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ORCIDBibTeX records: Nima Aghaeepour
@article{DBLP:journals/npjdm/ZahedaniMVAHARTWHS24,
author = {Ashkan Dehghani Zahedani and
Tracey McLaughlin and
Arvind Veluvali and
Nima Aghaeepour and
Amir Hosseinian and
Saransh Agarwal and
Jingyi Ruan and
Shital Tripathi and
Mark Woodward and
Noosheen Hashemi and
Michael Snyder},
title = {Correction: Digital health application integrating wearable data and
behavioral patterns improves metabolic health},
journal = {npj Digit. Medicine},
volume = {7},
number = {1},
year = {2024},
url = {https://doi.org/10.1038/s41746-024-00996-y},
doi = {10.1038/S41746-024-00996-Y},
timestamp = {Fri, 08 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/npjdm/ZahedaniMVAHARTWHS24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/aaai/FlemingLHJRTBGS24,
author = {Scott L. Fleming and
Alejandro Lozano and
William J. Haberkorn and
Jenelle A. Jindal and
Eduardo Pontes Reis and
Rahul Thapa and
Louis Blankemeier and
Julian Z. Genkins and
Ethan Steinberg and
Ashwin Nayak and
Birju S. Patel and
Chia{-}Chun Chiang and
Alison Callahan and
Zepeng Huo and
Sergios Gatidis and
Scott J. Adams and
Oluseyi Fayanju and
Shreya J. Shah and
Thomas Savage and
Ethan Goh and
Akshay S. Chaudhari and
Nima Aghaeepour and
Christopher D. Sharp and
Michael A. Pfeffer and
Percy Liang and
Jonathan H. Chen and
Keith E. Morse and
Emma P. Brunskill and
Jason A. Fries and
Nigam H. Shah},
editor = {Michael J. Wooldridge and
Jennifer G. Dy and
Sriraam Natarajan},
title = {MedAlign: {A} Clinician-Generated Dataset for Instruction Following
with Electronic Medical Records},
booktitle = {Thirty-Eighth {AAAI} Conference on Artificial Intelligence, {AAAI}
2024, Thirty-Sixth Conference on Innovative Applications of Artificial
Intelligence, {IAAI} 2024, Fourteenth Symposium on Educational Advances
in Artificial Intelligence, {EAAI} 2014, February 20-27, 2024, Vancouver,
Canada},
pages = {22021--22030},
publisher = {{AAAI} Press},
year = {2024},
url = {https://doi.org/10.1609/aaai.v38i20.30205},
doi = {10.1609/AAAI.V38I20.30205},
timestamp = {Tue, 02 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/aaai/FlemingLHJRTBGS24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2401-01620,
author = {Philip Chung and
Christine T. Fong and
Andrew M. Walters and
Nima Aghaeepour and
Meliha Yetisgen and
Vikas N. O'Reilly{-}Shah},
title = {Large Language Model Capabilities in Perioperative Risk Prediction
and Prognostication},
journal = {CoRR},
volume = {abs/2401.01620},
year = {2024},
url = {https://doi.org/10.48550/arXiv.2401.01620},
doi = {10.48550/ARXIV.2401.01620},
eprinttype = {arXiv},
eprint = {2401.01620},
timestamp = {Tue, 23 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2401-01620.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/npjdm/RavindraEBPZBCSMFMSTXGASHSEA23,
author = {Neal G. Ravindra and
Camilo Espinosa and
Elo{\"{\i}}se Berson and
Thanaphong Phongpreecha and
Peinan Zhao and
Martin Becker and
Alan L. Chang and
Sayane Shome and
Ivana Maric and
Davide De Francesco and
Samson Mataraso and
Geetha Saarunya and
Melan Thuraiappah and
Lei Xue and
Brice Gaudilliere and
Martin S. Angst and
Gary M. Shaw and
Erik D. Herzog and
David K. Stevenson and
Sarah K. England and
Nima Aghaeepour},
title = {Deep representation learning identifies associations between physical
activity and sleep patterns during pregnancy and prematurity},
journal = {npj Digit. Medicine},
volume = {6},
year = {2023},
url = {https://doi.org/10.1038/s41746-023-00911-x},
doi = {10.1038/S41746-023-00911-X},
timestamp = {Tue, 02 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/npjdm/RavindraEBPZBCSMFMSTXGASHSEA23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/npjdm/ZahedaniVMAHARTWHS23,
author = {Ashkan Dehghani Zahedani and
Arvind Veluvali and
Tracey McLaughlin and
Nima Aghaeepour and
Amir Hosseinian and
Saransh Agarwal and
Jingyi Ruan and
Shital Tripathi and
Mark Woodward and
Noosheen Hashemi and
Michael Snyder},
title = {Digital health application integrating wearable data and behavioral
patterns improves metabolic health},
journal = {npj Digit. Medicine},
volume = {6},
year = {2023},
url = {https://doi.org/10.1038/s41746-023-00956-y},
doi = {10.1038/S41746-023-00956-Y},
timestamp = {Fri, 08 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/npjdm/ZahedaniVMAHARTWHS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2308-14089,
author = {Scott L. Fleming and
Alejandro Lozano and
William J. Haberkorn and
Jenelle A. Jindal and
Eduardo Pontes Reis and
Rahul Thapa and
Louis Blankemeier and
Julian Z. Genkins and
Ethan Steinberg and
Ashwin Nayak and
Birju S. Patel and
Chia{-}Chun Chiang and
Alison Callahan and
Zepeng Huo and
Sergios Gatidis and
Scott J. Adams and
Oluseyi Fayanju and
Shreya J. Shah and
Thomas Savage and
Ethan Goh and
Akshay S. Chaudhari and
Nima Aghaeepour and
Christopher D. Sharp and
Michael A. Pfeffer and
Percy Liang and
Jonathan H. Chen and
Keith E. Morse and
Emma P. Brunskill and
Jason A. Fries and
Nigam H. Shah},
title = {MedAlign: {A} Clinician-Generated Dataset for Instruction Following
with Electronic Medical Records},
journal = {CoRR},
volume = {abs/2308.14089},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2308.14089},
doi = {10.48550/ARXIV.2308.14089},
eprinttype = {arXiv},
eprint = {2308.14089},
timestamp = {Mon, 18 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2308-14089.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}
}
@article{DBLP:journals/access/RashtianTRSA21,
author = {Hootan Rashtian and
Solmaz Shariat Torbaghan and
Salar Rahili and
Michael P. Snyder and
Nima Aghaeepour},
title = {Heart Rate and {CGM} Feature Representation Diabetes Detection From
Heart Rate: Learning Joint Features of Heart Rate and Continuous Glucose
Monitors Yields Better Representations},
journal = {{IEEE} Access},
volume = {9},
pages = {83234--83240},
year = {2021},
url = {https://doi.org/10.1109/ACCESS.2021.3085544},
doi = {10.1109/ACCESS.2021.3085544},
timestamp = {Tue, 13 Jul 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/access/RashtianTRSA21.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/corr/abs-2006-01395,
author = {J. Kenneth Tay and
Nima Aghaeepour and
Trevor Hastie and
Robert Tibshirani},
title = {Feature-weighted elastic net: using "features of features"
for better prediction},
journal = {CoRR},
volume = {abs/2006.01395},
year = {2020},
url = {https://arxiv.org/abs/2006.01395},
eprinttype = {arXiv},
eprint = {2006.01395},
timestamp = {Tue, 09 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2006-01395.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}
}
@article{DBLP:journals/bioinformatics/AghaeepourSKBSC18,
author = {Nima Aghaeepour and
Erin F. Simonds and
David J. H. F. Knapp and
Robert V. Bruggner and
Karen Sachs and
Anthony Culos and
Pier Federico Gherardini and
Nikolay Samusik and
Gabriela K. Fragiadakis and
Sean Bendall and
Brice Gaudilliere and
Martin S. Angst and
Connie J. Eaves and
William A. Weiss and
Wendy J. Fantl and
Garry P. Nolan},
title = {GateFinder: projection-based gating strategy optimization for flow
and mass cytometry},
journal = {Bioinform.},
volume = {34},
number = {23},
pages = {4131--4133},
year = {2018},
url = {https://doi.org/10.1093/bioinformatics/bty430},
doi = {10.1093/BIOINFORMATICS/BTY430},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/AghaeepourSKBSC18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/psb/SamusikAB17,
author = {Nikolay Samusik and
Nima Aghaeepour and
Sean Bendall},
editor = {Russ B. Altman and
A. Keith Dunker and
Lawrence Hunter and
Marylyn D. Ritchie and
Teri E. Klein},
title = {Session Introduction},
booktitle = {Biocomputing 2017: Proceedings of the Pacific Symposium, Kohala Coast,
Hawaii, USA, January 3-7, 2017},
pages = {557--563},
year = {2017},
url = {http://psb.stanford.edu/psb-online/proceedings/psb17/intro-single.pdf},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/psb/SamusikAB17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ONeillAPHKDB15,
author = {Kieran O'Neill and
Nima Aghaeepour and
Jeremy Parker and
Donna Hogge and
Aly Karsan and
Bakul Dalal and
Ryan Remy Brinkman},
title = {Deep profiling of multitube flow cytometry data},
journal = {Bioinform.},
volume = {31},
number = {10},
pages = {1623--1631},
year = {2015},
url = {https://doi.org/10.1093/bioinformatics/btv008},
doi = {10.1093/BIOINFORMATICS/BTV008},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ONeillAPHKDB15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ONeillJAHB14,
author = {Kieran O'Neill and
Adrin Jalali and
Nima Aghaeepour and
Holger H. Hoos and
Ryan Remy Brinkman},
title = {Enhanced flowType/RchyOptimyx: a Bioconductor pipeline for discovery
in high-dimensional cytometry data},
journal = {Bioinform.},
volume = {30},
number = {9},
pages = {1329--1330},
year = {2014},
url = {https://doi.org/10.1093/bioinformatics/btt770},
doi = {10.1093/BIOINFORMATICS/BTT770},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ONeillJAHB14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/AghaeepourH13,
author = {Nima Aghaeepour and
Holger H. Hoos},
title = {Ensemble-based prediction of {RNA} secondary structures},
journal = {{BMC} Bioinform.},
volume = {14},
pages = {139},
year = {2013},
url = {https://doi.org/10.1186/1471-2105-14-139},
doi = {10.1186/1471-2105-14-139},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/AghaeepourH13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/ONeillASB13,
author = {Kieran O'Neill and
Nima Aghaeepour and
Josef Spidlen and
Ryan Remy Brinkman},
title = {Flow Cytometry Bioinformatics},
journal = {PLoS Comput. Biol.},
volume = {9},
number = {12},
year = {2013},
url = {https://doi.org/10.1371/journal.pcbi.1003365},
doi = {10.1371/JOURNAL.PCBI.1003365},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/ONeillASB13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/AghaeepourCGOZJHRB12,
author = {Nima Aghaeepour and
Pratip K. Chattopadhyay and
Anuradha Ganesan and
Kieran O'Neill and
Habil Zare and
Adrin Jalali and
Holger H. Hoos and
Mario Roederer and
Ryan Remy Brinkman},
title = {Early immunologic correlates of {HIV} protection can be identified
from computational analysis of complex multivariate T-cell flow cytometry
assays},
journal = {Bioinform.},
volume = {28},
number = {7},
pages = {1009--1016},
year = {2012},
url = {https://doi.org/10.1093/bioinformatics/bts082},
doi = {10.1093/BIOINFORMATICS/BTS082},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/AghaeepourCGOZJHRB12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@incollection{DBLP:series/sci/KhanlooDAM09,
author = {Bahman Yari Saeed Khanloo and
Daryanaz Dargahi and
Nima Aghaeepour and
Ali Masoudi{-}Nejad},
editor = {Ajith Abraham and
Aboul Ella Hassanien and
Andr{\'{e}} Carlos Ponce de Leon Ferreira de Carvalho and
V{\'{a}}clav Sn{\'{a}}sel},
title = {Support Vector Clustering: From Local Constraint to Global Stability},
booktitle = {Foundations of Computational Intelligence - Volume 6: Data Mining},
series = {Studies in Computational Intelligence},
volume = {206},
pages = {209--227},
publisher = {Springer},
year = {2009},
url = {https://doi.org/10.1007/978-3-642-01091-0\_10},
doi = {10.1007/978-3-642-01091-0\_10},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/series/sci/KhanlooDAM09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/robocup/DashtiAABDDGKPS05,
author = {HesamAddin Dashti and
Nima Aghaeepour and
Sahar Asadi and
Meysam Bastani and
Zahra Delafkar and
Fatemeh Miri Disfani and
Serveh Ghaderi and
Shahin Kamali and
Sepideh Pashami and
Alireza Siahpirani},
editor = {Ansgar Bredenfeld and
Adam Jacoff and
Itsuki Noda and
Yasutake Takahashi},
title = {Dynamic Positioning Based on Voronoi Cells {(DPVC)}},
booktitle = {RoboCup 2005: Robot Soccer World Cup {IX}},
series = {Lecture Notes in Computer Science},
volume = {4020},
pages = {219--229},
publisher = {Springer},
year = {2005},
url = {https://doi.org/10.1007/11780519\_20},
doi = {10.1007/11780519\_20},
timestamp = {Thu, 23 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/robocup/DashtiAABDDGKPS05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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