Stephan C. Schürer

39 papers Journal 28Unranked 11

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	Advancing the bioassay ontology through integrated PK/PD and safety pharmacology representation. J. Biomed. Semant. Joan Glenny-Pescov, Caty Chung, Nicolette Ross, Jiaming Hu, Michael Sinclair, Rabia Khurshid, Anneli Karlsson, Stephan C. Schürer
2023	J	`jnl`	AI-Assisted chemical probe discovery for the understudied Calcium-Calmodulin Dependent Kinase, PNCK. PLoS Comput. Biol. Derek J. Essegian, Valery Chavez, Rabia Khurshid, Jaime R. Merchan, Stephan C. Schürer
2023	J	`jnl`	An extension of the BioAssay Ontology to include pharmacokinetic/pharmacodynamic terminology for the enrichment of scientific workflows. J. Biomed. Semant. Steve Penn, Jane Lomax, Anneli Karlsson, Vincent Antonucci, Carl-Dieter Zachmann, Samantha Kanza, Stephan C. Schürer, John Turner
2023	J	`jnl`	Correction: AI-Assisted chemical probe discovery for the understudied Calcium-Calmodulin Dependent Kinase, PNCK. PLoS Comput. Biol. Derek J. Essegian, Valery Chavez, Rabia Khurshid, Jaime R. Merchan, Stephan C. Schürer
2023	J	`jnl`	Pharos 2023: an integrated resource for the understudied human proteome. Nucleic Acids Res. 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, Ajay Pillai, Cristian Bologa, Jeremy S. Edwards, Ewy A. Mathé, Tudor I. Oprea
2022	J	`jnl`	SigCom LINCS: data and metadata search engine for a million gene expression signatures. Nucleic Acids Res. 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, Avi Ma'ayan
2022	J	`jnl`	The Clinical Kinase Index (CKI): A user friendly application to prioritize kinases as prospective cancer drug targets. Softw. Impacts Rimpi Khurana, Stephan C. Schürer
2021	J	`jnl`	TCRD and Pharos 2021: mining the human proteome for disease biology. Nucleic Acids Res. 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, Jayme Holmes, Giovanni Bocci, Noel Southall, Poorva Dharkar, Ewy A. Mathé, Anton Simeonov, Tudor I. Oprea
2020	J	`jnl`	LINCS Data Portal 2.0: next generation access point for perturbation-response signatures. Nucleic Acids Res. 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, John Erol Evangelista, Avi Ma'ayan, Mario Medvedovic, Stephan C. Schürer
2020	J	`jnl`	piNET: a versatile web platform for downstream analysis and visualization of proteomics data. Nucleic Acids Res. Behrouz Shamsaei, Szymon Chojnacki, Marcin Pilarczyk, Mehdi Fazel-Najafabadi, Wen Niu, Chuming Chen, Karen Ross, Andrea Matlock, Jeremy Muhlich, Somchai Chutipongtanate, Jie Zheng, John Turner, Dusica Vidovic, Jake Jaffe, Michael J. MacCoss, Cathy Wu, Ajay Pillai, Avi Ma'ayan, Stephan C. Schürer, Michal Kouril, Mario Medvedovic, Jarek Meller
2019	J	`jnl`	DrugCentral 2018: an update. Nucleic Acids Res. Oleg Ursu, Jayme Holmes, Cristian Bologa, Jeremy J. Yang, Stephen L. Mathias, Vasileios Stathias, Dac-Trung Nguyen, Stephan C. Schürer, Tudor I. Oprea
2019	J	`jnl`	OSCI: standardized stem cell ontology representation and use cases for stem cell investigation. BMC Bioinform. 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, Sirarat Sarntivijai, Stephan C. Schürer, K. Sue O'Shea, Alexander D. Diehl
2018	—	`conf`	A Gene Family-led Meta-Analysis of Drug-Target Interactions. BIBM Qiong Cheng, Saurabh Mehta, Stephan C. Schürer
2018	—	`conf`	CEDAR: Semantic Web Technology to Support Open Science. WWW (Companion Volume) Mark A. Musen, Susanna-Assunta Sansone, Kei-Hoi Cheung, Steven H. Kleinstein, Morgan Crafts, Stephan C. Schürer, John B. Graybeal
2018	J	`jnl`	Data Portal for the Library of Integrated Network-based Cellular Signatures (LINCS) program: integrated access to diverse large-scale cellular perturbation response data. Nucleic Acids Res. 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, Kathleen M. Jagodnik, Lily Wang, Sherry L. Jenkins, Christopher Mader, Wen Niu, Mehdi Fazel, Naim Al Mahi, Marcin Pilarczyk, Nicholas A. Clark, Behrouz Shamsaei, Jarek Meller, Juozas Vasiliauskas, John Reichard, Mario Medvedovic, Avi Ma'ayan, Ajay Pillai, Stephan C. Schürer
2017	J	`jnl`	Developing a framework for digital objects in the Big Data to Knowledge (BD2K) commons: Report from the Commons Framework Pilots workshop. J. Biomed. Informatics 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, Ajay Pillai, Avi Ma'ayan
2017	J	`jnl`	Drug target ontology to classify and integrate drug discovery data. J. Biomed. Semant. 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, Vasileios Stathias, Jianbin Duan, Nooshin Nabizadeh, Caty Chung, Christopher Mader, Ubbo Visser, Jeremy J. Yang, Cristian Bologa, Tudor I. Oprea, Stephan C. Schürer
2017	—	`conf`	Learning reference-enriched approach towards large scale active ontology alignment and integration. BIBM Qiong Cheng, Oleg Ursu, Tudor I. Oprea, Stephan C. Schürer
2017	J	`jnl`	Ontological representation, integration, and analysis of LINCS cell line cells and their cellular responses. BMC Bioinform. 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
2017	J	`jnl`	Pharos: Collating protein information to shed light on the druggable genome. Nucleic Acids Res. 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, Geetha Mandava, Subramani Mani, Saurabh Mehta, John P. Overington, Juhee Patel, Andrew D. Rouillard, Stephan C. Schürer, Timothy Sheils, Anton Simeonov, Larry A. Sklar, Noel Southall, Oleg Ursu, Dusica Vidovic, Anna Waller, Jeremy J. Yang, Ajit Jadhav, Tudor I. Oprea, Rajarshi Guha
2017	J	`jnl`	TIN-X: target importance and novelty explorer. Bioinform. 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
2017	—	`conf`	The SmartAPI Ecosystem for Making Web APIs FAIR. ISWC (Posters, Demos & Industry Tracks) 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, Ruben Verborgh, Chunlei Wu, Michel Dumontier
2017	—	`conf`	The ontology reference model for visual selectivity analysis in drug-target interactions. BIBM Qiong Cheng, Felix A. Lopez, Celia Duran, Christopher Camarillo, Tudor I. Oprea, Stephan C. Schürer
2016	—	`conf`	Building Concordant Ontologies for Drug Discovery. ICBO/BioCreative Hande Küçük-McGinty, Saurabh Mehta, Yu Lin, Nooshin Nabizadeh, Vasileios Stathias, Dusica Vidovic, Amar Koleti, Christopher Mader, Jianbin Duan, Ubbo Visser, Stephan C. Schürer
2016	—	`conf`	The Cell Line Ontology Integration and Analysis of the Knowledge of LINCS Cell Lines. ICBO/BioCreative Edison Ong, Jiangan Xie, Zhaohui Ni, Qingping Liu, Yu Lin, Vasileios Stathias, Caty Chung, Stephan C. Schürer, Yongqun He
2015	J	`jnl`	BioAssay Research Database (BARD): chemical biology and probe-development enabled by structured metadata and result types. Nucleic Acids Res. 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, Zihan Liu, Jamie N. Rose, X. Xiang, Jacob K. Asiedu, D. Durkin, J. Levine, J. J. Yang, Stephan C. Schürer, John C. Braisted, Noel Southall, Mark R. Southern, T. D. Y. Chung, Steve Brudz, C. Tanega, Stuart L. Schreiber, Joshua A. Bittker, Rajarshi Guha, Paul A. Clemons
2014	J	`jnl`	CLO: The cell line ontology. J. Biomed. Semant. 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, Kaoru Saijo, Hiroshi Masuya, Yukio Nakamura, Matthew H. Brush, Melissa A. Haendel, Jie Zheng, Christian J. Stoeckert Jr., Bjoern Peters, Christopher J. Mungall, Thomas E. Carey, David J. States, Brian D. Athey, Yongqun He
2014	J	`jnl`	Evolving BioAssay Ontology (BAO): modularization, integration and applications. J. Biomed. Semant. 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, Arturo J. Morales, Martin Romacker, David Twomey, Svetlana Bureeva, Vance P. Lemmon, Stephan C. Schürer
2013	J	`jnl`	GPCR ontology: development and application of a G protein-coupled receptor pharmacology knowledge framework. Bioinform. Magdalena Przydzial, Barun Bhhatarai, Amar Koleti, Uma Vempati, Stephan C. Schürer
2013	J	`jnl`	Kinome-wide Activity Modeling from Diverse Public High-Quality Data Sets. J. Chem. Inf. Model. Stephan C. Schürer, Steven M. Muskal
2013	—	`conf`	PrOntoLearn: Unsupervised Lexico-Semantic Ontology Generation Using Probabilistic Methods. URSW (LNCS Vol.) Saminda Abeyruwan, Ubbo Visser, Vance P. Lemmon, Stephan C. Schürer
2012	J	`jnl`	Novel Kinase Inhibitors by Reshuffling Ligand Functionalities Across the Human Kinome. J. Chem. Inf. Model. Dusica Vidovic, Steven M. Muskal, Stephan C. Schürer
2011	J	`jnl`	BioAssay Ontology (BAO): A Semantic Description of Bioassays and High-Throughput Screening Results. BMC Bioinform. Ubbo Visser, Saminda Abeyruwan, Uma Vempati, Robin P. Smith, Vance P. Lemmon, Stephan C. Schürer
2011	—	`conf`	Bioassay Ontology to Describe High-Throughput Screening Assays and their Results. ICBO 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
2011	—	`conf`	Cell Line Ontology: Redesigning the Cell Line Knowledgebase to Aid Integrative Translational Informatics. ICBO 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
2011	J	`jnl`	Distinct functional and conformational states of the human lymphoid tyrosine phosphatase catalytic domain can be targeted by choice of the inhibitor chemotype. J. Comput. Aided Mol. Des. Dusica Vidovic, Yuli Xie, Alison Rinderspacher, Shi-Xian Deng, Donald W. Landry, Caty Chung, Deborah H. Smith, Lutz Tautz, Stephan C. Schürer
2010	—	`conf`	PrOntoLearn: Unsupervised Lexico-Semantic Ontology Generation using Probabilistic Methods. URSW Saminda Abeyruwan, Ubbo Visser, Vance P. Lemmon, Stephan C. Schürer
2008	J	`jnl`	Utilizing high throughput screening data for predictive toxicology models: protocols and application to MLSCN assays. J. Comput. Aided Mol. Des. Rajarshi Guha, Stephan C. Schürer
2005	J	`jnl`	Prospective Exploration of Synthetically Feasible, Medicinally Relevant Chemical Space. J. Chem. Inf. Model. Stephan C. Schürer, Prashant Tyagi, Steven M. Muskal