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ORCIDBibTeX records: Natalie Stanley
@article{DBLP:journals/bmcbi/ShahirSP24,
author = {Jamshaid A. Shahir and
Natalie Stanley and
Jeremy E. Purvis},
title = {Cellograph: a semi-supervised approach to analyzing multi-condition
single-cell RNA-sequencing data using graph neural networks},
journal = {{BMC} Bioinform.},
volume = {25},
number = {1},
pages = {25},
year = {2024},
url = {https://doi.org/10.1186/s12859-024-05641-9},
doi = {10.1186/S12859-024-05641-9},
timestamp = {Fri, 19 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/ShahirSP24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ncs/0003NESFBBCSCFF23,
author = {Martin Becker and
Huda Nassar and
Camilo Espinosa and
Ina A. Stelzer and
Dorien Feyaerts and
Elo{\"{\i}}se Berson and
Neda Hajiakhoond Bidoki and
Alan L. Chang and
Geetha Saarunya and
Anthony Culos and
Davide De Francesco and
Ramin Fallahzadeh and
Qun Liu and
Yeasul Kim and
Ivana Maric and
Samson Mataraso and
Seyedeh Neelufar Payrovnaziri and
Thanaphong Phongpreecha and
Neal G. Ravindra and
Natalie Stanley and
Sayane Shome and
Yuqi Tan and
Melan Thuraiappah and
Maria Xenochristou and
Lei Xue and
Gary M. Shaw and
David K. Stevenson and
Martin S. Angst and
Brice Gaudilliere and
Nima Aghaeepour},
title = {Large-scale correlation network construction for unraveling the coordination
of complex biological systems},
journal = {Nat. Comput. Sci.},
volume = {3},
number = {4},
pages = {346--359},
year = {2023},
url = {https://doi.org/10.1038/s43588-023-00429-y},
doi = {10.1038/S43588-023-00429-Y},
timestamp = {Mon, 08 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ncs/0003NESFBBCSCFF23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/patterns/MaricCMSFHTSWTE22,
author = {Ivana Maric and
K{\'{e}}vin Contrepois and
Mira N. Moufarrej and
Ina A. Stelzer and
Dorien Feyaerts and
Xiaoyuan Han and
Andy Tang and
Natalie Stanley and
Ronald J. Wong and
Gavin M. Traber and
Mathew Ellenberger and
Alan L. Chang and
Ramin Fallahzadeh and
Huda Nassar and
Martin Becker and
Maria Xenochristou and
Camilo Espinosa and
Davide De Francesco and
Mohammad S. Ghaemi and
Elizabeth K. Costello and
Anthony Culos and
Xuefeng Bruce Ling and
Karl G. Sylvester and
Gary L. Darmstadt and
Virginia D. Winn and
Gary M. Shaw and
David A. Relman and
Stephen R. Quake and
Martin S. Angst and
Michael P. Snyder and
David K. Stevenson and
Brice Gaudilliere and
Nima Aghaeepour},
title = {Early prediction and longitudinal modeling of preeclampsia from multiomics},
journal = {Patterns},
volume = {3},
number = {12},
pages = {100655},
year = {2022},
url = {https://doi.org/10.1016/j.patter.2022.100655},
doi = {10.1016/J.PATTER.2022.100655},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/patterns/MaricCMSFHTSWTE22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bcb/ShanBYRSO22,
author = {Siyuan Shan and
Vishal Athreya Baskaran and
Haidong Yi and
Jolene Ranek and
Natalie Stanley and
Junier B. Oliva},
title = {Transparent single-cell set classification with kernel mean embeddings},
booktitle = {{BCB} '22: 13th {ACM} International Conference on Bioinformatics,
Computational Biology and Health Informatics, Northbrook, Illinois,
USA, August 7 - 10, 2022},
pages = {25:1--25:10},
publisher = {{ACM}},
year = {2022},
url = {https://doi.org/10.1145/3535508.3545538},
doi = {10.1145/3535508.3545538},
timestamp = {Mon, 01 Aug 2022 11:48:53 +0200},
biburl = {https://dblp.org/rec/conf/bcb/ShanBYRSO22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bcb/BaskaranRSSO22,
author = {Vishal Athreya Baskaran and
Jolene Ranek and
Siyuan Shan and
Natalie Stanley and
Junier B. Oliva},
title = {Distribution-based sketching of single-cell samples},
booktitle = {{BCB} '22: 13th {ACM} International Conference on Bioinformatics,
Computational Biology and Health Informatics, Northbrook, Illinois,
USA, August 7 - 10, 2022},
pages = {26:1--26:10},
publisher = {{ACM}},
year = {2022},
url = {https://doi.org/10.1145/3535508.3545539},
doi = {10.1145/3535508.3545539},
timestamp = {Mon, 01 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/bcb/BaskaranRSSO22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bcb/YiS22,
author = {Haidong Yi and
Natalie Stanley},
title = {CytoEMD: detecting and visualizing between-sample variation in relation
to phenotype with earth mover's distance},
booktitle = {{BCB} '22: 13th {ACM} International Conference on Bioinformatics,
Computational Biology and Health Informatics, Northbrook, Illinois,
USA, August 7 - 10, 2022},
pages = {28:1--28:14},
publisher = {{ACM}},
year = {2022},
url = {https://doi.org/10.1145/3535508.3545525},
doi = {10.1145/3535508.3545525},
timestamp = {Mon, 01 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/bcb/YiS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2201-07322,
author = {Siyuan Shan and
Vishal Baskaran and
Haidong Yi and
Jolene Ranek and
Natalie Stanley and
Junier Oliva},
title = {Interpretable Single-Cell Set Classification with Kernel Mean Embeddings},
journal = {CoRR},
volume = {abs/2201.07322},
year = {2022},
url = {https://arxiv.org/abs/2201.07322},
eprinttype = {arXiv},
eprint = {2201.07322},
timestamp = {Fri, 21 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2201-07322.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2207-00584,
author = {Vishal Athreya Baskaran and
Jolene Ranek and
Siyuan Shan and
Natalie Stanley and
Junier B. Oliva},
title = {Distribution-based Sketching of Single-Cell Samples},
journal = {CoRR},
volume = {abs/2207.00584},
year = {2022},
url = {https://doi.org/10.48550/arXiv.2207.00584},
doi = {10.48550/ARXIV.2207.00584},
eprinttype = {arXiv},
eprint = {2207.00584},
timestamp = {Wed, 06 Jul 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2207-00584.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bcb/YiS21,
author = {Haidong Yi and
Natalie Stanley},
editor = {Hongmei Jiang and
Xiuzhen Huang and
Jiajie Zhang},
title = {CytoSet: predicting clinical outcomes via set-modeling of cytometry
data},
booktitle = {{BCB} '21: 12th {ACM} International Conference on Bioinformatics,
Computational Biology and Health Informatics, Gainesville, Florida,
USA, August 1-4, 2021},
pages = {47:1--47:8},
publisher = {{ACM}},
year = {2021},
url = {https://doi.org/10.1145/3459930.3469529},
doi = {10.1145/3459930.3469529},
timestamp = {Wed, 04 Aug 2021 13:34:07 +0200},
biburl = {https://dblp.org/rec/conf/bcb/YiS21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/natmi/CulosTSBGMFTNEX20,
author = {Anthony Culos and
Amy Tsai and
Natalie Stanley and
Martin Becker and
Mohammad Sajjad Ghaemi and
David Mcilwain and
Ramin Fallahzadeh and
Athena Tanada and
Huda Nassar and
Camilo Espinosa and
Maria Xenochristou and
Edward Ganio and
Laura Peterson and
Xiaoyuan Han and
Ina A. Stelzer and
Kazuo Ando and
Dyani Gaudilliere and
Thanaphong Phongpreecha and
Ivana Maric and
Alan L. Chang and
Gary M. Shaw and
David K. Stevenson and
Sean Bendall and
Kara L. Davis and
Wendy J. Fantl and
Garry P. Nolan and
Trevor Hastie and
Robert Tibshirani and
Martin S. Angst and
Brice Gaudilliere and
Nima Aghaeepour},
title = {Integration of mechanistic immunological knowledge into a machine
learning pipeline improves predictions},
journal = {Nat. Mach. Intell.},
volume = {2},
number = {10},
pages = {619--628},
year = {2020},
url = {https://doi.org/10.1038/s42256-020-00232-8},
doi = {10.1038/S42256-020-00232-8},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/natmi/CulosTSBGMFTNEX20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ans/StanleyBKNM19,
author = {Natalie Stanley and
Thomas Bonacci and
Roland Kwitt and
Marc Niethammer and
Peter J. Mucha},
title = {Stochastic block models with multiple continuous attributes},
journal = {Appl. Netw. Sci.},
volume = {4},
number = {1},
pages = {54:1--54:22},
year = {2019},
url = {https://doi.org/10.1007/s41109-019-0170-z},
doi = {10.1007/S41109-019-0170-Z},
timestamp = {Sat, 09 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ans/StanleyBKNM19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GhaemiDCCNLLRMR19,
author = {Mohammad Sajjad Ghaemi and
Daniel B. DiGiulio and
K{\'{e}}vin Contrepois and
Benjamin J. Callahan and
Thuy T. M. Ngo and
Brittany Lee{-}McMullen and
Benoit Lehallier and
Anna Robaczewska and
David Mcilwain and
Yael Rosenberg{-}Hasson and
Ronald J. Wong and
Cecele Quaintance and
Anthony Culos and
Natalie Stanley and
Athena Tanada and
Amy Tsai and
Dyani Gaudilliere and
Edward Ganio and
Xiaoyuan Han and
Kazuo Ando and
Leslie McNeil and
Martha Tingle and
Paul H. Wise and
Ivana Maric and
Marina Sirota and
Tony Wyss{-}Coray and
Virginia D. Winn and
Maurice L. Druzin and
Ronald Gibbs and
Gary L. Darmstadt and
David B. Lewis and
Vahid Partovi Nia and
Bruno Agard and
Robert Tibshirani and
Garry P. Nolan and
Michael P. Snyder and
David A. Relman and
Stephen R. Quake and
Gary M. Shaw and
David K. Stevenson and
Martin S. Angst and
Brice Gaudilliere and
Nima Aghaeepour},
title = {Multiomics modeling of the immunome, transcriptome, microbiome, proteome
and metabolome adaptations during human pregnancy},
journal = {Bioinform.},
volume = {35},
number = {1},
pages = {95--103},
year = {2019},
url = {https://doi.org/10.1093/bioinformatics/bty537},
doi = {10.1093/BIOINFORMATICS/BTY537},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/GhaemiDCCNLLRMR19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@phdthesis{DBLP:phd/basesearch/Stanley18,
author = {Natalie Stanley},
title = {Adapting Community Detection Approaches to Large, Multilayer, and
Attributed Networks},
school = {University of North Carolina, Chapel Hill, {USA}},
year = {2018},
url = {https://doi.org/10.17615/g4qf-w514},
doi = {10.17615/G4QF-W514},
timestamp = {Fri, 20 Jan 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/phd/basesearch/Stanley18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/miccai/ZhangSMYLS18,
author = {Han Zhang and
Natalie Stanley and
Peter J. Mucha and
Weiyan Yin and
Weili Lin and
Dinggang Shen},
editor = {Alejandro F. Frangi and
Julia A. Schnabel and
Christos Davatzikos and
Carlos Alberola{-}L{\'{o}}pez and
Gabor Fichtinger},
title = {Multi-layer Large-Scale Functional Connectome Reveals Infant Brain
Developmental Patterns},
booktitle = {Medical Image Computing and Computer Assisted Intervention - {MICCAI}
2018 - 21st International Conference, Granada, Spain, September 16-20,
2018, Proceedings, Part {III}},
series = {Lecture Notes in Computer Science},
volume = {11072},
pages = {136--144},
publisher = {Springer},
year = {2018},
url = {https://doi.org/10.1007/978-3-030-00931-1\_16},
doi = {10.1007/978-3-030-00931-1\_16},
timestamp = {Wed, 27 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/miccai/ZhangSMYLS18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1803-02726,
author = {Natalie Stanley and
Thomas Bonacci and
Roland Kwitt and
Marc Niethammer and
Peter J. Mucha},
title = {Stochastic Block Models with Multiple Continuous Attributes},
journal = {CoRR},
volume = {abs/1803.02726},
year = {2018},
url = {http://arxiv.org/abs/1803.02726},
eprinttype = {arXiv},
eprint = {1803.02726},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-1803-02726.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1805-07375,
author = {Natalie Stanley and
Marc Niethammer and
Peter J. Mucha},
title = {Testing Alignment of Node Attributes with Network Structure Through
Label Propagation},
journal = {CoRR},
volume = {abs/1805.07375},
year = {2018},
url = {http://arxiv.org/abs/1805.07375},
eprinttype = {arXiv},
eprint = {1805.07375},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-1805-07375.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/asplos/ZhangSGCS17,
author = {Rui Zhang and
Natalie Stanley and
Christopher Griggs and
Andrew Chi and
Cynthia Sturton},
editor = {Yunji Chen and
Olivier Temam and
John Carter},
title = {Identifying Security Critical Properties for the Dynamic Verification
of a Processor},
booktitle = {Proceedings of the Twenty-Second International Conference on Architectural
Support for Programming Languages and Operating Systems, {ASPLOS}
2017, Xi'an, China, April 8-12, 2017},
pages = {541--554},
publisher = {{ACM}},
year = {2017},
url = {https://doi.org/10.1145/3037697.3037734},
doi = {10.1145/3037697.3037734},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/asplos/ZhangSGCS17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/ShaiSGTM17,
author = {Saray Shai and
Natalie Stanley and
Clara Granell and
Dane Taylor and
Peter J. Mucha},
title = {Case studies in network community detection},
journal = {CoRR},
volume = {abs/1705.02305},
year = {2017},
url = {http://arxiv.org/abs/1705.02305},
eprinttype = {arXiv},
eprint = {1705.02305},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/ShaiSGTM17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/StanleyKNM17,
author = {Natalie Stanley and
Roland Kwitt and
Marc Niethammer and
Peter J. Mucha},
title = {Compressing networks with super nodes},
journal = {CoRR},
volume = {abs/1706.04110},
year = {2017},
url = {http://arxiv.org/abs/1706.04110},
eprinttype = {arXiv},
eprint = {1706.04110},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/StanleyKNM17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tnse/StanleySTM16,
author = {Natalie Stanley and
Saray Shai and
Dane Taylor and
Peter J. Mucha},
title = {Clustering Network Layers with the Strata Multilayer Stochastic Block
Model},
journal = {{IEEE} Trans. Netw. Sci. Eng.},
volume = {3},
number = {2},
pages = {95--105},
year = {2016},
url = {https://doi.org/10.1109/TNSE.2016.2537545},
doi = {10.1109/TNSE.2016.2537545},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tnse/StanleySTM16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/StanleySTM15,
author = {Natalie Stanley and
Saray Shai and
Dane Taylor and
Peter J. Mucha},
title = {Clustering Network Layers With the Strata Multilayer Stochastic Block
Model},
journal = {CoRR},
volume = {abs/1507.01826},
year = {2015},
url = {http://arxiv.org/abs/1507.01826},
eprinttype = {arXiv},
eprint = {1507.01826},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/StanleySTM15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/TaylorSSM15,
author = {Dane Taylor and
Saray Shai and
Natalie Stanley and
Peter J. Mucha},
title = {Enhanced detectability of community structure in multilayer networks
through layer aggregation},
journal = {CoRR},
volume = {abs/1511.05271},
year = {2015},
url = {http://arxiv.org/abs/1511.05271},
eprinttype = {arXiv},
eprint = {1511.05271},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/TaylorSSM15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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