Compression-Based Induction and Genome Data. - Rattikorn Hewett; John H. Leuchner; Choh Man Teng 001; Sean D. Mooney; Teri E. Klein (FLAIRS, 2002)

The functional importance of disease-associated mutation. - Sean D. Mooney; Teri E. Klein (BMC Bioinform., 2002)

Informatics Approaches in Structural Genomics - Session Introduction. - Sean D. Mooney; Patricia C. Babbitt (Pacific Symposium on Biocomputing, 2003)

MutDB: annotating human variation with functionally relevant data. - Sean D. Mooney; Russ B. Altman (Bioinform., 2003)

Analysis of Mutations in the COLIA1 Gene with Second-Order Rule Induction. - Rattikorn Hewett; John H. Leuchner; Sean D. Mooney; Teri E. Klein (Int. J. Pattern Recognit. Artif. Intell., 2003)

Session Introduction. - Sean D. Mooney; Philip E. Bourne; Patricia C. Babbitt (Pacific Symposium on Biocomputing, 2004)

Introduction to Informatics Approaches in Structural Genomics: Modeling and Representation of Function from Macromolecular STructure. - Patricia C. Babbitt; Philip E. Bourne; Sean D. Mooney (Pacific Symposium on Biocomputing, 2005)

Bioinformatics approaches and resources for single nucleotide polymorphism functional analysis. - Sean D. Mooney (Briefings Bioinform., 2005)

MutDB services: interactive structural analysis of mutation data. - Jessica Dantzer; Charles W. Moad; Randy W. Heiland; Sean D. Mooney (Nucleic Acids Res., 2005)

Refining Detection of RNA-Protein Binding Regions by Pyrosequencing of RNA Fragments. - Xin Wang 008; Guohua Wang; Changyu Shen; Lang Li 001; Xinguo Wang; Sean D. Mooney; Howard J. Edenberg; Jeremy Sanford; Yunlong Liu (BIOCOMP, 2007)

Gain and loss of phosphorylation sites in human cancer. - Predrag Radivojac; Peter H. Baenziger; Maricel G. Kann; Matthew E. Mort; Matthew W. Hahn; Sean D. Mooney (ECCB, 2008)

Extensible open source content management systems and frameworks: a solution for many needs of a bioinformatics group. - Sean D. Mooney; Peter H. Baenziger (Briefings Bioinform., 2008)

MutDB: update on development of tools for the biochemical analysis of genetic variation. - Arti Singh; Adebayo Olowoyeye; Peter H. Baenziger; Jessica Dantzer; Maricel G. Kann; Predrag Radivojac; Randy W. Heiland; Sean D. Mooney (Nucleic Acids Res., 2008)

Automated inference of molecular mechanisms of disease from amino acid substitutions. - Biao Li; Vidhya G. Krishnan; Matthew E. Mort; Fuxiao Xin; Kishore K. Kamati; David N. Cooper; Sean D. Mooney; Predrag Radivojac (Bioinform., 2009)

Loss of Post-Translational Modification Sites in Disease. - Shuyan Li; Lilia M. Iakoucheva; Sean D. Mooney; Predrag Radivojac (Pacific Symposium on Biocomputing, 2010)

Structure-based kernels for the prediction of catalytic residues and their involvement in human inherited disease. - Fuxiao Xin; Steven A. Myers; Yong Fuga Li; David N. Cooper; Sean D. Mooney; Predrag Radivojac (BMC Bioinform., 2010)

Identifying viral integration sites using SeqMap 2.0. - Troy B. Hawkins; Jessica Dantzer; Brandon Peters; Mary Dinauer; Keithanne Mockaitis; Sean D. Mooney; Kenneth Cornetta (Bioinform., 2011)

Introduction: Advances in Computational Systems Bioinformatics. - Tobias Wittkop; Sean D. Mooney (J. Bioinform. Comput. Biol., 2011)

Toward More Transparent and Reproducible Omics Studies Through a Common Metadata Checklist and Data Publications. - 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; et al. (Big Data, 2013)

STOP using just GO: a multi-ontology hypothesis generation tool for high throughput experimentation. - Tobias Wittkop; Emily TerAvest; Uday S. Evani; K. Mathew Fleisch; Ari E. Berman; Corey Powell; Nigam H. Shah; Sean D. Mooney (BMC Bioinform., 2013)

The automated function prediction SIG looks back at 2013 and prepares for 2014. - Mark N. Wass; Sean D. Mooney; Michal Linial; Predrag Radivojac; Iddo Friedberg (Bioinform., 2014)

A Probabilistic Model to Predict Clinical Phenotypic Traits from Genome Sequencing. - 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 (PLoS Comput. Biol., 2014)

Ten Simple Rules for a Community Computational Challenge. - Iddo Friedberg; Mark N. Wass; Sean D. Mooney; Predrag Radivojac (PLoS Comput. Biol., 2015)

A New Way of Representing Clinical Reports for Rapid Phenotyping. - Meliha Yetisgen; Lucy Vanderwende; Tony Black; Sean D. Mooney; Peter Tarczy-Hornoch (CRI, 2016)

Use of Genome Data in Newborns as a Starting Point for Life-Long Precision Medicine. - Steven E. Brenner; Stephen Kingsmore; Sean D. Mooney; Robert Nussbaum; Jennifer Puck (PSB, 2016)

Session Introduction. - Alexander A. Morgan; Sean D. Mooney; Bruce J. Aronow; Steven E. Brenner (PSB, 2016)

The Loss and Gain of Functional Amino Acid Residues Is a Common Mechanism Causing Human Inherited Disease. - Jose Lugo-Martinez; Vikas Pejaver; Kymberleigh A. Pagel; Shantanu Jain; Matthew E. Mort; David N. Cooper; Sean D. Mooney; Predrag Radivojac (PLoS Comput. Biol., 2016)

The feasibility of using smartphones to assess and remediate depression in Hispanic/Latino individuals nationally. - Abhishek Pratap; Joaquin A. Anguera; Brenna N. Renn; Elias Chaibub Neto; Joshua Volponi; Sean D. Mooney; Pat A. Areán (UbiComp/ISWC Adjunct, 2017)

Session Introduction. - Alexander A. Morgan; Dana C. Crawford; Joshua C. Denny; Sean D. Mooney; Bruce J. Aronow; Steven E. Brenner (PSB, 2017)

When loss-of-function is loss of function: assessing mutational signatures and impact of loss-of-function genetic variants. - 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 (Bioinform., 2017)

KTAO: A Kidney Tissue Atlas Ontology to Support Community-Based Kidney Knowledge Base Development and Data Integration. - 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; et al. (ICBO, 2018)

Uncovering exposures responsible for birth season - disease effects: a global study. - Mary Regina Boland; Pradipta Parhi; Li Li 062; 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; et al. (J. Am. Medical Informatics Assoc., 2018)

Detecting Seasonal, Holiday, and Rare Events from Trauma Data in the Electronic Health Record. - Timothy Bergquist; Vikas Pejaver; Noah Hammarlund; Sean D. Mooney; Stephen J. Mooney (AMIA, 2019)

OPMI: the Ontology of Precision Medicine and Investigation and its Support for Clinical Data and Metadata Representation and Analysis. - Yongqun He; Edison Ong; Jennifer Schaub; Frederick Dowd; John F. O'Toole; Anastasios Siapos; Christian G. Reich; Sarah Seager; Ling Wang 001; Hong Yu 014; Jie Zheng 001; Christian J. Stoeckert Jr.; et al. (ICBO, 2019)

Indicators of retention in remote digital health studies: A cross-study evaluation of 100, 000 participants. - 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; et al. (CoRR, 2019)

Automated retrieval, preprocessing, and visualization of gridded hydrometeorology data products for spatial-temporal exploratory analysis and intercomparison. - Jimmy Phuong; Christina Bandaragoda; Erkan Istanbulluoglu; Claire Beveridge; Ronda Strauch; Landung Setiawan; Sean D. Mooney (Environ. Model. Softw., 2019)

Continuing challenges swirl around bioinformatics service delivery. - Sean D. Mooney (J. Biomed. Informatics, 2019)

Pathogenicity and functional impact of non-frameshifting insertion/deletion variation in the human genome. - Kymberleigh A. Pagel; Danny Antaki; Aojie Lian; Matthew E. Mort; David N. Cooper; Jonathan Sebat; Lilia M. Iakoucheva; Sean D. Mooney; Predrag Radivojac (PLoS Comput. Biol., 2019)

Piloting a model-to-data approach to enable predictive analytics in health care through patient mortality prediction. - Timothy Bergquist; Yao Yan; Thomas Schaffter; Thomas Yu; Vikas Pejaver; Noah Hammarlund; Justin Prosser; Justin Guinney; Sean D. Mooney (J. Am. Medical Informatics Assoc., 2020)

Leaf: an open-source, model-agnostic, data-driven web application for cohort discovery and translational biomedical research. - 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 (J. Am. Medical Informatics Assoc., 2020)

Indicators of retention in remote digital health studies: a cross-study evaluation of 100, 000 participants. - 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; et al. (npj Digit. Medicine, 2020)

A Continuous Crowd-sourced Challenge for Benchmarking COVID-19 Health Outcome Prediction. - Yao Yan; Thomas Schaffter; Timothy Bergquist; Thomas Yu; Justin Prosser; Sean D. Mooney; Justin Guinney (AMIA, 2021)

Establishing the reliability of algorithms. - Lara M. Mangravite; Sean D. Mooney; Iddo Friedberg; Justin Guinney (PSB, 2021)

Information needs and priority use cases of population health researchers to improve preparedness for future hurricanes and floods. - Jimmy Phuong; Christina Bandaragoda; Shefali Haldar; Kari A. Stephens; Patricia Ordóñez 002; Sean D. Mooney; Andrea L. Hartzler (J. Am. Medical Informatics Assoc., 2021)

Considering the possibilities and pitfalls of Generative Pre-trained Transformer 3 (GPT-3) in healthcare delivery. - Diane M. Korngiebel; Sean D. Mooney (npj Digit. Medicine, 2021)

Assessing Machine Learning Based Generators for Synthetic Electronic Health Records: A Benchmarking. - Chao Yan 004; Yao Yan; Ziqi Zhang 005; Zhiyu Wan; Justin Guinney; Sean D. Mooney; Bradley A. Malin (AMIA, 2022)

Geospatial divide in real-world EHR data: Analytical workflow to assess regional biases and potential impact on health equity. - Serena Jinchen Xie; Flavia Kapos; Stephen J. Mooney; Sean D. Mooney; Kari A. Stephens; Andrea L. Hartzler; Abhishek Pratap (AMIA, 2022)

The NLP Sandbox: an efficient model-to-data system to enable federated and unbiased evaluation of clinical NLP models. - Yao Yan; Thomas Yu; Kathleen Muenzen; Sijia Liu 002; Connor Boyle; George Koslowski; Jiaxin Zheng; Nicholas J. Dobbins; Clement Essien; Hongfang Liu; Larsson Omberg; Meliha Yestigen; et al. (CoRR, 2022)

A Multifaceted Benchmarking of Synthetic Electronic Health Record Generation Models. - Chao Yan 004; Yao Yan; Zhiyu Wan; Ziqi Zhang 005; Larsson Omberg; Justin Guinney; Sean D. Mooney; Bradley A. Malin (CoRR, 2022)

Evaluation of crowdsourced mortality prediction models as a framework for assessing artificial intelligence in medicine. - Timothy Bergquist; Thomas Schaffter; Yao Yan; Thomas Yu; Justin Prosser; Jifan Gao; Guanhua Chen 002; Lukasz Charzewski; Zofia Nawalany; Ivan Brugere; Renata Retkute; Alidivinas Prusokas; et al. (J. Am. Medical Informatics Assoc., 2023)

Predicting decompression surgery by applying multimodal deep learning to patients' structured and unstructured health data. - Chethan Jujjavarapu; Pradeep Suri; Vikas Pejaver; Janna Friedly; Laura S. Gold; Eric Meier; Trevor Cohen; Sean D. Mooney; Patrick J. Heagerty; Jeffrey G. Jarvik (BMC Medical Informatics Decis. Mak., 2023)

Automated Survey Collection with LLM-based Conversational Agents. - Kurmanbek Kaiyrbekov; Nicholas J. Dobbins; Sean D. Mooney (CoRR, 2025)