Literature DB >> 31332378

Inflated performance measures in enhancer-promoter interaction-prediction methods.

Fan Cao1, Melissa J Fullwood2,3,4.   

Abstract

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Year:  2019        PMID： 31332378     DOI： 10.1038/s41588-019-0434-7

Source DB:  PubMed          Journal:  Nat Genet        ISSN： 1061-4036            Impact factor:   38.330


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  15 in total

Review 1.  Enhancer Predictions and Genome-Wide Regulatory Circuits.

Authors:  Michael A Beer; Dustin Shigaki; Danwei Huangfu
Journal:  Annu Rev Genomics Hum Genet       Date:  2020-05-22       Impact factor: 8.929

Review 2.  Navigating the pitfalls of applying machine learning in genomics.

Authors:  Sean Whalen; Jacob Schreiber; William S Noble; Katherine S Pollard
Journal:  Nat Rev Genet       Date:  2021-11-26       Impact factor: 53.242

3.  EPIXplorer: A web server for prediction, analysis and visualization of enhancer-promoter interactions.

Authors:  Li Tang; Zhizhou Zhong; Yisheng Lin; Yifei Yang; Jun Wang; James F Martin; Min Li
Journal:  Nucleic Acids Res       Date:  2022-05-25       Impact factor: 19.160

4.  Chromatin loop anchors predict transcript and exon usage.

Authors:  Yu Zhang; Yichao Cai; Xavier Roca; Chee Keong Kwoh; Melissa Jane Fullwood
Journal:  Brief Bioinform       Date:  2021-11-05       Impact factor: 11.622

5.  Predict long-range enhancer regulation based on protein-protein interactions between transcription factors.

Authors:  Hao Wang; Binbin Huang; Jianrong Wang
Journal:  Nucleic Acids Res       Date:  2021-10-11       Impact factor: 16.971

6.  A systematic study of motif pairs that may facilitate enhancer-promoter interactions.

Authors:  Saidi Wang; Haiyan Hu; Xiaoman Li
Journal:  J Integr Bioinform       Date:  2022-02-07

7.  Leveraging three-dimensional chromatin architecture for effective reconstruction of enhancer-target gene regulatory interactions.

Authors:  Elisa Salviato; Vera Djordjilović; Judith Mary Hariprakash; Ilario Tagliaferri; Koustav Pal; Francesco Ferrari
Journal:  Nucleic Acids Res       Date:  2021-09-27       Impact factor: 16.971

Review 8.  Exploring 3D chromatin contacts in gene regulation: The evolution of approaches for the identification of functional enhancer-promoter interaction.

Authors:  Hang Xu; Shijie Zhang; Xianfu Yi; Dariusz Plewczynski; Mulin Jun Li
Journal:  Comput Struct Biotechnol J       Date:  2020-02-28       Impact factor: 7.271

9.  Local Epigenomic Data are more Informative than Local Genome Sequence Data in Predicting Enhancer-Promoter Interactions Using Neural Networks.

Authors:  Mengli Xiao; Zhong Zhuang; Wei Pan
Journal:  Genes (Basel)       Date:  2019-12-29       Impact factor: 4.096

10.  A curated benchmark of enhancer-gene interactions for evaluating enhancer-target gene prediction methods.

Authors:  Jill E Moore; Henry E Pratt; Michael J Purcaro; Zhiping Weng
Journal:  Genome Biol       Date:  2020-01-22       Impact factor: 13.583
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