Sampling Properties of the Alternating Projection Distance Geometry Algorithm Applied to Unconstrained Polypeptide Chains. - Jonathan Edwards; Greg Chatham; William Kile Glunt; Daniel McDonald; Chris Wells; Tom L. Hayden (Comput. Chem., 1997)

Determining Protein Structure using the Distance Geometry Program APA. - Robert Reams; Greg Chatham; William Kile Glunt; Daniel McDonald; Tom L. Hayden (Comput. Chem., 1999)

Comparison of two approaches to building a vertical search tool: a case study in the nanotechnology domain. - Michael Chau; Hsinchun Chen; Jialun Qin; Yilu Zhou; Yi Qin; Wai-Ki Sung; Daniel McDonald (JCDL, 2002)

NanoPort: a web portal for nanoscale science and technology. - Michael Chau; Hsinchun Chen; Jialun Qin; Yilu Zhou; Wai-Ki Sung; Yongchi Chen; Yi Qin; Daniel McDonald; Ann M. Lally; Matthew Landon (JCDL, 2002)

Using sentence-selection heuristics to rank text segments in TXTRACTOR. - Daniel McDonald; Hsinchun Chen (JCDL, 2002)

Genescene: Biomedical Text And Data Mining. - Gondy Leroy; Hsinchun Chen; Jesse D. Martinez; Shauna Eggers; Ryan R. Falsey; Kerri L. Kislin; Zan Huang; Jiexun Li; Jennifer Jie Xu 001; Daniel McDonald; T. Gavin Ng (JCDL, 2003)

Extracting gene pathway relations using a hybrid grammar: the Arizona Relation Parser. - Daniel McDonald; Hsinchun Chen; Hua Su; Byron Marshall (Bioinform., 2004)

EBizPort: Collecting and analyzing business intelligence information. - Byron Marshall; Daniel McDonald; Hsinchun Chen; Wingyan Chung (J. Assoc. Inf. Sci. Technol., 2004)

Transforming Open-Source Documents to Terror Networks: The Arizona TerrorNet. - Daniel McDonald; Hsinchun Chen; Robert P. Schumaker (AAAI Spring Symposium: AI Technologies for Homeland Security, 2005)

Linking Ontological Resources Using Aggregatable Substance Identifiers to Organize Extracted Relations. - Byron Marshall; Hua Su; Daniel McDonald; Hsinchun Chen (Pacific Symposium on Biocomputing, 2005)

Aggregating Automatically Extracted Regulatory Pathway Relations. - Byron Marshall; Hua Su; Daniel McDonald; Shauna Eggers; Hsinchun Chen (IEEE Trans. Inf. Technol. Biomed., 2006)

Summary in context: Searching versus browsing. - Daniel McDonald; Hsinchun Chen (ACM Trans. Inf. Syst., 2006)

Comparison of methods for estimating the nucleotide substitution matrix. - Maribeth Oscamou; Daniel McDonald; Von Bing Yap; Gavin A. Huttley; Manuel E. Lladser; Rob Knight 001 (BMC Bioinform., 2008)

Ensemble dispatching on an IBM Blue Gene/L for a bioinformatics knowledge environment. - Paul Marshall; Matthew Woitaszek; Henry M. Tufo; Rob Knight 001; Daniel McDonald; Julia Goodrich (SC-MTAGS, 2009)

ALEX: mobile language assistant for low-literacy adults. - Cosmin Munteanu; Joanna Lumsden; Hélène Fournier; Rock Leung; Danny D'Amours; Daniel McDonald; Julie Maitland (Mobile HCI, 2010)

ALEX©: a mobile adult literacy experiential learning application. - Joanna Lumsden; Rock Leung; Danny D'Amours; Daniel McDonald (Int. J. Mob. Learn. Organisation, 2010)

"Showing off" your mobile device: adult literacy learning in the classroom and beyond. - Cosmin Munteanu; Heather Molyneaux; Daniel McDonald; Joanna Lumsden; Rock Leung; Hélène Fournier; Julie Maitland (Mobile HCI, 2011)

Boulder ALignment Editor (ALE): a web-based RNA alignment tool. - Jesse Stombaugh; Jeremy Widmann; Daniel McDonald; Rob Knight 001 (Bioinform., 2011)

Tale of two studies: challenges in field research with low-literacy adult learners in a developed country. - Cosmin Munteanu; Heather Molyneaux; Julie Maitland; Daniel McDonald; Rock Leung (CHI Extended Abstracts, 2012)

Automorphism Groups of Countably Categorical Linear Orders are Extremely Amenable. - François G. Dorais; Steven Gubkin; Daniel McDonald; Manuel Rivera (Order, 2013)

Hidden in plain sight: low-literacy adults in a developed country overcoming social and educational challenges through mobile learning support tools. - Cosmin Munteanu; Heather Molyneaux; Julie Maitland; Daniel McDonald; Rock Leung; Hélène Fournier; Joanna Lumsden (Pers. Ubiquitous Comput., 2014)

Using a hybrid data model to manage ultrasound signaling data. - Daniel McDonald; Justin McKay (J. Comput. Sci. Coll., 2015)

When Deceitful Chats Look Truthful. - Daniel McDonald; Randall J. Boyle; John Anderson 010 (J. Comput. Inf. Syst., 2016)

Minimax Density Estimation for Growing Dimension. - Daniel McDonald (AISTATS, 2017)

Using raspberry pi computers to teach lamp and wordpress. - Daniel McDonald; S. Jeff Cold (J. Comput. Sci. Coll., 2017)

Comparing python and wordpress assignments on a raspberry Pi. - Daniel McDonald (J. Comput. Sci. Coll., 2018)

Teaching C# using Xamarin and Android tablets. - Daniel McDonald; Kodey Crandall; Kimberly W. Bartholomew (J. Comput. Sci. Coll., 2019)

Competitive Analysis with Graph Embedding on Patent Networks. - Yunli Wang; René Richard; Daniel McDonald (CBI (1), 2020)

Porting and optimizing UniFrac for GPUs: Reducing microbiome analysis runtimes by orders of magnitude. - Igor Sfiligoi; Daniel McDonald; Rob Knight 001 (PEARC, 2020)

Porting and optimizing UniFrac for GPUs. - Igor Sfiligoi; Daniel McDonald; Rob Knight 001 (CoRR, 2020)

A system for automatic lexical acquisition from PubMed. - Daniel McDonald (J. Comput. Sci. Coll., 2020)

Galileo: Citizen-led Experimentation Using a Social Computing System. - Vineet Pandey; Tushar Koul; Chen Yang; Daniel McDonald; Mad Price Ball; Bastian Greshake Tzovaras; Rob Knight 001; Scott R. Klemmer (CHI, 2021)

Enabling microbiome research on personal devices. - Igor Sfiligoi; Daniel McDonald; Rob Knight 001 (e-Science, 2021)

Accelerating Key Bioinformatics Tasks 100-fold by Improving Memory Access. - Igor Sfiligoi; Daniel McDonald; Rob Knight 001 (PEARC, 2021)

Text analysis of research topics from nursing journals. - Daniel McDonald; Karina McDonald; Jace Johnson (J. Comput. Sci. Coll., 2021)

Applications and Comparison of Dimensionality Reduction Methods for Microbiome Data. - George Armstrong; Gibraan Rahman; Cameron Martino; Daniel McDonald; Antonio González; Gal Mishne; Rob Knight 001 (Frontiers Bioinform., 2022)

Course delivery preferences of students post-COVID 2022. - John E. Anderson 010; Daniel McDonald; Nicholas Ball (J. Comput. Sci. Coll., 2022)

Testing GitHub projects on custom resources using unprivileged Kubernetes runners. - Igor Sfiligoi; Daniel McDonald; Rob Knight 001; Frank Würthwein (PEARC, 2023)

Mitigating memory latency in FM Index search. - Igor Sfiligoi; Daniel McDonald; Rob Knight 001 (e-Science, 2024)

Scaling DEPP phylogenetic placement to ultra-large reference trees: a tree-aware ensemble approach. - Yueyu Jiang; Daniel McDonald; Daniela Perry; Rob Knight 001; Siavash Mirarab (Bioinform., 2024)

A Tale of Two Rovers: How Different Philosophies Foster Innovation in the 2023 University Rover Challenge [Competitions]. - Stephen Jacobs; Riley McAllister; Kendra Gillo; Tyler Robert Cook; Tyler Wolf; Parmis Hassani; Jack Ulbrich-Baker; Dhiluka Mapa; Nathan Adkins; Daniel McDonald; Chao Chen 033; Yu Gu 008 (IEEE Robotics Autom. Mag., 2025)