3D基因组折叠的深度学习模型的配方和成分。

IF 3.7 2区生物学 Q2 CELL BIOLOGY

Current Opinion in Genetics & Development Pub Date : 2025-01-24 DOI:10.1016/j.gde.2024.102308

Paulina N Smaruj , Yao Xiao , Geoffrey Fudenberg

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引用次数: 0

摘要

三维基因组折叠在基因调控和疾病中发挥作用。在这篇综述中，我们比较和对比了最近用于预测基因组接触图谱的深度学习模型。我们调查了预处理、架构、训练、评估和解释方法，强调了不同模型的功能和局限性。在每个领域，我们都强调了基因组折叠模型的挑战、机遇和潜在的未来方向。

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Recipes and ingredients for deep learning models of 3D genome folding

Three-dimensional genome folding plays roles in gene regulation and disease. In this review, we compare and contrast recent deep learning models for predicting genome contact maps. We survey preprocessing, architecture, training, evaluation, and interpretation methods, highlighting the capabilities and limitations of different models. In each area, we highlight challenges, opportunities, and potential future directions for genome-folding models.

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来源期刊

Current Opinion in Genetics & Development 生物-细胞生物学

CiteScore

7.90

自引率

0.00%

发文量

102

审稿时长

1 months

期刊介绍： Current Opinion in Genetics and Development aims to stimulate scientifically grounded, interdisciplinary, multi-scale debate and exchange of ideas. It contains polished, concise and timely reviews and opinions, with particular emphasis on those articles published in the past two years. In addition to describing recent trends, the authors are encouraged to give their subjective opinion of the topics discussed. In Current Opinion in Genetics and Development we help the reader by providing in a systematic manner: 1. The views of experts on current advances in their field in a clear and readable form. 2. Evaluations of the most interesting papers, annotated by experts, from the great wealth of original publications.[...] The subject of Genetics and Development is divided into six themed sections, each of which is reviewed once a year: • Cancer Genomics • Genome Architecture and Expression • Molecular and genetic basis of disease • Developmental mechanisms, patterning and evolution • Cell reprogramming, regeneration and repair • Genetics of Human Origin / Evolutionary genetics (alternate years)