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ORCIDBibTeX records: Anthony Gitter
@article{DBLP:journals/corr/abs-2401-15478,
author = {Daniel McNeela and
Frederic Sala and
Anthony Gitter},
title = {Product Manifold Representations for Learning on Biological Pathways},
journal = {CoRR},
volume = {abs/2401.15478},
year = {2024},
url = {https://doi.org/10.48550/arXiv.2401.15478},
doi = {10.48550/ARXIV.2401.15478},
eprinttype = {arXiv},
eprint = {2401.15478},
timestamp = {Thu, 08 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2401-15478.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/AlnammiLEAVGKHWG23,
author = {Moayad Alnammi and
Shengchao Liu and
Spencer S. Ericksen and
Gene E. Ananiev and
Andrew F. Voter and
Song Guo and
James L. Keck and
F. Michael Hoffmann and
Scott A. Wildman and
Anthony Gitter},
title = {Evaluating Scalable Supervised Learning for Synthesize-on-Demand Chemical
Libraries},
journal = {J. Chem. Inf. Model.},
volume = {63},
number = {17},
pages = {5513--5528},
year = {2023},
url = {https://doi.org/10.1021/acs.jcim.3c00912},
doi = {10.1021/ACS.JCIM.3C00912},
timestamp = {Wed, 01 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/AlnammiLEAVGKHWG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2302-04611,
author = {Shengchao Liu and
Yutao Zhu and
Jiarui Lu and
Zhao Xu and
Weili Nie and
Anthony Gitter and
Chaowei Xiao and
Jian Tang and
Hongyu Guo and
Anima Anandkumar},
title = {A Text-guided Protein Design Framework},
journal = {CoRR},
volume = {abs/2302.04611},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2302.04611},
doi = {10.48550/ARXIV.2302.04611},
eprinttype = {arXiv},
eprint = {2302.04611},
timestamp = {Thu, 31 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2302-04611.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/LeeGGRMTKLCSBCY22,
author = {Benjamin D. Lee and
Anthony Gitter and
Casey S. Greene and
Sebastian Raschka and
Finlay Maguire and
Alexander J. Titus and
Michael D. Kessler and
Alexandra J. Lee and
Marc G. Chevrette and
Paul Allen Stewart and
Thiago Britto{-}Borges and
Evan M. Cofer and
Kun{-}Hsing Yu and
Juan Jose Carmona and
Elana J. Fertig and
Alexandr A. Kalinin and
Brandon Signal and
Benjamin J. Lengerich and
Timothy J. Triche Jr. and
Simina M. Boca},
title = {Ten quick tips for deep learning in biology},
journal = {PLoS Comput. Biol.},
volume = {18},
number = {3},
year = {2022},
url = {https://doi.org/10.1371/journal.pcbi.1009803},
doi = {10.1371/JOURNAL.PCBI.1009803},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/LeeGGRMTKLCSBCY22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2212-05991,
author = {Chris S. Magnano and
Anthony Gitter},
title = {Graph algorithms for predicting subcellular localization at the pathway
level},
journal = {CoRR},
volume = {abs/2212.05991},
year = {2022},
url = {https://doi.org/10.48550/arXiv.2212.05991},
doi = {10.48550/ARXIV.2212.05991},
eprinttype = {arXiv},
eprint = {2212.05991},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2212-05991.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/pnas/GelmanFHRG21,
author = {Sam Gelman and
Sarah A. Fahlberg and
Pete Heinzelman and
Philip A. Romero and
Anthony Gitter},
title = {Neural networks to learn protein sequence-function relationships from
deep mutational scanning data},
journal = {Proc. Natl. Acad. Sci. {USA}},
volume = {118},
number = {48},
pages = {e2104878118},
year = {2021},
url = {https://doi.org/10.1073/pnas.2104878118},
doi = {10.1073/PNAS.2104878118},
timestamp = {Mon, 27 Dec 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/pnas/GelmanFHRG21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/jcdl/RandoBMHRRVGG21,
author = {Halie M. Rando and
Simina M. Boca and
Lucy D'Agostino McGowan and
Daniel S. Himmelstein and
Michael P. Robson and
Vincent Rubinetti and
Ryan Velazquez and
Casey S. Greene and
Anthony Gitter},
editor = {Wolf{-}Tilo Balke and
Anita de Waard and
Yuanxi Fu and
Bolin Hua and
Jodi Schneider and
Ningyuan Song and
Xiaoguang Wang},
title = {An Open-Publishing Response to the {COVID-19} Infodemic},
booktitle = {Proceedings of the Workshop on Digital Infrastructures for Scholarly
Content Objects {(DISCO} 2021) co-located with {ACM/IEEE} Joint Conference
on Digital Libraries 2021(JCDL 2021), Online (Due to the Global Pandemic),
September 30, 2021},
series = {{CEUR} Workshop Proceedings},
volume = {2976},
pages = {29--38},
publisher = {CEUR-WS.org},
year = {2021},
url = {https://ceur-ws.org/Vol-2976/paper-2.pdf},
timestamp = {Fri, 10 Mar 2023 16:22:11 +0100},
biburl = {https://dblp.org/rec/conf/jcdl/RandoBMHRRVGG21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2105-14372,
author = {Benjamin D. Lee and
Anthony Gitter and
Casey S. Greene and
Sebastian Raschka and
Finlay Maguire and
Alexander J. Titus and
Michael D. Kessler and
Alexandra J. Lee and
Marc G. Chevrette and
Paul Allen Stewart and
Thiago Britto{-}Borges and
Evan M. Cofer and
Kun{-}Hsing Yu and
Juan Jose Carmona and
Elana J. Fertig and
Alexandr A. Kalinin and
Beth Signal and
Benjamin J. Lengerich and
Timothy J. Triche Jr. and
Simina M. Boca},
title = {Ten Quick Tips for Deep Learning in Biology},
journal = {CoRR},
volume = {abs/2105.14372},
year = {2021},
url = {https://arxiv.org/abs/2105.14372},
eprinttype = {arXiv},
eprint = {2105.14372},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2105-14372.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2109-08633,
author = {Halie M. Rando and
Simina M. Boca and
Lucy D'Agostino McGowan and
Daniel S. Himmelstein and
Michael P. Robson and
Vincent Rubinetti and
Ryan Velazquez and
Casey S. Greene and
Anthony Gitter},
title = {An Open-Publishing Response to the {COVID-19} Infodemic},
journal = {CoRR},
volume = {abs/2109.08633},
year = {2021},
url = {https://arxiv.org/abs/2109.08633},
eprinttype = {arXiv},
eprint = {2109.08633},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2109-08633.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ChanderengG20,
author = {Thevaa Chandereng and
Anthony Gitter},
title = {Lag penalized weighted correlation for time series clustering},
journal = {{BMC} Bioinform.},
volume = {21},
number = {1},
pages = {21},
year = {2020},
url = {https://doi.org/10.1186/s12859-019-3324-1},
doi = {10.1186/S12859-019-3324-1},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ChanderengG20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2005-14062,
author = {David Merrell and
Anthony Gitter},
title = {Inferring Signaling Pathways with Probabilistic Programming},
journal = {CoRR},
volume = {abs/2005.14062},
year = {2020},
url = {https://arxiv.org/abs/2005.14062},
eprinttype = {arXiv},
eprint = {2005.14062},
timestamp = {Sat, 23 Jan 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2005-14062.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/LiuAEVAKHWG19,
author = {Shengchao Liu and
Moayad Alnammi and
Spencer S. Ericksen and
Andrew F. Voter and
Gene E. Ananiev and
James L. Keck and
F. Michael Hoffmann and
Scott A. Wildman and
Anthony Gitter},
title = {Practical Model Selection for Prospective Virtual Screening},
journal = {J. Chem. Inf. Model.},
volume = {59},
number = {1},
pages = {282--293},
year = {2019},
url = {https://doi.org/10.1021/acs.jcim.8b00363},
doi = {10.1021/ACS.JCIM.8B00363},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/LiuAEVAKHWG19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/MeyerLMCG19,
author = {Jesse G. Meyer and
Shengchao Liu and
Ian J. Miller and
Joshua J. Coon and
Anthony Gitter},
title = {Learning Drug Functions from Chemical Structures with Convolutional
Neural Networks and Random Forests},
journal = {J. Chem. Inf. Model.},
volume = {59},
number = {10},
pages = {4438--4449},
year = {2019},
url = {https://doi.org/10.1021/acs.jcim.9b00236},
doi = {10.1021/ACS.JCIM.9B00236},
timestamp = {Tue, 01 Jun 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/MeyerLMCG19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/HimmelsteinRSHM19,
author = {Daniel S. Himmelstein and
Vincent Rubinetti and
David R. Slochower and
Dongbo Hu and
Venkat S. Malladi and
Casey S. Greene and
Anthony Gitter},
title = {Open collaborative writing with Manubot},
journal = {PLoS Comput. Biol.},
volume = {15},
number = {6},
year = {2019},
url = {https://doi.org/10.1371/journal.pcbi.1007128},
doi = {10.1371/JOURNAL.PCBI.1007128},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/HimmelsteinRSHM19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/ZhangELAWYMGWHW19,
author = {Huikun Zhang and
Spencer S. Ericksen and
Ching{-}pei Lee and
Gene E. Ananiev and
Nathan Wlodarchak and
Peng Yu and
Julie C. Mitchell and
Anthony Gitter and
Stephen J. Wright and
F. Michael Hoffmann and
Scott A. Wildman and
Michael A. Newton},
title = {Predicting kinase inhibitors using bioactivity matrix derived informer
sets},
journal = {PLoS Comput. Biol.},
volume = {15},
number = {8},
year = {2019},
url = {https://doi.org/10.1371/journal.pcbi.1006813},
doi = {10.1371/JOURNAL.PCBI.1006813},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/ploscb/ZhangELAWYMGWHW19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/aaai/LiuLG19,
author = {Shengchao Liu and
Yingyu Liang and
Anthony Gitter},
title = {Loss-Balanced Task Weighting to Reduce Negative Transfer in Multi-Task
Learning},
booktitle = {The Thirty-Third {AAAI} Conference on Artificial Intelligence, {AAAI}
2019, The Thirty-First Innovative Applications of Artificial Intelligence
Conference, {IAAI} 2019, The Ninth {AAAI} Symposium on Educational
Advances in Artificial Intelligence, {EAAI} 2019, Honolulu, Hawaii,
USA, January 27 - February 1, 2019},
pages = {9977--9978},
publisher = {{AAAI} Press},
year = {2019},
url = {https://doi.org/10.1609/aaai.v33i01.33019977},
doi = {10.1609/AAAI.V33I01.33019977},
timestamp = {Mon, 04 Sep 2023 12:29:24 +0200},
biburl = {https://dblp.org/rec/conf/aaai/LiuLG19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/MacGilvraySCPGC18,
author = {Matthew E. MacGilvray and
Evgenia Shishkova and
Deborah Chasman and
Michael Place and
Anthony Gitter and
Joshua J. Coon and
Audrey P. Gasch},
title = {Network inference reveals novel connections in pathways regulating
growth and defense in the yeast salt response},
journal = {PLoS Comput. Biol.},
volume = {14},
number = {5},
year = {2018},
url = {https://doi.org/10.1371/journal.pcbi.1006088},
doi = {10.1371/JOURNAL.PCBI.1006088},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/MacGilvraySCPGC18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/TuncbagGKSGF16,
author = {Nurcan Tuncbag and
Sara J. C. Gosline and
Amanda J. Kedaigle and
Anthony R. Soltis and
Anthony Gitter and
Ernest Fraenkel},
title = {Network-Based Interpretation of Diverse High-Throughput Datasets through
the Omics Integrator Software Package},
journal = {PLoS Comput. Biol.},
volume = {12},
number = {4},
year = {2016},
url = {https://doi.org/10.1371/journal.pcbi.1004879},
doi = {10.1371/JOURNAL.PCBI.1004879},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/TuncbagGKSGF16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/GitterHVFA16,
author = {Anthony Gitter and
Furong Huang and
Ragupathyraj Valluvan and
Ernest Fraenkel and
Animashree Anandkumar},
title = {Unsupervised learning of transcriptional regulatory networks via latent
tree graphical models},
journal = {CoRR},
volume = {abs/1609.06335},
year = {2016},
url = {http://arxiv.org/abs/1609.06335},
eprinttype = {arXiv},
eprint = {1609.06335},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/GitterHVFA16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/JainGB14,
author = {Siddhartha Jain and
Anthony Gitter and
Ziv Bar{-}Joseph},
title = {Multitask Learning of Signaling and Regulatory Networks with Application
to Studying Human Response to Flu},
journal = {PLoS Comput. Biol.},
volume = {10},
number = {12},
year = {2014},
url = {https://doi.org/10.1371/journal.pcbi.1003943},
doi = {10.1371/JOURNAL.PCBI.1003943},
timestamp = {Thu, 18 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/ploscb/JainGB14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/psb/GitterBPBBCZF14,
author = {Anthony Gitter and
Alfredo Braunstein and
Andrea Pagnani and
Carlo Baldassi and
Christian Borgs and
Jennifer T. Chayes and
Riccardo Zecchina and
Ernest Fraenkel},
editor = {Russ B. Altman and
A. Keith Dunker and
Lawrence Hunter and
Teri E. Klein and
Marylyn D. Ritchie},
title = {Sharing Information to Reconstruct Patient-Specific Pathways in Heterogeneous
Diseases},
booktitle = {Biocomputing 2014: Proceedings of the Pacific Symposium, Kohala Coast,
Hawaii, USA, January 3-7, 2014},
pages = {39--50},
year = {2014},
url = {http://psb.stanford.edu/psb-online/proceedings/psb14/gitter.pdf},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/psb/GitterBPBBCZF14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GitterB13,
author = {Anthony Gitter and
Ziv Bar{-}Joseph},
title = {Identifying proteins controlling key disease signaling pathways},
journal = {Bioinform.},
volume = {29},
number = {13},
pages = {227--236},
year = {2013},
url = {https://doi.org/10.1093/bioinformatics/btt241},
doi = {10.1093/BIOINFORMATICS/BTT241},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/GitterB13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcsb/SchulzDGZEB12,
author = {Marcel H. Schulz and
William E. Devanny and
Anthony Gitter and
Shan Zhong and
Jason Ernst and
Ziv Bar{-}Joseph},
title = {{DREM} 2.0: Improved reconstruction of dynamic regulatory networks
from time-series expression data},
journal = {{BMC} Syst. Biol.},
volume = {6},
pages = {104},
year = {2012},
url = {https://doi.org/10.1186/1752-0509-6-104},
doi = {10.1186/1752-0509-6-104},
timestamp = {Sat, 09 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcsb/SchulzDGZEB12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/NavlakhaGB12,
author = {Saket Navlakha and
Anthony Gitter and
Ziv Bar{-}Joseph},
title = {A Network-based Approach for Predicting Missing Pathway Interactions},
journal = {PLoS Comput. Biol.},
volume = {8},
number = {8},
year = {2012},
url = {https://doi.org/10.1371/journal.pcbi.1002640},
doi = {10.1371/JOURNAL.PCBI.1002640},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/NavlakhaGB12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1108-6113,
author = {R{\'{e}}ka Albert and
Bhaskar DasGupta and
Anthony Gitter and
Gamze G{\"{u}}rsoy and
Rashmi Hegde and
Pradyut Paul and
Gowri Sangeetha Sivanathan and
Eduardo D. Sontag},
title = {A New Computationally Efficient Measure of Topological Redundancy
of Biological and Social Networks},
journal = {CoRR},
volume = {abs/1108.6113},
year = {2011},
url = {http://arxiv.org/abs/1108.6113},
eprinttype = {arXiv},
eprint = {1108.6113},
timestamp = {Fri, 02 Aug 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-1108-6113.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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