Prospective Exploration of Synthetically Feasible, Medicinally Relevant Chemical Space. - Stephan C. Schürer; Prashant Tyagi; Steven M. Muskal (J. Chem. Inf. Model., 2005)

Utilizing high throughput screening data for predictive toxicology models: protocols and application to MLSCN assays. - Rajarshi Guha; Stephan C. Schürer (J. Comput. Aided Mol. Des., 2008)

Cell Line Ontology: Redesigning the Cell Line Knowledgebase to Aid Integrative Translational Informatics. - Sirarat Sarntivijai; Zuoshuang Xiang; Terrence F. Meehan; Alexander D. Diehl; Uma Vempati; Stephan C. Schürer; Chao Pang; James Malone; Helen E. Parkinson; Brian D. Athey; Yongqun He (ICBO, 2011)

Bioassay Ontology to Describe High-Throughput Screening Assays and their Results. - Uma Vempati; Ubbo Visser; Saminda Abeyruwan; Kunie Sakurai; Magdalena Przydzial; Caty Chung; Robin P. Smith; Amar Koleti; Christopher Mader; Vance P. Lemmon; Stephan C. Schürer (ICBO, 2011)

BioAssay Ontology (BAO): A Semantic Description of Bioassays and High-Throughput Screening Results. - Ubbo Visser; Saminda Abeyruwan; Uma Vempati; Robin P. Smith; Vance P. Lemmon; Stephan C. Schürer (BMC Bioinform., 2011)

Distinct functional and conformational states of the human lymphoid tyrosine phosphatase catalytic domain can be targeted by choice of the inhibitor chemotype. - Dusica Vidovic; Yuli Xie; Alison Rinderspacher; Shi-Xian Deng; Donald W. Landry; Caty Chung; Deborah H. Smith; Lutz Tautz; Stephan C. Schürer (J. Comput. Aided Mol. Des., 2011)

Novel Kinase Inhibitors by Reshuffling Ligand Functionalities Across the Human Kinome. - Dusica Vidovic; Steven M. Muskal; Stephan C. Schürer (J. Chem. Inf. Model., 2012)

PrOntoLearn: Unsupervised Lexico-Semantic Ontology Generation Using Probabilistic Methods. - Saminda Abeyruwan; Ubbo Visser; Vance P. Lemmon; Stephan C. Schürer (URSW (LNCS Vol.), 2013)

GPCR ontology: development and application of a G protein-coupled receptor pharmacology knowledge framework. - Magdalena Przydzial; Barun Bhhatarai; Amar Koleti; Uma Vempati; Stephan C. Schürer (Bioinform., 2013)

Kinome-wide Activity Modeling from Diverse Public High-Quality Data Sets. - Stephan C. Schürer; Steven M. Muskal (J. Chem. Inf. Model., 2013)

Evolving BioAssay Ontology (BAO): modularization, integration and applications. - Saminda Abeyruwan; Uma D. Vempati; Hande Küçük-McGinty; Ubbo Visser; Amar Koleti; Ahsan Mir; Kunie Sakurai; Caty Chung; Joshua A. Bittker; Paul A. Clemons; Steve Brudz; Anosha Siripala; et al. (J. Biomed. Semant., 2014)

CLO: The cell line ontology. - Sirarat Sarntivijai; Yu Lin; Zuoshuang Xiang; Terrence F. Meehan; Alexander D. Diehl; Uma D. Vempati; Stephan C. Schürer; Chao Pang; James Malone; Helen E. Parkinson; Yue Liu; Terue Takatsuki; et al. (J. Biomed. Semant., 2014)

BioAssay Research Database (BARD): chemical biology and probe-development enabled by structured metadata and result types. - E. A. Howe; Andrea de Souza; David L. Lahr; S. Chatwin; Philip Montgomery; B. R. Alexander; Dac-Trung Nguyen; Yasel Cruz; D. A. Stonich; G. Walzer; J. T. Rose; Shaita C. Picard; et al. (Nucleic Acids Res., 2015)

Building Concordant Ontologies for Drug Discovery. - Hande Küçük-McGinty; Saurabh Mehta; Yu Lin; Nooshin Nabizadeh; Vasileios Stathias; Dusica Vidovic; Amar Koleti; Christopher Mader; Jianbin Duan; Ubbo Visser; Stephan C. Schürer (ICBO/BioCreative, 2016)

The Cell Line Ontology Integration and Analysis of the Knowledge of LINCS Cell Lines. - Edison Ong; Jiangan Xie; Zhaohui Ni; Qingping Liu; Yu Lin; Vasileios Stathias; Caty Chung; Stephan C. Schürer; Yongqun He (ICBO/BioCreative, 2016)

The ontology reference model for visual selectivity analysis in drug-target interactions. - Qiong Cheng; Felix A. Lopez; Celia Duran; Christopher Camarillo; Tudor I. Oprea; Stephan C. Schürer (BIBM, 2017)

Learning reference-enriched approach towards large scale active ontology alignment and integration. - Qiong Cheng; Oleg Ursu; Tudor I. Oprea; Stephan C. Schürer (BIBM, 2017)

The SmartAPI Ecosystem for Making Web APIs FAIR. - Shima Dastgheib; Trish Whetzel; Amrapali Zaveri; Cyrus Afrasiabi; Pedro Assis; Paul Avillach; Kathleen M. Jagodnik; Gabor Korodi; Marcin Pilarczyk; Jeff de Pons; Stephan C. Schürer; Raymond Terryn; et al. (ISWC (Posters, Demos & Industry Tracks), 2017)

TIN-X: target importance and novelty explorer. - Daniel Cannon; Jeremy J. Yang; Stephen L. Mathias; Oleg Ursu; Subramani Mani; Anna Waller; Stephan C. Schürer; Lars Juhl Jensen; Larry A. Sklar; Cristian Bologa; Tudor I. Oprea (Bioinform., 2017)

Drug target ontology to classify and integrate drug discovery data. - Yu Lin; Saurabh Mehta; Hande Küçük-McGinty; John Paul Turner; Dusica Vidovic; Michele Forlin; Amar Koleti; Dac-Trung Nguyen; Lars Juhl Jensen; Rajarshi Guha; Stephen L. Mathias; Oleg Ursu; et al. (J. Biomed. Semant., 2017)

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; Stephan C. Schürer; Yongqun He (BMC Bioinform., 2017)

Developing a framework for digital objects in the Big Data to Knowledge (BD2K) commons: Report from the Commons Framework Pilots workshop. - Kathleen M. Jagodnik; Simon Koplev; Sherry L. Jenkins; Lucila Ohno-Machado; Benedict Paten; Stephan C. Schürer; Michel Dumontier; Ruben Verborgh; Alex A. T. Bui; Peipei Ping; Neil J. McKenna; Ravi K. Madduri; et al. (J. Biomed. Informatics, 2017)

Pharos: Collating protein information to shed light on the druggable genome. - Dac-Trung Nguyen; Stephen L. Mathias; Cristian Bologa; Søren Brunak; Nicolas F. Fernandez; Anna Gaulton; Anne Hersey; Jayme Holmes; Lars Juhl Jensen; Anneli Karlsson; Guixia Liu; Avi Ma'ayan; et al. (Nucleic Acids Res., 2017)

A Gene Family-led Meta-Analysis of Drug-Target Interactions. - Qiong Cheng; Saurabh Mehta; Stephan C. Schürer (BIBM, 2018)

CEDAR: Semantic Web Technology to Support Open Science. - Mark A. Musen; Susanna-Assunta Sansone; Kei-Hoi Cheung; Steven H. Kleinstein; Morgan Crafts; Stephan C. Schürer; John B. Graybeal (WWW (Companion Volume), 2018)

Data Portal for the Library of Integrated Network-based Cellular Signatures (LINCS) program: integrated access to diverse large-scale cellular perturbation response data. - Amar Koleti; Raymond Terryn; Vasileios Stathias; Caty Chung; Daniel J. Cooper; John Paul Turner; Dusica Vidovic; Michele Forlin; Tanya T. Kelley; Alessandro D'Urso; Bryce K. Allen; Denis Torre; et al. (Nucleic Acids Res., 2018)

OSCI: standardized stem cell ontology representation and use cases for stem cell investigation. - Yongqun He; William D. Duncan; Daniel J. Cooper; Jens Hansen; Ravi Iyengar; Edison Ong; Kendal Walker; Omar Tibi; Sam Smith; Lucas M. Serra; Jie Zheng 001; Sirarat Sarntivijai; et al. (BMC Bioinform., 2019)

DrugCentral 2018: an update. - Oleg Ursu; Jayme Holmes; Cristian Bologa; Jeremy J. Yang; Stephen L. Mathias; Vasileios Stathias; Dac-Trung Nguyen; Stephan C. Schürer; Tudor I. Oprea (Nucleic Acids Res., 2019)

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 Ross; Andrea Matlock; Jeremy Muhlich; Somchai Chutipongtanate; Jie Zheng 001; John Turner; et al. (Nucleic Acids Res., 2020)

LINCS Data Portal 2.0: next generation access point for perturbation-response signatures. - Vasileios Stathias; John Paul Turner; Amar Koleti; Dusica Vidovic; Daniel J. Cooper; Mehdi Fazel-Najafabadi; Marcin Pilarczyk; Raymond Terryn; Caty Chung; Afoma Umeano; Daniel J. B. Clarke; Alexander Lachmann; et al. (Nucleic Acids Res., 2020)

TCRD and Pharos 2021: mining the human proteome for disease biology. - Timothy Sheils; Stephen L. Mathias; Keith J. Kelleher; Vishal B. Siramshetty; Dac-Trung Nguyen; Cristian Bologa; Lars Juhl Jensen; Dusica Vidovic; Amar Koleti; Stephan C. Schürer; Anna Waller; Jeremy J. Yang; et al. (Nucleic Acids Res., 2021)

SigCom LINCS: data and metadata search engine for a million gene expression signatures. - John Erol Evangelista; Daniel J. B. Clarke; Zhuorui Xie; Alexander Lachmann; Minji Jeon; Kerwin Chen; Kathleen M. Jagodnik; Sherry L. Jenkins; Maxim V. Kuleshov; Megan L. Wojciechowicz; Stephan C. Schürer; Mario Medvedovic; et al. (Nucleic Acids Res., 2022)

The Clinical Kinase Index (CKI): A user friendly application to prioritize kinases as prospective cancer drug targets. - Rimpi Khurana; Stephan C. Schürer (Softw. Impacts, 2022)

AI-Assisted chemical probe discovery for the understudied Calcium-Calmodulin Dependent Kinase, PNCK. - Derek J. Essegian; Valery Chavez; Rabia Khurshid; Jaime R. Merchan; Stephan C. Schürer (PLoS Comput. Biol., 2023)

Pharos 2023: an integrated resource for the understudied human proteome. - Keith J. Kelleher; Timothy Sheils; Stephen L. Mathias; Jeremy J. Yang; Vincent T. Metzger; Vishal B. Siramshetty; Dac-Trung Nguyen; Lars Juhl Jensen; Dusica Vidovic; Stephan C. Schürer; Jayme Holmes; Karlie R. Sharma; et al. (Nucleic Acids Res., 2023)

Correction: AI-Assisted chemical probe discovery for the understudied Calcium-Calmodulin Dependent Kinase, PNCK. - Derek J. Essegian; Valery Chavez; Rabia Khurshid; Jaime R. Merchan; Stephan C. Schürer (PLoS Comput. Biol., 2023)

An extension of the BioAssay Ontology to include pharmacokinetic/pharmacodynamic terminology for the enrichment of scientific workflows. - Steve Penn; Jane Lomax; Anneli Karlsson; Vincent Antonucci; Carl-Dieter Zachmann; Samantha Kanza; Stephan C. Schürer; John Turner (J. Biomed. Semant., 2023)