The Kipoi repository accelerates community exchange and reuse of predictive models for genomics

Žiga Avsec; Roman Kreuzhuber; Johnny Israeli; Nancy Xu; Jun Cheng; Avanti Shrikumar; Abhimanyu Banerjee; Daniel S. Kim; Thorsten Beier; Lara Urban; Anshul Kundaje; Oliver Stegle; Julien Gagneur

doi:10.1038/s41587-019-0140-0

The Kipoi repository accelerates community exchange and reuse of predictive models for genomics

Žiga Avsec, Roman Kreuzhuber, Johnny Israeli, Nancy Xu, Jun Cheng, Avanti Shrikumar, Abhimanyu Banerjee, Daniel S. Kim, Thorsten Beier, Lara Urban, Anshul Kundaje, Oliver Stegle, Julien Gagneur

Informatics 29 - Chair of Computational Molecular Medicine

Research output: Contribution to journal › Letter › peer-review

100 Scopus citations

Original language	English
Pages (from-to)	592-600
Number of pages	9
Journal	Nature Biotechnology
Volume	37
Issue number	6
DOIs	https://doi.org/10.1038/s41587-019-0140-0
State	Published - 1 Jun 2019

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@article{9a2744bce7a54c6b97bf63b1391f10f3,

title = "The Kipoi repository accelerates community exchange and reuse of predictive models for genomics",

author = "{\v Z}iga Avsec and Roman Kreuzhuber and Johnny Israeli and Nancy Xu and Jun Cheng and Avanti Shrikumar and Abhimanyu Banerjee and Kim, {Daniel S.} and Thorsten Beier and Lara Urban and Anshul Kundaje and Oliver Stegle and Julien Gagneur",

note = "Funding Information: We thank C.-S. Foo for early discussion on the manuscript and N. Zupan for implementing the website. We thank D. Quang for providing help with FactorNet and trained models for CEBPB and MAFK. We thank W. Huber for feedback on the manuscript. {\v Z}.A. and J.C. were supported by a Deutsche Forschungsgemeinschaft fellowship through the Graduate School of Quantitative Biosciences Munich. {\v Z}.A. and T.B. were supported by the German Bundesministerium f{\"u}r Bildung und Forschung (BMBF) through the project MechML (01IS18053F). J.C. was supported by the Competence Network for Technical, Scientific High Performance Computing in Bavaria KONWIHR. L.U. received support from core funding of the European Molecular Biology Laboratory and the European Union{\textquoteright}s Horizon 2020 research and innovation programme (grant agreement number N635290). J.I. is supported by a Stanford BioX Fellowship. A.S. is supported by an HHMI International Student Research Fellowship and a Stanford BioX Fellowship. D.S.K. is supported by a Stanford BioX Fellowship. A.B. is supported by NIH grant 1DP2OD022870. A.K. is supported by NIH grants 1DP2OD022870 and 1U01HG009431. This work was supported by an NVIDIA hardware grant providing a Titan X GPU card.",

year = "2019",

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doi = "10.1038/s41587-019-0140-0",

language = "English",

volume = "37",

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journal = "Nature Biotechnology",

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T1 - The Kipoi repository accelerates community exchange and reuse of predictive models for genomics

AU - Avsec, Žiga

AU - Kreuzhuber, Roman

AU - Israeli, Johnny

AU - Xu, Nancy

AU - Cheng, Jun

AU - Shrikumar, Avanti

AU - Banerjee, Abhimanyu

AU - Kim, Daniel S.

AU - Beier, Thorsten

AU - Urban, Lara

AU - Kundaje, Anshul

AU - Stegle, Oliver

AU - Gagneur, Julien

N1 - Funding Information: We thank C.-S. Foo for early discussion on the manuscript and N. Zupan for implementing the website. We thank D. Quang for providing help with FactorNet and trained models for CEBPB and MAFK. We thank W. Huber for feedback on the manuscript. Ž.A. and J.C. were supported by a Deutsche Forschungsgemeinschaft fellowship through the Graduate School of Quantitative Biosciences Munich. Ž.A. and T.B. were supported by the German Bundesministerium für Bildung und Forschung (BMBF) through the project MechML (01IS18053F). J.C. was supported by the Competence Network for Technical, Scientific High Performance Computing in Bavaria KONWIHR. L.U. received support from core funding of the European Molecular Biology Laboratory and the European Union’s Horizon 2020 research and innovation programme (grant agreement number N635290). J.I. is supported by a Stanford BioX Fellowship. A.S. is supported by an HHMI International Student Research Fellowship and a Stanford BioX Fellowship. D.S.K. is supported by a Stanford BioX Fellowship. A.B. is supported by NIH grant 1DP2OD022870. A.K. is supported by NIH grants 1DP2OD022870 and 1U01HG009431. This work was supported by an NVIDIA hardware grant providing a Titan X GPU card.

PY - 2019/6/1

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U2 - 10.1038/s41587-019-0140-0

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JO - Nature Biotechnology

JF - Nature Biotechnology

IS - 6

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The Kipoi repository accelerates community exchange and reuse of predictive models for genomics

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