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@article{DBLP:journals/ijhpca/ZvyaginBHDZBCKPMMIOVPWHEFXLSNRDV23,
  author       = {Maxim Zvyagin and
                  Alexander Brace and
                  Kyle Hippe and
                  Yuntian Deng and
                  Bin Zhang and
                  Cindy Orozco Bohorquez and
                  Austin Clyde and
                  Bharat Kale and
                  Danilo Perez{-}Rivera and
                  Heng Ma and
                  Carla M. Mann and
                  Michael W. Irvin and
                  Defne G. Ozgulbas and
                  Natalia Vassilieva and
                  J. Gregory Pauloski and
                  Logan T. Ward and
                  Val{\'{e}}rie Hayot{-}Sasson and
                  Murali Emani and
                  Sam Foreman and
                  Zhen Xie and
                  Diangen Lin and
                  Maulik Shukla and
                  Weili Nie and
                  Josh Romero and
                  Christian Dallago and
                  Arash Vahdat and
                  Chaowei Xiao and
                  Thomas Gibbs and
                  Ian T. Foster and
                  James J. Davis and
                  Michael E. Papka and
                  Thomas S. Brettin and
                  Rick Stevens and
                  Anima Anandkumar and
                  Venkatram Vishwanath and
                  Arvind Ramanathan},
  title        = {GenSLMs: Genome-scale language models reveal SARS-CoV-2 evolutionary
                  dynamics},
  journal      = {Int. J. High Perform. Comput. Appl.},
  volume       = {37},
  number       = {6},
  pages        = {683--705},
  year         = {2023},
  url          = {https://doi.org/10.1177/10943420231201154},
  doi          = {10.1177/10943420231201154},
  timestamp    = {Mon, 11 Dec 2023 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/ijhpca/ZvyaginBHDZBCKPMMIOVPWHEFXLSNRDV23.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/OlsonABCCDDDDKKLLMMMNNOOPPPPSSSTTVV23,
  author       = {Robert D. Olson and
                  Rida Assaf and
                  Thomas S. Brettin and
                  Neal Conrad and
                  Clark Cucinell and
                  James J. Davis and
                  Donald M. Dempsey and
                  Allan Dickerman and
                  Emily M. Dietrich and
                  Ronald W. Kenyon and
                  Mehmet Kuscuoglu and
                  Elliot J. Lefkowitz and
                  Jian Lu and
                  Dustin Machi and
                  Catherine Macken and
                  Chunhong Mao and
                  Anna Maria Niewiadomska and
                  Marcus Nguyen and
                  Gary J. Olsen and
                  Jamie C. Overbeek and
                  Bruce D. Parrello and
                  Victoria Parrello and
                  Jacob s Porter and
                  Gordon D. Pusch and
                  Maulik Shukla and
                  Indresh Singh and
                  Lucy Stewart and
                  Gene Tan and
                  Chris Thomas and
                  Margo VanOeffelen and
                  Veronika Vonstein and
                  Zachary S. Wallace and
                  Andrew S. Warren and
                  Alice R. Wattam and
                  Fangfang Xia and
                  Hyun Seung Yoo and
                  Yun Zhang and
                  Christian M. Zmasek and
                  Richard H. Scheuermann and
                  Rick L. Stevens},
  title        = {Introducing the Bacterial and Viral Bioinformatics Resource Center
                  {(BV-BRC):} a resource combining PATRIC, {IRD} and ViPR},
  journal      = {Nucleic Acids Res.},
  volume       = {51},
  number       = {{D1}},
  pages        = {678--689},
  year         = {2023},
  url          = {https://doi.org/10.1093/nar/gkac1003},
  doi          = {10.1093/NAR/GKAC1003},
  timestamp    = {Sat, 30 Sep 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/nar/OlsonABCCDDDDKKLLMMMNNOOPPPPSSSTTVV23.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/sc/NarykovZBEPSVDS23,
  author       = {Oleksandr Narykov and
                  Yitan Zhu and
                  Thomas S. Brettin and
                  Yvonne A. Evrard and
                  Alexander Partin and
                  Maulik Shukla and
                  Priyanka Vasanthakumari and
                  James H. Doroshow and
                  Rick Stevens},
  title        = {Entropy-Based Regularization on Deep Learning Models for Anti-Cancer
                  Drug Response Prediction},
  booktitle    = {Proceedings of the {SC} '23 Workshops of The International Conference
                  on High Performance Computing, Network, Storage, and Analysis, {SC-W}
                  2023, Denver, CO, USA, November 12-17, 2023},
  pages        = {121--122},
  publisher    = {{ACM}},
  year         = {2023},
  url          = {https://doi.org/10.1145/3624062.3624080},
  doi          = {10.1145/3624062.3624080},
  timestamp    = {Tue, 28 Nov 2023 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/conf/sc/NarykovZBEPSVDS23.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2310-04610,
  author       = {Shuaiwen Leon Song and
                  Bonnie Kruft and
                  Minjia Zhang and
                  Conglong Li and
                  Shiyang Chen and
                  Chengming Zhang and
                  Masahiro Tanaka and
                  Xiaoxia Wu and
                  Jeff Rasley and
                  Ammar Ahmad Awan and
                  Connor Holmes and
                  Martin Cai and
                  Adam Ghanem and
                  Zhongzhu Zhou and
                  Yuxiong He and
                  Pete Luferenko and
                  Divya Kumar and
                  Jonathan A. Weyn and
                  Ruixiong Zhang and
                  Sylwester Klocek and
                  Volodymyr Vragov and
                  Mohammed AlQuraishi and
                  Gustaf Ahdritz and
                  Christina Floristean and
                  Cristina Negri and
                  Rao Kotamarthi and
                  Venkatram Vishwanath and
                  Arvind Ramanathan and
                  Sam Foreman and
                  Kyle Hippe and
                  Troy Arcomano and
                  Romit Maulik and
                  Maxim Zvyagin and
                  Alexander Brace and
                  Bin Zhang and
                  Cindy Orozco Bohorquez and
                  Austin Clyde and
                  Bharat Kale and
                  Danilo Perez{-}Rivera and
                  Heng Ma and
                  Carla M. Mann and
                  Michael W. Irvin and
                  J. Gregory Pauloski and
                  Logan T. Ward and
                  Val{\'{e}}rie Hayot{-}Sasson and
                  Murali Emani and
                  Zhen Xie and
                  Diangen Lin and
                  Maulik Shukla and
                  Ian T. Foster and
                  James J. Davis and
                  Michael E. Papka and
                  Thomas S. Brettin and
                  Prasanna Balaprakash and
                  Gina Tourassi and
                  John Gounley and
                  Heidi A. Hanson and
                  Thomas E. Potok and
                  Massimiliano Lupo Pasini and
                  Kate Evans and
                  Dan Lu and
                  Dalton D. Lunga and
                  Junqi Yin and
                  Sajal Dash and
                  Feiyi Wang and
                  Mallikarjun Shankar and
                  Isaac Lyngaas and
                  Xiao Wang and
                  Guojing Cong and
                  Pei Zhang and
                  Ming Fan and
                  Siyan Liu and
                  Adolfy Hoisie and
                  Shinjae Yoo and
                  Yihui Ren and
                  William Tang and
                  Kyle Felker and
                  Alexey Svyatkovskiy and
                  Hang Liu and
                  Ashwin M. Aji and
                  Angela Dalton and
                  Michael J. Schulte and
                  Karl Schulz and
                  Yuntian Deng and
                  Weili Nie and
                  Josh Romero and
                  Christian Dallago and
                  Arash Vahdat and
                  Chaowei Xiao and
                  Thomas Gibbs and
                  Anima Anandkumar and
                  Rick Stevens},
  title        = {DeepSpeed4Science Initiative: Enabling Large-Scale Scientific Discovery
                  through Sophisticated {AI} System Technologies},
  journal      = {CoRR},
  volume       = {abs/2310.04610},
  year         = {2023},
  url          = {https://doi.org/10.48550/arXiv.2310.04610},
  doi          = {10.48550/ARXIV.2310.04610},
  eprinttype    = {arXiv},
  eprint       = {2310.04610},
  timestamp    = {Tue, 05 Mar 2024 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2310-04610.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/XiaABBGCCDDDEFG22,
  author       = {Fangfang Xia and
                  Jonathan E. Allen and
                  Prasanna Balaprakash and
                  Thomas S. Brettin and
                  Cristina Garcia{-}Cardona and
                  Austin Clyde and
                  Judith D. Cohn and
                  James H. Doroshow and
                  Xiaotian Duan and
                  Veronika Dubinkina and
                  Yvonne A. Evrard and
                  Ya Ju Fan and
                  Jason Gans and
                  Stewart He and
                  Pinyi Lu and
                  Sergei Maslov and
                  Alexander Partin and
                  Maulik Shukla and
                  Eric A. Stahlberg and
                  Justin M. Wozniak and
                  Hyun Seung Yoo and
                  George F. Zaki and
                  Yitan Zhu and
                  Rick Stevens},
  title        = {A cross-study analysis of drug response prediction in cancer cell
                  lines},
  journal      = {Briefings Bioinform.},
  volume       = {23},
  number       = {1},
  year         = {2022},
  url          = {https://doi.org/10.1093/bib/bbab356},
  doi          = {10.1093/BIB/BBAB356},
  timestamp    = {Tue, 07 May 2024 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bib/XiaABBGCCDDDEFG22.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ewc/ShuklaBPPM22,
  author       = {Vipin Shukla and
                  Mainak Bandyopadhyay and
                  Vivek Pandya and
                  A. Pandey and
                  Avirup Maulik},
  title        = {Artificial neural network based predictive negative hydrogen ion helicon
                  plasma source for fusion grade large sized ion source},
  journal      = {Eng. Comput.},
  volume       = {38},
  number       = {1},
  pages        = {347--364},
  year         = {2022},
  url          = {https://doi.org/10.1007/s00366-020-01060-5},
  doi          = {10.1007/S00366-020-01060-5},
  timestamp    = {Mon, 23 Oct 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/ewc/ShuklaBPPM22.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/fbinf/WallaceDNOSSZZS22,
  author       = {Zachary S. Wallace and
                  James J. Davis and
                  Anna Maria Niewiadomska and
                  Robert D. Olson and
                  Maulik Shukla and
                  Rick Stevens and
                  Yun Zhang and
                  Christian M. Zmasek and
                  Richard H. Scheuermann},
  title        = {Early detection of emerging SARS-CoV-2 variants of interest for experimental
                  evaluation},
  journal      = {Frontiers Bioinform.},
  volume       = {2},
  year         = {2022},
  url          = {https://doi.org/10.3389/fbinf.2022.1020189},
  doi          = {10.3389/FBINF.2022.1020189},
  timestamp    = {Sat, 30 Sep 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/fbinf/WallaceDNOSSZZS22.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/VanOeffelenNABD21,
  author       = {Margo VanOeffelen and
                  Marcus Nguyen and
                  Derya Aytan{-}Aktug and
                  Thomas S. Brettin and
                  Emily M. Dietrich and
                  Ronald W. Kenyon and
                  Dustin Machi and
                  Chunhong Mao and
                  Robert Olson and
                  Gordon D. Pusch and
                  Maulik Shukla and
                  Rick Stevens and
                  Veronika Vonstein and
                  Andrew S. Warren and
                  Alice R. Wattam and
                  Hyun Seung Yoo and
                  James J. Davis},
  title        = {A genomic data resource for predicting antimicrobial resistance from
                  laboratory-derived antimicrobial susceptibility phenotypes},
  journal      = {Briefings Bioinform.},
  volume       = {22},
  number       = {6},
  year         = {2021},
  url          = {https://doi.org/10.1093/bib/bbab313},
  doi          = {10.1093/BIB/BBAB313},
  timestamp    = {Sat, 30 Sep 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bib/VanOeffelenNABD21.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/PartinBEZYXJCSF21,
  author       = {Alexander Partin and
                  Thomas S. Brettin and
                  Yvonne A. Evrard and
                  Yitan Zhu and
                  Hyun Seung Yoo and
                  Fangfang Xia and
                  Songhao Jiang and
                  Austin Clyde and
                  Maulik Shukla and
                  Michael Fonstein and
                  James H. Doroshow and
                  Rick L. Stevens},
  title        = {Learning curves for drug response prediction in cancer cell lines},
  journal      = {{BMC} Bioinform.},
  volume       = {22},
  number       = {1},
  pages        = {252},
  year         = {2021},
  url          = {https://doi.org/10.1186/s12859-021-04163-y},
  doi          = {10.1186/S12859-021-04163-Y},
  timestamp    = {Sat, 30 Sep 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bmcbi/PartinBEZYXJCSF21.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/0002WABBBCCDDGG20,
  author       = {James J. Davis and
                  Alice R. Wattam and
                  Ramy K. Aziz and
                  Thomas S. Brettin and
                  Ralph Butler and
                  Rory Butler and
                  Philippe Chlenski and
                  Neal Conrad and
                  Allan Dickerman and
                  Emily M. Dietrich and
                  Joseph L. Gabbard and
                  Svetlana Gerdes and
                  Andrew Guard and
                  Ronald W. Kenyon and
                  Dustin Machi and
                  Chunhong Mao and
                  Daniel E. Murphy{-}Olson and
                  Marcus Nguyen and
                  Eric K. Nordberg and
                  Gary J. Olsen and
                  Robert Olson and
                  Jamie C. Overbeek and
                  Ross A. Overbeek and
                  Bruce D. Parrello and
                  Gordon D. Pusch and
                  Maulik Shukla and
                  Chris Thomas and
                  Margo VanOeffelen and
                  Veronika Vonstein and
                  Andrew S. Warren and
                  Fangfang Xia and
                  Dawen Xie and
                  Hyun Seung Yoo and
                  Rick Stevens},
  title        = {The {PATRIC} Bioinformatics Resource Center: expanding data and analysis
                  capabilities},
  journal      = {Nucleic Acids Res.},
  volume       = {48},
  number       = {Database-Issue},
  pages        = {D606--D612},
  year         = {2020},
  url          = {https://doi.org/10.1093/nar/gkz943},
  doi          = {10.1093/NAR/GKZ943},
  timestamp    = {Sat, 30 Sep 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/nar/0002WABBBCCDDGG20.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/NguyenOSVD20,
  author       = {Marcus Nguyen and
                  Robert Olson and
                  Maulik Shukla and
                  Margo VanOeffelen and
                  James J. Davis},
  title        = {Predicting antimicrobial resistance using conserved genes},
  journal      = {PLoS Comput. Biol.},
  volume       = {16},
  number       = {10},
  year         = {2020},
  url          = {https://doi.org/10.1371/journal.pcbi.1008319},
  doi          = {10.1371/JOURNAL.PCBI.1008319},
  timestamp    = {Sat, 30 Sep 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/ploscb/NguyenOSVD20.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2005-09572,
  author       = {Yitan Zhu and
                  Thomas S. Brettin and
                  Yvonne A. Evrard and
                  Alexander Partin and
                  Fangfang Xia and
                  Maulik Shukla and
                  Hyun Seung Yoo and
                  James H. Doroshow and
                  Rick Stevens},
  title        = {Ensemble Transfer Learning for the Prediction of Anti-Cancer Drug
                  Response},
  journal      = {CoRR},
  volume       = {abs/2005.09572},
  year         = {2020},
  url          = {https://arxiv.org/abs/2005.09572},
  eprinttype    = {arXiv},
  eprint       = {2005.09572},
  timestamp    = {Fri, 22 May 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2005-09572.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2011-12466,
  author       = {Alexander Partin and
                  Thomas S. Brettin and
                  Yvonne A. Evrard and
                  Yitan Zhu and
                  Hyun Seung Yoo and
                  Fangfang Xia and
                  Songhao Jiang and
                  Austin Clyde and
                  Maulik Shukla and
                  Michael Fonstein and
                  James H. Doroshow and
                  Rick Stevens},
  title        = {Learning Curves for Drug Response Prediction in Cancer Cell Lines},
  journal      = {CoRR},
  volume       = {abs/2011.12466},
  year         = {2020},
  url          = {https://arxiv.org/abs/2011.12466},
  eprinttype    = {arXiv},
  eprint       = {2011.12466},
  timestamp    = {Tue, 01 Dec 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2011-12466.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/AntonopoulosAAB19,
  author       = {Dionysios A. Antonopoulos and
                  Rida Assaf and
                  Ramy Karam Aziz and
                  Thomas S. Brettin and
                  Christopher Bun and
                  Neal Conrad and
                  James J. Davis and
                  Emily M. Dietrich and
                  Terry Disz and
                  Svetlana Gerdes and
                  Ronald W. Kenyon and
                  Dustin Machi and
                  Chunhong Mao and
                  Daniel E. Murphy{-}Olson and
                  Eric K. Nordberg and
                  Gary J. Olsen and
                  Robert Olson and
                  Ross A. Overbeek and
                  Bruce D. Parrello and
                  Gordon D. Pusch and
                  John Santerre and
                  Maulik Shukla and
                  Rick L. Stevens and
                  Margo VanOeffelen and
                  Veronika Vonstein and
                  Andrew S. Warren and
                  Alice R. Wattam and
                  Fangfang Xia and
                  Hyun Seung Yoo},
  title        = {{PATRIC} as a unique resource for studying antimicrobial resistance},
  journal      = {Briefings Bioinform.},
  volume       = {20},
  number       = {4},
  pages        = {1094--1102},
  year         = {2019},
  url          = {https://doi.org/10.1093/bib/bbx083},
  doi          = {10.1093/BIB/BBX083},
  timestamp    = {Sat, 30 Sep 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bib/AntonopoulosAAB19.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/XiaSBGCAMHDESS18,
  author       = {Fangfang Xia and
                  Maulik Shukla and
                  Thomas S. Brettin and
                  Cristina Garcia{-}Cardona and
                  Judith D. Cohn and
                  Jonathan E. Allen and
                  Sergei Maslov and
                  Susan L. Holbeck and
                  James H. Doroshow and
                  Yvonne A. Evrard and
                  Eric A. Stahlberg and
                  Rick L. Stevens},
  title        = {Predicting tumor cell line response to drug pairs with deep learning},
  journal      = {{BMC} Bioinform.},
  volume       = {19-S},
  number       = {18},
  pages        = {71--79},
  year         = {2018},
  url          = {https://doi.org/10.1186/s12859-018-2509-3},
  doi          = {10.1186/S12859-018-2509-3},
  timestamp    = {Sat, 30 Sep 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bmcbi/XiaSBGCAMHDESS18.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/WattamDABBBCDDG17,
  author       = {Alice R. Wattam and
                  James J. Davis and
                  Rida Assaf and
                  S{\'{e}}bastien Boisvert and
                  Thomas S. Brettin and
                  Christopher Bun and
                  Neal Conrad and
                  Emily M. Dietrich and
                  Terry Disz and
                  Joseph L. Gabbard and
                  Svetlana Gerdes and
                  Christopher S. Henry and
                  Ronald W. Kenyon and
                  Dustin Machi and
                  Chunhong Mao and
                  Eric K. Nordberg and
                  Gary J. Olsen and
                  Daniel E. Murphy{-}Olson and
                  Robert Olson and
                  Ross A. Overbeek and
                  Bruce D. Parrello and
                  Gordon D. Pusch and
                  Maulik Shukla and
                  Veronika Vonstein and
                  Andrew S. Warren and
                  Fangfang Xia and
                  Hyun Seung Yoo and
                  Rick L. Stevens},
  title        = {Improvements to PATRIC, the all-bacterial Bioinformatics Database
                  and Analysis Resource Center},
  journal      = {Nucleic Acids Res.},
  volume       = {45},
  number       = {Database-Issue},
  pages        = {D535--D542},
  year         = {2017},
  url          = {https://doi.org/10.1093/nar/gkw1017},
  doi          = {10.1093/NAR/GKW1017},
  timestamp    = {Sat, 30 Sep 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/nar/WattamDABBBCDDG17.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MaoAWWSYS15,
  author       = {Chunhong Mao and
                  David Abraham and
                  Alice R. Wattam and
                  Meredith J. C. Wilson and
                  Maulik Shukla and
                  Hyun Seung Yoo and
                  Bruno W. S. Sobral},
  title        = {Curation, integration and visualization of bacterial virulence factors
                  in {PATRIC}},
  journal      = {Bioinform.},
  volume       = {31},
  number       = {2},
  pages        = {252--258},
  year         = {2015},
  url          = {https://doi.org/10.1093/bioinformatics/btu631},
  doi          = {10.1093/BIOINFORMATICS/BTU631},
  timestamp    = {Sat, 30 Sep 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/MaoAWWSYS15.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WarrenABDEGHHLM15,
  author       = {Andrew S. Warren and
                  Cristina Aurrecoechea and
                  Brian P. Brunk and
                  Prerak Desai and
                  Scott J. Emrich and
                  Gloria I. Giraldo{-}Calder{\'{o}}n and
                  Omar S. Harb and
                  Deborah Hix and
                  Daniel Lawson and
                  Dustin Machi and
                  Chunhong Mao and
                  Michael McClelland and
                  Eric K. Nordberg and
                  Maulik Shukla and
                  Leslie B. Vosshall and
                  Alice R. Wattam and
                  Rebecca Will and
                  Hyun Seung Yoo and
                  Bruno W. S. Sobral},
  title        = {RNA-Rocket: an RNA-Seq analysis resource for infectious disease research},
  journal      = {Bioinform.},
  volume       = {31},
  number       = {9},
  pages        = {1496--1498},
  year         = {2015},
  url          = {https://doi.org/10.1093/bioinformatics/btv002},
  doi          = {10.1093/BIOINFORMATICS/BTV002},
  timestamp    = {Sat, 30 Sep 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/WarrenABDEGHHLM15.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/OverbeekOPODDEGPSVWXS14,
  author       = {Ross A. Overbeek and
                  Robert Olson and
                  Gordon D. Pusch and
                  Gary J. Olsen and
                  James J. Davis and
                  Terry Disz and
                  Robert A. Edwards and
                  Svetlana Gerdes and
                  Bruce D. Parrello and
                  Maulik Shukla and
                  Veronika Vonstein and
                  Alice R. Wattam and
                  Fangfang Xia and
                  Rick Stevens},
  title        = {The {SEED} and the Rapid Annotation of microbial genomes using Subsystems
                  Technology {(RAST)}},
  journal      = {Nucleic Acids Res.},
  volume       = {42},
  number       = {Database-Issue},
  pages        = {206--214},
  year         = {2014},
  url          = {https://doi.org/10.1093/nar/gkt1226},
  doi          = {10.1093/NAR/GKT1226},
  timestamp    = {Sat, 30 Sep 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/nar/OverbeekOPODDEGPSVWXS14.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/WattamADDDGGGHKMMNOOPSSSSVWWWYZZS14,
  author       = {Alice R. Wattam and
                  David Abraham and
                  Oral Dalay and
                  Terry Disz and
                  Timothy Driscoll and
                  Joseph L. Gabbard and
                  Joseph J. Gillespie and
                  Roger Gough and
                  Deborah Hix and
                  Ronald W. Kenyon and
                  Dustin Machi and
                  Chunhong Mao and
                  Eric K. Nordberg and
                  Robert Olson and
                  Ross A. Overbeek and
                  Gordon D. Pusch and
                  Maulik Shukla and
                  Julie Schulman and
                  Rick L. Stevens and
                  Daniel E. Sullivan and
                  Veronika Vonstein and
                  Andrew S. Warren and
                  Rebecca Will and
                  Meredith J. C. Wilson and
                  Hyun Seung Yoo and
                  Chengdong Zhang and
                  Yan Zhang and
                  Bruno W. S. Sobral},
  title        = {PATRIC, the bacterial bioinformatics database and analysis resource},
  journal      = {Nucleic Acids Res.},
  volume       = {42},
  number       = {Database-Issue},
  pages        = {581--591},
  year         = {2014},
  url          = {https://doi.org/10.1093/nar/gkt1099},
  doi          = {10.1093/NAR/GKT1099},
  timestamp    = {Sat, 30 Sep 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/nar/WattamADDDGGGHKMMNOOPSSSSVWWWYZZS14.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DriscollGMDSFHBS11,
  author       = {Timothy Driscoll and
                  Joseph L. Gabbard and
                  Chunhong Mao and
                  Oral Dalay and
                  Maulik Shukla and
                  Clark C. Freifeld and
                  Anne Gatewood Hoen and
                  John S. Brownstein and
                  Bruno W. S. Sobral},
  title        = {Integration and visualization of host-pathogen data related to infectious
                  diseases},
  journal      = {Bioinform.},
  volume       = {27},
  number       = {16},
  pages        = {2279--2287},
  year         = {2011},
  url          = {https://doi.org/10.1093/bioinformatics/btr391},
  doi          = {10.1093/BIOINFORMATICS/BTR391},
  timestamp    = {Sat, 09 Apr 2022 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/DriscollGMDSFHBS11.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/biostec/SobralMSSZ11,
  author       = {Bruno W. S. Sobral and
                  Chunhong Mao and
                  Maulik Shukla and
                  Daniel E. Sullivan and
                  Chengdong Zhang},
  editor       = {Ana L. N. Fred and
                  Joaquim Filipe and
                  Hugo Gamboa},
  title        = {Informatics-Driven Infectious Disease Research},
  booktitle    = {Biomedical Engineering Systems and Technologies - 4th International
                  Joint Conference, {BIOSTEC} 2011, Rome, Italy, January 26-29, 2011,
                  Revised Selected Papers},
  series       = {Communications in Computer and Information Science},
  volume       = {273},
  pages        = {3--11},
  publisher    = {Springer},
  year         = {2011},
  url          = {https://doi.org/10.1007/978-3-642-29752-6\_1},
  doi          = {10.1007/978-3-642-29752-6\_1},
  timestamp    = {Sun, 25 Oct 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/conf/biostec/SobralMSSZ11.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/SnyderKLNKSSTXYZDDGHHHJKMMNPSYGGHABBKMRVCCDEKWSS07,
  author       = {E. E. Snyder and
                  N. Kampanya and
                  J. Lu and
                  Eric K. Nordberg and
                  H. R. Karur and
                  Maulik Shukla and
                  Jeetendra Soneja and
                  Y. Tian and
                  Tian Xue and
                  Hyun Seung Yoo and
                  Fengkai Zhang and
                  C. Dharmanolla and
                  N. V. Dongre and
                  Joseph J. Gillespie and
                  J. Hamelius and
                  M. Hance and
                  K. I. Huntington and
                  D. Jukneliene and
                  J. Koziski and
                  L. Mackasmiel and
                  S. P. Mane and
                  V. Nguyen and
                  A. Purkayastha and
                  J. Shallom and
                  G. Yu and
                  Y. Guo and
                  Joseph L. Gabbard and
                  Deborah Hix and
                  A. F. Azad and
                  S. C. Baker and
                  S. M. Boyle and
                  Y. Khudyakov and
                  X. J. Meng and
                  C. Rupprecht and
                  J. Vinje and
                  Oswald Crasta and
                  M. J. Czar and
                  Allan Dickerman and
                  J. Dana Eckart and
                  Ron Kenyon and
                  Rebecca Will and
                  Jo{\~{a}}o C. Setubal and
                  Bruno W. S. Sobral},
  title        = {{PATRIC:} The {VBI} PathoSystems Resource Integration Center},
  journal      = {Nucleic Acids Res.},
  volume       = {35},
  number       = {Database-Issue},
  pages        = {401--406},
  year         = {2007},
  url          = {https://doi.org/10.1093/nar/gkl858},
  doi          = {10.1093/NAR/GKL858},
  timestamp    = {Sat, 30 Sep 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/nar/SnyderKLNKSSTXYZDDGHHHJKMMNPSYGGHABBKMRVCCDEKWSS07.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ipps/SiosonWVESKRHGCKW03,
  author       = {Allan A. Sioson and
                  Jonathan I. Watkinson and
                  Cecilia Vasquez{-}Robinet and
                  Margaret Ellis and
                  Maulik Shukla and
                  Deept Kumar and
                  Naren Ramakrishnan and
                  Lenwood S. Heath and
                  Ruth Grene and
                  Boris I. Chevone and
                  Karen Kafadar and
                  Layne T. Watson},
  title        = {Expresso and Chips: Creating a Next Generation Microarray Experiment
                  Management System},
  booktitle    = {17th International Parallel and Distributed Processing Symposium {(IPDPS}
                  2003), 22-26 April 2003, Nice, France, CD-ROM/Abstracts Proceedings},
  pages        = {209},
  publisher    = {{IEEE} Computer Society},
  year         = {2003},
  url          = {https://doi.org/10.1109/IPDPS.2003.1213384},
  doi          = {10.1109/IPDPS.2003.1213384},
  timestamp    = {Mon, 15 Apr 2024 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/conf/ipps/SiosonWVESKRHGCKW03.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/vissym/SomervellMNS02,
  author       = {Jacob P. Somervell and
                  D. Scott McCrickard and
                  Chris North and
                  Maulik Shukla},
  editor       = {David S. Ebert and
                  Pere Brunet and
                  Isabel Navazo},
  title        = {An Evaluation of Information Visualization in Attention-Limited Environments},
  booktitle    = {4th Joint Eurographics - {IEEE} {TCVG} Symposium on Visualization,
                  VisSym 2002, Barcelona, Spain, May 27-29, 2002},
  pages        = {211--216},
  publisher    = {Eurographics Association},
  year         = {2002},
  url          = {https://doi.org/10.2312/VisSym/VisSym02/211-216},
  doi          = {10.2312/VISSYM/VISSYM02/211-216},
  timestamp    = {Wed, 04 Nov 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/conf/vissym/SomervellMNS02.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
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