BibTeX records: Sanjay Joshua Swamidass

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@article{DBLP:journals/patterns/WatersIJKRSSGSZ24,
  author       = {Michael R. Waters and
                  Matthew Inkman and
                  Kay Jayachandran and
                  Roman M. Kowalchuk and
                  Clifford Robinson and
                  Julie K. Schwarz and
                  S. Joshua Swamidass and
                  Obi L. Griffith and
                  Jeffrey J. Szymanski and
                  Jin Zhang},
  title        = {GAiN: An integrative tool utilizing generative adversarial neural
                  networks for augmented gene expression analysis},
  journal      = {Patterns},
  volume       = {5},
  number       = {2},
  pages        = {100910},
  year         = {2024},
  url          = {https://doi.org/10.1016/j.patter.2023.100910},
  doi          = {10.1016/J.PATTER.2023.100910},
  timestamp    = {Thu, 29 Feb 2024 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/patterns/WatersIJKRSSGSZ24.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/jcisd/FlynnS23,
  author       = {Noah R. Flynn and
                  S. Joshua Swamidass},
  title        = {Message Passing Neural Networks Improve Prediction of Metabolite Authenticity},
  journal      = {J. Chem. Inf. Model.},
  volume       = {63},
  number       = {6},
  pages        = {1675--1694},
  year         = {2023},
  url          = {https://doi.org/10.1021/acs.jcim.2c01383},
  doi          = {10.1021/ACS.JCIM.2C01383},
  timestamp    = {Sat, 29 Apr 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/jcisd/FlynnS23.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@inproceedings{DBLP:conf/icaart/DattaS22,
  author       = {Arghya Datta and
                  S. Joshua Swamidass},
  editor       = {Ana Paula Rocha and
                  Luc Steels and
                  H. Jaap van den Herik},
  title        = {Fair-Net: {A} Network Architecture for Reducing Performance Disparity
                  between Identifiable Sub-populations},
  booktitle    = {Proceedings of the 14th International Conference on Agents and Artificial
                  Intelligence, {ICAART} 2022, Volume 3, Online Streaming, February
                  3-5, 2022},
  pages        = {645--654},
  publisher    = {{SCITEPRESS}},
  year         = {2022},
  url          = {https://doi.org/10.5220/0010877400003116},
  doi          = {10.5220/0010877400003116},
  timestamp    = {Tue, 06 Jun 2023 14:58:00 +0200},
  biburl       = {https://dblp.org/rec/conf/icaart/DattaS22.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/ploscb/DattaFBWMS21,
  author       = {Arghya Datta and
                  Noah R. Flynn and
                  Dustyn A. Barnette and
                  Keith F. Woeltje and
                  Grover P. Miller and
                  S. Joshua Swamidass},
  title        = {Machine learning liver-injuring drug interactions with non-steroidal
                  anti-inflammatory drugs (NSAIDs) from a retrospective electronic health
                  record {(EHR)} cohort},
  journal      = {PLoS Comput. Biol.},
  volume       = {17},
  number       = {7},
  year         = {2021},
  url          = {https://doi.org/10.1371/journal.pcbi.1009053},
  doi          = {10.1371/JOURNAL.PCBI.1009053},
  timestamp    = {Sun, 02 Oct 2022 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/ploscb/DattaFBWMS21.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/titb/DattaMDMWYS21,
  author       = {Arghya Datta and
                  Matthew K. Matlock and
                  Na Le Dang and
                  Thiago C. Moulin and
                  Keith F. Woeltje and
                  Elizabeth L. Yanik and
                  Sanjay Joshua Swamidass},
  title        = {'Black Box' to 'Conversational' Machine Learning: Ondansetron Reduces
                  Risk of Hospital-Acquired Venous Thromboembolism},
  journal      = {{IEEE} J. Biomed. Health Informatics},
  volume       = {25},
  number       = {6},
  pages        = {2204--2214},
  year         = {2021},
  url          = {https://doi.org/10.1109/JBHI.2020.3033405},
  doi          = {10.1109/JBHI.2020.3033405},
  timestamp    = {Sat, 31 Jul 2021 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/titb/DattaMDMWYS21.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@inproceedings{DBLP:conf/ijcnn/DattaFS21,
  author       = {Arghya Datta and
                  Noah R. Flynn and
                  S. Joshua Swamidass},
  title        = {Cal-Net: Jointly Learning Classification and Calibration On Imbalanced
                  Binary Classification Tasks},
  booktitle    = {International Joint Conference on Neural Networks, {IJCNN} 2021, Shenzhen,
                  China, July 18-22, 2021},
  pages        = {1--8},
  publisher    = {{IEEE}},
  year         = {2021},
  url          = {https://doi.org/10.1109/IJCNN52387.2021.9534411},
  doi          = {10.1109/IJCNN52387.2021.9534411},
  timestamp    = {Mon, 03 Jan 2022 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/conf/ijcnn/DattaFS21.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/corr/abs-2106-00720,
  author       = {Arghya Datta and
                  S. Joshua Swamidass},
  title        = {Fair-Net: {A} Network Architecture For Reducing Performance Disparity
                  Between Identifiable Sub-Populations},
  journal      = {CoRR},
  volume       = {abs/2106.00720},
  year         = {2021},
  url          = {https://arxiv.org/abs/2106.00720},
  eprinttype    = {arXiv},
  eprint       = {2106.00720},
  timestamp    = {Sun, 02 Oct 2022 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2106-00720.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/jcisd/DangMHS20,
  author       = {Na Le Dang and
                  Matthew K. Matlock and
                  Tyler B. Hughes and
                  S. Joshua Swamidass},
  title        = {The Metabolic Rainbow: Deep Learning Phase {I} Metabolism in Five
                  Colors},
  journal      = {J. Chem. Inf. Model.},
  volume       = {60},
  number       = {3},
  pages        = {1146--1164},
  year         = {2020},
  url          = {https://doi.org/10.1021/acs.jcim.9b00836},
  doi          = {10.1021/ACS.JCIM.9B00836},
  timestamp    = {Tue, 01 Jun 2021 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/jcisd/DangMHS20.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/jcisd/FlynnDWS20,
  author       = {Noah R. Flynn and
                  Na Le Dang and
                  Michael D. Ward and
                  S. Joshua Swamidass},
  title        = {XenoNet: Inference and Likelihood of Intermediate Metabolite Formation},
  journal      = {J. Chem. Inf. Model.},
  volume       = {60},
  number       = {7},
  pages        = {3431--3449},
  year         = {2020},
  url          = {https://doi.org/10.1021/acs.jcim.0c00361},
  doi          = {10.1021/ACS.JCIM.0C00361},
  timestamp    = {Tue, 01 Jun 2021 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/jcisd/FlynnDWS20.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/jcisd/HughesDKFS20,
  author       = {Tyler B. Hughes and
                  Na Le Dang and
                  Ayush Kumar and
                  Noah R. Flynn and
                  S. Joshua Swamidass},
  title        = {Metabolic Forest: Predicting the Diverse Structures of Drug Metabolites},
  journal      = {J. Chem. Inf. Model.},
  volume       = {60},
  number       = {10},
  pages        = {4702--4716},
  year         = {2020},
  url          = {https://doi.org/10.1021/acs.jcim.0c00360},
  doi          = {10.1021/ACS.JCIM.0C00360},
  timestamp    = {Tue, 01 Jun 2021 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/jcisd/HughesDKFS20.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@inproceedings{DBLP:conf/ijcnn/MatlockDDJS19,
  author       = {Matthew K. Matlock and
                  Arghya Datta and
                  Na Le Dang and
                  Kevin Jiang and
                  S. Joshua Swamidass},
  title        = {Deep learning long-range information in undirected graphs with wave
                  networks},
  booktitle    = {International Joint Conference on Neural Networks, {IJCNN} 2019 Budapest,
                  Hungary, July 14-19, 2019},
  pages        = {1--8},
  publisher    = {{IEEE}},
  year         = {2019},
  url          = {https://doi.org/10.1109/IJCNN.2019.8852455},
  doi          = {10.1109/IJCNN.2019.8852455},
  timestamp    = {Sat, 05 Sep 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/conf/ijcnn/MatlockDDJS19.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/jcisd/MatlockHDS18,
  author       = {Matthew K. Matlock and
                  Tyler B. Hughes and
                  Jayme L. Dahlin and
                  S. Joshua Swamidass},
  title        = {Modeling Small-Molecule Reactivity Identifies Promiscuous Bioactive
                  Compounds},
  journal      = {J. Chem. Inf. Model.},
  volume       = {58},
  number       = {8},
  pages        = {1483--1500},
  year         = {2018},
  url          = {https://doi.org/10.1021/acs.jcim.8b00104},
  doi          = {10.1021/ACS.JCIM.8B00104},
  timestamp    = {Tue, 01 Jun 2021 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/jcisd/MatlockHDS18.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/tmi/MarshMKLSGS18,
  author       = {Jon N. Marsh and
                  Matthew K. Matlock and
                  Satoru Kudose and
                  Ta{-}Chiang Liu and
                  Thaddeus S. Stappenbeck and
                  Joseph P. Gaut and
                  S. Joshua Swamidass},
  title        = {Deep Learning Global Glomerulosclerosis in Transplant Kidney Frozen
                  Sections},
  journal      = {{IEEE} Trans. Medical Imaging},
  volume       = {37},
  number       = {12},
  pages        = {2718--2728},
  year         = {2018},
  url          = {https://doi.org/10.1109/TMI.2018.2851150},
  doi          = {10.1109/TMI.2018.2851150},
  timestamp    = {Sat, 05 Sep 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/tmi/MarshMKLSGS18.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@inproceedings{DBLP:conf/psb/SoutherlandSPWW18,
  author       = {William M. Southerland and
                  S. Joshua Swamidass and
                  Philip R. O. Payne and
                  Laura K. Wiley and
                  ClarLynda R. Williams{-}DeVane},
  editor       = {Russ B. Altman and
                  A. Keith Dunker and
                  Lawrence Hunter and
                  Marylyn D. Ritchie and
                  Teri E. Klein},
  title        = {The diversity and disparity in biomedical informatics {(DDBI)} workshop},
  booktitle    = {Biocomputing 2018: Proceedings of the Pacific Symposium, The Big Island
                  of Hawaii, Hawaii, USA, January 3-7, 2018},
  pages        = {614--617},
  year         = {2018},
  url          = {http://psb.stanford.edu/psb-online/proceedings/psb18/wkshop-diversity.pdf},
  timestamp    = {Thu, 12 Mar 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/conf/psb/SoutherlandSPWW18.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/corr/abs-1810-12153,
  author       = {Matthew K. Matlock and
                  Arghya Datta and
                  Na Le Dang and
                  Kevin Jiang and
                  S. Joshua Swamidass},
  title        = {Deep learning long-range information in undirected graphs with wave
                  networks},
  journal      = {CoRR},
  volume       = {abs/1810.12153},
  year         = {2018},
  url          = {http://arxiv.org/abs/1810.12153},
  eprinttype    = {arXiv},
  eprint       = {1810.12153},
  timestamp    = {Thu, 01 Nov 2018 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/corr/abs-1810-12153.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bioinformatics/RuanSS17,
  author       = {Shuxiang Ruan and
                  S. Joshua Swamidass and
                  Gary D. Stormo},
  title        = {{BEESEM:} estimation of binding energy models using {HT-SELEX} data},
  journal      = {Bioinform.},
  volume       = {33},
  number       = {15},
  pages        = {2288--2295},
  year         = {2017},
  url          = {https://doi.org/10.1093/bioinformatics/btx191},
  doi          = {10.1093/BIOINFORMATICS/BTX191},
  timestamp    = {Sat, 05 Sep 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/RuanSS17.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bib/LiZCBSL16,
  author       = {Jiao Li and
                  Si Zheng and
                  Bin Chen and
                  Atul J. Butte and
                  S. Joshua Swamidass and
                  Zhiyong Lu},
  title        = {A survey of current trends in computational drug repositioning},
  journal      = {Briefings Bioinform.},
  volume       = {17},
  number       = {1},
  pages        = {2--12},
  year         = {2016},
  url          = {https://doi.org/10.1093/bib/bbv020},
  doi          = {10.1093/BIB/BBV020},
  timestamp    = {Wed, 02 Nov 2022 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bib/LiZCBSL16.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bioinformatics/DangHKS16,
  author       = {Na Le Dang and
                  Tyler B. Hughes and
                  Varun Krishnamurthy and
                  S. Joshua Swamidass},
  title        = {A simple model predicts UGT-mediated metabolism},
  journal      = {Bioinform.},
  volume       = {32},
  number       = {20},
  pages        = {3183--3189},
  year         = {2016},
  url          = {https://doi.org/10.1093/bioinformatics/btw350},
  doi          = {10.1093/BIOINFORMATICS/BTW350},
  timestamp    = {Sat, 05 Sep 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/DangHKS16.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bioinformatics/MatlockHS15,
  author       = {Matthew K. Matlock and
                  Tyler B. Hughes and
                  Sanjay Joshua Swamidass},
  title        = {XenoSite server: a web-available site of metabolism prediction tool},
  journal      = {Bioinform.},
  volume       = {31},
  number       = {7},
  pages        = {1136--1137},
  year         = {2015},
  url          = {https://doi.org/10.1093/bioinformatics/btu761},
  doi          = {10.1093/BIOINFORMATICS/BTU761},
  timestamp    = {Mon, 02 Mar 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/MatlockHS15.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bioinformatics/ZaretzkiBHS15,
  author       = {Jed M. Zaretzki and
                  Michael R. Browning and
                  Tyler B. Hughes and
                  S. Joshua Swamidass},
  title        = {Extending {P450} site-of-metabolism models with region-resolution
                  data},
  journal      = {Bioinform.},
  volume       = {31},
  number       = {12},
  pages        = {1966--1973},
  year         = {2015},
  url          = {https://doi.org/10.1093/bioinformatics/btv100},
  doi          = {10.1093/BIOINFORMATICS/BTV100},
  timestamp    = {Sat, 05 Sep 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/ZaretzkiBHS15.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bioinformatics/KumarSSGB15,
  author       = {Runjun D. Kumar and
                  Adam C. Searleman and
                  S. Joshua Swamidass and
                  Obi L. Griffith and
                  Ron Bose},
  title        = {Statistically identifying tumor suppressors and oncogenes from pan-cancer
                  genome-sequencing data},
  journal      = {Bioinform.},
  volume       = {31},
  number       = {22},
  pages        = {3561--3568},
  year         = {2015},
  url          = {https://doi.org/10.1093/bioinformatics/btv430},
  doi          = {10.1093/BIOINFORMATICS/BTV430},
  timestamp    = {Sat, 05 Sep 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/KumarSSGB15.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/jcheminf/LusciBFSB15,
  author       = {Alessandro Lusci and
                  Michael R. Browning and
                  David Fooshee and
                  S. Joshua Swamidass and
                  Pierre Baldi},
  title        = {Accurate and efficient target prediction using a potency-sensitive
                  influence-relevance voter},
  journal      = {J. Cheminformatics},
  volume       = {7},
  pages        = {63:1--63:13},
  year         = {2015},
  url          = {https://doi.org/10.1186/s13321-015-0110-6},
  doi          = {10.1186/S13321-015-0110-6},
  timestamp    = {Sat, 05 Sep 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/jcheminf/LusciBFSB15.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/jcisd/ZaretzkiBS15,
  author       = {Jed Zaretzki and
                  Kevin Michael Boehm and
                  Sanjay Joshua Swamidass},
  title        = {Improved Prediction of CYP-Mediated Metabolism with Chemical Fingerprints},
  journal      = {J. Chem. Inf. Model.},
  volume       = {55},
  number       = {5},
  pages        = {972--982},
  year         = {2015},
  url          = {https://doi.org/10.1021/ci5005652},
  doi          = {10.1021/CI5005652},
  timestamp    = {Fri, 22 Dec 2023 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/jcisd/ZaretzkiBS15.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/jcamd/EkinsCSLW14,
  author       = {Sean Ekins and
                  Alex M. Clark and
                  S. Joshua Swamidass and
                  Nadia K. Litterman and
                  Antony J. Williams},
  title        = {Bigger data, collaborative tools and the future of predictive drug
                  discovery},
  journal      = {J. Comput. Aided Mol. Des.},
  volume       = {28},
  number       = {10},
  pages        = {997--1008},
  year         = {2014},
  url          = {https://doi.org/10.1007/s10822-014-9762-y},
  doi          = {10.1007/S10822-014-9762-Y},
  timestamp    = {Thu, 16 Apr 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/jcamd/EkinsCSLW14.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/jcisd/MatlockS14,
  author       = {Matthew K. Matlock and
                  S. Joshua Swamidass},
  title        = {Sharing Chemical Relationships Does Not Reveal Structures},
  journal      = {J. Chem. Inf. Model.},
  volume       = {54},
  number       = {1},
  pages        = {37--48},
  year         = {2014},
  url          = {https://doi.org/10.1021/ci400399a},
  doi          = {10.1021/CI400399A},
  timestamp    = {Fri, 06 Mar 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/jcisd/MatlockS14.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@inproceedings{DBLP:conf/psb/SwamidassLAB14,
  author       = {S. Joshua Swamidass and
                  Zhiyong Lu and
                  Pankaj Agarwal and
                  Atul J. Butte},
  editor       = {Russ B. Altman and
                  A. Keith Dunker and
                  Lawrence Hunter and
                  Teri E. Klein and
                  Marylyn D. Ritchie},
  title        = {Session Introduction},
  booktitle    = {Biocomputing 2014: Proceedings of the Pacific Symposium, Kohala Coast,
                  Hawaii, USA, January 3-7, 2014},
  pages        = {110--113},
  year         = {2014},
  url          = {http://psb.stanford.edu/psb-online/proceedings/psb14/intro-cdr.pdf},
  timestamp    = {Thu, 12 Mar 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/conf/psb/SwamidassLAB14.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bib/SloutskyJSN13,
  author       = {Roman Sloutsky and
                  Nicolas Jimenez and
                  S. Joshua Swamidass and
                  Kristen M. Naegle},
  title        = {Accounting for noise when clustering biological data},
  journal      = {Briefings Bioinform.},
  volume       = {14},
  number       = {4},
  pages        = {423--436},
  year         = {2013},
  url          = {https://doi.org/10.1093/bib/bbs057},
  doi          = {10.1093/BIB/BBS057},
  timestamp    = {Thu, 04 Jun 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bib/SloutskyJSN13.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bioinformatics/ZaretzkiBHRSB13,
  author       = {Jed Zaretzki and
                  Charles Bergeron and
                  Tao{-}wei Huang and
                  Patrik Rydberg and
                  S. Joshua Swamidass and
                  Curt M. Breneman},
  title        = {RS-WebPredictor: a server for predicting CYP-mediated sites of metabolism
                  on drug-like molecules},
  journal      = {Bioinform.},
  volume       = {29},
  number       = {4},
  pages        = {497--498},
  year         = {2013},
  url          = {https://doi.org/10.1093/bioinformatics/bts705},
  doi          = {10.1093/BIOINFORMATICS/BTS705},
  timestamp    = {Mon, 02 Mar 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/ZaretzkiBHRSB13.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bioinformatics/MatlockZS13,
  author       = {Matthew K. Matlock and
                  Jed Zaretzki and
                  S. Joshua Swamidass},
  title        = {Scaffold network generator: a tool for mining molecular structures},
  journal      = {Bioinform.},
  volume       = {29},
  number       = {20},
  pages        = {2655--2656},
  year         = {2013},
  url          = {https://doi.org/10.1093/bioinformatics/btt448},
  doi          = {10.1093/BIOINFORMATICS/BTT448},
  timestamp    = {Mon, 02 Mar 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/MatlockZS13.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/jcamd/BrowningCS13,
  author       = {Michael R. Browning and
                  Bradley T. Calhoun and
                  Sanjay Joshua Swamidass},
  title        = {Managing missing measurements in small-molecule screens},
  journal      = {J. Comput. Aided Mol. Des.},
  volume       = {27},
  number       = {5},
  pages        = {469--478},
  year         = {2013},
  url          = {https://doi.org/10.1007/s10822-013-9642-x},
  doi          = {10.1007/S10822-013-9642-X},
  timestamp    = {Thu, 16 Apr 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/jcamd/BrowningCS13.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/jcisd/ZaretzkiMS13,
  author       = {Jed Zaretzki and
                  Matthew K. Matlock and
                  S. Joshua Swamidass},
  title        = {XenoSite: Accurately Predicting CYP-Mediated Sites of Metabolism with
                  Neural Networks},
  journal      = {J. Chem. Inf. Model.},
  volume       = {53},
  number       = {12},
  pages        = {3373--3383},
  year         = {2013},
  url          = {https://doi.org/10.1021/ci400518g},
  doi          = {10.1021/CI400518G},
  timestamp    = {Fri, 06 Mar 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/jcisd/ZaretzkiMS13.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/jcisd/SwamidassCBBC12,
  author       = {S. Joshua Swamidass and
                  Bradley T. Calhoun and
                  Joshua A. Bittker and
                  Nicole E. Bodycombe and
                  Paul A. Clemons},
  title        = {Utility-Aware Screening with Clique-Oriented Prioritization},
  journal      = {J. Chem. Inf. Model.},
  volume       = {52},
  number       = {1},
  pages        = {29--37},
  year         = {2012},
  url          = {https://doi.org/10.1021/ci2003285},
  doi          = {10.1021/CI2003285},
  timestamp    = {Fri, 06 Mar 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/jcisd/SwamidassCBBC12.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bib/Swamidass11,
  author       = {Sanjay Joshua Swamidass},
  title        = {Mining small-molecule screens to repurpose drugs},
  journal      = {Briefings Bioinform.},
  volume       = {12},
  number       = {4},
  pages        = {327--335},
  year         = {2011},
  url          = {https://doi.org/10.1093/bib/bbr028},
  doi          = {10.1093/BIB/BBR028},
  timestamp    = {Thu, 04 Jun 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bib/Swamidass11.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bioinformatics/SwamidassCBBC11,
  author       = {Sanjay Joshua Swamidass and
                  Bradley T. Calhoun and
                  Joshua A. Bittker and
                  Nicole E. Bodycombe and
                  Paul A. Clemons},
  title        = {Enhancing the rate of scaffold discovery with diversity-oriented prioritization},
  journal      = {Bioinform.},
  volume       = {27},
  number       = {16},
  pages        = {2271--2278},
  year         = {2011},
  url          = {https://doi.org/10.1093/bioinformatics/btr369},
  doi          = {10.1093/BIOINFORMATICS/BTR369},
  timestamp    = {Mon, 02 Mar 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/SwamidassCBBC11.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bioinformatics/SwamidassADB10,
  author       = {Sanjay Joshua Swamidass and
                  Chlo{\'{e}}{-}Agathe Azencott and
                  Kenny Daily and
                  Pierre Baldi},
  title        = {A {CROC} stronger than {ROC:} measuring, visualizing and optimizing
                  early retrieval},
  journal      = {Bioinform.},
  volume       = {26},
  number       = {10},
  pages        = {1348--1356},
  year         = {2010},
  url          = {https://doi.org/10.1093/bioinformatics/btq140},
  doi          = {10.1093/BIOINFORMATICS/BTQ140},
  timestamp    = {Mon, 02 Mar 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/SwamidassADB10.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@inproceedings{DBLP:conf/wirn/BaldiAS10,
  author       = {Pierre Baldi and
                  Chlo{\'{e}}{-}Agathe Azencott and
                  Sanjay Joshua Swamidass},
  editor       = {Bruno Apolloni and
                  Simone Bassis and
                  Anna Esposito and
                  Francesco Carlo Morabito},
  title        = {Bridging the Gap Between Neural Network and Kernel Methods: Applications
                  to Drug Discovery},
  booktitle    = {Neural Nets {WIRN10} - Proceedings of the 20th Italian Workshop on
                  Neural Nets, Vietri sul Mare, Salerno, Italy, May 27-29 2010},
  series       = {Frontiers in Artificial Intelligence and Applications},
  volume       = {226},
  pages        = {3--13},
  publisher    = {{IOS} Press},
  year         = {2010},
  url          = {https://doi.org/10.3233/978-1-60750-692-8-3},
  doi          = {10.3233/978-1-60750-692-8-3},
  timestamp    = {Sat, 05 Sep 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/conf/wirn/BaldiAS10.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/jcheminf/NasrSB09,
  author       = {Ramzi Nasr and
                  Sanjay Joshua Swamidass and
                  Pierre Baldi},
  title        = {Large scale study of multiple-molecule queries},
  journal      = {J. Cheminformatics},
  volume       = {1},
  pages        = {7},
  year         = {2009},
  url          = {https://doi.org/10.1186/1758-2946-1-7},
  doi          = {10.1186/1758-2946-1-7},
  timestamp    = {Thu, 14 Feb 2019 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/jcheminf/NasrSB09.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/jcisd/SwamidassALGTB09,
  author       = {S. Joshua Swamidass and
                  Chlo{\'{e}}{-}Agathe Azencott and
                  Ting{-}Wan Lin and
                  Hugo Gramajo and
                  Shiou{-}Chuan Tsai and
                  Pierre Baldi},
  title        = {Influence Relevance Voting: An Accurate And Interpretable Virtual
                  High Throughput Screening Method},
  journal      = {J. Chem. Inf. Model.},
  volume       = {49},
  number       = {4},
  pages        = {756--766},
  year         = {2009},
  url          = {https://doi.org/10.1021/ci8004379},
  doi          = {10.1021/CI8004379},
  timestamp    = {Fri, 06 Mar 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/jcisd/SwamidassALGTB09.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/jcisd/BenzSB08,
  author       = {Ryan W. Benz and
                  S. Joshua Swamidass and
                  Pierre Baldi},
  title        = {Discovery of Power-Laws in Chemical Space},
  journal      = {J. Chem. Inf. Model.},
  volume       = {48},
  number       = {6},
  pages        = {1138--1151},
  year         = {2008},
  url          = {https://doi.org/10.1021/ci700353m},
  doi          = {10.1021/CI700353M},
  timestamp    = {Sat, 30 Sep 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/jcisd/BenzSB08.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bioinformatics/ChenLSWB07,
  author       = {Jonathan H. Chen and
                  Erik Linstead and
                  Sanjay Joshua Swamidass and
                  Dennis Wang and
                  Pierre Baldi},
  title        = {ChemDB update - full-text search and virtual chemical space},
  journal      = {Bioinform.},
  volume       = {23},
  number       = {17},
  pages        = {2348--2351},
  year         = {2007},
  url          = {https://doi.org/10.1093/bioinformatics/btm341},
  doi          = {10.1093/BIOINFORMATICS/BTM341},
  timestamp    = {Thu, 14 Oct 2021 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/ChenLSWB07.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/jcisd/SwamidassB07,
  author       = {S. Joshua Swamidass and
                  Pierre Baldi},
  title        = {Bounds and Algorithms for Fast Exact Searches of Chemical Fingerprints
                  in Linear and Sublinear Time},
  journal      = {J. Chem. Inf. Model.},
  volume       = {47},
  number       = {2},
  pages        = {302--317},
  year         = {2007},
  url          = {https://doi.org/10.1021/ci600358f},
  doi          = {10.1021/CI600358F},
  timestamp    = {Fri, 06 Mar 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/jcisd/SwamidassB07.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/jcisd/SwamidassB07a,
  author       = {S. Joshua Swamidass and
                  Pierre Baldi},
  title        = {Mathematical Correction for Fingerprint Similarity Measures to Improve
                  Chemical Retrieval},
  journal      = {J. Chem. Inf. Model.},
  volume       = {47},
  number       = {3},
  pages        = {952--964},
  year         = {2007},
  url          = {https://doi.org/10.1021/ci600526a},
  doi          = {10.1021/CI600526A},
  timestamp    = {Fri, 06 Mar 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/jcisd/SwamidassB07a.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/jcisd/AzencottKSCRB07,
  author       = {Chlo{\'{e}}{-}Agathe Azencott and
                  Alexandre Ksikes and
                  S. Joshua Swamidass and
                  Jonathan H. Chen and
                  Liva Ralaivola and
                  Pierre Baldi},
  title        = {One- to Four-Dimensional Kernels for Virtual Screening and the Prediction
                  of Physical, Chemical, and Biological Properties},
  journal      = {J. Chem. Inf. Model.},
  volume       = {47},
  number       = {3},
  pages        = {965--974},
  year         = {2007},
  url          = {https://doi.org/10.1021/ci600397p},
  doi          = {10.1021/CI600397P},
  timestamp    = {Thu, 14 Oct 2021 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/jcisd/AzencottKSCRB07.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/jcisd/BaldiBHS07,
  author       = {Pierre Baldi and
                  Ryan W. Benz and
                  Daniel S. Hirschberg and
                  S. Joshua Swamidass},
  title        = {Lossless Compression of Chemical Fingerprints Using Integer Entropy
                  Codes Improves Storage and Retrieval},
  journal      = {J. Chem. Inf. Model.},
  volume       = {47},
  number       = {6},
  pages        = {2098--2109},
  year         = {2007},
  url          = {https://doi.org/10.1021/ci700200n},
  doi          = {10.1021/CI700200N},
  timestamp    = {Sat, 30 Sep 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/jcisd/BaldiBHS07.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/tcbb/DanzigerSZDLCCHSLBBL06,
  author       = {Samuel A. Danziger and
                  Sanjay Joshua Swamidass and
                  Jue Zeng and
                  Lawrence R. Dearth and
                  Qiang Lu and
                  Jonathan H. Chen and
                  Jianlin Cheng and
                  Vinh P. Hoang and
                  Hiroto Saigo and
                  Ray Luo and
                  Pierre Baldi and
                  Rainer K. Brachmann and
                  Richard H. Lathrop},
  title        = {Functional Census of Mutation Sequence Spaces: The Example of p53
                  Cancer Rescue Mutants},
  journal      = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
  volume       = {3},
  number       = {2},
  pages        = {114--125},
  year         = {2006},
  url          = {https://doi.org/10.1109/TCBB.2006.22},
  doi          = {10.1109/TCBB.2006.22},
  timestamp    = {Mon, 24 Apr 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/tcbb/DanzigerSZDLCCHSLBBL06.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bioinformatics/ChenSDBB05,
  author       = {Jonathan H. Chen and
                  Sanjay Joshua Swamidass and
                  Yimeng Dou and
                  Jocelyne Bruand and
                  Pierre Baldi},
  title        = {ChemDB: a public database of small molecules and related chemoinformatics
                  resources},
  journal      = {Bioinform.},
  volume       = {21},
  number       = {22},
  pages        = {4133--4139},
  year         = {2005},
  url          = {https://doi.org/10.1093/bioinformatics/bti683},
  doi          = {10.1093/BIOINFORMATICS/BTI683},
  timestamp    = {Thu, 14 Oct 2021 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/ChenSDBB05.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/nn/RalaivolaSSB05,
  author       = {Liva Ralaivola and
                  Sanjay Joshua Swamidass and
                  Hiroto Saigo and
                  Pierre Baldi},
  title        = {Graph kernels for chemical informatics},
  journal      = {Neural Networks},
  volume       = {18},
  number       = {8},
  pages        = {1093--1110},
  year         = {2005},
  url          = {https://doi.org/10.1016/j.neunet.2005.07.009},
  doi          = {10.1016/J.NEUNET.2005.07.009},
  timestamp    = {Mon, 26 Oct 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/nn/RalaivolaSSB05.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@inproceedings{DBLP:conf/ismb/SwamidassCBPRB05,
  author       = {Sanjay Joshua Swamidass and
                  Jonathan H. Chen and
                  Jocelyne Bruand and
                  Peter Phung and
                  Liva Ralaivola and
                  Pierre Baldi},
  title        = {Kernels for small molecules and the prediction of mutagenicity, toxicity
                  and anti-cancer activity},
  booktitle    = {Proceedings Thirteenth International Conference on Intelligent Systems
                  for Molecular Biology 2005, Detroit, MI, USA, 25-29 June 2005},
  pages        = {359--368},
  year         = {2005},
  url          = {https://doi.org/10.1093/bioinformatics/bti1055},
  doi          = {10.1093/BIOINFORMATICS/BTI1055},
  timestamp    = {Thu, 14 Oct 2021 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/conf/ismb/SwamidassCBPRB05.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@inproceedings{DBLP:conf/wilf/SwamidassB05,
  author       = {Sanjay Joshua Swamidass and
                  Pierre Baldi},
  editor       = {Isabelle Bloch and
                  Alfredo Petrosino and
                  Andrea Tettamanzi},
  title        = {Statistical Distribution of Chemical Fingerprints},
  booktitle    = {Fuzzy Logic and Applications, 6th International Workshop, {WILF} 2005,
                  Crema, Italy, September 15-17, 2005, Revised Selected Papers},
  series       = {Lecture Notes in Computer Science},
  volume       = {3849},
  pages        = {11--18},
  publisher    = {Springer},
  year         = {2005},
  url          = {https://doi.org/10.1007/11676935\_2},
  doi          = {10.1007/11676935\_2},
  timestamp    = {Sun, 02 Jun 2019 21:16:27 +0200},
  biburl       = {https://dblp.org/rec/conf/wilf/SwamidassB05.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
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