Sean D. Mooney

54 papers C 1Misc 13Journal 35Unranked 5

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	Automated Survey Collection with LLM-based Conversational Agents. CoRR Kurmanbek Kaiyrbekov, Nicholas J. Dobbins, Sean D. Mooney
2025	J	`jnl`	Transformer patient embedding using electronic health records enables patient stratification and progression analysis. npj Digit. Medicine Su Xian, Monika E. Grabowska, Iftikhar J. Kullo, Yuan Luo, Jordan W. Smoller, Theresa L. Walunas, Wei-Qi Wei, Gail P. Jarvik, Sean D. Mooney, David R. Crosslin
2023	J	`jnl`	Evaluation of crowdsourced mortality prediction models as a framework for assessing artificial intelligence in medicine. J. Am. Medical Informatics Assoc. Timothy Bergquist, Thomas Schaffter, Yao Yan, Thomas Yu, Justin Prosser, Jifan Gao, Guanhua Chen, Lukasz Charzewski, Zofia Nawalany, Ivan Brugere, Renata Retkute, Alidivinas Prusokas, Augustinas Prusokas, Yonghwa Choi, Sanghoon Lee, Junseok Choe, Inggeol Lee, Sunkyu Kim, Jaewoo Kang, Sean D. Mooney, Justin Guinney
2023	J	`jnl`	Predicting decompression surgery by applying multimodal deep learning to patients' structured and unstructured health data. BMC Medical Informatics Decis. Mak. Chethan Jujjavarapu, Pradeep Suri, Vikas Pejaver, Janna Friedly, Laura S. Gold, Eric Meier, Trevor Cohen, Sean D. Mooney, Patrick J. Heagerty, Jeffrey G. Jarvik
2022	J	`jnl`	A Multifaceted Benchmarking of Synthetic Electronic Health Record Generation Models. CoRR Chao Yan, Yao Yan, Zhiyu Wan, Ziqi Zhang, Larsson Omberg, Justin Guinney, Sean D. Mooney, Bradley A. Malin
2022	Misc	`conf`	Assessing Machine Learning Based Generators for Synthetic Electronic Health Records: A Benchmarking. AMIA Chao Yan, Yao Yan, Ziqi Zhang, Zhiyu Wan, Justin Guinney, Sean D. Mooney, Bradley A. Malin
2022	Misc	`conf`	Geospatial divide in real-world EHR data: Analytical workflow to assess regional biases and potential impact on health equity. AMIA Serena Jinchen Xie, Flavia Kapos, Stephen J. Mooney, Sean D. Mooney, Kari A. Stephens, Andrea L. Hartzler, Abhishek Pratap
2022	J	`jnl`	The NLP Sandbox: an efficient model-to-data system to enable federated and unbiased evaluation of clinical NLP models. CoRR Yao Yan, Thomas Yu, Kathleen Muenzen, Sijia Liu, Connor Boyle, George Koslowski, Jiaxin Zheng, Nicholas J. Dobbins, Clement Essien, Hongfang Liu, Larsson Omberg, Meliha Yestigen, Bradley Taylor, James A. Eddy, Justin Guinney, Sean D. Mooney, Thomas Schaffter
2021	Misc	`conf`	A Continuous Crowd-sourced Challenge for Benchmarking COVID-19 Health Outcome Prediction. AMIA Yao Yan, Thomas Schaffter, Timothy Bergquist, Thomas Yu, Justin Prosser, Sean D. Mooney, Justin Guinney
2021	J	`jnl`	Considering the possibilities and pitfalls of Generative Pre-trained Transformer 3 (GPT-3) in healthcare delivery. npj Digit. Medicine Diane M. Korngiebel, Sean D. Mooney
2021	Misc	`conf`	Establishing the reliability of algorithms. PSB Lara M. Mangravite, Sean D. Mooney, Iddo Friedberg, Justin Guinney
2021	J	`jnl`	Information needs and priority use cases of population health researchers to improve preparedness for future hurricanes and floods. J. Am. Medical Informatics Assoc. Jimmy Phuong, Christina Bandaragoda, Shefali Haldar, Kari A. Stephens, Patricia Ordóñez, Sean D. Mooney, Andrea L. Hartzler
2020	J	`jnl`	Indicators of retention in remote digital health studies: a cross-study evaluation of 100, 000 participants. npj Digit. Medicine Abhishek Pratap, Elias Chaibub Neto, Phil Snyder, Carl Stepnowsky, Noémie Elhadad, Daniel Grant, Matthew H. Mohebbi, Sean D. Mooney, Christine Suver, John Wilbanks, Lara M. Mangravite, Patrick J. Heagerty, Pat A. Areán, Larsson Omberg
2020	J	`jnl`	Leaf: an open-source, model-agnostic, data-driven web application for cohort discovery and translational biomedical research. J. Am. Medical Informatics Assoc. Nicholas J. Dobbins, Clifford H. Spital, Robert A. Black, Jason M. Morrison, Bas de Veer, Elizabeth Zampino, Robert D. Harrington, Bethene D. Britt, Kari A. Stephens, Adam B. Wilcox, Peter Tarczy-Hornoch, Sean D. Mooney
2020	J	`jnl`	Piloting a model-to-data approach to enable predictive analytics in health care through patient mortality prediction. J. Am. Medical Informatics Assoc. Timothy Bergquist, Yao Yan, Thomas Schaffter, Thomas Yu, Vikas Pejaver, Noah Hammarlund, Justin Prosser, Justin Guinney, Sean D. Mooney
2019	J	`jnl`	Automated retrieval, preprocessing, and visualization of gridded hydrometeorology data products for spatial-temporal exploratory analysis and intercomparison. Environ. Model. Softw. Jimmy Phuong, Christina Bandaragoda, Erkan Istanbulluoglu, Claire Beveridge, Ronda Strauch, Landung Setiawan, Sean D. Mooney
2019	J	`jnl`	Continuing challenges swirl around bioinformatics service delivery. J. Biomed. Informatics Sean D. Mooney
2019	Misc	`conf`	Detecting Seasonal, Holiday, and Rare Events from Trauma Data in the Electronic Health Record. AMIA Timothy Bergquist, Vikas Pejaver, Noah Hammarlund, Sean D. Mooney, Stephen J. Mooney
2019	J	`jnl`	Indicators of retention in remote digital health studies: A cross-study evaluation of 100, 000 participants. CoRR Abhishek Pratap, Elias Chaibub Neto, Phil Snyder, Carl Stepnowsky, Noémie Elhadad, Daniel Grant, Matthew H. Mohebbi, Sean D. Mooney, Christine Suver, John Wilbanks, Lara M. Mangravite, Patricki J. Heagerty, Pat A. Areán, Larsson Omberg
2019	—	`conf`	OPMI: the Ontology of Precision Medicine and Investigation and its Support for Clinical Data and Metadata Representation and Analysis. ICBO Yongqun He, Edison Ong, Jennifer Schaub, Frederick Dowd, John F. O'Toole, Anastasios Siapos, Christian G. Reich, Sarah Seager, Ling Wang, Hong Yu, Jie Zheng, Christian J. Stoeckert Jr., Xiaolin Yang, Sheng Yang, Becky Steck, Christopher Park, Laura Barisoni, Matthias Kretzler, Jonathan Himmelfarb, Ravi Iyengar, Sean D. Mooney
2019	J	`jnl`	Pathogenicity and functional impact of non-frameshifting insertion/deletion variation in the human genome. PLoS Comput. Biol. Kymberleigh A. Pagel, Danny Antaki, Aojie Lian, Matthew E. Mort, David N. Cooper, Jonathan Sebat, Lilia M. Iakoucheva, Sean D. Mooney, Predrag Radivojac
2018	—	`conf`	KTAO: A Kidney Tissue Atlas Ontology to Support Community-Based Kidney Knowledge Base Development and Data Integration. ICBO Yongqun He, Becky Steck, Edison Ong, Laura Mariani, Chrysta Lienczewski, Ulysses J. Balis, Matthias Kretzler, Jonathan Himmelfarb, John F. Bertram, Evren U. Azeloglu, Ravi Iyengar, Deborah Hoshizaki, Sean D. Mooney
2018	J	`jnl`	Uncovering exposures responsible for birth season - disease effects: a global study. J. Am. Medical Informatics Assoc. Mary Regina Boland, Pradipta Parhi, Li Li, Riccardo Miotto, Robert J. Carroll, Usman Iqbal, Phung-Anh (Alex) Nguyen, Martijn J. Schuemie, Seng Chan You, Donahue Smith, Sean D. Mooney, Patrick B. Ryan, Yu-Chuan (Jack) Li, Rae Woong Park, Joshua C. Denny, Joel T. Dudley, George Hripcsak, Pierre Gentine, Nicholas P. Tatonetti
2017	Misc	`conf`	Session Introduction. PSB Alexander A. Morgan, Dana C. Crawford, Joshua C. Denny, Sean D. Mooney, Bruce J. Aronow, Steven E. Brenner
2017	—	`conf`	The feasibility of using smartphones to assess and remediate depression in Hispanic/Latino individuals nationally. UbiComp/ISWC Adjunct Abhishek Pratap, Joaquin A. Anguera, Brenna N. Renn, Elias Chaibub Neto, Joshua Volponi, Sean D. Mooney, Pat A. Areán
2017	J	`jnl`	When loss-of-function is loss of function: assessing mutational signatures and impact of loss-of-function genetic variants. Bioinform. Kymberleigh A. Pagel, Vikas Pejaver, Guan Ning Lin, Hyun-Jun Nam, Matthew E. Mort, David N. Cooper, Jonathan Sebat, Lilia M. Iakoucheva, Sean D. Mooney, Predrag Radivojac
2016	—	`conf`	A New Way of Representing Clinical Reports for Rapid Phenotyping. CRI Meliha Yetisgen, Lucy Vanderwende, Tony Black, Sean D. Mooney, Peter Tarczy-Hornoch
2016	Misc	`conf`	Session Introduction. PSB Alexander A. Morgan, Sean D. Mooney, Bruce J. Aronow, Steven E. Brenner
2016	J	`jnl`	The Loss and Gain of Functional Amino Acid Residues Is a Common Mechanism Causing Human Inherited Disease. PLoS Comput. Biol. Jose Lugo-Martinez, Vikas Pejaver, Kymberleigh A. Pagel, Shantanu Jain, Matthew E. Mort, David N. Cooper, Sean D. Mooney, Predrag Radivojac
2016	Misc	`conf`	Use of Genome Data in Newborns as a Starting Point for Life-Long Precision Medicine. PSB Steven E. Brenner, Stephen Kingsmore, Sean D. Mooney, Robert Nussbaum, Jennifer Puck
2015	J	`jnl`	Ten Simple Rules for a Community Computational Challenge. PLoS Comput. Biol. Iddo Friedberg, Mark N. Wass, Sean D. Mooney, Predrag Radivojac
2014	J	`jnl`	A Probabilistic Model to Predict Clinical Phenotypic Traits from Genome Sequencing. PLoS Comput. Biol. Yun-Ching Chen, Christopher Douville, Cheng Wang, Noushin Niknafs, Grace H. T. Yeo, Violeta Beleva Guthrie, Hannah Carter, Peter D. Stenson, David N. Cooper, Biao Li, Sean D. Mooney, Rachel Karchin
2014	J	`jnl`	The automated function prediction SIG looks back at 2013 and prepares for 2014. Bioinform. Mark N. Wass, Sean D. Mooney, Michal Linial, Predrag Radivojac, Iddo Friedberg
2013	J	`jnl`	STOP using just GO: a multi-ontology hypothesis generation tool for high throughput experimentation. BMC Bioinform. Tobias Wittkop, Emily TerAvest, Uday S. Evani, K. Mathew Fleisch, Ari E. Berman, Corey Powell, Nigam H. Shah, Sean D. Mooney
2013	J	`jnl`	Toward More Transparent and Reproducible Omics Studies Through a Common Metadata Checklist and Data Publications. Big Data Eugene Kolker, Vural Özdemir, Lennart Martens, William Hancock, Gordon A. Anderson, Nathaniel Anderson, Sukru Aynacioglu, Ancha V. Baranova, Shawn R. Campagna, Rui Chen, John Choiniere, Stephen P. Dearth, Wu-chun Feng, Lynnette Ferguson, Geoffrey C. Fox, Dmitrij Frishman, Robert Grossman, Allison P. Heath, Roger Higdon, Mara H. Hutz, Imre Janko, Lihua Jiang, Sanjay Joshi, Alexander E. Kel, Joseph W. Kemnitz, Isaac S. Kohane, Natali Kolker, Doron Lancet, Elaine Lee, Weizhong Li, Andrey Lisitsa, Adrian Llerena, Courtney MacNealy-Koch, Jean-Claude Marshall, Paola Masuzzo, Amanda May, George Mias, Matthew E. Monroe, Elizabeth Montague, Sean D. Mooney, Alexey I. Nesvizhskii, Santosh Noronha, Gilbert S. Omenn, Harsha Rajasimha, Preveen Ramamoorthy, Jerry Sheehan, Larry Smarr, Charles V. Smith, Todd Smith, Michael Snyder, Srikanth Rapole, Sanjeeva Srivastava, Larissa Stanberry, Elizabeth Stewart, Stefano Toppo, Peter Uetz, Kenneth Verheggen, Brynn H. Voy, Louise Warnich, Steven W. Wilhelm, Gregory Yandl
2011	J	`jnl`	Identifying viral integration sites using SeqMap 2.0. Bioinform. Troy B. Hawkins, Jessica Dantzer, Brandon Peters, Mary Dinauer, Keithanne Mockaitis, Sean D. Mooney, Kenneth Cornetta
2011	J	`jnl`	Introduction: Advances in Computational Systems Bioinformatics. J. Bioinform. Comput. Biol. Tobias Wittkop, Sean D. Mooney
2010	Misc	`conf`	Loss of Post-Translational Modification Sites in Disease. Pacific Symposium on Biocomputing Shuyan Li, Lilia M. Iakoucheva, Sean D. Mooney, Predrag Radivojac
2010	J	`jnl`	Structure-based kernels for the prediction of catalytic residues and their involvement in human inherited disease. Bioinform. Fuxiao Xin, Steven A. Myers, Yong Fuga Li, David N. Cooper, Sean D. Mooney, Predrag Radivojac
2010	J	`jnl`	Structure-based kernels for the prediction of catalytic residues and their involvement in human inherited disease. BMC Bioinform. Fuxiao Xin, Steven A. Myers, Yong Fuga Li, David N. Cooper, Sean D. Mooney, Predrag Radivojac
2009	J	`jnl`	Automated inference of molecular mechanisms of disease from amino acid substitutions. Bioinform. Biao Li, Vidhya G. Krishnan, Matthew E. Mort, Fuxiao Xin, Kishore K. Kamati, David N. Cooper, Sean D. Mooney, Predrag Radivojac
2008	J	`jnl`	Extensible open source content management systems and frameworks: a solution for many needs of a bioinformatics group. Briefings Bioinform. Sean D. Mooney, Peter H. Baenziger
2008	C	`conf`	Gain and loss of phosphorylation sites in human cancer. ECCB Predrag Radivojac, Peter H. Baenziger, Maricel G. Kann, Matthew E. Mort, Matthew W. Hahn, Sean D. Mooney
2008	J	`jnl`	MutDB: update on development of tools for the biochemical analysis of genetic variation. Nucleic Acids Res. Arti Singh, Adebayo Olowoyeye, Peter H. Baenziger, Jessica Dantzer, Maricel G. Kann, Predrag Radivojac, Randy W. Heiland, Sean D. Mooney
2007	—	`conf`	Refining Detection of RNA-Protein Binding Regions by Pyrosequencing of RNA Fragments. BIOCOMP Xin Wang, Guohua Wang, Changyu Shen, Lang Li, Xinguo Wang, Sean D. Mooney, Howard J. Edenberg, Jeremy Sanford, Yunlong Liu
2005	J	`jnl`	Bioinformatics approaches and resources for single nucleotide polymorphism functional analysis. Briefings Bioinform. Sean D. Mooney
2005	Misc	`conf`	Introduction to Informatics Approaches in Structural Genomics: Modeling and Representation of Function from Macromolecular STructure. Pacific Symposium on Biocomputing Patricia C. Babbitt, Philip E. Bourne, Sean D. Mooney
2005	J	`jnl`	MutDB services: interactive structural analysis of mutation data. Nucleic Acids Res. Jessica Dantzer, Charles W. Moad, Randy W. Heiland, Sean D. Mooney
2004	Misc	`conf`	Session Introduction. Pacific Symposium on Biocomputing Sean D. Mooney, Philip E. Bourne, Patricia C. Babbitt
2003	J	`jnl`	Analysis of Mutations in the COLIA1 Gene with Second-Order Rule Induction. Int. J. Pattern Recognit. Artif. Intell. Rattikorn Hewett, John H. Leuchner, Sean D. Mooney, Teri E. Klein
2003	Misc	`conf`	Informatics Approaches in Structural Genomics - Session Introduction. Pacific Symposium on Biocomputing Sean D. Mooney, Patricia C. Babbitt
2003	J	`jnl`	MutDB: annotating human variation with functionally relevant data. Bioinform. Sean D. Mooney, Russ B. Altman
2002	Misc	`conf`	Compression-Based Induction and Genome Data. FLAIRS Rattikorn Hewett, John H. Leuchner, Choh Man Teng, Sean D. Mooney, Teri E. Klein
2002	J	`jnl`	The functional importance of disease-associated mutation. BMC Bioinform. Sean D. Mooney, Teri E. Klein