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Journal Articles
- 2024
[j34]Ashley C. Griffin, Karen H. Wang, Tiffany I. Leung, Julio C. Facelli
:
Recommendations to promote fairness and inclusion in biomedical AI research and clinical use. J. Biomed. Informatics 157: 104693 (2024)- [j33]Kristal N. Varela, Gabriel I. Pagola, Albert M. Lund, Marta B. Ferraro, Anita M. Orendt, Julio C. Facelli:
An open science grid implementation of the steady state genetic algorithm for crystal structure prediction. J. Comput. Sci. 82: 102415 (2024) - 2023
- [j32]Sejal Mistry, Naomi O. Riches, Ramkiran Gouripeddi, Julio C. Facelli:
Environmental exposures in machine learning and data mining approaches to diabetes etiology: A scoping review. Artif. Intell. Medicine 135: 102461 (2023) - [j31]Sejal Mistry, Ramkiran Gouripeddi, Vandana Raman, Julio C. Facelli:
Sequential data mining of infection patterns as predictors for onset of type 1 diabetes in genetically at-risk individuals. J. Biomed. Informatics 142: 104385 (2023) - [j30]Carlo Combi, Julio C. Facelli, Peter Haddawy, John H. Holmes, Sabine Koch, Hongfang Liu, Jochen Meyer, Mor Peleg, Giuseppe Pozzi, Gregor Stiglic, Pierangelo Veltri, Christopher C. Yang:
The IHI Rochester Report 2022 on Healthcare Informatics Research: Resuming After the CoViD-19. J. Heal. Informatics Res. 7(2): 169-202 (2023) - 2022
- [j29]Alan H. Morris, Christopher Horvat, Brian Stagg, David W. Grainger, Michael Lanspa, James Orme, Terry P. Clemmer, Lindell K. Weaver, Frank Thomas, Colin K. Grissom, Ellie Hirshberg, Thomas D. East, Carrie Jane Wallace, Michael P. Young, Dean F. Sittig, Mary Suchyta, James E. Pearl, Antinio Pesenti, Michela Bombino, Eduardo Beck, Katherine A. Sward, Charlene R. Weir, Shobha Phansalkar, Gordon R. Bernard, B. Taylor Thompson, Roy Brower, Jonathon D. Truwit, Jay S. Steingrub, R. Duncan Hite, Douglas F. Willson, Jerry J. Zimmerman, Vinay Nadkarni, Adrienne G. Randolph, Martha A. Q. Curley, Christopher J. L. Newth, Jacques Lacroix, Michael S. D. Agus, Kang Hoe Lee, Bennett P. deBoisblanc, Frederick Alan Moore, R. Scott Evans, Dean K. Sorenson, Anthony Wong, Michael V. Boland, Willard H. Dere, Alan S. Crandall, Julio C. Facelli, Stanley M. Huff, Peter J. Haug, Ulrike Pielmeier, Stephen Edward Rees, Dan S. Karbing, Steen Andreassen, Eddy Fan, Roberta M. Goldring, Kenneth I Berger, Beno W. Oppenheimer, Eugene Wesley Ely, Brian W. Pickering, David A. Schoenfeld, Irena Tocino, Russell S. Gonnering, Peter J. Pronovost, Lucy A. Savitz, Didier Dreyfuss, Arthur S. Slutsky, James D. Crapo, Michael R. Pinsky, Brent James, Donald M. Berwick:
Computer clinical decision support that automates personalized clinical care: a challenging but needed healthcare delivery strategy. J. Am. Medical Informatics Assoc. 30(1): 178-194 (2022) - [j28]Janette Vazquez, Julio C. Facelli:
Conformal Prediction in Clinical Medical Sciences. J. Heal. Informatics Res. 6(3): 241-252 (2022) - 2021
- [j27]Yulan Wang, Bernard Li, Ramkiran Gouripeddi, Julio C. Facelli:
Human activity pattern implications for modeling SARS-CoV-2 transmission. Comput. Methods Programs Biomed. 199: 105896 (2021) - [j26]Alan H. Morris, Brian Stagg, Michael Lanspa, James Orme, Terry P. Clemmer, Lindell K. Weaver, Frank Thomas, Colin K. Grissom, Ellie Hirshberg, Thomas D. East, Carrie Jane Wallace, Michael P. Young, Dean F. Sittig, Antonio Pesenti, Michela Bombino, Eduardo Beck, Katherine A. Sward, Charlene R. Weir, Shobha S. Phansalkar, Gordon R. Bernard, B. Taylor Thompson, Roy Brower, Jonathon D. Truwit, Jay S. Steingrub, R. Duncan Hite, Douglas F. Willson, Jerry J. Zimmerman, Vinay M. Nadkarni, Adrienne Randolph, Martha A. Q. Curley, Christopher J. L. Newth, Jacques Lacroix, Michael S. D. Agus, Kang H. Lee, Bennett P. deBoisblanc, R. Scott Evans, Dean K. Sorenson, Anthony Wong, Michael V. Boland, David W. Grainger, Willard H. Dere, Alan S. Crandall, Julio C. Facelli, Stanley M. Huff, Peter J. Haug, Ulrike Pielmeier, Stephen Edward Rees, Dan S. Karbing, Steen Andreassen, Eddy Fan, Roberta M. Goldring, Kenneth I. Berger, Beno W. Oppenheimer, Eugene Wesley Ely, Ognjen Gajic, Brian W. Pickering, David A. Schoenfeld, Irena Tocino, Russell S. Gonnering, Peter J. Pronovost, Lucy A. Savitz, Didier Dreyfuss, Arthur S. Slutsky, James D. Crapo, Derek C. Angus, Michael R. Pinsky, Brent James, Donald M. Berwick:
Enabling a learning healthcare system with automated computer protocols that produce replicable and personalized clinician actions. J. Am. Medical Informatics Assoc. 28(6): 1330-1344 (2021) - 2020
- [j25]Xiangyang Ye, Qing T. Zeng, Julio C. Facelli, Diana I. Brixner, Mike Conway, Bruce E. Bray:
Predicting Optimal Hypertension Treatment Pathways Using Recurrent Neural Networks. Int. J. Medical Informatics 139: 104122 (2020) - 2019
- [j24]Naresh Sundar Rajan, Ramkiran Gouripeddi, Peter Mo, Randy Madsen, Julio C. Facelli:
Towards a content agnostic computable knowledge repository for data quality assessment. Comput. Methods Programs Biomed. 177: 193-201 (2019) - 2018
- [j23]Juan M. R. Albano, Nahuel Mussini, Roxana Toriano, Julio C. Facelli, Marta B. Ferraro, Mónica Pickholz:
Calcium interactions with Cx26 hemmichannel: Spatial association between MD simulations biding sites and variant pathogenicity. Comput. Biol. Chem. 77: 331-342 (2018) - [j22]Tiago K. Colicchio, Guilherme Del Fiol, Debra L. Scammon, Julio C. Facelli, Watson A. Bowes III, Scott P. Narus:
Comprehensive methodology to monitor longitudinal change patterns during EHR implementations: a case study at a large health care delivery network. J. Biomed. Informatics 83: 40-53 (2018) - 2017
- [j21]Anne M. Turner, Julio C. Facelli, Monique W. M. Jaspers, Thomas Wetter, Daniel Pfeifer, Laël Cranmer Gatewood, Terry Adam, Yu-Chuan Li, Ming-Chin Lin, R. Scott Evans, Anna L. Beukenhorst, Hugo Johan Theodoore van Mens, Esmée Tensen, Christian Bock, Laura Fendrich, Peter Seitz, Julian Suleder, Ranyah Aldekhyyel, Kent Bridgeman, Zhen Hu, Aaron Sattler, Shin-Yi Guo, Md. Mohaimenul Islam, Dina Nur Anggraini Ningrum, Hsin-Ru Tung, Jiantao Bian, Joseph M. Plasek, Casey A. Rommel, Juandalyn Burke, Harkirat Sohi:
Solving Interoperability in Translational Health. Appl. Clin. Inform. 08(02): 651-659 (2017) - [j20]Tiago K. Colicchio, Guilherme Del Fiol, Debra L. Scammon, Watson A. Bowes III, Julio C. Facelli, Scott P. Narus:
Development and classification of a robust inventory of near real-time outcome measurements for assessing information technology interventions in health care. J. Biomed. Informatics 73: 62-75 (2017) - 2016
- [j19]David E. Jones, Hamidreza Ghandehari, Julio C. Facelli:
A review of the applications of data mining and machine learning for the prediction of biomedical properties of nanoparticles. Comput. Methods Programs Biomed. 132: 93-103 (2016) - [j18]Tiago K. Colicchio, Julio C. Facelli, Guilherme Del Fiol, Debra L. Scammon, Watson A. Bowes III, Scott P. Narus:
Health information technology adoption: Understanding research protocols and outcome measurements for IT interventions in health care. J. Biomed. Informatics 63: 33-44 (2016) - 2014
- [j17]Jingran Wen, Daniel R. Scoles, Julio C. Facelli:
Structure prediction of polyglutamine disease proteins: comparison of methods. BMC Bioinform. 15(S-7): S11 (2014) - [j16]Wayne B. Bradford, John F. Hurdle, Bernie LaSalle, Julio C. Facelli:
Development of a HIPAA-compliant environment for translational research data and analytics. J. Am. Medical Informatics Assoc. 21(1): 185-189 (2014) - [j15]Shan He, Scott P. Narus, Julio C. Facelli, Lee Min Lau, Jeffrey R. Botkin, John F. Hurdle:
A domain analysis model for eIRB systems: Addressing the weak link in clinical research informatics. J. Biomed. Informatics 52: 121-129 (2014) - [j14]Julien C. Thibault, Daniel R. Roe, Julio C. Facelli, Thomas E. Cheatham III:
Data model, dictionaries, and desiderata for biomolecular simulation data indexing and sharing. J. Cheminformatics 6(1): 4 (2014) - [j13]Julien C. Thibault, Thomas E. Cheatham III, Julio C. Facelli:
iBIOMES Lite: Summarizing Biomolecular Simulation Data in Limited Settings. J. Chem. Inf. Model. 54(6): 1810-1819 (2014) - 2013
- [j12]Julien C. Thibault, Julio C. Facelli, Thomas E. Cheatham III:
iBIOMES: Managing and Sharing Biomolecular Simulation Data in a Distributed Environment. J. Chem. Inf. Model. 53(3): 726-736 (2013) - 2012
- [j11]Victor Maojo, Martin Fritts, Fernando Martín-Sánchez, Diana de la Iglesia, Raul E. Cachau, Miguel García-Remesal, José Crespo, Joyce A. Mitchell, Alberto Anguita, Nathan A. Baker, José María Barreiro, Sonia E. Benitez, Guillermo de la Calle, Julio C. Facelli, Peter Ghazal, Antoine Geissbühler, Fernando D. González Nilo, Norbert M. Graf, Pierre Grangeat, Isabel Hermosilla, Rada Hussein, Josipa Kern, Sabine Koch, Yannick Legré, Victoria López-Alonso, Guillermo López-Campos, Luciano Milanesi, Vassilis Moustakis, Cristian R. Munteanu, Paula Otero, Alejandro Pazos, David Pérez-Rey, George Potamias, Ferran Sanz, Casimir A. Kulikowski:
Nanoinformatics: developing new computing applications for nanomedicine. Computing 94(6): 521-539 (2012) - [j10]David K. Crockett, Elaine Lyon, Marc S. Williams, Scott P. Narus, Julio C. Facelli, Joyce A. Mitchell:
Utility of gene-specific algorithms for predicting pathogenicity of uncertain gene variants. J. Am. Medical Informatics Assoc. 19(2): 207-211 (2012) - [j9]Kailah Davis, Catherine J. Staes, Jeffrey Duncan, Sean Igo, Julio C. Facelli:
Identification of pneumonia and influenza deaths using the death certificate pipeline. BMC Medical Informatics Decis. Mak. 12: 37 (2012) - [j8]Julio C. Facelli:
An agenda for ultra-large-scale system research for global health informatics. SIGHIT Rec. 2(1): 12 (2012) - 2011
- [j7]Mark T. W. Ebbert, Roy R. L. Bastien, Kenneth M. Boucher, Miguel Martín, Eva Carrasco, Rosalía Caballero, Inge J. Stijleman, Philip S. Bernard, Julio C. Facelli:
Characterization of uncertainty in the classification of multivariate assays: application to PAM50 centroid-based genomic predictors for breast cancer treatment plans. J. Clin. Bioinform. 1: 37 (2011) - 2010
- [j6]Nephi A. Walton, Mollie R. Poynton, Per H. Gesteland, Christopher G. Maloney, Catherine J. Staes, Julio C. Facelli:
Predicting the start week of respiratory syncytial virus outbreaks using real time weather variables. BMC Medical Informatics Decis. Mak. 10: 68 (2010) - 2009
- [j5]Seonah Kim, Anita M. Orendt, Marta B. Ferraro, Julio C. Facelli:
Crystal structure prediction of flexible molecules using parallel genetic algorithms with a standard force field. J. Comput. Chem. 30(13): 1973-1985 (2009) - [j4]Catherine J. Staes, Wu Xu, Samuel D. LeFevre, Ronald C. Price, Scott P. Narus, Adi V. Gundlapalli, Robert T. Rolfs, Barry Nangle, Matthew H. Samore, Julio C. Facelli:
A case for using grid architecture for state public health informatics: the Utah perspective. BMC Medical Informatics Decis. Mak. 9: 32 (2009) - 2008
- [j3]Tobias Rausch, Alun Thomas, Nicola J. Camp, Lisa A. Cannon-Albright, Julio C. Facelli:
A parallel genetic algorithm to discover patterns in genetic markers that indicate predisposition to multifactorial disease. Comput. Biol. Medicine 38(7): 826-836 (2008) - 2006
- [j2]Thanh N. Truong, Manohar Nayak, Hung H. Huynh, Tom Cook, Priya Mahajan, Le-Thuy T. Tran, Jannu Bharath, Shrish Jain, Ha B. Pham, Chaiwoot Boonyasiriwat, Nhat Nguyen, Evan Andersen, Yong Kim, Suengkeol Choe, Jihoon Choi, Thomas E. Cheatham III, Julio C. Facelli:
Computational Science and Engineering Online (CSE-Online): A Cyber-Infrastructure for Scientific Computing. J. Chem. Inf. Model. 46(3): 971-984 (2006) - 2005
- [j1]Victor E. Bazterra, Martin Cuma, Marta B. Ferraro, Julio C. Facelli:
A general framework to understand parallel performance in heterogeneous clusters: analysis of a new adaptive parallel genetic algorithm. J. Parallel Distributed Comput. 65(1): 48-57 (2005)
Conference and Workshop Papers
- 2023
- [c30]Ryan Gardner, Joshua Wilkins, Sejal Mistry, Ramkiran Gouripeddi, Julio C. Facelli:
Structural Homology of Epitope Binding Mimicry in the Onset of Type 1 Diabetes Mellitus. BIBM 2023: 3708-3713 - [c29]Carlo Combi, Julio C. Facelli, Peter Haddawy, John H. Holmes, Sabine Koch, Hongfang Liu, Jochen Meyer, Mor Peleg, Giuseppe Pozzi, Gregor Stiglic, Pierangelo Veltri, Christopher C. Yang:
Resuming HealthCare Informatics Research after CoViD-19: the HealthCare System Perspective. ICHI 2023: 760-762 - [c28]Alexander S. Millar, John Arnn, Sam Himes, Julio C. Facelli:
Uncertainty in Breast Cancer Risk Prediction: A Conformal Prediction Study of Race Stratification. MedInfo 2023: 991-995 - 2020
- [c27]Le-Thuy T. Tran, Ramkiran Gouripeddi, Julio C. Facelli:
A Harmonized Framework to Evaluate Impacts of ECHO Pain and Opioid Training on Patients and Clinicians. AMIA 2020 - [c26]Lance T. Pflieger, Stefan M. Pulst, Julio C. Facelli:
Characterization of Analytic and Experimental Uncertainty of RNA-seq Co-expression Network Determination: Application to SCA2. ICHI 2020: 1-11 - 2019
- [c25]Ramkiran Gouripeddi, Le-Thuy T. Tran, Tanvi Gangadhar, Randy K. Madsen, Julio C. Facelli, Katherine A. Sward:
Assimilating Pollen into Exposomes for Pediatric Asthma Research. AMIA 2019 - [c24]Ramkiran Gouripeddi, Le-Thuy T. Tran, Randy Madsen, Tanvi Gangadhar, Peter Mo, Nicole Burnett, Ryan Butcher, Katherine A. Sward, Julio C. Facelli:
An Architecture for Metadata-driven Integration of Heterogeneous Sensor and Health Data for Translational Exposomic Research. BHI 2019: 1-4 - [c23]Richard L. Bradshaw, Ramkiran Gouripeddi, Julio C. Facelli:
Concept Bag: A New Method for Computing Concept Similarity in Biomedical Data. IWBBIO (2) 2019: 15-23 - [c22]Danielle Groat, Ramkiran Gouripeddi, Randy Madsen, Yu Kuei Lin, Julio C. Facelli:
An Architecture to Support Real-World Studies that Investigate the Autonomic Nervous System. Poly/DMAH@VLDB 2019: 196-203 - 2017
- [c21]Samir E. AbdelRahman, Julio C. Facelli, Bruce E. Bray, Rashmee U. Shah, Guilherme Del Fiol:
Extraction of Patient Temporal Patterns and Clusters from Clinical Data. AMIA 2017 - [c20]Tiago K. Colicchio, Guilherme Del Fiol, Watson A. Bowes III, Julio C. Facelli, Debra L. Scammon, Scott P. Narus:
The Impact of Health IT Adoption: Are We Measuring the Right Outcomes? AMIA 2017 - [c19]Ramkiran Gouripeddi, Nicole Burnett, Mollie R. Cummins, Julio C. Facelli, Katherine A. Sward:
A Conceptual Representation of Exposome in Translational Research. AMIA 2017 - 2016
- [c18]Tiago K. Colicchio, Julio C. Facelli, Guilherme Del Fiol, Debra L. Scammon, Watson A. Bowes III, Scott P. Narus:
Assessment of the Heterogeneity of Outcome Measurements for IT Interventions in Health Care. AMIA 2016 - 2014
- [c17]Ramkiran Gouripeddi, Naresh Sundar Rajan, Randy Madsen, Phillip B. Warner, Julio C. Facelli:
Federating Air Quality Data with Clinical Data. AMIA 2014 - [c16]Phillip B. Warner, Peter Mo, N. Dustin Schultz, Ramkiran Gouripeddi, Jeffrey Duncan, Julio C. Facelli:
VIRGO: Virtual Identity Resolution on the Go. ICHI 2014: 366 - 2013
- [c15]Richard L. Bradshaw, N. Dustin Schultz, Julio C. Facelli, Randy Madsen, Ramkiran Gouripeddi, Ryan Butcher, Bernie LaSalle:
Going FURTHeR with Three Federated Query Types. AMIA 2013 - [c14]Ryan Butcher, Ramkiran Gouripeddi, Randy Madsen, Julio C. Facelli:
Using Primitive Role Relationships in SNOMED to Enhance Concept Searching by Limiting Semantic Variability in FURTHeR. AMIA 2013 - [c13]Ramkiran Gouripeddi, Julio C. Facelli, Richard L. Bradshaw, Dustin Schultz, Bernie LaSalle, Phillip B. Warner, Ryan Butcher, Randy Madsen, Peter Mo:
FURTHeR: An Infrastructure for Clinical, Translational and Comparative Effectiveness Research. AMIA 2013 - [c12]Randy Madsen, Richard L. Bradshaw, N. Dustin Schultz, Ryan Butcher, Ramkiran Gouripeddi, Joyce A. Mitchell, Julio C. Facelli:
Knowledge Driven Inclusion and Exclusion Criteria Refinement within the FURTHeR Framework. AMIA 2013 - [c11]Peter Mo, Randy Madsen, Richard L. Bradshaw, N. Dustin Schultz, Ryan Butcher, Bernie LaSalle, Ramkiran Gouripeddi, Julio C. Facelli:
Federating caTissue with FURTHeR. AMIA 2013 - [c10]Dustin Schultz, Bernie LaSalle, Shan He, Ramkiran Gouripeddi, Ryan Butcher, Julio C. Facelli:
Creating a Secure, Easily Accessible Environment for PHI Data Exports within FURTHeR utilizing REDCap. AMIA 2013 - [c9]Phillip B. Warner, Peter Mo, N. Dustin Schultz, Ramkiran Gouripeddi, Scott P. Narus, Julio C. Facelli:
On the Fly Linkage of Records Containing Protected Health Information (PHI) Within the FURTHeR Framework. AMIA 2013 - [c8]Kailah Davis, Ronald C. Price, Julio C. Facelli:
Implementing public health analytical services: Grid enabling of MetaMap. CBMS 2013: 113-118 - [c7]Monique W. M. Jaspers, George Demiris, Julio C. Facelli, Lael C. Gatewood, Alexander Hörbst, J. Li, Daniel Pfeifer, Thomas Wetter:
International Collaborations in Health Informatics Education: Globalizing Health and Biomedical Informatics Curricula. MedInfo 2013: 1249 - 2012
- [c6]Ronald C. Price, Derick Huth, Jody Smith, Steve Harper, Wilson Pace, Gerald Pulver, Michael G. Kahn, Lisa M. Schilling, Julio C. Facelli:
Federated Queries for Comparative Effectiveness Research: Performance Analysis. HealthGrid 2012: 9-18 - 2009
- [c5]Marta B. Ferraro, Anita M. Orendt, Julio C. Facelli:
Parallel Genetic Algorithms for Crystal Structure Prediction: Successes and Failures in Predicting Bicalutamide Polymorphs. ICIC (1) 2009: 120-129 - 2008
- [c4]Ronald C. Price, Wayne B. Bradford, Victor E. Bazterra, Julio C. Facelli:
Digital Sherpa: a set of high level tools to manage scientific applications in a computational grid. Mardi Gras Conference 2008: 36 - 2006
- [c3]Ronald C. Price, Victor E. Bazterra, Wayne B. Bradford, Julio C. Facelli:
Poster reception - Digital Sherpa. SC 2006: 156 - 2001
- [c2]David B. Jackson, Brian D. Haymore, Julio C. Facelli, Quinn Snell:
Improving Cluster Utilization through Set Based Allocation Policies. ICPP Workshops 2001: 355-360 - 1992
- [c1]Julio C. Facelli, Jeff Nichols:
How Changing High Performance Computing Technology Changes the Way in Whigh We Do Computational Chemistry. SC 1992: 382-383
Editorship
- 2020
- [e1]Taesung Park, Young-Rae Cho, Xiaohua Hu, Illhoi Yoo, Hyun Goo Woo, Jianxin Wang, Julio C. Facelli, Seungyoon Nam, Mingon Kang:
IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2020, Virtual Event, South Korea, December 16-19, 2020. IEEE 2020, ISBN 978-1-7281-6215-7 [contents]
Informal and Other Publications
- 2019
- [i2]Albert M. Lund, Ramkiran Gouripeddi, Julio C. Facelli:
Generation and Classification of Activity Sequences for Spatiotemporal Modeling of Human Populations. CoRR abs/1911.05476 (2019) - 2013
- [i1]Naresh Sundar Rajan, Ramkiran Gouripeddi, Julio C. Facelli:
A Service Oriented Framework to Assess the Quality of Electronic Health Data for Clinical Research. ICHI 2013: 482
Coauthor Index
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