of drug candidates for clear cell renal cell carcinoma using a systems biology-based drug repositioning approach
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45. Analysis of Single‐Cell Transcriptome and Surface Protein Expression in Ankylosing Spondylitis Identifies OX40 ‐Positive and Glucocorticoid‐Induced Tumor Necrosis Factor Receptor–Positive Pathogenic Th17 Cells
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46. Unveiling the Genomic Basis of Chemosensitivity in Sarcomas of the Extremities: An Integrated Approach for an Unmet Clinical Need
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47. Pathway-based assessment of single chemicals and mixtures by a high-throughput transcriptomics approach
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48. Connectivity map-based drug repositioning of bortezomib to reverse the metastatic effect of GALNT14 in lung cancer
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49. Transcriptional Regulation of Cancer Immune Checkpoints: Emerging Strategies for Immunotherapy
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50. An acetyl-histone vulnerability in PI3K/AKT inhibition-resistant cancers is targetable by both BET and HDAC inhibitors
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51. Proteomics of resistance to Notch1 inhibition in acute lymphoblastic leukemia reveals targetable kinase signatures
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52. Integrated bioinformatic analysis reveals the underlying molecular mechanism of and potential drugs for pulmonary arterial hypertension
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53. Generative AI Models for Drug Discovery
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55. Analysis of Infected Host Gene Expression Reveals Repurposed Drug Candidates and Time-Dependent Host Response Dynamics for COVID-19
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56. Deep generative modeling of sample-level heterogeneity in single-cell genomics
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57. Network approaches for modeling the effect of drugs and diseases
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59. Regulating the cell shift of endothelial cell-like myofibroblasts in pulmonary fibrosis
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69. Unsupervised Learning in Drug Design from Self-Organization to Deep Chemistry
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74. Integrated landscape of plasma metabolism and proteome of patients with post-traumatic deep vein thrombosis
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75. A multiplex single-cell RNA-Seq pharmacotranscriptomics pipeline for drug discovery
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90. Computational drug repurposing by exploiting large-scale gene expression data: Strategy, methods and applications
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91. Signature analysis of high-throughput transcriptomics screening data for mechanistic inference and chemical grouping
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93. m5C RNA Methylation Primarily Affects the ErbB and PI3K–Akt Signaling Pathways in Gastrointestinal Cancer
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94. Classification of pediatric gliomas based on immunological profiling: Implications for immunotherapy strategies
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95. Integrative computational approach identifies drug targets in CD4+ T-cell-mediated immune disorders
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96. Identification of candidate repurposable drugs to combat COVID-19 using a signature-based approach
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98. Immune-Associated Gene Signatures and Subtypes to Predict the Progression of Atherosclerotic Plaques Based on Machine Learning
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99. DGKB mediates radioresistance by regulating DGAT1-dependent lipotoxicity in glioblastoma
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100. cSurvival: a web resource for biomarker interactions in cancer outcomes and in cell lines
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