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Literature DB >> 26252139

Deep learning for regulatory genomics.

Yongjin Park¹, Manolis Kellis¹.

Abstract

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Year: 2015 PMID： 26252139 DOI： 10.1038/nbt.3313

Source DB: PubMed Journal: Nat Biotechnol ISSN： 1087-0156 Impact factor: 54.908

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8 in total

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Review 5. Deep learning.

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6. Evaluation of methods for modeling transcription factor sequence specificity.

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Journal: Nat Biotechnol Date: 2013-01-27 Impact factor: 54.908

7. An integrated encyclopedia of DNA elements in the human genome.

Authors:
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8. Integrative analysis of 111 reference human epigenomes.

Authors: Anshul Kundaje; Wouter Meuleman; Jason Ernst; Misha Bilenky; Angela Yen; Alireza Heravi-Moussavi; Pouya Kheradpour; Zhizhuo Zhang; Jianrong Wang; Michael J Ziller; Viren Amin; John W Whitaker; Matthew D Schultz; Lucas D Ward; Abhishek Sarkar; Gerald Quon; Richard S Sandstrom; Matthew L Eaton; Yi-Chieh Wu; Andreas R Pfenning; Xinchen Wang; Melina Claussnitzer; Yaping Liu; Cristian Coarfa; R Alan Harris; Noam Shoresh; Charles B Epstein; Elizabeta Gjoneska; Danny Leung; Wei Xie; R David Hawkins; Ryan Lister; Chibo Hong; Philippe Gascard; Andrew J Mungall; Richard Moore; Eric Chuah; Angela Tam; Theresa K Canfield; R Scott Hansen; Rajinder Kaul; Peter J Sabo; Mukul S Bansal; Annaick Carles; Jesse R Dixon; Kai-How Farh; Soheil Feizi; Rosa Karlic; Ah-Ram Kim; Ashwinikumar Kulkarni; Daofeng Li; Rebecca Lowdon; GiNell Elliott; Tim R Mercer; Shane J Neph; Vitor Onuchic; Paz Polak; Nisha Rajagopal; Pradipta Ray; Richard C Sallari; Kyle T Siebenthall; Nicholas A Sinnott-Armstrong; Michael Stevens; Robert E Thurman; Jie Wu; Bo Zhang; Xin Zhou; Arthur E Beaudet; Laurie A Boyer; Philip L De Jager; Peggy J Farnham; Susan J Fisher; David Haussler; Steven J M Jones; Wei Li; Marco A Marra; Michael T McManus; Shamil Sunyaev; James A Thomson; Thea D Tlsty; Li-Huei Tsai; Wei Wang; Robert A Waterland; Michael Q Zhang; Lisa H Chadwick; Bradley E Bernstein; Joseph F Costello; Joseph R Ecker; Martin Hirst; Alexander Meissner; Aleksandar Milosavljevic; Bing Ren; John A Stamatoyannopoulos; Ting Wang; Manolis Kellis
Journal: Nature Date: 2015-02-19 Impact factor: 69.504

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Review 3. Deep learning in pharmacogenomics: from gene regulation to patient stratification.

Authors: Alexandr A Kalinin; Gerald A Higgins; Narathip Reamaroon; Sayedmohammadreza Soroushmehr; Ari Allyn-Feuer; Ivo D Dinov; Kayvan Najarian; Brian D Athey
Journal: Pharmacogenomics Date: 2018-04-26 Impact factor: 2.533

4. DeepDeath: Learning to predict the underlying cause of death with Big Data.

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Journal: Conf Proc IEEE Eng Med Biol Soc Date: 2017-07

5. DeepTACT: predicting 3D chromatin contacts via bootstrapping deep learning.

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6. RicENN: Prediction of Rice Enhancers with Neural Network Based on DNA Sequences.

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7. Prediction of regulatory motifs from human Chip-sequencing data using a deep learning framework.

Authors: Jinyu Yang; Anjun Ma; Adam D Hoppe; Cankun Wang; Yang Li; Chi Zhang; Yan Wang; Bingqiang Liu; Qin Ma
Journal: Nucleic Acids Res Date: 2019-09-05 Impact factor: 16.971

8. Predicting enhancer-promoter interaction from genomic sequence with deep neural networks.

Authors: Shashank Singh; Yang Yang; Barnabás Póczos; Jian Ma
Journal: Quant Biol Date: 2019-06

9. Large-scale DNA-based phenotypic recording and deep learning enable highly accurate sequence-function mapping.

Authors: Simon Höllerer; Laetitia Papaxanthos; Anja Cathrin Gumpinger; Katrin Fischer; Christian Beisel; Karsten Borgwardt; Yaakov Benenson; Markus Jeschek
Journal: Nat Commun Date: 2020-07-15 Impact factor: 14.919

Review 10. Opportunities and obstacles for deep learning in biology and medicine.

Authors: Travers Ching; Daniel S Himmelstein; Brett K Beaulieu-Jones; Alexandr A Kalinin; Brian T Do; Gregory P Way; Enrico Ferrero; Paul-Michael Agapow; Michael Zietz; Michael M Hoffman; Wei Xie; Gail L Rosen; Benjamin J Lengerich; Johnny Israeli; Jack Lanchantin; Stephen Woloszynek; Anne E Carpenter; Avanti Shrikumar; Jinbo Xu; Evan M Cofer; Christopher A Lavender; Srinivas C Turaga; Amr M Alexandari; Zhiyong Lu; David J Harris; Dave DeCaprio; Yanjun Qi; Anshul Kundaje; Yifan Peng; Laura K Wiley; Marwin H S Segler; Simina M Boca; S Joshua Swamidass; Austin Huang; Anthony Gitter; Casey S Greene
Journal: J R Soc Interface Date: 2018-04 Impact factor: 4.293