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ORCIDBibTeX records: Peter N. Robinson
@article{DBLP:journals/bioinformatics/CaufieldHEHJMKMRHRM24,
author = {J. Harry Caufield and
Harshad Hegde and
Vincent Emonet and
Nomi L. Harris and
Marcin P. Joachimiak and
Nicolas Matentzoglu and
Hyeongsik Kim and
Sierra A. T. Moxon and
Justin T. Reese and
Melissa A. Haendel and
Peter N. Robinson and
Christopher J. Mungall},
title = {Structured Prompt Interrogation and Recursive Extraction of Semantics
{(SPIRES):} a method for populating knowledge bases using zero-shot
learning},
journal = {Bioinform.},
volume = {40},
number = {3},
year = {2024},
url = {https://doi.org/10.1093/bioinformatics/btae104},
doi = {10.1093/BIOINFORMATICS/BTAE104},
timestamp = {Mon, 01 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/CaufieldHEHJMKMRHRM24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/data/SenHDHCWORNLNMWPGWBLPBHSJRKTPBNBLS24,
author = {Anando Sen and
Victoria Hedley and
Eva Degraeuwe and
Steven Hirschfeld and
Ronald Cornet and
Ramona Walls and
John Owen and
Peter N. Robinson and
Edward G. Neilan and
Thomas Liener and
Giovanni Nisato and
Neena Modi and
Simon Woodworth and
Avril Palmeri and
Ricarda Gaentzsch and
Melissa Walsh and
Teresa Berkery and
Joanne Lee and
Laura Persijn and
Kasey Baker and
Kristina An Haack and
Sonia Segovia Simon and
Julius O. B. Jacobsen and
Giorgio Reggiardo and
Melissa A. Kirwin and
Jessie Trueman and
Claudia Pansieri and
Donato Bonifazi and
Sin{\'{e}}ad Nally and
Fedele Bonifazi and
Rebecca Leary and
Volker Straub},
title = {Learning from conect4children: {A} Collaborative Approach towards
Standardisation of Disease-Specific Paediatric Research Data},
journal = {Data},
volume = {9},
number = {4},
pages = {55},
year = {2024},
url = {https://doi.org/10.3390/data9040055},
doi = {10.3390/DATA9040055},
timestamp = {Wed, 08 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/data/SenHDHCWORNLNMWPGWBLPBHSJRKTPBNBLS24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/KarlebachR24,
author = {Guy Karlebach and
Peter N. Robinson},
title = {Computing Minimal Boolean Models of Gene Regulatory Networks},
journal = {J. Comput. Biol.},
volume = {31},
number = {2},
pages = {117--127},
year = {2024},
url = {https://doi.org/10.1089/cmb.2023.0122},
doi = {10.1089/CMB.2023.0122},
timestamp = {Sat, 16 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/KarlebachR24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/midm/GrozaCGBHRMR24,
author = {Tudor Groza and
J. Harry Caufield and
Dylan Gration and
Gareth Baynam and
Melissa A. Haendel and
Peter N. Robinson and
Christopher J. Mungall and
Justin T. Reese},
title = {An evaluation of {GPT} models for phenotype concept recognition},
journal = {{BMC} Medical Informatics Decis. Mak.},
volume = {24},
number = {1},
pages = {30},
year = {2024},
url = {https://doi.org/10.1186/s12911-024-02439-w},
doi = {10.1186/S12911-024-02439-W},
timestamp = {Tue, 13 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/midm/GrozaCGBHRMR24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/biostec/NicoliniMCCMPRR24,
author = {Marco Nicolini and
Dario Malchiodi and
Alberto Cabri and
Emanuele Cavalleri and
Marco Mesiti and
Alberto Paccanaro and
Peter N. Robinson and
Justin T. Reese and
Elena Casiraghi and
Giorgio Valentini},
editor = {Maria Pedro Guarino and
Kazuhiro Hotta and
Malik Yousef and
Hui Liu and
Giovanni Saggio and
Ana L. N. Fred and
Hugo Gamboa},
title = {Fine-Tuning of Conditional Transformers Improves the Generation of
Functionally Characterized Proteins},
booktitle = {Proceedings of the 17th International Joint Conference on Biomedical
Engineering Systems and Technologies, {BIOSTEC} 2024, Volume 1, Rome,
Italy, February 21-23, 2024},
pages = {561--568},
publisher = {{SCITEPRESS}},
year = {2024},
url = {https://doi.org/10.5220/0012567900003657},
doi = {10.5220/0012567900003657},
timestamp = {Tue, 07 May 2024 20:01:01 +0200},
biburl = {https://dblp.org/rec/conf/biostec/NicoliniMCCMPRR24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KarlebachCSCHRMVR23,
author = {Guy Karlebach and
Leigh Carmody and
Jagadish Chandrabose Sundaramurthi and
Elena Casiraghi and
Peter Hansen and
Justin T. Reese and
Christopher J. Mungall and
Giorgio Valentini and
Peter N. Robinson},
title = {An expectation-maximization framework for comprehensive prediction
of isoform-specific functions},
journal = {Bioinform.},
volume = {39},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad132},
doi = {10.1093/BIOINFORMATICS/BTAD132},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/KarlebachCSCHRMVR23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GrozaWDDHBDLLR23,
author = {Tudor Groza and
Honghan Wu and
Marcel E. Dinger and
Daniel Danis and
Coleman Hilton and
Anita Bagley and
Jon R. Davids and
Ling Luo and
Zhiyong Lu and
Peter N. Robinson},
title = {Term-BLAST-like alignment tool for concept recognition in noisy clinical
texts},
journal = {Bioinform.},
volume = {39},
number = {12},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad716},
doi = {10.1093/BIOINFORMATICS/BTAD716},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/GrozaWDDHBDLLR23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biomedsem/ChanTDMSGVMRMH23,
author = {Lauren E. Chan and
Anne E. Thessen and
William D. Duncan and
Nicolas Matentzoglu and
Charles Schmitt and
Cynthia J. Grondin and
Nicole A. Vasilevsky and
Julie A. McMurry and
Peter N. Robinson and
Christopher J. Mungall and
Melissa A. Haendel},
title = {The Environmental Conditions, Treatments, and Exposures Ontology {(ECTO):}
connecting toxicology and exposure to human health and beyond},
journal = {J. Biomed. Semant.},
volume = {14},
number = {1},
pages = {3},
year = {2023},
url = {https://doi.org/10.1186/s13326-023-00283-x},
doi = {10.1186/S13326-023-00283-X},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biomedsem/ChanTDMSGVMRMH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jbi/CasiraghiWHCNETBLCCBBMSJSRRPVHW23,
author = {Elena Casiraghi and
Rachel Wong and
Margaret Hall and
Ben D. Coleman and
Marco Notaro and
Michael D. Evans and
Jena S. Tronieri and
Hannah Blau and
Bryan Laraway and
Tiffany J. Callahan and
Lauren E. Chan and
Carolyn T. Bramante and
John B. Buse and
Richard A. Moffitt and
Til Sturmer and
Steven G. Johnson and
Yu Raymond Shao and
Justin T. Reese and
Peter N. Robinson and
Alberto Paccanaro and
Giorgio Valentini and
Jared D. Huling and
Kenneth Wilkins},
title = {A method for comparing multiple imputation techniques: {A} case study
on the {U.S.} national {COVID} cohort collaborative},
journal = {J. Biomed. Informatics},
volume = {139},
pages = {104295},
year = {2023},
url = {https://doi.org/10.1016/j.jbi.2023.104295},
doi = {10.1016/J.JBI.2023.104295},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jbi/CasiraghiWHCNETBLCCBBMSJSRRPVHW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ncs/CappellettiFCRC23,
author = {Luca Cappelletti and
Tommaso Fontana and
Elena Casiraghi and
Vida Ravanmehr and
Tiffany J. Callahan and
Carlos Cano and
Marcin P. Joachimiak and
Christopher J. Mungall and
Peter N. Robinson and
Justin T. Reese and
Giorgio Valentini},
title = {{GRAPE} for fast and scalable graph processing and random-walk-based
embedding},
journal = {Nat. Comput. Sci.},
volume = {3},
number = {6},
pages = {552--568},
year = {2023},
url = {https://doi.org/10.1038/s43588-023-00465-8},
doi = {10.1038/S43588-023-00465-8},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ncs/CappellettiFCRC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/npjdm/CallahanSWZOBBBCCCDFLMMMRSTTVWZDR23,
author = {Tiffany J. Callahan and
Adrianne L. Stefanski and
Jordan M. Wyrwa and
Chenjie Zeng and
Anna Ostropolets and
Juan M. Banda and
William A. Baumgartner Jr. and
Richard D. Boyce and
Elena Casiraghi and
Ben D. Coleman and
Janine H. Collins and
Sara J. Deakyne Davies and
James A. Feinstein and
Asiyah Y. Lin and
Blake Martin and
Nicolas A. Matentzoglu and
Daniella Meeker and
Justin T. Reese and
Jessica Sinclair and
Sanya Bathla Taneja and
Katy E. Trinkley and
Nicole A. Vasilevsky and
Andrew E. Williams and
Xingmin Aaron Zhang and
Joshua C. Denny and
Patrick B. Ryan and
George Hripcsak and
Tellen D. Bennett and
Melissa A. Haendel and
Peter N. Robinson and
Lawrence E. Hunter and
Michael G. Kahn},
title = {Ontologizing health systems data at scale: making translational discovery
a reality},
journal = {npj Digit. Medicine},
volume = {6},
year = {2023},
url = {https://doi.org/10.1038/s41746-023-00830-x},
doi = {10.1038/S41746-023-00830-X},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/npjdm/CallahanSWZOBBBCCCDFLMMMRSTTVWZDR23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/iwbbio/CappellettiTFJR23,
author = {Luca Cappelletti and
Stefano Taverni and
Tommaso Fontana and
Marcin P. Joachimiak and
Justin T. Reese and
Peter N. Robinson and
Elena Casiraghi and
Giorgio Valentini},
editor = {Ignacio Rojas and
Olga Valenzuela and
Fernando Rojas Ruiz and
Luis Javier Herrera and
Francisco M. Ortu{\~{n}}o},
title = {Degree-Normalization Improves Random-Walk-Based Embedding Accuracy
in {PPI} Graphs},
booktitle = {Bioinformatics and Biomedical Engineering - 10th International Work-Conference,
{IWBBIO} 2023, Meloneras, Gran Canaria, Spain, July 12-14, 2023 Proceedings,
Part {II}},
series = {Lecture Notes in Computer Science},
volume = {13920},
pages = {372--383},
publisher = {Springer},
year = {2023},
url = {https://doi.org/10.1007/978-3-031-34960-7\_26},
doi = {10.1007/978-3-031-34960-7\_26},
timestamp = {Tue, 26 Dec 2023 17:13:20 +0100},
biburl = {https://dblp.org/rec/conf/iwbbio/CappellettiTFJR23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2302-10800,
author = {J. Harry Caufield and
Tim E. Putman and
Kevin Schaper and
Deepak R. Unni and
Harshad Hegde and
Tiffany J. Callahan and
Luca Cappelletti and
Sierra A. T. Moxon and
Vida Ravanmehr and
Seth Carbon and
Lauren E. Chan and
Katherina Cortes and
Kent A. Shefchek and
Glass Elsarboukh and
James P. Balhoff and
Tommaso Fontana and
Nicolas Matentzoglu and
Richard M. Bruskiewich and
Anne E. Thessen and
Nomi L. Harris and
Monica C. Munoz{-}Torres and
Melissa A. Haendel and
Peter N. Robinson and
Marcin P. Joachimiak and
Christopher J. Mungall and
Justin T. Reese},
title = {KG-Hub - Building and Exchanging Biological Knowledge Graphs},
journal = {CoRR},
volume = {abs/2302.10800},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2302.10800},
doi = {10.48550/ARXIV.2302.10800},
eprinttype = {arXiv},
eprint = {2302.10800},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2302-10800.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2304-02711,
author = {J. Harry Caufield and
Harshad Hegde and
Vincent Emonet and
Nomi L. Harris and
Marcin P. Joachimiak and
Nicolas Matentzoglu and
HyeongSik Kim and
Sierra A. T. Moxon and
Justin T. Reese and
Melissa A. Haendel and
Peter N. Robinson and
Christopher J. Mungall},
title = {Structured prompt interrogation and recursive extraction of semantics
{(SPIRES):} {A} method for populating knowledge bases using zero-shot
learning},
journal = {CoRR},
volume = {abs/2304.02711},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2304.02711},
doi = {10.48550/ARXIV.2304.02711},
eprinttype = {arXiv},
eprint = {2304.02711},
timestamp = {Tue, 18 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2304-02711.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2307-05727,
author = {Tiffany J. Callahan and
Ignacio J. Tripodi and
Adrianne L. Stefanski and
Luca Cappelletti and
Sanya Bathla Taneja and
Jordan M. Wyrwa and
Elena Casiraghi and
Nicolas A. Matentzoglu and
Justin T. Reese and
Jonathan C. Silverstein and
Charles Tapley Hoyt and
Richard D. Boyce and
Scott A. Malec and
Deepak R. Unni and
Marcin P. Joachimiak and
Peter N. Robinson and
Christopher J. Mungall and
Emanuele Cavalleri and
Tommaso Fontana and
Giorgio Valentini and
Marco Mesiti and
Lucas A. Gillenwater and
Brook E. Santangelo and
Nicole A. Vasilevsky and
Robert Hoehndorf and
Tellen D. Bennett and
Patrick B. Ryan and
George Hripcsak and
Michael G. Kahn and
Michael Bada and
William A. Baumgartner Jr. and
Lawrence E. Hunter},
title = {An Open-Source Knowledge Graph Ecosystem for the Life Sciences},
journal = {CoRR},
volume = {abs/2307.05727},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2307.05727},
doi = {10.48550/ARXIV.2307.05727},
eprinttype = {arXiv},
eprint = {2307.05727},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2307-05727.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2309-17169,
author = {Tudor Groza and
J. Harry Caufield and
Dylan Gration and
Gareth Baynam and
Melissa A. Haendel and
Peter N. Robinson and
Chris Mungall and
Justin T. Reese},
title = {An evaluation of {GPT} models for phenotype concept recognition},
journal = {CoRR},
volume = {abs/2309.17169},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2309.17169},
doi = {10.48550/ARXIV.2309.17169},
eprinttype = {arXiv},
eprint = {2309.17169},
timestamp = {Tue, 17 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2309-17169.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2312-00183,
author = {Emanuele Cavalleri and
Alberto Cabri and
Mauricio Soto Gomez and
Sara Bonfitto and
Paolo Perlasca and
Jessica Gliozzo and
Tiffany J. Callahan and
Justin T. Reese and
Peter N. Robinson and
Elena Casiraghi and
Giorgio Valentini and
Marco Mesiti},
title = {{RNA-KG:} An ontology-based knowledge graph for representing interactions
involving {RNA} molecules},
journal = {CoRR},
volume = {abs/2312.00183},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2312.00183},
doi = {10.48550/ARXIV.2312.00183},
eprinttype = {arXiv},
eprint = {2312.00183},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2312-00183.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/JacobsenKCRS22,
author = {Julius O. B. Jacobsen and
Catherine Kelly and
Valentina Cipriani and
Peter N. Robinson and
Damian Smedley},
title = {Evaluation of phenotype-driven gene prioritization methods for Mendelian
diseases},
journal = {Briefings Bioinform.},
volume = {23},
number = {5},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac188},
doi = {10.1093/BIB/BBAC188},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/JacobsenKCRS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jamia/ThomasFZMPWHCGW22,
author = {Jason A. Thomas and
Randi E. Foraker and
Noa Zamstein and
Jon D. Morrow and
Philip R. O. Payne and
Adam B. Wilcox and
Melissa A. Haendel and
Christopher G. Chute and
Kenneth R. Gersing and
Anita Walden and
Tellen D. Bennett and
David A. Eichmann and
Justin Guinney and
Warren A. Kibbe and
Hongfang Liu and
Emily R. Pfaff and
Peter N. Robinson and
Joel H. Saltz and
Heidi Spratt and
Justin Starren and
Christine Suver and
Chunlei Wu and
Davera Gabriel and
Stephanie S. Hong and
Kristin Kostka and
Harold P. Lehmann and
Richard A. Moffitt and
Michele Morris and
Matvey B. Palchuk and
Xiaohan Tanner Zhang and
Richard L. Zhu and
Benjamin R. C. Amor and
Mark M. Bissell and
Marshall Clark and
Andrew T. Girvin and
Adam M. Lee and
Robert T. Miller and
Kellie M. Walters and
Yooree Chae and
Connor Cook and
Alexandra Dest and
Racquel R. Dietz and
Thomas Dillon and
Patricia A. Francis and
Rafael Fuentes and
Alexis Graves and
Andrew J. Neumann and
Shawn T. O'Neil and
Usman Sheikh and
Andr{\'{e}}a M. Volz and
Elizabeth Zampino and
Christopher P. Austin and
Samuel Bozzette and
Mariam Deacy and
Nicole Garbarini and
Michael G. Kurilla and
Sam G. Michael and
Joni L. Rutter and
Meredith Temple{-}O'Connor and
Katie Rebecca Bradwell and
Amin Manna and
Nabeel Qureshi and
Mary Morrison Saltz and
Julie A. McMurry and
Carolyn T. Bramante and
Jeremy Richard Harper and
Wenndy Hernandez and
Farrukh M. Koraishy and
Federico Mariona and
Saidulu Mattapally and
Amit Saha and
Satyanarayana Vedula and
Yujuan Fu and
Nisha Mathews and
Ofer Mendelevitch},
title = {Demonstrating an approach for evaluating synthetic geospatial and
temporal epidemiologic data utility: results from analyzing {\textgreater}1.8
million SARS-CoV-2 tests in the United States National {COVID} Cohort
Collaborative {(N3C)}},
journal = {J. Am. Medical Informatics Assoc.},
volume = {29},
number = {8},
pages = {1350--1365},
year = {2022},
url = {https://doi.org/10.1093/jamia/ocac045},
doi = {10.1093/JAMIA/OCAC045},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jamia/ThomasFZMPWHCGW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jbi/YanLLVOXGSRL22,
author = {Shankai Yan and
Ling Luo and
Po{-}Ting Lai and
Daniel Veltri and
Andrew J. Oler and
Sandhya Xirasagar and
Rajarshi Ghosh and
Morgan Similuk and
Peter N. Robinson and
Zhiyong Lu},
title = {PhenoRerank: {A} re-ranking model for phenotypic concept recognition
pre-trained on human phenotype ontology},
journal = {J. Biomed. Informatics},
volume = {129},
pages = {104059},
year = {2022},
url = {https://doi.org/10.1016/j.jbi.2022.104059},
doi = {10.1016/J.JBI.2022.104059},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jbi/YanLLVOXGSRL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/SteinhausRS22,
author = {Robin Steinhaus and
Peter N. Robinson and
Dominik Seelow},
title = {FABIAN-variant: predicting the effects of {DNA} variants on transcription
factor binding},
journal = {Nucleic Acids Res.},
volume = {50},
number = {{W1}},
pages = {322--329},
year = {2022},
url = {https://doi.org/10.1093/nar/gkac393},
doi = {10.1093/NAR/GKAC393},
timestamp = {Thu, 09 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/nar/SteinhausRS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/SteinhausPSSRS22,
author = {Robin Steinhaus and
Sebastian Proft and
Evelyn Seelow and
Tobias Schalau and
Peter N. Robinson and
Dominik Seelow},
title = {Deep phenotyping: symptom annotation made simple with {SAMS}},
journal = {Nucleic Acids Res.},
volume = {50},
number = {{W1}},
pages = {677--681},
year = {2022},
url = {https://doi.org/10.1093/nar/gkac329},
doi = {10.1093/NAR/GKAC329},
timestamp = {Thu, 09 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/nar/SteinhausPSSRS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bibm/KarlebachR22,
author = {Guy Karlebach and
Peter N. Robinson},
editor = {Donald A. Adjeroh and
Qi Long and
Xinghua Mindy Shi and
Fei Guo and
Xiaohua Hu and
Srinivas Aluru and
Giri Narasimhan and
Jianxin Wang and
Mingon Kang and
Ananda Mondal and
Jin Liu},
title = {Computing Minimal Boolean Models of Gene Regulatory Networks},
booktitle = {{IEEE} International Conference on Bioinformatics and Biomedicine,
{BIBM} 2022, Las Vegas, NV, USA, December 6-8, 2022},
pages = {2519--2525},
publisher = {{IEEE}},
year = {2022},
url = {https://doi.org/10.1109/BIBM55620.2022.9995023},
doi = {10.1109/BIBM55620.2022.9995023},
timestamp = {Thu, 12 Jan 2023 09:26:28 +0100},
biburl = {https://dblp.org/rec/conf/bibm/KarlebachR22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ifip12/PetriniNGCRCV22,
author = {Alessandro Petrini and
Marco Notaro and
Jessica Gliozzo and
Tiziana Castrignan{\`{o}} and
Peter N. Robinson and
Elena Casiraghi and
Giorgio Valentini},
editor = {Ilias Maglogiannis and
Lazaros Iliadis and
John MacIntyre and
Paulo Cortez},
title = {ParSMURF-NG: {A} Machine Learning High Performance Computing System
for the Analysis of Imbalanced Big Omics Data},
booktitle = {Artificial Intelligence Applications and Innovations. {AIAI} 2022
{IFIP} {WG} 12.5 International Workshops - {MHDW} 2022, 5G-PINE 2022,
{AIBMG} 2022, ML@HC 2022, and {AIBEI} 2022, Hersonissos, Crete, Greece,
June 17-20, 2022, Proceedings},
series = {{IFIP} Advances in Information and Communication Technology},
volume = {652},
pages = {424--435},
publisher = {Springer},
year = {2022},
url = {https://doi.org/10.1007/978-3-031-08341-9\_34},
doi = {10.1007/978-3-031-08341-9\_34},
timestamp = {Wed, 05 Oct 2022 21:11:03 +0200},
biburl = {https://dblp.org/rec/conf/ifip12/PetriniNGCRCV22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2206-06444,
author = {Elena Casiraghi and
Rachel Wong and
Margaret Hall and
Ben D. Coleman and
Marco Notaro and
Michael D. Evans and
Jena S. Tronieri and
Hannah Blau and
Bryan Laraway and
Tiffany J. Callahan and
Lauren E. Chan and
Carolyn T. Bramante and
John B. Buse and
Richard A. Moffitt and
Til Sturmer and
Steven G. Johnson and
Yu Raymond Shao and
Justin T. Reese and
Peter N. Robinson and
Alberto Paccanaro and
Giorgio Valentini and
Jared D. Huling and
Kenneth Wilkins},
title = {Tell Bennet, Christopher Chute, Peter DeWitt, Kenneth Gersing, Andrew
Girvin, Melissa Haendel, Jeremy Harper, Janos Hajagos, Stephanie Hong,
Emily Pfaff, Jane Reusch, Corneliu Antoniescu, Kimberly Robaski: {A}
Methodological Framework for the Comparative Evaluation of Multiple
Imputation Methods: Multiple Imputation of Race, Ethnicity and Body
Mass Index in the {U.S.} National {COVID} Cohort Collaborative},
journal = {CoRR},
volume = {abs/2206.06444},
year = {2022},
url = {https://doi.org/10.48550/arXiv.2206.06444},
doi = {10.48550/ARXIV.2206.06444},
eprinttype = {arXiv},
eprint = {2206.06444},
timestamp = {Wed, 09 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2206-06444.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2209-04732,
author = {Tiffany J. Callahan and
Adrianne L. Stefanski and
Jordan M. Wyrwa and
Chenjie Zeng and
Anna Ostropolets and
Juan M. Banda and
William A. Baumgartner Jr. and
Richard D. Boyce and
Elena Casiraghi and
Ben D. Coleman and
Janine H. Collins and
Sara J. Deakyne Davies and
James A. Feinstein and
Melissa A. Haendel and
Asiyah Y. Lin and
Blake Martin and
Nicolas Matentzoglu and
Daniella Meeker and
Justin T. Reese and
Jessica Sinclair and
Sanya Bathla Taneja and
Katy E. Trinkley and
Nicole A. Vasilevsky and
Andrew E. Williams and
Xingman A. Zhang and
Peter N. Robinson and
Patrick B. Ryan and
George Hripcsak and
Tellen D. Bennett and
Lawrence E. Hunter and
Michael G. Kahn},
title = {Ontologizing Health Systems Data at Scale: Making Translational Discovery
a Reality},
journal = {CoRR},
volume = {abs/2209.04732},
year = {2022},
url = {https://doi.org/10.48550/arXiv.2209.04732},
doi = {10.48550/ARXIV.2209.04732},
eprinttype = {arXiv},
eprint = {2209.04732},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2209-04732.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LuoYLVOXGSRL21,
author = {Ling Luo and
Shankai Yan and
Po{-}Ting Lai and
Daniel Veltri and
Andrew J. Oler and
Sandhya Xirasagar and
Rajarshi Ghosh and
Morgan Similuk and
Peter N. Robinson and
Zhiyong Lu},
title = {PhenoTagger: a hybrid method for phenotype concept recognition using
human phenotype ontology},
journal = {Bioinform.},
volume = {37},
number = {13},
pages = {1884--1890},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab019},
doi = {10.1093/BIOINFORMATICS/BTAB019},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LuoYLVOXGSRL21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/NotaroFPGCRV21,
author = {Marco Notaro and
Marco Frasca and
Alessandro Petrini and
Jessica Gliozzo and
Elena Casiraghi and
Peter N. Robinson and
Giorgio Valentini},
title = {{HEMDAG:} a family of modular and scalable hierarchical ensemble methods
to improve Gene Ontology term prediction},
journal = {Bioinform.},
volume = {37},
number = {23},
pages = {4526--4533},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab485},
doi = {10.1093/BIOINFORMATICS/BTAB485},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/NotaroFPGCRV21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jamia/HaendelCBEGKPPR21,
author = {Melissa A. Haendel and
Christopher G. Chute and
Tellen D. Bennett and
David A. Eichmann and
Justin Guinney and
Warren A. Kibbe and
Philip R. O. Payne and
Emily R. Pfaff and
Peter N. Robinson and
Joel H. Saltz and
Heidi Spratt and
Christine Suver and
John Wilbanks and
Adam B. Wilcox and
Andrew E. Williams and
Chunlei Wu and
Clair Blacketer and
Robert L. Bradford and
James J. Cimino and
Marshall Clark and
Evan W. Colmenares and
Patricia A. Francis and
Davera Gabriel and
Alexis Graves and
Raju Hemadri and
Stephanie S. Hong and
George Hripcsak and
Dazhi Jiao and
Jeffrey G. Klann and
Kristin Kostka and
Adam M. Lee and
Harold P. Lehmann and
Lora Lingrey and
Robert T. Miller and
Michele Morris and
Shawn N. Murphy and
Karthik Natarajan and
Matvey B. Palchuk and
Usman Sheikh and
Harold Solbrig and
Shyam Visweswaran and
Anita Walden and
Kellie M. Walters and
Griffin M. Weber and
Xiaohan Tanner Zhang and
Richard L. Zhu and
Benjamin R. C. Amor and
Andrew T. Girvin and
Amin Manna and
Nabeel Qureshi and
Michael G. Kurilla and
Sam G. Michael and
Lili M. Portilla and
Joni L. Rutter and
Christopher P. Austin and
Ken R. Gersing},
title = {The National {COVID} Cohort Collaborative {(N3C):} Rationale, design,
infrastructure, and deployment},
journal = {J. Am. Medical Informatics Assoc.},
volume = {28},
number = {3},
pages = {427--443},
year = {2021},
url = {https://doi.org/10.1093/jamia/ocaa196},
doi = {10.1093/JAMIA/OCAA196},
timestamp = {Thu, 08 Sep 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jamia/HaendelCBEGKPPR21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jimaging/ScarabelliZCFPE21,
author = {Alice Scarabelli and
Massimo Zilocchi and
Elena Casiraghi and
Pierangelo Fasani and
Guido Giovanni Plensich and
Alessandro Andrea Esposito and
Elvira Stellato and
Alessandro Petrini and
Justin T. Reese and
Peter N. Robinson and
Giorgio Valentini and
Gianpaolo Carrafiello},
title = {Abdominal Computed Tomography Imaging Findings in Hospitalized {COVID-19}
Patients: {A} Year-Long Experience and Associations Revealed by Explainable
Artificial Intelligence},
journal = {J. Imaging},
volume = {7},
number = {12},
pages = {258},
year = {2021},
url = {https://doi.org/10.3390/jimaging7120258},
doi = {10.3390/JIMAGING7120258},
timestamp = {Wed, 09 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jimaging/ScarabelliZCFPE21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/0001GMCLVDBBBCC21,
author = {Sebastian K{\"{o}}hler and
Michael A. Gargano and
Nicolas Matentzoglu and
Leigh Carmody and
David Lewis{-}Smith and
Nicole A. Vasilevsky and
Daniel Danis and
Ganna Balagura and
Gareth Baynam and
Amy M. Brower and
Tiffany J. Callahan and
Christopher G. Chute and
Johanna L. Est and
Peter D. Galer and
Shiva Ganesan and
Matthias Griese and
Matthias Haimel and
Julia Pazmandi and
Marc Hanauer and
Nomi L. Harris and
Michael Hartnett and
Maximilian Hastreiter and
Fabian Hauck and
Yongqun He and
Tim Jeske and
Hugh Kearney and
Gerhard Kindle and
Christoph Klein and
Katrin Knoflach and
Roland Krause and
David Lagorce and
Julie A. McMurry and
Jillian A. Miller and
Monica C. Munoz{-}Torres and
Rebecca L. Peters and
Christina K. Rapp and
Ana Rath and
Shahmir A. Rind and
Avi Z. Rosenberg and
Michael M. Segal and
Markus G. Seidel and
Damian Smedley and
Tomer Talmy and
Yarlalu Thomas and
Samuel A. Wiafe and
Julie Xian and
Zafer Y{\"{u}}ksel and
Ingo Helbig and
Christopher J. Mungall and
Melissa A. Haendel and
Peter N. Robinson},
title = {The Human Phenotype Ontology in 2021},
journal = {Nucleic Acids Res.},
volume = {49},
number = {Database-Issue},
pages = {D1207--D1217},
year = {2021},
url = {https://doi.org/10.1093/nar/gkaa1043},
doi = {10.1093/NAR/GKAA1043},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/0001GMCLVDBBBCC21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/patterns/ReeseUCCRCSGBFB21,
author = {Justin T. Reese and
Deepak R. Unni and
Tiffany J. Callahan and
Luca Cappelletti and
Vida Ravanmehr and
Seth Carbon and
Kent A. Shefchek and
Benjamin M. Good and
James P. Balhoff and
Tommaso Fontana and
Hannah Blau and
Nicolas Matentzoglu and
Nomi L. Harris and
Monica C. Munoz{-}Torres and
Melissa A. Haendel and
Peter N. Robinson and
Marcin P. Joachimiak and
Christopher J. Mungall},
title = {{KG-COVID-19:} {A} Framework to Produce Customized Knowledge Graphs
for {COVID-19} Response},
journal = {Patterns},
volume = {2},
number = {1},
pages = {100155},
year = {2021},
url = {https://doi.org/10.1016/j.patter.2020.100155},
doi = {10.1016/J.PATTER.2020.100155},
timestamp = {Thu, 23 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/patterns/ReeseUCCRCSGBFB21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/amia/LiuSMBSBSSABCGR21,
author = {Feifan Liu and
Noha Sharafeldin and
Vithal Madhira and
Katie R. Bradwell and
Qianqian Song and
Benjamin Bates and
Yu R. Shao and
Jing Su and
Alfred Anzalone and
Timothym Bergquist and
Sarah Cutrona and
Ben S. Gerber and
Peter N. Robinson and
Justin Guinney and
Umit Topaloglu},
title = {{COVID-19} Mortality Prediction among Patients with Cancer Using a
Large National Cohort},
booktitle = {{AMIA} 2021, American Medical Informatics Association Annual Symposium,
San Diego, CA, USA, October 30, 2021 - November 3, 2021},
publisher = {{AMIA}},
year = {2021},
url = {https://knowledge.amia.org/74229-amia-1.4622266/t004-1.4626008/t004-1.4626009/3577654-1.4626223/3577343-1.4626220},
timestamp = {Wed, 17 Apr 2024 11:46:53 +0200},
biburl = {https://dblp.org/rec/conf/amia/LiuSMBSBSSABCGR21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icbo/VasilevskyTMJHR21,
author = {Nicole A. Vasilevsky and
Sabrina Toro and
Nicolas Matentzoglu and
Dazhi Jiao and
Melissa A. Haendel and
Peter N. Robinson and
Christopher J. Mungall},
editor = {Janna Hastings and
Adrien Barton},
title = {Reclassification of Infectious Disease in the Mondo Disease Ontology},
booktitle = {Proceedings of the International Conference on Biomedical Ontologies
2021 co-located with the Workshop on Ontologies for the Behavioural
and Social Sciences (OntoBess 2021) as part of the Bolzano Summer
of Knowledge {(BOSK} 2021), Bozen-Bolzano, Italy, 16-18 September,
2021},
series = {{CEUR} Workshop Proceedings},
volume = {3073},
pages = {104--109},
publisher = {CEUR-WS.org},
year = {2021},
url = {https://ceur-ws.org/Vol-3073/paper14.pdf},
timestamp = {Fri, 10 Mar 2023 16:22:23 +0100},
biburl = {https://dblp.org/rec/conf/icbo/VasilevskyTMJHR21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2101-01425,
author = {Giorgio Valentini and
Elena Casiraghi and
Luca Cappelletti and
Vida Ravanmehr and
Tommaso Fontana and
Justin T. Reese and
Peter N. Robinson},
title = {Het-node2vec: second order random walk sampling for heterogeneous
multigraphs embedding},
journal = {CoRR},
volume = {abs/2101.01425},
year = {2021},
url = {https://arxiv.org/abs/2101.01425},
eprinttype = {arXiv},
eprint = {2101.01425},
timestamp = {Mon, 02 Aug 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2101-01425.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2110-06196,
author = {Luca Cappelletti and
Tommaso Fontana and
Elena Casiraghi and
Vida Ravanmehr and
Tiffany J. Callahan and
Marcin P. Joachimiak and
Christopher J. Mungall and
Peter N. Robinson and
Justin T. Reese and
Giorgio Valentini},
title = {GraPE: fast and scalable Graph Processing and Embedding},
journal = {CoRR},
volume = {abs/2110.06196},
year = {2021},
url = {https://arxiv.org/abs/2110.06196},
eprinttype = {arXiv},
eprint = {2110.06196},
timestamp = {Fri, 22 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2110-06196.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/access/CasiraghiMTFCFE20,
author = {Elena Casiraghi and
Dario Malchiodi and
Gabriella Trucco and
Marco Frasca and
Luca Cappelletti and
Tommaso Fontana and
Alessandro Andrea Esposito and
Emanuele Avola and
Alessandro Jachetti and
Justin T. Reese and
Alessandro Rizzi and
Peter N. Robinson and
Giorgio Valentini},
title = {Explainable Machine Learning for Early Assessment of {COVID-19} Risk
Prediction in Emergency Departments},
journal = {{IEEE} Access},
volume = {8},
pages = {196299--196325},
year = {2020},
url = {https://doi.org/10.1109/ACCESS.2020.3034032},
doi = {10.1109/ACCESS.2020.3034032},
timestamp = {Mon, 02 Aug 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/access/CasiraghiMTFCFE20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/ShefchekHGMUBKC20,
author = {Kent A. Shefchek and
Nomi L. Harris and
Michael A. Gargano and
Nicolas Matentzoglu and
Deepak R. Unni and
Matthew H. Brush and
Dan Keith and
Tom Conlin and
Nicole A. Vasilevsky and
Xingmin Aaron Zhang and
James P. Balhoff and
Larry Babb and
Susan M. Bello and
Hannah Blau and
Yvonne M. Bradford and
Seth Carbon and
Leigh Carmody and
Lauren E. Chan and
Valentina Cipriani and
Alayne Cuzick and
Maria G. Della Rocca and
Nathan A. Dunn and
Shahim Essaid and
Petra Fey and
Christian A. Grove and
Jean{-}Philippe F. Gourdine and
Ada Hamosh and
Midori A. Harris and
Ingo Helbig and
Maureen E. Hoatlin and
Marcin P. Joachimiak and
Simon Jupp and
Kenneth B. Lett and
Suzanna E. Lewis and
Craig McNamara and
Zo{\"{e}} May Pendlington and
Clare Pilgrim and
Tim E. Putman and
Vida Ravanmehr and
Justin T. Reese and
Erin Rooney Riggs and
Sofia M. C. Robb and
Paola Roncaglia and
James Seager and
Erik Segerdell and
Morgan Similuk and
Andrea L. Storm and
Courtney Thaxon and
Anne E. Thessen and
Julius O. B. Jacobsen and
Julie A. McMurry and
Tudor Groza and
Sebastian K{\"{o}}hler and
Damian Smedley and
Peter N. Robinson and
Christopher J. Mungall and
Melissa A. Haendel and
Monica C. Munoz{-}Torres and
David Osumi{-}Sutherland},
title = {The Monarch Initiative in 2019: an integrative data and analytic platform
connecting phenotypes to genotypes across species},
journal = {Nucleic Acids Res.},
volume = {48},
number = {Database-Issue},
pages = {D704--D715},
year = {2020},
url = {https://doi.org/10.1093/nar/gkz997},
doi = {10.1093/NAR/GKZ997},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/ShefchekHGMUBKC20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icbo/VasilevskyEMHHR20,
author = {Nicole A. Vasilevsky and
Shahim Essaid and
Nicolas Matentzoglu and
Nomi L. Harris and
Melissa A. Haendel and
Peter N. Robinson and
Christopher J. Mungall},
editor = {Janna Hastings and
Frank Loebe},
title = {Mondo Disease Ontology: Harmonizing Disease Concepts Across the World
(short paper)},
booktitle = {Proceedings of the 11th International Conference on Biomedical Ontologies
{(ICBO)} joint with the 10th Workshop on Ontologies and Data in Life
Sciences {(ODLS)} and part of the Bolzano Summer of Knowledge (BoSK
2020), Virtual conference hosted in Bolzano, Italy, September 17,
2020},
series = {{CEUR} Workshop Proceedings},
volume = {2807},
pages = {1--2},
publisher = {CEUR-WS.org},
year = {2020},
url = {https://ceur-ws.org/Vol-2807/abstractY.pdf},
timestamp = {Fri, 10 Mar 2023 16:22:24 +0100},
biburl = {https://dblp.org/rec/conf/icbo/VasilevskyEMHHR20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2009-08478,
author = {Ling Luo and
Shankai Yan and
Po{-}Ting Lai and
Daniel Veltri and
Andrew J. Oler and
Sandhya Xirasagar and
Rajarshi Ghosh and
Morgan Similuk and
Peter N. Robinson and
Zhiyong Lu},
title = {PhenoTagger: {A} Hybrid Method for Phenotype Concept Recognition using
Human Phenotype Ontology},
journal = {CoRR},
volume = {abs/2009.08478},
year = {2020},
url = {https://arxiv.org/abs/2009.08478},
eprinttype = {arXiv},
eprint = {2009.08478},
timestamp = {Wed, 01 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2009-08478.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/GourdineBVSKMMM19,
author = {Jean{-}Philippe F. Gourdine and
Matthew H. Brush and
Nicole A. Vasilevsky and
Kent A. Shefchek and
Sebastian K{\"{o}}hler and
Nicolas Matentzoglu and
Monica C. Munoz{-}Torres and
Julie A. McMurry and
Xingmin Aaron Zhang and
Peter N. Robinson and
Melissa A. Haendel},
title = {Representing glycophenotypes: semantic unification of glycobiology
resources for disease discovery},
journal = {Database J. Biol. Databases Curation},
volume = {2019},
pages = {baz114},
year = {2019},
url = {https://doi.org/10.1093/database/baz114},
doi = {10.1093/DATABASE/BAZ114},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biodb/GourdineBVSKMMM19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/KohlerCVJDGGHMM19,
author = {Sebastian K{\"{o}}hler and
Leigh Carmody and
Nicole A. Vasilevsky and
Julius O. B. Jacobsen and
Daniel Danis and
Jean{-}Philippe F. Gourdine and
Michael A. Gargano and
Nomi L. Harris and
Nicolas Matentzoglu and
Julie A. McMurry and
David Osumi{-}Sutherland and
Valentina Cipriani and
James P. Balhoff and
Tom Conlin and
Hannah Blau and
Gareth Baynam and
Richard Palmer and
Dylan Gratian and
Hugh J. S. Dawkins and
Michael Segal and
Anna C. Jansen and
Ahmed Muaz and
Willie H. Chang and
Jenna Bergerson and
Stanley J. F. Laulederkind and
Zafer Y{\"{u}}ksel and
Sergi Beltran and
Alexandra F. Freeman and
Panagiotis I. Sergouniotis and
Daniel Durkin and
Andrea L. Storm and
Marc Hanauer and
Michael Brudno and
Susan M. Bello and
Murat Sincan and
Kayli Rageth and
Matthew T. Wheeler and
Renske Oegema and
Halima Lourghi and
Maria G. Della Rocca and
Rachel Thompson and
Francisco Castellanos and
James Priest and
Charlotte Cunningham{-}Rundles and
Ayushi Hegde and
Ruth C. Lovering and
Catherine Hajek and
Annie Olry and
Luigi Notarangelo and
Morgan Similuk and
Xingmin Aaron Zhang and
David G{\'{o}}mez{-}Andr{\'{e}}s and
Hanns Lochm{\"{u}}ller and
H{\'{e}}l{\`{e}}ne Dollfus and
Sergio Rosenzweig and
Shruti Marwaha and
Ana Rath and
Kathleen Sullivan and
Cynthia L. Smith and
Joshua D. Milner and
Doroth{\'{e}}e Leroux and
Cornelius F. Boerkoel and
Amy Klion and
Melody C. Carter and
Tudor Groza and
Damian Smedley and
Melissa A. Haendel and
Chris Mungall and
Peter N. Robinson},
title = {Expansion of the Human Phenotype Ontology {(HPO)} knowledge base and
resources},
journal = {Nucleic Acids Res.},
volume = {47},
number = {Database-Issue},
pages = {D1018--D1027},
year = {2019},
url = {https://doi.org/10.1093/nar/gky1105},
doi = {10.1093/NAR/GKY1105},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/KohlerCVJDGGHMM19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/npjdm/ZhangYVGCCDJRPC19,
author = {Xingmin Aaron Zhang and
Amy Yates and
Nicole A. Vasilevsky and
Jean{-}Philippe F. Gourdine and
Tiffany J. Callahan and
Leigh C. Carmody and
Daniel Danis and
Marcin P. Joachimiak and
Vida Ravanmehr and
Emily R. Pfaff and
James Champion and
Kimberly Robasky and
Hao Xu and
Karamarie Fecho and
Nephi A. Walton and
Richard L. Zhu and
Justin Ramsdill and
Christopher J. Mungall and
Sebastian K{\"{o}}hler and
Melissa A. Haendel and
Clement J. McDonald and
Daniel J. Vreeman and
David B. Peden and
Tellen D. Bennett and
James A. Feinstein and
Blake Martin and
Adrianne L. Stefanski and
Lawrence E. Hunter and
Christopher G. Chute and
Peter N. Robinson},
title = {Semantic integration of clinical laboratory tests from electronic
health records for deep phenotyping and biomarker discovery},
journal = {npj Digit. Medicine},
volume = {2},
year = {2019},
url = {https://doi.org/10.1038/s41746-019-0110-4},
doi = {10.1038/S41746-019-0110-4},
timestamp = {Fri, 08 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/npjdm/ZhangYVGCCDJRPC19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icbo/CarmodyZVMMR19,
author = {Leigh C. Carmody and
Xingmin Aaron Zhang and
Nicole A. Vasilevsky and
Christopher J. Mungall and
Nicolas Matentzoglu and
Peter N. Robinson},
editor = {Alexander D. Diehl and
William D. Duncan and
Gloria Sanso},
title = {Medical Action Ontology (MAxO)},
booktitle = {Proceedings of the 10th International Conference on Biomedical Ontology
{(ICBO} 2019), Buffalo, New York, USA, July 30 - August 2, 2019},
series = {{CEUR} Workshop Proceedings},
volume = {2931},
pages = {1},
publisher = {CEUR-WS.org},
year = {2019},
url = {https://ceur-ws.org/Vol-2931/ICBO\_2019\_paper\_60.pdf},
timestamp = {Fri, 10 Mar 2023 16:22:23 +0100},
biburl = {https://dblp.org/rec/conf/icbo/CarmodyZVMMR19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HeinrichKMRK17,
author = {Verena Heinrich and
Tom Kamphans and
Stefan Mundlos and
Peter N. Robinson and
Peter M. Krawitz},
title = {A likelihood ratio-based method to predict exact pedigrees for complex
families from next-generation sequencing data},
journal = {Bioinform.},
volume = {33},
number = {1},
pages = {72--78},
year = {2017},
url = {https://doi.org/10.1093/bioinformatics/btw550},
doi = {10.1093/BIOINFORMATICS/BTW550},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HeinrichKMRK17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/NotaroSRV17,
author = {Marco Notaro and
Max Schubach and
Peter N. Robinson and
Giorgio Valentini},
title = {Prediction of Human Phenotype Ontology terms by means of hierarchical
ensemble methods},
journal = {{BMC} Bioinform.},
volume = {18},
number = {1},
pages = {449:1--449:18},
year = {2017},
url = {https://doi.org/10.1186/s12859-017-1854-y},
doi = {10.1186/S12859-017-1854-Y},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/NotaroSRV17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/PenzkoferJFBMRZ17,
author = {Tobias Penzkofer and
Marten J{\"{a}}ger and
Marek Figlerowicz and
Richard Badge and
Stefan Mundlos and
Peter N. Robinson and
Tomasz Zemojtel},
title = {L1Base 2: more retrotransposition-active LINE-1s, more mammalian genomes},
journal = {Nucleic Acids Res.},
volume = {45},
number = {Database-Issue},
pages = {D68--D73},
year = {2017},
url = {https://doi.org/10.1093/nar/gkw925},
doi = {10.1093/NAR/GKW925},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/PenzkoferJFBMRZ17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/MungallM0BBBCCD17,
author = {Christopher J. Mungall and
Julie A. McMurry and
Sebastian K{\"{o}}hler and
James P. Balhoff and
Charles D. Borromeo and
Matthew H. Brush and
Seth Carbon and
Tom Conlin and
Nathan A. Dunn and
Mark Engelstad and
Erin Foster and
Jean{-}Philippe F. Gourdine and
Julius O. B. Jacobsen and
Dan Keith and
Bryan Laraway and
Suzanna E. Lewis and
Jeremy NguyenXuan and
Kent A. Shefchek and
Nicole A. Vasilevsky and
Zhou Yuan and
Nicole L. Washington and
Harry Hochheiser and
Tudor Groza and
Damian Smedley and
Peter N. Robinson and
Melissa A. Haendel},
title = {The Monarch Initiative: an integrative data and analytic platform
connecting phenotypes to genotypes across species},
journal = {Nucleic Acids Res.},
volume = {45},
number = {Database-Issue},
pages = {D712--D722},
year = {2017},
url = {https://doi.org/10.1093/nar/gkw1128},
doi = {10.1093/NAR/GKW1128},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/MungallM0BBBCCD17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/0001VEFMABBBBBB17,
author = {Sebastian K{\"{o}}hler and
Nicole A. Vasilevsky and
Mark Engelstad and
Erin Foster and
Julie A. McMurry and
S{\'{e}}gol{\`{e}}ne Aym{\'{e}} and
Gareth Baynam and
Susan M. Bello and
Cornelius F. Boerkoel and
Kym M. Boycott and
Michael Brudno and
Orion J. Buske and
Patrick F. Chinnery and
Valentina Cipriani and
Laureen E. Connell and
Hugh J. S. Dawkins and
Laura E. DeMare and
Andrew Devereau and
Bert B. A. de Vries and
Helen V. Firth and
Kathleen Freson and
Daniel Greene and
Ada Hamosh and
Ingo Helbig and
Courtney Hum and
Johanna J{\"{a}}hn and
Roger James and
Roland Krause and
Stanley J. F. Laulederkind and
Hanns Lochm{\"{u}}ller and
Gholson J. Lyon and
Soichi Ogishima and
Annie Olry and
Willem H. Ouwehand and
Nikolas Pontikos and
Ana Rath and
Franz Schaefer and
Richard H. Scott and
Michael Segal and
Panagiotis I. Sergouniotis and
Richard Sever and
Cynthia L. Smith and
Volker Straub and
Rachel Thompson and
Catherine Turner and
Ernest Turro and
Marijcke W. M. Veltman and
Tom Vulliamy and
Jing Yu and
Julie von Ziegenweidt and
Andreas Zankl and
Stephan Z{\"{u}}chner and
Tomasz Zemojtel and
Julius O. B. Jacobsen and
Tudor Groza and
Damian Smedley and
Christopher J. Mungall and
Melissa A. Haendel and
Peter N. Robinson},
title = {The Human Phenotype Ontology in 2017},
journal = {Nucleic Acids Res.},
volume = {45},
number = {Database-Issue},
pages = {D865--D876},
year = {2017},
url = {https://doi.org/10.1093/nar/gkw1039},
doi = {10.1093/NAR/GKW1039},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/0001VEFMABBBBBB17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cibb/NotaroSFMRV17,
author = {Marco Notaro and
Max Schubach and
Marco Frasca and
Marco Mesiti and
Peter N. Robinson and
Giorgio Valentini},
editor = {Massimo Bartoletti and
Annalisa Barla and
Andrea Bracciali and
Gunnar W. Klau and
Leif E. Peterson and
Alberto Policriti and
Roberto Tagliaferri},
title = {Ensembling Descendant Term Classifiers to Improve Gene - Abnormal
Phenotype Predictions},
booktitle = {Computational Intelligence Methods for Bioinformatics and Biostatistics
- 14th International Meeting, {CIBB} 2017, Cagliari, Italy, September
7-9, 2017, Revised Selected Papers},
series = {Lecture Notes in Computer Science},
volume = {10834},
pages = {70--80},
publisher = {Springer},
year = {2017},
url = {https://doi.org/10.1007/978-3-030-14160-8\_8},
doi = {10.1007/978-3-030-14160-8\_8},
timestamp = {Sun, 02 Jun 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/cibb/NotaroSFMRV17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icbo/VasilevskyBMO0B17,
author = {Nicole A. Vasilevsky and
James P. Balhoff and
Christopher J. Mungall and
David Osumi{-}Sutherland and
Sebastian K{\"{o}}hler and
Susan M. Bello and
Cynthia L. Smith and
Peter N. Robinson and
Melissa A. Haendel},
editor = {Matthew Horridge and
Phillip Lord and
Jennifer D. Warrender},
title = {Aligning the Human Phenotype and Mammalian Phenotype Ontology using
Dead Simple Ontology Design Patterns},
booktitle = {Proceedings of the 8th International Conference on Biomedical Ontology
{(ICBO} 2017), Newcastle-upon-Tyne, United Kingdom, September 13th
- 15th, 2017},
series = {{CEUR} Workshop Proceedings},
volume = {2137},
publisher = {CEUR-WS.org},
year = {2017},
url = {https://ceur-ws.org/Vol-2137/paper\_22.pdf},
timestamp = {Fri, 10 Mar 2023 16:22:24 +0100},
biburl = {https://dblp.org/rec/conf/icbo/VasilevskyBMO0B17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/OellrichCGRSBBG16,
author = {Anika Oellrich and
Nigel Collier and
Tudor Groza and
Dietrich Rebholz{-}Schuhmann and
Nigam Shah and
Olivier Bodenreider and
Mary Regina Boland and
Ivo I. Georgiev and
Hongfang Liu and
Kevin M. Livingston and
Augustin Luna and
Ann{-}Marie Mallon and
Prashanti Manda and
Peter N. Robinson and
Gabriella Rustici and
Michelle Simon and
Liqin Wang and
Rainer Winnenburg and
Michel Dumontier},
title = {The digital revolution in phenotyping},
journal = {Briefings Bioinform.},
volume = {17},
number = {5},
pages = {819--830},
year = {2016},
url = {https://doi.org/10.1093/bib/bbv083},
doi = {10.1093/BIB/BBV083},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/OellrichCGRSBBG16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icbo/VasilevskyEFMR016,
author = {Nicole A. Vasilevsky and
Mark Engelstad and
Erin Foster and
Chris Mungall and
Peter N. Robinson and
Sebastian K{\"{o}}hler and
Melissa A. Haendel},
editor = {Pankaj Jaiswal and
Robert Hoehndorf and
Cecilia N. Arighi and
Austin Meier},
title = {Enhancing the Human Phenotype Ontology for Use by the Layperson},
booktitle = {Proceedings of the Joint International Conference on Biological Ontology
and BioCreative, Corvallis, Oregon, United States, August 1-4, 2016},
series = {{CEUR} Workshop Proceedings},
volume = {1747},
publisher = {CEUR-WS.org},
year = {2016},
url = {https://ceur-ws.org/Vol-1747/IT402\_ICBO2016.pdf},
timestamp = {Fri, 10 Mar 2023 16:22:23 +0100},
biburl = {https://dblp.org/rec/conf/icbo/VasilevskyEFMR016.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/CollierGSROR15,
author = {Nigel Collier and
Tudor Groza and
Damian Smedley and
Peter N. Robinson and
Anika Oellrich and
Dietrich Rebholz{-}Schuhmann},
title = {PhenoMiner: from text to a database of phenotypes associated with
{OMIM} diseases},
journal = {Database J. Biol. Databases Curation},
volume = {2015},
year = {2015},
url = {https://doi.org/10.1093/database/bav104},
doi = {10.1093/DATABASE/BAV104},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biodb/CollierGSROR15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/GrozaKDCOSCBZR15,
author = {Tudor Groza and
Sebastian K{\"{o}}hler and
Sandra C. Doelken and
Nigel Collier and
Anika Oellrich and
Damian Smedley and
Francisco M. Couto and
Gareth Baynam and
Andreas Zankl and
Peter N. Robinson},
title = {Automatic concept recognition using the Human Phenotype Ontology reference
and test suite corpora},
journal = {Database J. Biol. Databases Curation},
volume = {2015},
year = {2015},
url = {https://doi.org/10.1093/database/bav005},
doi = {10.1093/DATABASE/BAV005},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biodb/GrozaKDCOSCBZR15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KuchenbeckerNHN15,
author = {L{\'{e}}on Kuchenbecker and
Mikalai Nienen and
Jochen Hecht and
Avidan U. Neumann and
Nina Babel and
Knut Reinert and
Peter N. Robinson},
title = {{IMSEQ} - a fast and error aware approach to immunogenetic sequence
analysis},
journal = {Bioinform.},
volume = {31},
number = {18},
pages = {2963--2971},
year = {2015},
url = {https://doi.org/10.1093/bioinformatics/btv309},
doi = {10.1093/BIOINFORMATICS/BTV309},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/KuchenbeckerNHN15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhuHDHRMKK15,
author = {Na Zhu and
Verena Heinrich and
Thorsten Dickhaus and
Jochen Hecht and
Peter N. Robinson and
Stefan Mundlos and
Tom Kamphans and
Peter M. Krawitz},
title = {Strategies to improve the performance of rare variant association
studies by optimizing the selection of controls},
journal = {Bioinform.},
volume = {31},
number = {22},
pages = {3577--3583},
year = {2015},
url = {https://doi.org/10.1093/bioinformatics/btv457},
doi = {10.1093/BIOINFORMATICS/BTV457},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhuHDHRMKK15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biomedsem/GrozaTRZ15,
author = {Tudor Groza and
Tania Tudorache and
Peter N. Robinson and
Andreas Zankl},
title = {Capturing domain knowledge from multiple sources: the rare bone disorders
use case},
journal = {J. Biomed. Semant.},
volume = {6},
pages = {21},
year = {2015},
url = {https://doi.org/10.1186/s13326-015-0008-2},
doi = {10.1186/S13326-015-0008-2},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biomedsem/GrozaTRZ15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/iwbbio/ValentiniKRNR15,
author = {Giorgio Valentini and
Sebastian K{\"{o}}hler and
Matteo R{\'{e}} and
Marco Notaro and
Peter N. Robinson},
editor = {Francisco M. Ortu{\~{n}}o Guzman and
Ignacio Rojas},
title = {Prediction of Human Gene - Phenotype Associations by Exploiting the
Hierarchical Structure of the Human Phenotype Ontology},
booktitle = {Bioinformatics and Biomedical Engineering - Third International Conference,
{IWBBIO} 2015, Granada, Spain, April 15-17, 2015. Proceedings, Part
{I}},
series = {Lecture Notes in Computer Science},
volume = {9043},
pages = {66--77},
publisher = {Springer},
year = {2015},
url = {https://doi.org/10.1007/978-3-319-16483-0\_7},
doi = {10.1007/978-3-319-16483-0\_7},
timestamp = {Tue, 14 May 2019 10:00:48 +0200},
biburl = {https://dblp.org/rec/conf/iwbbio/ValentiniKRNR15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/mcs/RobinsonFKNRV15,
author = {Peter N. Robinson and
Marco Frasca and
Sebastian K{\"{o}}hler and
Marco Notaro and
Matteo Re and
Giorgio Valentini},
editor = {Friedhelm Schwenker and
Fabio Roli and
Josef Kittler},
title = {A Hierarchical Ensemble Method for DAG-Structured Taxonomies},
booktitle = {Multiple Classifier Systems - 12th International Workshop, {MCS} 2015,
G{\"{u}}nzburg, Germany, June 29 - July 1, 2015, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {9132},
pages = {15--26},
publisher = {Springer},
year = {2015},
url = {https://doi.org/10.1007/978-3-319-20248-8\_2},
doi = {10.1007/978-3-319-20248-8\_2},
timestamp = {Sat, 09 Apr 2022 12:40:52 +0200},
biburl = {https://dblp.org/rec/conf/mcs/RobinsonFKNRV15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SmedleyKCABHVZR14,
author = {Damian Smedley and
Sebastian K{\"{o}}hler and
Johanna Christina Czeschik and
Joanna S. Amberger and
Carol A. Bocchini and
Ada Hamosh and
Julian Veldboer and
Tomasz Zemojtel and
Peter N. Robinson},
title = {Walking the interactome for candidate prioritization in exome sequencing
studies of Mendelian diseases},
journal = {Bioinform.},
volume = {30},
number = {22},
pages = {3215--3222},
year = {2014},
url = {https://doi.org/10.1093/bioinformatics/btu508},
doi = {10.1093/BIOINFORMATICS/BTU508},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/SmedleyKCABHVZR14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biomedsem/OellrichKWMLHRS14,
author = {Anika Oellrich and
Sebastian K{\"{o}}hler and
Nicole L. Washington and
Chris Mungall and
Suzanna Lewis and
Melissa A. Haendel and
Peter N. Robinson and
Damian Smedley},
title = {The influence of disease categories on gene candidate predictions
from model organism phenotypes},
journal = {J. Biomed. Semant.},
volume = {5},
number = {{S-1}},
pages = {S4},
year = {2014},
url = {https://doi.org/10.1186/2041-1480-5-S1-S4},
doi = {10.1186/2041-1480-5-S1-S4},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biomedsem/OellrichKWMLHRS14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/MasinoDDWSKPRW14,
author = {Aaron J. Masino and
Elizabeth T. Dechene and
Matthew C. Dulik and
Alisha Wilkens and
Nancy B. Spinner and
Ian D. Krantz and
Jeffrey W. Pennington and
Peter N. Robinson and
Peter S. White},
title = {Clinical phenotype-based gene prioritization: an initial study using
semantic similarity and the human phenotype ontology},
journal = {{BMC} Bioinform.},
volume = {15},
pages = {248},
year = {2014},
url = {https://doi.org/10.1186/1471-2105-15-248},
doi = {10.1186/1471-2105-15-248},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/MasinoDDWSKPRW14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/KohlerDM14,
author = {Sebastian K{\"{o}}hler and
Sandra C. Doelken and
Christopher J. Mungall and
Sebastian Bauer and
Helen V. Firth and
Isabelle Bailleul{-}Forestier and
Graeme C. M. Black and
Danielle L. Brown and
Michael Brudno and
Jennifer Campbell and
David R. FitzPatrick and
Janan T. Eppig and
Andrew P. Jackson and
Kathleen Freson and
Marta G{\^{\i}}rdea and
Ingo Helbig and
Jane A. Hurst and
Johanna J{\"{a}}hn and
Laird G. Jackson and
Anne M. Kelly and
David H. Ledbetter and
Sahar Mansour and
Christa L. Martin and
Celia Moss and
Andrew D. Mumford and
Willem H. Ouwehand and
Soo{-}Mi Park and
Erin Rooney Riggs and
Richard H. Scott and
Sanjay Sisodiya and
Steven Van Vooren and
Ronald J. Wapner and
Andrew O. M. Wilkie and
Caroline F. Wright and
Anneke T. Vulto{-}van Silfhout and
Nicole de Leeuw and
Bert B. A. de Vries and
Nicole L. Washington and
Cynthia L. Smith and
Monte Westerfield and
Paul N. Schofield and
Barbara J. Ruef and
Georgios V. Gkoutos and
Melissa A. Haendel and
Damian Smedley and
Suzanna E. Lewis and
Peter N. Robinson},
title = {The Human Phenotype Ontology project: linking molecular biology and
disease through phenotype data},
journal = {Nucleic Acids Res.},
volume = {42},
number = {Database-Issue},
pages = {966--974},
year = {2014},
url = {https://doi.org/10.1093/nar/gkt1026},
doi = {10.1093/NAR/GKT1026},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/KohlerDM14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/SmedleyOKRWRLM13,
author = {Damian Smedley and
Anika Oellrich and
Sebastian K{\"{o}}hler and
Barbara J. Ruef and
Monte Westerfield and
Peter N. Robinson and
Suzanna Lewis and
Christopher J. Mungall},
title = {PhenoDigm: analyzing curated annotations to associate animal models
with human diseases},
journal = {Database J. Biol. Databases Curation},
volume = {2013},
year = {2013},
url = {https://doi.org/10.1093/database/bat025},
doi = {10.1093/DATABASE/BAT025},
timestamp = {Thu, 13 Aug 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biodb/SmedleyOKRWRLM13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/medinfo/GrosjeanMSLCRD13,
author = {Julien Grosjean and
Tayeb Merabti and
Lina Fatima Soualmia and
Catherine Letord and
Jean Charlet and
Peter N. Robinson and
St{\'{e}}fan Jacques Darmoni},
editor = {Christoph Ulrich Lehmann and
Elske Ammenwerth and
Christian N{\o}hr},
title = {Integrating the Human Phenotype Ontology into HeTOP Terminology-Ontology
Server},
booktitle = {{MEDINFO} 2013 - Proceedings of the 14th World Congress on Medical
and Health Informatics, 20-13 August 2013, Copenhagen, Denmark},
series = {Studies in Health Technology and Informatics},
volume = {192},
pages = {961},
publisher = {{IOS} Press},
year = {2013},
url = {https://doi.org/10.3233/978-1-61499-289-9-961},
doi = {10.3233/978-1-61499-289-9-961},
timestamp = {Wed, 03 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/medinfo/GrosjeanMSLCRD13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BauerKSR12,
author = {Sebastian Bauer and
Sebastian K{\"{o}}hler and
Marcel H. Schulz and
Peter N. Robinson},
title = {Bayesian ontology querying for accurate and noise-tolerant semantic
searches},
journal = {Bioinform.},
volume = {28},
number = {19},
pages = {2502--2508},
year = {2012},
url = {https://doi.org/10.1093/bioinformatics/bts471},
doi = {10.1093/BIOINFORMATICS/BTS471},
timestamp = {Sat, 09 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/BauerKSR12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/midm/TaboadaMPJRS12,
author = {Maria Taboada and
Diego Mart{\'{\i}}nez Hern{\'{a}}ndez and
Bel{\'{e}}n Pilo and
Adriano Jim{\'{e}}nez{-}Escrig and
Peter N. Robinson and
Mar{\'{\i}}a Jes{\'{u}}s Sobrido},
title = {Querying phenotype-genotype relationships on patient datasets using
semantic web technology: the example of cerebrotendinous xanthomatosis},
journal = {{BMC} Medical Informatics Decis. Mak.},
volume = {12},
pages = {78},
year = {2012},
url = {https://doi.org/10.1186/1472-6947-12-78},
doi = {10.1186/1472-6947-12-78},
timestamp = {Sun, 25 Jul 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/midm/TaboadaMPJRS12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RodelspergerKBHBBCSR11,
author = {Christian R{\"{o}}delsperger and
Peter M. Krawitz and
Sebastian Bauer and
Jochen Hecht and
Abigail W. Bigham and
Michael Bamshad and
Birgit Jonske de Condor and
Michal R. Schweiger and
Peter N. Robinson},
title = {Identity-by-descent filtering of exome sequence data for disease-gene
identification in autosomal recessive disorders},
journal = {Bioinform.},
volume = {27},
number = {6},
pages = {829--836},
year = {2011},
url = {https://doi.org/10.1093/bioinformatics/btr022},
doi = {10.1093/BIOINFORMATICS/BTR022},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/RodelspergerKBHBBCSR11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BauerRG11,
author = {Sebastian Bauer and
Peter N. Robinson and
Julien Gagneur},
title = {Model-based gene set analysis for Bioconductor},
journal = {Bioinform.},
volume = {27},
number = {13},
pages = {1882--1883},
year = {2011},
url = {https://doi.org/10.1093/bioinformatics/btr296},
doi = {10.1093/BIOINFORMATICS/BTR296},
timestamp = {Tue, 08 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/BauerRG11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/KohlerBMCSSGR11,
author = {Sebastian K{\"{o}}hler and
Sebastian Bauer and
Chris Mungall and
Gabriele Carletti and
Cynthia L. Smith and
Paul N. Schofield and
Georgios V. Gkoutos and
Peter N. Robinson},
title = {Improving ontologies by automatic reasoning and evaluation of logical
definitions},
journal = {{BMC} Bioinform.},
volume = {12},
pages = {418},
year = {2011},
url = {https://doi.org/10.1186/1471-2105-12-418},
doi = {10.1186/1471-2105-12-418},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/KohlerBMCSSGR11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/SchulzKBR11,
author = {Marcel H. Schulz and
Sebastian K{\"{o}}hler and
Sebastian Bauer and
Peter N. Robinson},
title = {Exact score distribution computation for ontological similarity searches},
journal = {{BMC} Bioinform.},
volume = {12},
pages = {441},
year = {2011},
url = {https://doi.org/10.1186/1471-2105-12-441},
doi = {10.1186/1471-2105-12-441},
timestamp = {Sat, 09 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/SchulzKBR11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KrawitzRJJBR10,
author = {Peter M. Krawitz and
Christian R{\"{o}}delsperger and
Marten J{\"{a}}ger and
Luke Jostins and
Sebastian Bauer and
Peter N. Robinson},
title = {Microindel detection in short-read sequence data},
journal = {Bioinform.},
volume = {26},
number = {6},
pages = {722--729},
year = {2010},
url = {https://doi.org/10.1093/bioinformatics/btq027},
doi = {10.1093/BIOINFORMATICS/BTQ027},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/KrawitzRJJBR10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/SchulzKBVR09,
author = {Marcel H. Schulz and
Sebastian K{\"{o}}hler and
Sebastian Bauer and
Martin Vingron and
Peter N. Robinson},
editor = {Steven Salzberg and
Tandy J. Warnow},
title = {Exact Score Distribution Computation for Similarity Searches in Ontologies},
booktitle = {Algorithms in Bioinformatics, 9th International Workshop, {WABI} 2009,
Philadelphia, PA, USA, September 12-13, 2009. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {5724},
pages = {298--309},
publisher = {Springer},
year = {2009},
url = {https://doi.org/10.1007/978-3-642-04241-6\_25},
doi = {10.1007/978-3-642-04241-6\_25},
timestamp = {Sat, 09 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/wabi/SchulzKBVR09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BauerGVR08,
author = {Sebastian Bauer and
Steffen Grossmann and
Martin Vingron and
Peter N. Robinson},
title = {Ontologizer 2.0 - a multifunctional tool for {GO} term enrichment
analysis and data exploration},
journal = {Bioinform.},
volume = {24},
number = {14},
pages = {1650--1651},
year = {2008},
url = {https://doi.org/10.1093/bioinformatics/btn250},
doi = {10.1093/BIOINFORMATICS/BTN250},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/BauerGVR08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ijbra/SchulzBR08,
author = {Marcel H. Schulz and
Sebastian Bauer and
Peter N. Robinson},
title = {The generalised k-Truncated Suffix Tree for time-and space-efficient
searches in multiple {DNA} or protein sequences},
journal = {Int. J. Bioinform. Res. Appl.},
volume = {4},
number = {1},
pages = {81--95},
year = {2008},
url = {https://doi.org/10.1504/IJBRA.2008.017165},
doi = {10.1504/IJBRA.2008.017165},
timestamp = {Sat, 09 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ijbra/SchulzBR08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GrossmannBRV07,
author = {Steffen Grossmann and
Sebastian Bauer and
Peter N. Robinson and
Martin Vingron},
title = {Improved detection of overrepresentation of Gene-Ontology annotations
with parent-child analysis},
journal = {Bioinform.},
volume = {23},
number = {22},
pages = {3024--3031},
year = {2007},
url = {https://doi.org/10.1093/bioinformatics/btm440},
doi = {10.1093/BIOINFORMATICS/BTM440},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/GrossmannBRV07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/GilleR06,
author = {Christoph Gille and
Peter N. Robinson},
title = {HotSwap for bioinformatics: {A} {STRAP} tutorial},
journal = {{BMC} Bioinform.},
volume = {7},
pages = {64},
year = {2006},
url = {https://doi.org/10.1186/1471-2105-7-64},
doi = {10.1186/1471-2105-7-64},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/GilleR06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/BeattieR06,
author = {Bradley J. Beattie and
Peter N. Robinson},
title = {Binary State Pattern Clustering: {A} Digital Paradigm for Class and
Biomarker Discovery in Gene Microarray Studies of Cancer},
journal = {J. Comput. Biol.},
volume = {13},
number = {5},
pages = {1114--1130},
year = {2006},
url = {https://doi.org/10.1089/cmb.2006.13.1114},
doi = {10.1089/CMB.2006.13.1114},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcb/BeattieR06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/GrossmannBRV06,
author = {Steffen Grossmann and
Sebastian Bauer and
Peter N. Robinson and
Martin Vingron},
editor = {Alberto Apostolico and
Concettina Guerra and
Sorin Istrail and
Pavel A. Pevzner and
Michael S. Waterman},
title = {An Improved Statistic for Detecting Over-Represented Gene Ontology
Annotations in Gene Sets},
booktitle = {Research in Computational Molecular Biology, 10th Annual International
Conference, {RECOMB} 2006, Venice, Italy, April 2-5, 2006, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {3909},
pages = {85--98},
publisher = {Springer},
year = {2006},
url = {https://doi.org/10.1007/11732990\_9},
doi = {10.1007/11732990\_9},
timestamp = {Mon, 13 May 2019 09:30:09 +0200},
biburl = {https://dblp.org/rec/conf/recomb/GrossmannBRV06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RobinsonWBB04,
author = {Peter N. Robinson and
Andreas Wollstein and
Ulrike B{\"{o}}hme and
Bradley J. Beattie},
title = {Ontologizing gene-expression microarray data: characterizing clusters
with Gene Ontology},
journal = {Bioinform.},
volume = {20},
number = {6},
pages = {979--981},
year = {2004},
url = {https://doi.org/10.1093/bioinformatics/bth040},
doi = {10.1093/BIOINFORMATICS/BTH040},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/RobinsonWBB04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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