TY - JOUR
T1 - The Nucleome Data Bank
T2 - Web-based resources to simulate and analyze the three-dimensional genome
AU - Contessoto, Vinícius G.
AU - Cheng, Ryan R.
AU - Hajitaheri, Arya
AU - Dodero-Rojas, Esteban
AU - Mello, Matheus F.
AU - Lieberman-Aiden, Erez
AU - Wolynes, Peter G.
AU - Di Pierro, Michele
AU - Onuchic, José N.
N1 - Publisher Copyright:
© 2021 The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.
PY - 2021/1/8
Y1 - 2021/1/8
N2 - We introduce the Nucleome Data Bank (NDB), a web-based platform to simulate and analyze the three-dimensional (3D) organization of genomes. The NDB enables physics-based simulation of chromosomal structural dynamics through the MEGABASE + MiChroM computational pipeline. The input of the pipeline consists of epigenetic information sourced from the Encode database; the output consists of the trajectories of chromosomal motions that accurately predict Hi-C and fluorescence insitu hybridization data, as well as multiple observations of chromosomal dynamics in vivo. As an intermediate step, users can also generate chromosomal sub-compartment annotations directly from the same epigenetic input, without the use of any DNA-DNA proximity ligation data. Additionally, the NDB freely hosts both experimental and computational structural genomics data. Besides being able to perform their own genome simulations and download the hosted data, users can also analyze and visualize the same data through custom-designed web-based tools. In particular, the one-dimensional genetic and epigenetic data can be overlaid onto accurate 3D structures of chromosomes, to study the spatial distribution of genetic and epigenetic features. The NDB aims to be a shared resource to biologists, biophysicists and all genome scientists. The NDB is available at https://ndb.rice.edu.
AB - We introduce the Nucleome Data Bank (NDB), a web-based platform to simulate and analyze the three-dimensional (3D) organization of genomes. The NDB enables physics-based simulation of chromosomal structural dynamics through the MEGABASE + MiChroM computational pipeline. The input of the pipeline consists of epigenetic information sourced from the Encode database; the output consists of the trajectories of chromosomal motions that accurately predict Hi-C and fluorescence insitu hybridization data, as well as multiple observations of chromosomal dynamics in vivo. As an intermediate step, users can also generate chromosomal sub-compartment annotations directly from the same epigenetic input, without the use of any DNA-DNA proximity ligation data. Additionally, the NDB freely hosts both experimental and computational structural genomics data. Besides being able to perform their own genome simulations and download the hosted data, users can also analyze and visualize the same data through custom-designed web-based tools. In particular, the one-dimensional genetic and epigenetic data can be overlaid onto accurate 3D structures of chromosomes, to study the spatial distribution of genetic and epigenetic features. The NDB aims to be a shared resource to biologists, biophysicists and all genome scientists. The NDB is available at https://ndb.rice.edu.
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U2 - 10.1093/nar/gkaa818
DO - 10.1093/nar/gkaa818
M3 - Article
C2 - 33021634
AN - SCOPUS:85095707350
SN - 0305-1048
VL - 49
SP - D172-D182
JO - Nucleic Acids Research
JF - Nucleic Acids Research
IS - D1
ER -