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 (LSGRID, 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 (LSGRID, 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 (SAG, 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; et al. (New Gener. Comput., 2004)

Seismic image reconstruction using complex wavelets. - Mark A. Miller; Nick G. Kingsbury; Richard W. Hobbs (Computational Imaging, 2005)

Seismic Imaging Using Complex Wavelets. - Mark A. Miller; Nick G. Kingsbury; Richard W. Hobbs (ICASSP (2), 2005)

Statistical Image Modelling Using Interscale Phase Relationships of Complex Wavelet Coefficients. - Mark A. Miller; Nick G. Kingsbury (ICASSP (2), 2006)

SWAMI: Integrating Biological Databases and Analysis Tools Within User Friendly Environment. - Rami Rifaieh; Roger Unwin; Jeremy Carver; Mark A. Miller (DILS, 2007)

Image Modeling Using Interscale Phase Properties of Complex Wavelet Coefficients. - Mark A. Miller; Nick G. Kingsbury (IEEE Trans. Image Process., 2008)

Image Denoising Using Derotated Complex Wavelet Coefficients. - Mark A. Miller; Nick G. Kingsbury (IEEE Trans. Image Process., 2008)

The CIPRES science gateway: a community resource for phylogenetic analyses. - Mark A. Miller; Wayne Pfeiffer; Terri Schwartz (TG, 2011)

The CIPRES science gateway: enabling high-impact science for phylogenetics researchers with limited resources. - Mark A. Miller; Wayne Pfeiffer; Terri Schwartz (XSEDE, 2012)

Authoring a Science Gateway Cookbook. - Suresh Marru; Rion Dooley; Nancy Wilkins-Diehr; Marlon E. Pierce; Mark A. Miller; Sudhakar Pamidighantam; Julie Wernert (CLUSTER, 2013)

Embedding CIPRES science gateway capabilities in phylogenetics software environments. - Mark A. Miller; Terri Schwartz; Wayne Pfeiffer (XSEDE, 2013)

The CIPRES workbench: a flexible framework for creating science gateways. - Mark A. Miller; Terri Schwartz; Paul Hoover; Kenneth Yoshimoto; Subhashini Sivagnanam; Amitava Majumdar 001 (XSEDE, 2015)

User behavior and usage patterns for a highly accessed science gateway. - Mark A. Miller; Terri Schwartz; Wayne Pfeiffer (XSEDE, 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 001; Dan Gunter; Ray Idaszak; Steven R. Brandt; Mark A. Miller; Sandra Gesing; Nick D. Jones; Nic Weber; et al. (CoRR, 2016)

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 001; Mark A. Miller (PEARC, 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)

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 (ICBO, 2018)

Towards a Science Gateway Reference Architecture. - Marlon E. Pierce; Mark A. Miller; Emre H. Brookes; Mona Wong; Yan Liu 009; Enis Afgan; Sandra Gesing; Maytal Dahan; Suresh Marru; Tony Walker (IWSG, 2018)

A Collaborative, Realism-Based, Electronic Healthcare Graph: Public Data, Common Data Models, and Practical Instantiation. - Mark A. Miller; Christian J. Stoeckert Jr. (ICBO, 2019)

Web of Trust Tool for Gateway User Vetting. - Kenneth Yoshimoto; Nicholas T. Carnevale; Subhashini Sivagnanam; Amitava Majumdar 001; Mark A. Miller (PEARC, 2019)

Scaling and Querying a Semantically Rich, Electronic Healthcare Graph. - Hayden Freedman; Mark A. Miller; Heather Williams; Christian J. Stoeckert Jr. (ICBO/ODLS, 2020)

A Robust, Self-Training Classifier for Medication Strings, with Quantitative and Semantic Confidence Metrics. - Mark A. Miller; Hayden Freedman; Christian J. Stoeckert Jr. (ICBO/ODLS, 2020)

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; et al. (ICBO, 2021)

Bringing Schemas to the Schemaless. - Mark A. Miller; Rebecca C. Jackson; Christopher J. Mungall (ICBO, 2021)

The Linked Data Modeling Language (LinkML): A General-Purpose Data Modeling Framework Grounded in Machine-Readable Semantics. - Sierra A. T. Moxon; Harold Solbrig; Deepak R. Unni; Dazhi Jiao; Richard M. Bruskiewich; James P. Balhoff; Gaurav Vaidya; William D. Duncan; Harshad Hegde; Mark A. Miller; Matthew H. Brush; Nomi L. Harris; et al. (ICBO, 2021)

Standardization of assay representation in the Ontology for Biomedical Investigations. - Randi Vita; Jie Zheng 001; 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; et al. (Database J. Biol. Databases Curation, 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 001; et al. (Concurr. Comput. Pract. Exp., 2021)

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 (Appl. Ontology, 2024)