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Daniel McDonald

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2020 – today

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2024
[j14]
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Yueyu Jiang, Daniel McDonald, Daniela Perry, Rob Knight, Siavash Mirarab:
Scaling DEPP phylogenetic placement to ultra-large reference trees: a tree-aware ensemble approach. Bioinform. 40(6) (2024)
[c18]
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Igor Sfiligoi, Daniel McDonald, Rob Knight:
Mitigating memory latency in FM Index search. e-Science 2024: 1-2
2023
[c17]
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Igor Sfiligoi, Daniel McDonald, Rob Knight, Frank Würthwein:
Testing GitHub projects on custom resources using unprivileged Kubernetes runners. PEARC 2023: 332-335
[i4]
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  - journals/corr/abs-2305-10346
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Igor Sfiligoi, Daniel McDonald, Rob Knight, Frank Würthwein:
Testing GitHub projects on custom resources using unprivileged Kubernetes runners. CoRR abs/2305.10346 (2023)
2022
[j13]
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  - journals/fbinf/ArmstrongRMMGMK22
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George Armstrong, Gibraan Rahman, Cameron Martino, Daniel McDonald, Antonio González, Gal Mishne, Rob Knight:
Applications and Comparison of Dimensionality Reduction Methods for Microbiome Data. Frontiers Bioinform. 2: 821861 (2022)
2021
[c16]
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Vineet Pandey, Tushar Koul, Chen Yang, Daniel McDonald, Mad Price Ball, Bastian Greshake Tzovaras, Rob Knight, Scott R. Klemmer:
Galileo: Citizen-led Experimentation Using a Social Computing System. CHI 2021: 565:1-565:14
[c15]
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Igor Sfiligoi, Daniel McDonald, Rob Knight:
Enabling microbiome research on personal devices. e-Science 2021: 229-230
[c14]
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Igor Sfiligoi, Daniel McDonald, Rob Knight:
Accelerating Key Bioinformatics Tasks 100-fold by Improving Memory Access. PEARC 2021: 7:1-7:5
[i3]
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  - journals/corr/abs-2104-09565
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Igor Sfiligoi, Daniel McDonald, Rob Knight:
Accelerating key bioinformatics tasks 100-fold by improving memory access. CoRR abs/2104.09565 (2021)
[i2]
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  - journals/corr/abs-2107-05397
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Igor Sfiligoi, Daniel McDonald, Rob Knight:
Enabling microbiome research on personal devices. CoRR abs/2107.05397 (2021)
2020
[c13]
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  - conf/wecwis/WangRM20
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Yunli Wang, René Richard, Daniel McDonald:
Competitive Analysis with Graph Embedding on Patent Networks. CBI (1) 2020: 10-19
[c12]
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Igor Sfiligoi, Daniel McDonald, Rob Knight:
Porting and optimizing UniFrac for GPUs: Reducing microbiome analysis runtimes by orders of magnitude. PEARC 2020: 500-504
[i1]
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  - journals/corr/abs-2005-05826
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Igor Sfiligoi, Daniel McDonald, Rob Knight:
Porting and optimizing UniFrac for GPUs. CoRR abs/2005.05826 (2020)

2010 – 2019

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2017
[c11]
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Daniel McDonald:
Minimax Density Estimation for Growing Dimension. AISTATS 2017: 194-203
2016
[j12]
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Daniel McDonald, Randall J. Boyle, John Anderson:
When Deceitful Chats Look Truthful. J. Comput. Inf. Syst. 56(4): 331-340 (2016)
2014
[j11]
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  - journals/puc/MunteanuMMMLFL14
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Cosmin Munteanu, Heather Molyneaux, Julie Maitland, Daniel McDonald, Rock Leung, Hélène Fournier, Joanna Lumsden:
Hidden in plain sight: low-literacy adults in a developed country overcoming social and educational challenges through mobile learning support tools. Pers. Ubiquitous Comput. 18(6): 1455-1469 (2014)
2013
[j10]
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  - journals/order/DoraisGMR13
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François G. Dorais, Steven Gubkin, Daniel McDonald, Manuel Rivera:
Automorphism Groups of Countably Categorical Linear Orders are Extremely Amenable. Order 30(2): 415-426 (2013)
2012
[c10]
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Cosmin Munteanu, Heather Molyneaux, Julie Maitland, Daniel McDonald, Rock Leung:
Tale of two studies: challenges in field research with low-literacy adult learners in a developed country. CHI Extended Abstracts 2012: 489-504
2011
[j9]
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  - journals/bioinformatics/StombaughWMK11
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Jesse Stombaugh, Jeremy Widmann, Daniel McDonald, Rob Knight:
Boulder ALignment Editor (ALE): a web-based RNA alignment tool. Bioinform. 27(12): 1706-1707 (2011)
[c9]
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Cosmin Munteanu, Heather Molyneaux, Daniel McDonald, Joanna Lumsden, Rock Leung, Hélène Fournier, Julie Maitland:
"Showing off" your mobile device: adult literacy learning in the classroom and beyond. Mobile HCI 2011: 95-104
2010
[j8]
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Joanna Lumsden, Rock Leung, Danny D'Amours, Daniel McDonald:
ALEX^©: a mobile adult literacy experiential learning application. Int. J. Mob. Learn. Organisation 4(2): 172-191 (2010)
[c8]
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Cosmin Munteanu, Joanna Lumsden, Hélène Fournier, Rock Leung, Danny D'Amours, Daniel McDonald, Julie Maitland:
ALEX: mobile language assistant for low-literacy adults. Mobile HCI 2010: 427-430

2000 – 2009

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2009
[c7]
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Paul Marshall, Matthew Woitaszek, Henry M. Tufo, Rob Knight, Daniel McDonald, Julia Goodrich:
Ensemble dispatching on an IBM Blue Gene/L for a bioinformatics knowledge environment. SC-MTAGS 2009
2008
[j7]
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  - journals/bmcbi/OscamouMYHLK08
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Maribeth Oscamou, Daniel McDonald, Von Bing Yap, Gavin A. Huttley, Manuel E. Lladser, Rob Knight:
Comparison of methods for estimating the nucleotide substitution matrix. BMC Bioinform. 9 (2008)
2006
[j6]
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  - journals/titb/MarshallSMEC06
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Byron Marshall, Hua Su, Daniel McDonald, Shauna Eggers, Hsinchun Chen:
Aggregating Automatically Extracted Regulatory Pathway Relations. IEEE Trans. Inf. Technol. Biomed. 10(1): 100-108 (2006)
[j5]
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  - journals/tois/McDonaldC06
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Daniel McDonald, Hsinchun Chen:
Summary in context: Searching versus browsing. ACM Trans. Inf. Syst. 24(1): 111-141 (2006)
2005
[c6]
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Daniel McDonald, Hsinchun Chen, Robert P. Schumaker:
Transforming Open-Source Documents to Terror Networks: The Arizona TerrorNet. AAAI Spring Symposium: AI Technologies for Homeland Security 2005: 62-69
[c5]
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Byron Marshall, Hua Su, Daniel McDonald, Hsinchun Chen:
Linking Ontological Resources Using Aggregatable Substance Identifiers to Organize Extracted Relations. Pacific Symposium on Biocomputing 2005
2004
[j4]
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Daniel McDonald, Hsinchun Chen, Hua Su, Byron Marshall:
Extracting gene pathway relations using a hybrid grammar: the Arizona Relation Parser. Bioinform. 20(18): 3370-3378 (2004)
[j3]
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  - journals/jasis/MarshallMCC04
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Byron Marshall, Daniel McDonald, Hsinchun Chen, Wingyan Chung:
EBizPort: Collecting and analyzing business intelligence information. J. Assoc. Inf. Sci. Technol. 55(10): 873-891 (2004)
2003
[c4]
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  - conf/jcdl/LeroyCMEFKHLXMN03
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Gondy Leroy, Hsinchun Chen, Jesse D. Martinez, Shauna Eggers, Ryan R. Falsey, Kerri L. Kislin, Zan Huang, Jiexun Li, Jennifer Jie Xu, Daniel McDonald, T. Gavin Ng:
Genescene: Biomedical Text And Data Mining. JCDL 2003: 116-118
2002
[c3]
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Daniel McDonald, Hsinchun Chen:
Using sentence-selection heuristics to rank text segments in TXTRACTOR. JCDL 2002: 28-35
[c2]
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  - conf/jcdl/ChauCQZQSM02
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Michael Chau, Hsinchun Chen, Jialun Qin, Yilu Zhou, Yi Qin, Wai-Ki Sung, Daniel McDonald:
Comparison of two approaches to building a vertical search tool: a case study in the nanotechnology domain. JCDL 2002: 135-144
[c1]
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Michael Chau, Hsinchun Chen, Jialun Qin, Yilu Zhou, Wai-Ki Sung, Yongchi Chen, Yi Qin, Daniel McDonald, Ann M. Lally, Matthew Landon:
NanoPort: a web portal for nanoscale science and technology. JCDL 2002: 373

1990 – 1999

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1999
[j2]
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  - journals/candc/ReamsCGMH99
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Robert Reams, Greg Chatham, William Kile Glunt, Daniel McDonald, Tom L. Hayden:
Determining Protein Structure using the Distance Geometry Program APA. Comput. Chem. 23(2): 153-163 (1999)
1997
[j1]
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  - journals/candc/EdwardsCGMWH97
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Jonathan Edwards, Greg Chatham, William Kile Glunt, Daniel McDonald, Chris Wells, Tom L. Hayden:
Sampling Properties of the Alternating Projection Distance Geometry Algorithm Applied to Unconstrained Polypeptide Chains. Comput. Chem. 21(2): 115-124 (1997)

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