Mark A. Miller

According to our database, Mark A. Miller authored at least 30 papers between 2004 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2024

The Artificial Intelligence Ontology: LLM-assisted construction of AI concept hierarchies.

Marcin P. Joachimiak, Mark A. Miller, J. Harry Caufield, Ryan Ly, Nomi L. Harris, Andrew J. Tritt, Christopher J. Mungall, Kristofer E. Bouchard

CoRR, 2024

2021

Measuring success for a future vision: Defining impact in science gateways/virtual research environments.

Prasad Calyam, Nancy Wilkins-Diehr, Mark A. Miller, Emre H. Brookes, Ritu Arora, Amit Chourasia, Douglas M. Jennewein, Viswanath Nandigam, M. Drew LaMar, Sean B. Cleveland, Greg Newman, Shaowen Wang, Ilya Zaslavsky, Michael A. Cianfrocco, Kevin M. Ellett, David Tarboton, Keith G. Jeffery, Zhiming Zhao, Juan González-Aranda, Mark J. Perri, Gregory E. Tucker, Leonardo Candela, Tamás Kiss, Sandra Gesing

Concurr. Comput. Pract. Exp., 2021

Standardization of assay representation in the Ontology for Biomedical Investigations.

Randi Vita, Jie Zheng, Rebecca C. Jackson, Damion M. Dooley, James A. Overton, Mark A. Miller, Daniel C. Berrios, Richard H. Scheuermann, Yongqun He, Hande Küçük-McGinty, Mathias Brochhausen, Aisyah Yu Lin, Sagar B. Jain, Marcus C. Chibucos, John Judkins, Michelle G. Giglio, Irene Y. Feng, Gully Burns, Matthew H. Brush, Bjoern Peters, Christian J. Stoeckert Jr.

Database J. Biol. Databases Curation, 2021

Bringing Schemas to the Schemaless.

Mark A. Miller, Rebecca C. Jackson, Christopher J. Mungall

Proceedings of the International Conference on Biomedical Ontologies 2021 co-located with the Workshop on Ontologies for the Behavioural and Social Sciences (OntoBess 2021) as part of the Bolzano Summer of Knowledge (BOSK 2021), 2021

Leveraging Ontologies within the National Microbiome Data Collaborative.

William D. Duncan, Faiza Ahmed, Fnu Anubhav, Jeffrey Baumes, Jonathan Beezley, Mark Borkum, Lisa M. Bramer, Shane Canon, Patrick S. G. Chain, Danielle Christianson, Yuri Corilo, Karen Davenport, Brandon Davis, Meghan Drake, Kjiersten Fagnan, Mark Flynn, David Hays, Bin Hu, Marcel Huntemann, Julia Kelliher, Sofya Lebedeva, Po-E Li, Mary Lipton, Chien-Chi Lo, Douglas Mans, Stanton Martin, Lee Ann McCue, David Millard, Kayd Miller, Nigel Mouncey, Paul D. Piehowski, Elais Player Jackson, Anastasiya Prymolenna, Samuel O. Purvine, T. B. K. Reddy, Rachel Richardson, Migun Shakya, Montana Smith, Jagadish Chandrabose Sundaramurthi, Mark A. Miller, Deepak R. Unni, Pajau Vangay, Bruce Wilson, Donald Winston, Elisha M. Wood-Charlson, Yan Xu, Emiley A. Eloe-Fadrosh, Christopher J. Mungall

Proceedings of the International Conference on Biomedical Ontologies 2021 co-located with the Workshop on Ontologies for the Behavioural and Social Sciences (OntoBess 2021) as part of the Bolzano Summer of Knowledge (BOSK 2021), 2021

2020

A Robust, Self-Training Classifier for Medication Strings, with Quantitative and Semantic Confidence Metrics.

Mark A. Miller, Hayden Freedman, Christian J. Stoeckert Jr.

Proceedings of the 11th International Conference on Biomedical Ontologies (ICBO) joint with the 10th Workshop on Ontologies and Data in Life Sciences (ODLS) and part of the Bolzano Summer of Knowledge (BoSK 2020), 2020

Scaling and Querying a Semantically Rich, Electronic Healthcare Graph.

Hayden Freedman, Mark A. Miller, Heather Williams, Christian J. Stoeckert Jr.

Proceedings of the 11th International Conference on Biomedical Ontologies (ICBO) joint with the 10th Workshop on Ontologies and Data in Life Sciences (ODLS) and part of the Bolzano Summer of Knowledge (BoSK 2020), 2020

2019

Web of Trust Tool for Gateway User Vetting.

Kenneth Yoshimoto, Nicholas T. Carnevale, Subhashini Sivagnanam, Amitava Majumdar, Mark A. Miller

Proceedings of the Practice and Experience in Advanced Research Computing on Rise of the Machines (learning), 2019

A Collaborative, Realism-Based, Electronic Healthcare Graph: Public Data, Common Data Models, and Practical Instantiation.

Mark A. Miller, Christian J. Stoeckert Jr.

Proceedings of the 10th International Conference on Biomedical Ontology (ICBO 2019), Buffalo, New York, USA, July 30, 2019

2018

Towards a Science Gateway Reference Architecture.

Marlon E. Pierce, Mark A. Miller, Emre H. Brookes, Mona Wong, Yan Liu, Enis Afgan, Sandra Gesing, Maytal Dahan, Suresh Marru, Tony Walker

Proceedings of the 10th International Workshop on Science Gateways, 2018

Transforming and Unifying Research with Biomedical Ontologies: The Penn TURBO Project.

Christian J. Stoeckert Jr., David L. Birtwell, Hayden Freedman, Mark A. Miller, Heather Williams

Proceedings of the 9th International Conference on Biological Ontology (ICBO 2018), 2018

2017

T-BAS: Tree-Based Alignment Selector toolkit for phylogenetic-based placement, alignment downloads and metadata visualization: an example with the Pezizomycotina tree of life.

Ignazio Carbone, James B. White, Jolanta Miadlikowska, A. Elizabeth Arnold, Mark A. Miller

Bioinform., 2017

Apache Airavata Sharing Service: A Tool for Enabling User Collaboration in Science Gateways.

Supun Nakandala, Suresh Marru, Marlon E. Pierce, Sudhakar Pamidighantam, Kenneth Yoshimoto, Terri Schwartz, Subhashini Sivagnanam, Amitava Majumdar, Mark A. Miller

Proceedings of the Practice and Experience in Advanced Research Computing 2017: Sustainability, 2017

2016

Report on the Third Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE3).

Daniel S. Katz, Sou-Cheng T. Choi, Kyle E. Niemeyer, James Hetherington, Frank Löffler, Dan Gunter, Ray Idaszak, Steven R. Brandt, Mark A. Miller, Sandra Gesing, Nick D. Jones, Nic Weber, Suresh Marru, Gabrielle Allen, Birgit Penzenstadler, Colin C. Venters, Ethan Davis, Lorraine J. Hwang, Ilian T. Todorov, Abani K. Patra, Miguel de Val-Borro

CoRR, 2016

User behavior and usage patterns for a highly accessed science gateway.

Mark A. Miller, Terri Schwartz, Wayne Pfeiffer

Proceedings of the XSEDE16 Conference on Diversity, 2016

2015

The CIPRES workbench: a flexible framework for creating science gateways.

Mark A. Miller, Terri Schwartz, Paul Hoover, Kenneth Yoshimoto, Subhashini Sivagnanam, Amitava Majumdar

Proceedings of the 2015 XSEDE Conference: Scientific Advancements Enabled by Enhanced Cyberinfrastructure, St. Louis, MO, USA, July 26, 2015

2013

Embedding CIPRES science gateway capabilities in phylogenetics software environments.

Mark A. Miller, Terri Schwartz, Wayne Pfeiffer

Proceedings of the Extreme Science and Engineering Discovery Environment: Gateway to Discovery, 2013

Authoring a Science Gateway Cookbook.

Suresh Marru, Rion Dooley, Nancy Wilkins-Diehr, Marlon E. Pierce, Mark A. Miller, Sudhakar Pamidighantam, Julie Wernert

Proceedings of the 2013 IEEE International Conference on Cluster Computing, 2013

2012

The CIPRES science gateway: enabling high-impact science for phylogenetics researchers with limited resources.

Mark A. Miller, Wayne Pfeiffer, Terri Schwartz

Proceedings of the 1st Conference of the Extreme Science and Engineering Discovery Environment, 2012

2011

The CIPRES science gateway: a community resource for phylogenetic analyses.

Mark A. Miller, Wayne Pfeiffer, Terri Schwartz

Proceedings of the 2011 TeraGrid Conference - Extreme Digital Discovery, 2011

2008

Image Denoising Using Derotated Complex Wavelet Coefficients.

Mark A. Miller, Nick G. Kingsbury

IEEE Trans. Image Process., 2008

Image Modeling Using Interscale Phase Properties of Complex Wavelet Coefficients.

Mark A. Miller, Nick G. Kingsbury

IEEE Trans. Image Process., 2008

2007

SWAMI: Integrating Biological Databases and Analysis Tools Within User Friendly Environment.

Rami Rifaieh, Roger Unwin, Jeremy Carver, Mark A. Miller

Proceedings of the Data Integration in the Life Sciences, 4th International Workshop, 2007

2006

Statistical Image Modelling Using Interscale Phase Relationships of Complex Wavelet Coefficients.

Mark A. Miller, Nick G. Kingsbury

Proceedings of the 2006 IEEE International Conference on Acoustics Speech and Signal Processing, 2006

2005

Seismic Imaging Using Complex Wavelets.

Mark A. Miller, Nick G. Kingsbury, Richard W. Hobbs

Proceedings of the 2005 IEEE International Conference on Acoustics, 2005

Seismic image reconstruction using complex wavelets.

Mark A. Miller, Nick G. Kingsbury, Richard W. Hobbs

Proceedings of the Computational Imaging III, San Jose, 2005

2004

The Encyclopedia of Life Project: Grid Software and Deployment.

Wilfred W. Li, Robert W. Byrnes, Jim Hayes, Adam Birnbaum, Vicente M. Reyes, Atif Shahab, Coleman Mosley, Dmitry Pekurovsky, Greg B. Quinn, Ilya N. Shindyalov, Henri Casanova, Larry Ang, Fran Berman, Peter W. Arzberger, Mark A. Miller, Philip E. Bourne

New Gener. Comput., 2004

A Framework for the Design and Reuse of Grid Workflows.

Ilkay Altintas, Adam Birnbaum, Kim K. Baldridge, Wibke Sudholt, Mark A. Miller, Céline Amoreira, Yohann Potier, Bertram Ludäscher

Proceedings of the Scientific Applications of Grid Computing, First International Workshop, 2004

Grid Portal Interface for Interactive Use and Monitoring of High-Throughput Proteome Annotation.

Atif Shahab, Danny Chuon, Toyotaro Suzumura, Wilfred W. Li, Robert W. Byrnes, Kouji Tanaka, Larry Ang, Satoshi Matsuoka, Philip E. Bourne, Mark A. Miller, Peter W. Arzberger

Proceedings of the Grid Computing in Life Science, 2004

Grid Workflow Software for a High-Throughput Proteome Annotation Pipeline.

Adam Birnbaum, James Hayes, Wilfred W. Li, Mark A. Miller, Peter W. Arzberger, Philip E. Bourne, Henri Casanova

Proceedings of the Grid Computing in Life Science, 2004