Large-scale Comparative Study of Hi-C-based Chromatin 3D Structure Modeling Methods

الموضوعات

علوم تطبيقية وتكنولوجية

الملخص

Chromatin is a complex polymer molecule in eukaryotic cells, primarily consisting of DNA and histones. Many works have shown that the 3D folding of chromatin structure plays an important role in DNA expression. The recently proposed Chro- mosome Conformation Capture technologies, especially the Hi-C assays, provide us an opportunity to study how the 3D structures of the chromatin are organized. Based on the data from Hi-C experiments, many chromatin 3D structure modeling methods have been proposed. However, there is limited ground truth to validate these methods and no robust chromatin structure alignment algorithms to evaluate the performance of these methods.In our work, we first made a thorough literature review of 25 publicly available population Hi-C-based chromatin 3D structure modeling methods. Furthermore, to evaluate and to compare the performance of these methods, we proposed a novel data simulation method, which combined the population Hi-C data and single-cell Hi-C data without ad hoc parameters. Also, we designed a global and a local alignment algorithms to measure the similarity between the templates and the chromatin struc- tures predicted by different modeling methods. Finally, the results from large-scale comparative tests indicated that our alignment algorithms significantly outperform the algorithms in literature.

روابط وملفات

التعريف والنوع

رقم الوثيقة

0ac7c042-c5b4-41b8-8b66-0e10832a4180

رقم العقد

0

نوع الوسائط

Crawler

نوع المحتوى

الرسائل العلمية

صيغة المصدر

رسائل ماجيستير

نوع الملف

pdf text

أسماء الملفات

1699067_1.pdf

بيانات النشر

ألقاب المؤلفين

[{"name_ar":"Cheng Wang","title_ar":"اعداد","title_en":"Preparation"},{"name_ar":"Xin Gao","title_ar":"اشراف","title_en":"Supervision"}]

اللغة

English

المصدر والدورية

اسم المصدر

Large-scale Comparative Study of Hi-C-based Chromatin 3D Structure Modeling Methods

المحتوى والصفحات

عدد الصفحات

0

كلمات الباحثين

chromatin 3D structure , data simulation , Hi-C , structure alignment , structure modeling

إشراف وإعداد

الإشراف

Xin Gao

الإعداد

Cheng Wang

الاقتباسات الببليوغرافية