Unexplored therapeutic opportunities in the human genome

Oprea, Tudor I., Bologa, Cristian G., Brunak, Søren, Campbell, Allen, Gan, Gregory N., Gaulton, Anna, Gomez, Shawn M., Guha, Rajarshi +33 more·2018·Nature Reviews Drug Discovery

Cited by (378)

Items 301–378 of 378

  1. Illuminating the Druggable Genome through Patent Bioactivity Data
    María Paula Magariños, Anna Gaulton, Eloy Félix · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
  2. DNA-encoded Library Machine Learning Applications
    Eric A. Sigel · 2025 · Royal Society of Chemistry eBooks
  3. Ultrasmall chemogenetic tags with group-transfer ligands
    Vedagopuram Sreekanth, Shaimaa H. Sindi, Santosh Kumar Chaudhary et al. · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  4. Age- and Sex- Driven Transcriptional and Metabolic Diversity in Myeloid-Derived Suppressor Cells After Mouse Sepsis
    Christine E. Rodhouse, Dayuan Wang, Hongru Tang, Valerie E. Polcz, Miguel Hernández-Ríos, Xuanxuan Yu, Leandro Balzano‐Nogueira, Jaimar C. Rincon, Angel M. Charles, Seiichiro Fujishima et al. · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  5. Commentary: Integrative Analysis of Multiple Sclerosis Using a Systems Biology Approach
    Holger Husi · 2018 · Journal of Neurology and Neuromedicine
  6. Trendbericht Biochemie Teil 3: Adhäsions‐GPCR ‐‐ Hindernisse und Perspektiven
    Nicole Scholz, Simone Prömel, Ines Liebscher · 2019 · Nachrichten aus der Chemie
  7. Leveraging genetic data to investigate molecular targets and drug repurposing candidates for treating alcohol use disorder and hepatotoxicity
    Joshua C. Gray, Mikela A. Murphy, Lorenzo Leggio · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
  8. Practical Chemogenomic Modeling and Molecule Discovery Strategies Unveiled by Active Learning
    J.B. Brown · 2019 · Systems Medicine
  9. Chemical Strategies for Evaluating New Drug Targets
    Adrian J. Carter, Raina Seupel, Paul E. Brennan, M. Sundström, Andrea Introini, Anke Mueller‐Fahrnow · 2019 · Methods and principles in medicinal chemistry
  10. Fast Small-Scale Membrane Protein Purification and Grid Preparation for Single-Particle Electron Microscopy
    Natalie Bärland, Camilo Pérez · 2020 · Methods in molecular biology
  11. DNA-encoded Chemistry and Its Use in Discovering Chemical Probes
    Anthony D. Keefe · 2020 · Royal Society of Chemistry eBooks
  12. Curative and Preventive Treatment for Cardiovascular Disease (CVD) Targeting Multiple Etiology
    Josefino B. Tunac · 2021 · Cardiology and Cardiovascular Research
  13. Prevalent mouse phenotypes in the unexplored druggable genome
    Olga Gulyaeva, Zicheng Hu, Tudor Ionel Oprea, K. C. Kent Lloyd, Shawn M. Gomez, Bryan L. Roth, Michael T. McManus · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
  14. Epigenetic Target Prediction with Accurate Machine Learning Models
    Norberto Sánchez‐Cruz, José L. Medina‐Franco · 2021 · ChemRxiv
  15. Drug Discovery: Overview
    Terry Kenakin · 2022 · Elsevier eBooks
  16. Faculty Opinions recommendation of DrugCentral 2018: an update.
    Christopher Southan · 2018 · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature
  17. Small Molecule Modulation of the Archetypal UbiB protein COQ8
    Nathan H. Murray, Adam Lewis, Christopher R. M. Asquith, Juan Pablo Rincon Pabon, Zixiang Fang, Naomi Ptak, Robert Smith, James D. Vasta, Chad Zimprich, Cesear R. Corona et al. · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
  18. Faculty Opinions recommendation of Target-Based Evaluation of "Drug-Like" Properties and Ligand Efficiencies.
    John A. Lowe III · 2021 · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature
  19. Excited about Receptors
    Stephen H Safe · 2022 · Receptors
  20. Mechanism Study of Proteins under Membrane Environment
    Yue Zhang, Xiaohong Zhu, Honghui Zhang · 2022 · Membranes
  21. Drug discovery: Standing on the shoulders of giants
    Susan M. Miller, Walter H. Moos, Barbara H. Munk, Stephen A. Munk, Charles P. Hart, David C. Spellmeyer · 2023 · Elsevier eBooks
  22. Model Agnostic Semi-Supervised Meta-Learning Elucidates Understudied Out-of-distribution Molecular Interactions
    You Wu, Li Xie, Li Xie · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  23. Broad functional profiling of fission yeast proteins using phenomics and machine learning
    Maria Rodríguez‐López, Nicola Bordin, Jonathan Lees, Harry M. Scholes, Shaimaa Hassan, Quentin Saintain, Stephan Kamrad, Christine Anne Orengo, Jürg Bähler · 2023 · eLife
  24. eLife Assessment: Broad functional profiling of fission yeast proteins using phenomics and machine learning
    Adèle L. Marston · 2023 · eLife
  25. Reviewer #1 (Public Review): Broad functional profiling of fission yeast proteins using phenomics and machine learning
    Rodríguez-López María, Nicola Bordin, Lees Jon · 2023 · eLife
  26. Reviewer #3 (Public Review): Broad functional profiling of fission yeast proteins using phenomics and machine learning
    Rodríguez-López María, Bordin Nicola, Lees Jon · 2023 · eLife
  27. Reviewer #2 (Public Review): Broad functional profiling of fission yeast proteins using phenomics and machine learning
    Rodríguez-López María, Nicola Bordin, Lees Jon · 2023 · eLife
  28. Broad functional profiling of fission yeast proteins using phenomics and machine learning
    Rodríguez-López, María, Bordin, Nicola, Lees, Jon, Scholes, Harry, Hassan, Shaimaa, Saintain, Quentin, Kamrad, Stephan, Orengo, Christine, Bähler, Jürg · 2023
  29. Das funktionelle Unbekanntom
    Manfred Spitzer · 2023 · Nervenheilkunde
  30. Pharos and TCRD : Informatics Tools for Illuminating Dark Targets
    Keith J. Kelleher, Timothy K. Sheils, Stephen L. Mathias, Ðắc-Trung Nguyễn, Vishal B. Siramshetty, Ajay Pillai, Jeremy J. Yang, Cristian Bologa, Jeremy S. Edwards, Tudor Ionel Oprea et al. · 2023 · Methods and principles in medicinal chemistry
  31. Peer Review #2 of "Integrated single-dose kinome profiling data is predictive of cancer cell line sensitivity to kinase inhibitors (v0.1)"
    2023 · PeerJ
  32. Peer Review #1 of "Integrated single-dose kinome profiling data is predictive of cancer cell line sensitivity to kinase inhibitors (v0.1)"
    2023 · PeerJ
  33. Peer Review #2 of "Integrated single-dose kinome profiling data is predictive of cancer cell line sensitivity to kinase inhibitors (v0.3)"
    2023 · PeerJ
  34. Peer Review #2 of "Integrated single-dose kinome profiling data is predictive of cancer cell line sensitivity to kinase inhibitors (v0.2)"
    2023 · PeerJ
  35. Meta-Research: understudied genes are lost in a leaky pipeline between genome-wide assays and reporting of results
    Reese A. K. Richardson, Heliodoro Tejedor Navarro, Luı́s A. Nunes Amaral, Thomas Stoeger · 2023 · eLife
  36. Unveiling the role of Tdark genes in genetic diseases and phenotypes through bioinformatics-based functional enrichment and network analyses
    Doris Kafita, Kevin Dzobo, Panji Nkhoma, Musalula Sinkala · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  37. Meta-Research: understudied genes are lost in a leaky pipeline between genome-wide assays and reporting of results
    Richardson, Reese AK, Navarro, Heliodoro Tejedor, Nunes Amaral, Luis A, Stoeger, Thomas · 2024
  38. Identification of Suitable Target/E3 Ligase Pairs for PROTAC Development using a Rapamycin-induced Proximity Assay (RiPA)
    Adhikari, Bikash, Schneider, Katharina, Diebold, Mathias, Sotriffer, Christoph, Wolf, Elmar · 2024
  39. Multifaceted perspectives of detecting and targeting solid tumors
    Abhishek Bhattacharya, Anjan Kr. Dasgupta · 2024 · International review of cytology
  40. Initial Characterization of WDR5B Reveals a Role in the Proliferation of Retinal Pigment Epithelial Cells
    Jeff Bailey, Dzwokai Ma, Dennis Clegg · 2024 · Cells
  41. Defining degradability landscape of protein degraders
    Olivier Elemento, Wei Du · 2024 · Research Square
  42. Identification of Suitable Target/E3 Ligase Pairs for PROTAC Development using a Rapamycin-induced Proximity Assay (RiPA)
    Bikash Adhikari, Katharina Schneider, Mathias Diebold, Christoph Sotriffer, Elmar Wolf · 2024 · eLife
  43. eLife Assessment: Identification of Suitable Target/E3 Ligase Pairs for PROTAC Development using a Rapamycin-induced Proximity Assay (RiPA)
    Agnieszka Chacińska · 2024 · eLife
  44. Reviewer #1 (Public Review): Identification of Suitable Target/E3 Ligase Pairs for PROTAC Development using a Rapamycin-induced Proximity Assay (RiPA)
    Bikash Adhikari, Katharina Schneider, Mathias Diebold · 2024 · eLife
  45. Reviewer #2 (Public Review): Identification of Suitable Target/E3 Ligase Pairs for PROTAC Development using a Rapamycin-induced Proximity Assay (RiPA)
    Bikash Adhikari, Katharina Schneider, Mathias Diebold · 2024 · eLife
  46. Meta-Research: Assessing the Alignment of Biomedical Research and Clinical Translation
    Mengyi Sun, Thomas Stoeger, Luı́s A. Nunes Amaral · 2024 · medRxiv
  47. Identification of Suitable Target/E3 Ligase Pairs for PROTAC Development using a Rapamycin-induced Proximity Assay (RiPA)
    Bikash Adhikari, Katharina Schneider, Mathias Diebold, Christoph Sotriffer, Elmar Wolf · 2024 · eLife
  48. SmartGraph API: Programmatic Knowledge Mining in Network-Pharmacology Setting
    Gergely Zahoránszky-Köhalmi, Brandon Walker, Nathan Miller et al. · 2024 · Journal of Chemical Information and Modeling
  49. Therapeutic Implications of Recent Genomic Discoveries in Schizophrenia
    Steven J. Clapcote · 2024 · Royal Society of Chemistry eBooks
  50. Designing Pharmaceuticals Through Ligand-Centric Approaches
    Spoorthi R Kulkarni, Vidya Niranjan, Shradha Anand Mulimani · 2025 · IGI Global eBooks
  51. LigExtract: Large-scale Automated Identification of Ligands from Protein Structures in the Protein Data Bank
    Natália Aniceto, Nuno Martinho, Ismael Rufino · 2025 · Genomics Proteomics & Bioinformatics
  52. TICTAC: target illumination clinical trial analytics with cheminformatics
    Jeremiah I. Abok, Jeremy S. Edwards, Jeremy J. Yang · 2025 · Frontiers in Bioinformatics
  53. A magyar gyógyszerkutatás és -fejlesztés a 21. Században
    István Greiner, András M. Kotschy, Balázs Volk, Miklós György Keserû · 2025 · Magyar Tudomány
  54. Integrated Genomic Profiling Reveals Mechanisms of Broad Drug Resistance and Opportunities for Phenotypic Reprogramming in Cancer Cells
    Ian Mersich, Brian S. J. Blagg, Aktar Ali · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  55. Ultrasmall Chemogenetic Tags with Group‐Transfer Ligands
    Vedagopuram Sreekanth, Shaimaa H. Sindi, Santosh Kumar Chaudhary et al. · 2025 · Angewandte Chemie
  56. Pharmacophore-driven antibody discovery on the yeast surface
    Manjie Huang, Sean J. Williams, Vikas D. Trivedi, Nikhil U. Nair, James A. Van Deventer · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  57. Research towards selective inhibition of the CLK3 kinase
    D. K. Singh, Frédéric Justaud, Dabbugoddu Brahmaiah · 2025 · Beilstein Journal of Organic Chemistry
  58. Use of Adult T-Cell Leukemia/Lymphoma Cell Lines in a Novel Proteomic Approach for Clarifying the Function of Human Proteins of Unknown Function
    Yasuhiro Tonoyama, Yo-ichi Ishida · 2025 · Lymphatics
  59. Decoding the dark genome reveals its organisation into modular disease networks
    Doris Kafita, Kevin Dzobo, Panji Nkhoma, Musalula Sinkala · 2026 · Scientific Reports
  60. Exploring the YANK family: Emerging therapeutic targets for various diseases
    Qian He, Yue Cheng, Shuang Zhao · 2026 · Oncology and Translational Medicine
  61. Harnessing Targeted Protein Degradation for Developing Brain Cancer Therapy
    Osaid Muhammad, Sophie White, Carina Jungha Dumo, Thomas I‐H. Park, Peter J. Choi, Jiney Jose · 2026 · Bioconjugate Chemistry
  62. How many protein pairs can we chemically target?
    Maria J. Falaguera, Tudor Ionel Oprea, Jordi Mestres · 2026 · Drug Discovery Today
  63. A heterogeneous biomedical knowledge network framework for rare disease drug candidate prioritization: integrating Orphadata and DisGeNET via gene-bridge harmonization
    Diya Ramani · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  64. A Systematic Direct-to-Biology Approach Identified Potent Cereblon HaloPROTACs
    Rebecca Stevens, Kwok-Ho Chan, Alice Moore · 2026 · ACS Chemical Biology
  65. A quantitative approach for defining the degradability landscape of protein degraders
    Wei Du, Lamberto De Boni, Benjamin David Hopkins, Olivier Elemento · 2026 · Nature Communications
  66. Modulating the human gut microbiome-host system: a new drug discovery paradigm
    Gonzalo Colmenarejo · 2026 · Frontiers in Drug Discovery
  67. Evaluation of deep learning architectures for predicting ligand interactions with neurologically relevant GPCRs
    Souvik Dey, Pinyi Lu, Anders Wallqvist, Mohamed Diwan M. AbdulHameed · 2026 · Journal of Cheminformatics
  68. Deep contrastive learning and single-cell kinetic analysis: dual-engine breakthroughs in genome-wide ligand discovery
    Haoran Zhang, Bing Ye, Shenghua Gao · 2026 · 中国科学通报:英文版
  69. Cross-Ancestry Proteogenomic Analyses Identified New Therapeutic Insights for Ischemic Heart Disease
    Mohsen Mazidi, Neil Wright, Alfred Pozarickij, Iona Y. Millwood, Robin Walters, Christiana Kartsonaki, Derrick Bennett, Pang Yao, Huaidong Du, Hannah Fry et al. · 2026 · Journal of the American College of Cardiology
  70. Physics-informed deep learning: A new paradigm for macromolecular recognition and rational protein design
    Haobo Xie, Hao Wang, Xiaojun Yao, Jinyan Li, Yi Pan, Aiping Lü, Xiangxiang Zeng, Dongsheng Cao, Xiangzheng Fu · 2026 · The Innovation Drug Discovery
  71. ‘Superdark’ protein looks like a G-protein-coupled receptor — but shows unconventional behaviour
    Nil Casajuana-Martín, M. Madan Babu · 2026 · Nature
  72. KinaseDB: an integrated multi-omics platform for the human kinome with disease-specific target prioritization
    Sadiyah Afroz, Idhant Arora, Harsh Hingorani · 2026 · Nucleic Acids Research
  73. World models for biomedicine
    Ayush Noori, Nic Fishman, Ada Fang, Lukas Fesser, Marinka Žitnik · 2026 · Cell
  74. Dark proteome and emerging technologies for functional characterization and drug discovery
    Md Azizul Haque, Jong-Joo Kim, Danishuddin · 2026 · Drug Discovery Today
  75. CAST as a Tumor-Specific Suppressor in Colorectal Cancer: Discovery Through Integrative Analysis of Unannotated Isoforms, Proteomics, and Epigenetic Regulation
    alireza ebadi, Maryam Hashemi · 2026 · medRxiv
  76. Synthesis, Characterization, and Cytotoxic Evaluation of 2-Thioxoquinazolin-4(1H)-one Derivatives: Interaction with Paclitaxel in HeLa Cervical Cancer Cells and Selectivity for HaCaT Normal Keratinocytes
    B. Rashid, A. Anwar, M. S. AHMAD · 2026 · Molecular Biology
  77. Temporally Validated Models for Target “Tclin-likeness”
    Mohammed A. Quazi, Suman Sirimulla, Cristian Bologa, Alexei O. Pushechnikov, Bill Farley, Nikolay Savchuk, Tudor Ionel Oprea · 2026 · Journal of Chemical Information and Modeling
  78. Can Natural Products Drug the Dark Proteome by Exploiting Uncharacterized Binding Sites, Structural Disorder, and Previously Untapped Protein Biology?
    Olivia Bennett, Harry Collins, Jack Foster, Ethan Wright · 2026 · International Journal of Pharmaceutical and Phytopharmacological Research