The Library of Integrated Network-Based Cellular Signatures NIH Program: System-Level Cataloging of Human Cells Response to Perturbations

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Items 101–200 of 429

1. Systems-Wide Approaches in Induced Pluripotent Stem Cell Models
   Edward Lau, David T. Paik, Joseph C. Wu · 2018 · Annual Review of Pathology Mechanisms of Disease
2. Editorial: Drug Repositioning: Current Advances and Future Perspectives
   Yuhei Nishimura, Hideaki Hara · 2018 · Frontiers in Pharmacology
3. Modulating the transcriptional landscape of SARS-CoV-2 as an effective method for developing antiviral compounds
   Daisy A. Hoagland, Daniel J. B. Clarke, Rasmus Møller, Yuling Han, Liuliu Yang, Megan L. Wojciechowicz, Alexander Lachmann, Kasopefoluwa Y. Oguntuyo, Christian S. Stevens, Benhur Lee et al. · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
4. Drug repositioning for cancer in the era of AI, big omics, and real-world data
   Robert Wieder, Nabil R. Adam · 2022 · Critical Reviews in Oncology/Hematology
5. Senescence-associated microvascular endothelial dysfunction: A focus on the blood-brain and blood-retinal barriers
   Sung Young Kim, Jaejoung Cheon · 2024 · Ageing Research Reviews
6. RETRACTED ARTICLE: Computational Drug Repositioning for Gastric Cancer using Reversal Gene Expression Profiles
   In‐Wha Kim, Ha-Young Jang, Jae Hyun Kim, Myeong Gyu Kim, Sangsoo Kim, Jung Mi Oh · 2019 · Scientific Reports · Retracted
7. Towards Biomanufacturing of Cell-Derived Matrices
   Weng Wan Chan, Fang Yu, Bach Quang Le, Sixun Chen, Marcus Yee, Deepak Choudhury · 2021 · International Journal of Molecular Sciences
8. Repurposing Drugs via Network Analysis: Opportunities for Psychiatric Disorders
   Trang T. T. Truong, Bruna Panizzutti, Jee Hyun Kim, Ken R. Walder · 2022 · Pharmaceutics
9. Unlocking biological insights from differentially expressed genes: Concepts, methods, and future perspectives
   Huachun Yin, Hongrui Duo, Song Li, Dan Qin, Lingling Xie, Yingxue Xiao, Jing Sun, Jingxin Tao, Xiaoxi Zhang, Yinghong Li et al. · 2024 · Journal of Advanced Research
10. Structure-based drug repositioning explains ibrutinib as VEGFR2 inhibitor
    Melissa F. Adasme, Daniele Parisi, Kristien Van Belle, Sebastian Salentin, V. Joachim Haupt, Gary S. Jennings, Jörg C. Heinrich, Jean Herman, Ben Sprangers, Thierry Louat et al. · 2020 · PLoS ONE
11. Automatic identification of small molecules that promote cell conversion and reprogramming
    Francesco Napolitano, Trisevgeni Rapakoulia, Patrizia Annunziata, Akira Hasegawa, Mélissa Cardon, Sara Napolitano, Lorenzo Vaccaro, Antonella Iuliano, Luca G. Wanderlingh, Takeya Kasukawa et al. · 2021 · Stem Cell Reports
12. Drug repurposing in silico screening platforms
    Jonathan G.L. Mullins · 2022 · Biochemical Society Transactions
13. A Transient Metabolic State in Melanoma Persister Cells Mediated by Chemotherapeutic Treatments
    Prashant Karki, Vahideh Angardi, Juan Carlos Mier, Mehmet A. Orman · 2022 · Frontiers in Molecular Biosciences
14. Building Containerized Workflows Using the BioDepot-Workflow-Builder
    Ling‐Hong Hung, Jiaming Hu, Trevor Meiss, Alyssa Ingersoll, Wes Lloyd, Daniel Kristiyanto, Yuguang Xiong, Eric A. Sobie, Ka Yee Yeung · 2019 · Cell Systems
15. Transcriptomics for Clinical and Experimental Biology Research: Hang on a Seq
    Tanner Stokes, Haoning Howard Cen, Philipp Kapranov, Iain J. Gallagher, Andrew A. Pitsillides, Claude‐Henry Volmar, William E. Kraus, James D. Johnson, Stuart M. Phillips, Claes Wahlestedt et al. · 2023 · Advanced Genetics
16. Insights into respiratory disease through bioinformatics
    Bhavna Hurgobin, Emma de Jong, Anthony Bosco · 2018 · Respirology
17. Connectivity Mapping Identifies BI-2536 as a Potential Drug to Treat Diabetic Kidney Disease
    Lu Zhang, Zichen Wang, Ruijie Liu, Zhengzhe Li, Jennifer Lin, Megan L. Wojciechowicz, Jiyi Huang, Kyung Lee, Avi Ma’ayan, Cijiang He · 2020 · Diabetes
18. A Bayesian approach to accurate and robust signature detection on LINCS L1000 data
    Yue Qiu, Tianhuan Lu, Hansaim Lim, Lei Xie · 2020 · Bioinformatics
19. Inferring kinase activity from phosphoproteomic data: Tool comparison and recent applications
    Sander R. Piersma, Andrea Vallés‐Martí, Frank Rolfs, Thang V. Pham, Alex A. Henneman, Connie R. Jiménez · 2022 · Mass Spectrometry Reviews
20. A library of induced pluripotent stem cells from clinically well-characterized, diverse healthy human individuals
    Schaniel, Christoph, Dhanan, Priyanka, Hu, Bin, Xiong, Yuguang, Raghunandan, Teeya, Gonzalez, David M., Dariolli, Rafael, D'Souza, Sunita L., Yadaw, Arjun S., Hansen, Jens et al. · 2021 · Stem Cell Reports
21. Validating Small Molecule Chemical Probes for Biological Discovery
    Victoria Vu, Magdalena M. Szewczyk, David Y. Nie, C.H. Arrowsmith, Dalia Baršytė-Lovejoy · 2022 · Annual Review of Biochemistry
22. Repositioning linifanib as a potent anti-necroptosis agent for sepsis
    Liang Yu, Kai Yang, Xiaoyan He, Min Li, Lin Gao, Yunhong Zha · 2023 · Cell Death Discovery
23. piNET: a versatile web platform for downstream analysis and visualization of proteomics data
    Behrouz Shamsaei, Szymon Chojnacki, Marcin Pilarczyk, Mehdi Fazel Najafabadi, Wen Niu, Chuming Chen, Karen E. ROSS, Andrea D. Matlock, Jeremy L. Muhlich, Somchai Chutipongtanate et al. · 2020 · Nucleic Acids Research
24. PI3K signaling through a biochemical systems lens
    Ralitsa Radostinova Madsen, Alex Toker · 2023 · Journal of Biological Chemistry
25. BET Inhibitors Synergize with Carfilzomib to Induce Cell Death in Cancer Cells via Impairing Nrf1 Transcriptional Activity and Exacerbating the Unfolded Protein Response
    Janakiram Reddy Vangala, Ajay S Potluri, Senthil K. Radhakrishnan · 2020 · Biomolecules
26. The Advantages of Connectivity Map Applied in Traditional Chinese Medicine
    Huimin Jiang, Cheng Hu, Meijuan Chen · 2021 · Frontiers in Pharmacology
27. Morphodynamical cell state description via live-cell imaging trajectory embedding
    Jeremy Copperman, Sean M. Gross, Young Hwan Chang, Laura M. Heiser, Daniel M. Zuckerman · 2023 · Communications Biology
28. Inhibition of the neuromuscular acetylcholine receptor with atracurium activates FOXO/DAF‐16‐induced longevity
    Rebecca L. McIntyre, Simone W. Denis, Rashmi Kamble, Marte Molenaars, Michael Angelo Petr, Bauke V. Schomakers, Mizanur Rahman, Siddhartha Datta Gupta, Márton L. Tóth, Siva A. Vanapalli et al. · 2021 · Aging Cell
29. Investigations of nitazoxanide molecular targets and pathways for the treatment of hepatocellular carcinoma using network pharmacology and molecular docking
    Shakeel Ahmad Khan, Terence K. Lee · 2022 · Frontiers in Pharmacology
30. A review of computational methods for predicting cancer drug response at the single-cell level through integration with bulk RNAseq data
    Danielle Maeser, Weijie Zhang, Yingbo Huang, R. Stephanie Huang · 2023 · Current Opinion in Structural Biology
31. Supervised chemical graph mining improves drug-induced liver injury prediction
    Sangsoo Lim, Young‐Kuk Kim, Jeonghyeon Gu, Sunho Lee, Wonseok Shin, Sun Kim · 2022 · iScience
32. lncHUB2: aggregated and inferred knowledge about human and mouse lncRNAs
    Giacomo B. Marino, Megan L. Wojciechowicz, Daniel J. B. Clarke, Maxim V. Kuleshov, Zhuorui Xie, Minji Jeon, Alexander Lachmann, Avi Ma’ayan · 2023 · Database
33. Toxicology knowledge graph for structural birth defects
    John Erol Evangelista, Daniel J. B. Clarke, Zhuorui Xie, Giacomo B. Marino, Vivian Utti, Sherry L. Jenkins, Taha Mohseni Ahooyi, Cristian Bologa, Jeremy J. Yang, Jessica Binder et al. · 2023 · Communications Medicine
34. Deep representation learning determines drug mechanism of action from cell painting images
    Daniel R. Wong, David J. Logan, Santosh Hariharan, Robert V. Stanton, Djork-Arné Clevert, Andrew J. M. Kiruluta · 2023 · Digital Discovery
35. Differential Sensitivity Analysis for Resistant Malignancies (DISARM) Identifies Common Candidate Therapies across Platinum-Resistant Cancers
    Carl Michael Gay, Pan Tong, Robert J. Cardnell, Triparna Sen, Xiao Hua Su, Jun Ma, Rasha O. Bara, Faye M. Johnson, Chris Wakefield, John Victor Heymach et al. · 2018 · Clinical Cancer Research
36. Predicting gastrointestinal drug effects using contextualized metabolic models
    Marouen Ben Guebila, Ines Thiele · 2019 · PLoS Computational Biology
37. State-of-the-Art and Future Directions in Structural Proteomics
    Lotta Happonen, Markku T Varjosalo · 2025 · Molecular & Cellular Proteomics
38. A human-based multi-gene signature enables quantitative drug repurposing for metabolic disease
    James A. Timmons, Andrew Anighoro, Robert James Brogan, Jack Stahl, Claes Wahlestedt, David Gordon Farquhar, Jake P. Taylor‐King, Claude‐Henry Volmar, William E Kraus, Stuart M. Phillips · 2021 · eLife
39. A Gene Co-Expression Network-Based Drug Repositioning Approach Identifies Candidates for Treatment of Hepatocellular Carcinoma
    Meng Yuan, Ko Eun Shong, Xiangyü Li, Sajda Ashraf, Mengnan Shi, Woonghee Kim, Jens Nielsen, Hasan Türkez, Saeed Shoaie, Mathias Uhlén et al. · 2022 · Cancers
40. Signature-driven repurposing of Midostaurin for combination with MEK1/2 and KRASG12C inhibitors in lung cancer
    Irati Macaya, Marta Román, Connor Welch, Rodrigo Entrialgo‐Cadierno, Marina Salmón, Alba Santos, Iker Feliu, Joanna R. Kovalski, Inés López, María Rodríguez‐Remírez et al. · 2023 · Nature Communications
41. From Phenotypic Hit to Chemical Probe: Chemical Biology Approaches to Elucidate Small Molecule Action in Complex Biological Systems
    Quentin T. L. Pasquer, Ioannis A. Tsakoumagkos, Sascha Hoogendoorn · 2020 · Molecules
42. Responsiveness to perturbations is a hallmark of transcription factors that maintain cell identity in vitro
    Ian A. Mellis, Hailey I. Edelstein, Rachel Truitt, Yogesh Goyal, Lauren E. Beck, Orsolya Symmons, Margaret C. Dunagin, Ricardo Linares-Saldana, Parisha P. Shah, Juan A. Pérez-Bermejo et al. · 2021 · Cell Systems
43. Functional Assays to Screen and Dissect Genomic Hits
    Kiran Musunuru, Daniel Bernstein, Francis Sessions Cole, Mustafa Kezar Khokha, Frank S. Lee, Shin Lin, Thomas V. McDonald, Ivan P. G. Moskowitz, Thomas Quertermous, Vijay G. Sankaran et al. · 2018 · Circulation Genomic and Precision Medicine
44. Evaluating the consistency of large-scale pharmacogenomic studies
    Raziur Rahman, Saugato Rahman Dhruba, Kevin Matlock, Carlos De Niz, Souparno Ghosh, Ranadip Pal · 2018 · Briefings in Bioinformatics
45. L1000 Viewer: A Search Engine and Web Interface for the LINCS Data Repository
    Aliyu Musa, Shailesh Tripathi, Matthias Dehmer, Frank Emmert‐Streib · 2019 · Frontiers in Genetics
46. Hierarchical Multi-Omics Data Integration and Modeling to Predict Novel Chemical-Induced Cell-Specific Proteomics Profiles for Systems Pharmacology
    You Wu, Qiao Liu, Lei Xie · 2022 · Cell Reports Methods
47. Metabolic mapping of the human solute carrier superfamily
    Tabea Wiedmer, Shao Thing Teoh, Eirini Christodoulaki, Gernot Wolf, Chengzhe Tian, Vitaly Sedlyarov, Abigail P Jarret, Philipp Leippe, Fabian Frommelt, Álvaro Inglés‐Prieto et al. · 2025 · Molecular Systems Biology
48. Network-Based Assessment of Adverse Drug Reaction Risk in Polypharmacy Using High-Throughput Screening Data
    Guillermo de Anda‐Jáuregui, Kai Guo, Junguk Hur · 2019 · International Journal of Molecular Sciences
49. DDSBC: A Stacking Ensemble Classifier-Based Approach for Breast Cancer Drug-Pair Cell Synergy Prediction
    Aamir Mehmood, Aman Chandra Kaushik, Dong‐Qing Wei · 2024 · Journal of Chemical Information and Modeling
50. Transcriptome‑based drug repositioning identifies TPCA‑1 as a potential selective inhibitor of esophagus squamous carcinoma cell viability
    Zongyang Li, Linjun Zou, Zhi‐Xiong Jim Xiao, Jian Yang · 2022 · International Journal of Molecular Medicine
51. Navigating Transcriptomic Connectivity Mapping Workflows to Link Chemicals with Bioactivities
    Shah, Imran, Bundy, Joseph, Chambers, Bryant, Everett, Logan J., Haggard, Derik, Harrill, Joshua, Judson, Richard S., Nyffeler, Johanna, Patlewicz, Grace · 2022 · Chemical Research in Toxicology
52. Turning omics data into therapeutic insights
    Amanda J. Kedaigle, Ernest Fraenkel · 2018 · Current Opinion in Pharmacology
53. TomahaqCompanion: A Tool for the Creation and Analysis of Isobaric Label Based Multiplexed Targeted Assays
    Christopher M. Rose, Brian K. Erickson, Devin K. Schweppe, Rosa Viner, Jae Hyuk Choi, John C. Rogers, Ryan D. Bomgarden, Steven P. Gygi, Donald S. Kirkpatrick · 2018 · Journal of Proteome Research
54. Systems biology: perspectives on multiscale modeling in research on endocrine-related cancers
    Robert C. Clarke, John J. Tyson, Ming Tony Tan, William T. Baumann, Jin Lu, Jianhua Xuan, Yue Wang · 2019 · Endocrine Related Cancer
55. 2017 WONOEP appraisal: Studying epilepsy as a network disease using systems biology approaches
    John Matthew Mahoney, James Dominic Mills, Angelika Mühlebner, Jeffrey L. Noebels, Heidrun Potschka, Michele Simonato, Katja Kobow · 2019 · Epilepsia
56. A pharmacogenomic analysis using L1000CDS2 identifies BX-795 as a potential anticancer drug for primary pancreatic ductal adenocarcinoma cells
    Eun Ah Choi, Yeon-Sook Choi, Eun Ji Lee, Shree Ram Singh, Song Cheol Kim, Suhwan Chang · 2019 · Cancer Letters
57. AlphaFold3 in Drug Discovery: A Comprehensive Assessment of Capabilities, Limitations, and Applications
    Haiyang Zheng, Hanfeng Lin, Adebowale A. Alade, Jingjing Chen, Erika Y. Monroy, Min Zhang, Jin Wang · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
58. L2S2: chemical perturbation and CRISPR KO LINCS L1000 signature search engine
    Giacomo B. Marino, John Erol Evangelista, Daniel J. B. Clarke, Avi Ma’ayan · 2025 · Nucleic Acids Research
59. Opioids and immune checkpoint inhibitors differentially regulate a common immune network in triple-negative breast cancer
    Joseph R. Scarpa, Giacomo Montagna, George Plitas, Amitabh Gulati, Gregory W. Fischer, Joshua S. Mincer · 2023 · Frontiers in Oncology
60. HDAC1/2 inhibitor therapy improves multiple organ systems in aged mice
    Alessandra Tammaro, Eileen G. Daniels, Iman Man Hu, Kelly C. ‘t Hart, Kim Reid, Rio Putra Juni, Loes M. Butter, Goutham Vasam, Rashmi Kamble, Aldo Jongejan et al. · 2023 · iScience
61. An Application of Computational Drug Repurposing Based on Transcriptomic Signatures
    Evangelos Karatzas, George C. Kolios, George M. Spyrou · 2018 · Methods in molecular biology
62. Identification of pathways associated with chemosensitivity through network embedding
    Sheng Wang, Edward W Huang, Junmei Cairns, Jian Peng, Liewei Wang, Saurabh Sinha · 2019 · PLoS Computational Biology
63. Accelerating drug discovery and repurposing by combining transcriptional signature connectivity with docking
    Alexander William Thorman, James K. Reigle, Somchai Chutipongtanate, Juechen Yang, Behrouz Shamsaei, Marcin Pilarczyk, Mehdi Fazel‐Najafabadi, Rafał Adamczak, Michal Kouril, Surbhi Bhatnagar et al. · 2024 · Science Advances
64. Harnessing the biological complexity of Big Data from LINCS gene expression signatures
    Aliyu Musa, Shailesh Tripathi, Meenakshisundaram Kandhavelu, Matthias Dehmer, Frank Emmert‐Streib · 2018 · PLoS ONE
65. Pharmacokinetic Profiles Determine Optimal Combination Treatment Schedules in Computational Models of Drug Resistance
    Itziar Irurzun‐Arana, Thomas O. McDonald, Iñaki F. Trocóniz, Franziska Michor A · 2020 · Cancer Research
66. Prediction of Synergistic Drug Combinations for Prostate Cancer by Transcriptomic and Network Characteristics
    Shiqi Li, Fuhui Zhang, Xiuchan Xiao, Yanzhi Guo, Zhining Wen, Menglong Li, Xuemei Pu · 2021 · Frontiers in Pharmacology
67. Evolution of precision oncology‐guided treatment paradigms
    Ramanuj DasGupta, Aixin Yap, Elena Yaqing Yong, Shumei Chia · 2022 · WIREs Mechanisms of Disease
68. Screening of Drug Repositioning Candidates for Castration Resistant Prostate Cancer
    In‐Wha Kim, Jae Hyun Kim, Jung Mi Oh · 2019 · Frontiers in Oncology
69. Integrating Mathematical Modeling with High-Throughput Imaging Explains How Polyploid Populations Behave in Nutrient-Sparse Environments
    Gregory J. Kimmel, Mark A. Dane, Laura M. Heiser, Philipp M. Altrock, Noemi Andor · 2020 · Cancer Research
70. Artificial intelligence to guide precision anticancer therapy with multitargeted kinase inhibitors
    Manali Singha, Limeng Pu, Brent A. Stanfield, Ifeanyi Kingsley Uche, Paul J. F. Rider, Konstantin Gus Kousoulas, Jagannathan Ramanujam, Michał Bryliński · 2022 · BMC Cancer
71. Drug Repurposing: Insights into Current Advances and Future Applications
    T Bhatia, Shweta Sharma · 2023 · Current Medicinal Chemistry
72. Interactions between integrin α9β1 and VCAM-1 promote neutrophil hyperactivation and mediate poststroke DVT
    Nilesh O. Pandey, Harpreet Kaur, Mehul R. Chorawala, Sumit Kumar Anand, Lakshmi Chandaluri, Megan E. Butler, Richa Aishwarya, Shiva Jashwanth Gaddam, Xinggui Shen, Mabruka Alfaidi et al. · 2024 · Blood Advances
73. Towards the routine use of in silico screenings for drug discovery using metabolic modelling
    Tamara Bintener, Maria Pires Pacheco, Thomas Sauter · 2020 · Biochemical Society Transactions
74. Strategies to identify candidate repurposable drugs: COVID-19 treatment as a case example
    Ali Sajid Imami, Robert Erne McCullumsmith, Sinead Marie O'Donovan · 2021 · Translational Psychiatry
75. secDrug: a pipeline to discover novel drug combinations to kill drug-resistant multiple myeloma cells using a greedy set cover algorithm and single-cell multi-omics
    Harish Kumar, Suman Mazumder, Sayak Chakravarti, Neeraj Sharma, Ujjal Kumar Mukherjee, Shaji Kunnathu Kumar, Linda Banovic Baughn, Brian G. Van Ness, Amit Mitra · 2022 · Blood Cancer Journal
76. Investigation of drugs for the prevention of doxorubicin-induced cardiac events using big data analysis
    Shiori Nishiuchi, Kenta Yagi, Hiroumi Saito, Yoshito Zamami, Takahiro Niimura, Kôji Miyata, Yoshika Sakamoto, Kimiko Fukunaga, Shunsuke Ishida, Hirofumi Hamano et al. · 2022 · European Journal of Pharmacology
77. Kaleidoscope: A New Bioinformatics Pipeline Web Application for In Silico Hypothesis Exploration of Omics Signatures
    Khaled Alganem, Rammohan Shukla, Hunter Eby, Mackenzie E. Abel, Xiaolu Zhang, William Brett McIntyre, Jiwon Lee, Christy Au‐Yeung, Roshanak Asgariroozbehani, Roshni Panda et al. · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
78. Computational frameworks for enhanced extracellular vesicle biomarker discovery
    Jina Kim, Ju Dong Yang, Vatche Garen Agopian, Yazhen Zhu, Hsian‐Rong Tseng, Sungyong You · 2026 · Experimental & Molecular Medicine
79. Characterization of Cancer Stem Cells in Laryngeal Squamous Cell Carcinoma by Single-cell RNA Sequencing
    Yanguo Li, Lin Chen, Yidian Chu, Zhengyu Wei, Qi Ding, Shanshan Gu, Hongxia Deng, Qi Liao, Zhisen Shen · 2024 · Genomics Proteomics & Bioinformatics
80. Learning to encode cellular responses to systematic perturbations with deep generative models
    Yifan Xue, Michael Qi Ding, Xinghua Lu · 2020 · npj Systems Biology and Applications
81. Predicting Lyme Disease From Patients' Peripheral Blood Mononuclear Cells Profiled With RNA-Sequencing
    Daniel J. B. Clarke, Alison W. Rebman, Allison Bailey, Megan L. Wojciechowicz, Sherry L. Jenkins, John Erol Evangelista, Matteo Danieletto, Jinshui Fan, Mark W. Eshoo, Michael R. Mosel et al. · 2021 · Frontiers in Immunology
82. Computational Drug Repurposing for Neurodegenerative Diseases
    Kyriaki Savva, Margarita Zachariou, Anastasis Oulas, George Minadakis, Kleitos Sokratous, Nikolas Dietis, George M. Spyrou · 2019 · Elsevier eBooks
83. Proteomic profiling dataset of chemical perturbations in multiple biological backgrounds
    Deborah O. Dele-Oni, Karen E. Christianson, Shawn B. Egri, Alvaro Sebastian Vaca Jácome, Katherine C. DeRuff, James Mullahoo, Vagisha Sharma, Desiree Davison, Tak Ko, Michael Bula et al. · 2021 · Scientific Data
84. Drug and single-cell gene expression integration identifies sensitive and resistant glioblastoma cell populations
    Robert K. Suter, Anna M. Jermakowicz, Rithvik Veeramachaneni, Matthew D’Antuono, L.G. Zhang, Rishika Chowdary, Simon Kaeppeli, Madison Sharp, Pravallika Palwai, Vasileios Stathias et al. · 2026 · Nature Communications
85. Mass spectrometry-based profiling of single-cell histone post-translational modifications to dissect chromatin heterogeneity
    Ronald R. Cutler, Laura Corveleyn, Claudia Ctortecka, Francesca Licausi, Joshua Cantlon-Bruce, Alvaro Sebastian Vaca Jácome, Dieter L. D. Deforce, Jan Vijg, Maarten Dhaenens, Malvina Papanastasiou et al. · 2025 · Nature Communications
86. Integration of Multiple Data Sources for Gene Network Inference Using Genetic Perturbation Data
    Xiao Yang Liang, William Chad Young, Ling‐Hong Hung, Adrian E. Raftery, Ka Yee Yeung · 2019 · Journal of Computational Biology
87. Identifying Gene Signatures for Cancer Drug Repositioning Based on Sample Clustering
    Fei Wang, Yulian Ding, Xiujuan Lei, Bo Liao, Fang‐Xiang Wu · 2020 · IEEE Transactions on Computational Biology and Bioinformatics
88. LINCS gene expression signature analysis revealed bosutinib as a radiosensitizer of breast cancer cells by targeting eIF4G1
    Sai Hu, Ping‐Kun Zhou, Xiaodan Liu, Xiaodan Liu, Dafei Xie, Bo Huang, Hua Guan · 2021 · International Journal of Molecular Medicine
89. Connectivity Map Analysis of a Single-Cell RNA-Sequencing -Derived Transcriptional Signature of mTOR Signaling
    Naim Al Mahi, Erik Y. Zhang, Susan G. Sherman, Jane J. Yu, Mario Medvedovic · 2021 · International Journal of Molecular Sciences
90. A primer on applying AI synergistically with domain expertise to oncology
    Jason Kim, Rebecca L. Kusko, Benjamin J. Zeskind, Jenny Zhang, Renan Escalante-Chong · 2021 · Biochimica et Biophysica Acta (BBA) - Reviews on Cancer
91. New drug candidates for osteosarcoma: Drug repurposing based on gene expression signature
    Raissa Coelho Andrade, Mariana Boroni, Marion Kielmanowicz Amazonas, Fernando Regla Vargas · 2021 · Computers in Biology and Medicine
92. Integrated Genomic and Bioinformatics Approaches to Identify Molecular Links between Endocrine Disruptors and Adverse Outcomes
    Jacopo Umberto Verga, Matthew L. Huff, Diarmuid Owens, Bethany Jacobs Wolf, Gary Hardiman · 2022 · International Journal of Environmental Research and Public Health
93. COVID-19-specific transcriptomic signature detectable in blood across multiple cohorts
    Tommi Välikangas, Sini Junttila, Kalle T. Rytkönen, Anu Kukkonen-Macchi, Tomi Suomi, Laura L. Elo · 2022 · Frontiers in Genetics
94. Datasets2Tools, repository and search engine for bioinformatics datasets, tools and canned analyses
    Denis Torre, Patrycja Krawczuk, Kathleen M. Jagodnik, Alexander Lachmann, Zichen Wang, Lily Wang, Maxim V. Kuleshov, Avi Ma’ayan · 2018 · Scientific Data
95. Identifying shared transcriptional risk patterns between atherosclerosis and cancer
    Richard A. Baylis, Hua Gao, Fu-Di Wang, C. Bell, Lingfeng Luo, J. Björkegren, N. Leeper · 2023 · iScience
96. Ontological representation, integration, and analysis of LINCS cell line cells and their cellular responses
    Edison Ong, Jiangan Xie, Zhaohui Ni, Qingping Liu, Sirarat Sarntivijai, Yu Lin, Daniel J. Cooper, Raymond Terryn, Vasileios Stathias, Caty Chung et al. · 2017 · BMC Bioinformatics
97. Repurposing of Anticancer Stem Cell Drugs in Brain Tumors
    Hisham F. Bahmad, Darine Daher, Abed Alhalim Aljamal, Mohamad K. Elajami, Kei Shing Oh, Juan Carlos Alvarez Moreno, Ruben G. Delgado, Richard Suarez, Ana Zaldivar, Roshanak Azimi et al. · 2021 · Journal of Histochemistry & Cytochemistry
98. Systematic indication extension for drugs using patient stratification insights generated by combinatorial analytics
    Sayoni Das, Krystyna Taylor, Simon A. Beaulah, Steve Gardner · 2022 · Patterns
99. Systems Pharmacology Identifies an Arterial Wall Regulatory Gene Network Mediating Coronary Artery Disease Side Effects of Antiretroviral Therapy
    Itziar Frades, Ben Readhead, Letizia Amadori, Simon Koplev, Husain Ahammad Talukdar, Heidi M. Crane, Paul K. Crane, Jason Ciril Kovacic, Joel T. Dudley, Chiara Giannarelli et al. · 2019 · Circulation Genomic and Precision Medicine
100. Association of Antineoplastic Therapy With Decreased SARS-CoV-2 Infection Rates in Patients With Cancer
     Michael Bonner Foote, James Robert White, Justin Jee, Guillem Argilés, Jonathan C. M. Wan, Benoı̂t Rousseau, Melissa S. Pessin, Luis Alberto Diaz · 2021 · JAMA Oncology