Cargando…

An integrated 3-Dimensional Genome Modeling Engine for data-driven simulation of spatial genome organization

ChIA-PET is a high-throughput mapping technology that reveals long-range chromatin interactions and provides insights into the basic principles of spatial genome organization and gene regulation mediated by specific protein factors. Recently, we showed that a single ChIA-PET experiment provides info...

Descripción completa

Detalles Bibliográficos
Autores principales:	Szałaj, Przemysław, Tang, Zhonghui, Michalski, Paul, Pietal, Michal J., Luo, Oscar J., Sadowski, Michał, Li, Xingwang, Radew, Kamen, Ruan, Yijun, Plewczynski, Dariusz
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Cold Spring Harbor Laboratory Press 2016
Materias:	Method
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5131821/ https://www.ncbi.nlm.nih.gov/pubmed/27789526 http://dx.doi.org/10.1101/gr.205062.116

Ejemplares similares

3D-GNOME 2.0: a three-dimensional genome modeling engine for predicting structural variation-driven alterations of chromatin spatial structure in the human genome
por: Wlasnowolski, Michal, et al.
Publicado: (2020)

Spatial chromatin architecture alteration by structural variations in human genomes at the population scale
por: Sadowski, Michal, et al.
Publicado: (2019)

Correction to: Spatial chromatin architecture alteration by structural variations in human genomes at the population scale
por: Sadowski, Michal, et al.
Publicado: (2019)

3D-GNOME: an integrated web service for structural modeling of the 3D genome
por: Szalaj, Przemyslaw, et al.
Publicado: (2016)

Three-dimensional organization and dynamics of the genome
por: Szalaj, Przemyslaw, et al.
Publicado: (2018)

NanoForms: an integrated server for processing, analysis and assembly of raw sequencing data of microbial genomes, from Oxford Nanopore technology
por: Czmil, Anna, et al.
Publicado: (2022)

3D-GNOME 3.0: a three-dimensional genome modelling engine for analysing changes of promoter-enhancer contacts in the human genome
por: Wlasnowolski, Michal, et al.
Publicado: (2023)

Chromatin topology reorganization and transcription repression by PML-RARα in acute promyeloid leukemia
por: Wang, Ping, et al.
Publicado: (2020)

Three-dimensional Epigenome Statistical Model: Genome-wide Chromatin Looping Prediction
por: Al Bkhetan, Ziad, et al.
Publicado: (2018)

Enhanced performance of gene expression predictive models with protein-mediated spatial chromatin interactions
por: Chiliński, Mateusz, et al.
Publicado: (2023)

Enhanced performance of gene expression predictive models with protein-mediated spatial chromatin interactions
por: Chiliński, Mateusz, et al.
Publicado: (2023)

A genome annotation-driven approach to cloning the human ORFeome
por: Collins, John E, et al.
Publicado: (2004)

Chrom3D: three-dimensional genome modeling from Hi-C and nuclear lamin-genome contacts
por: Paulsen, Jonas, et al.
Publicado: (2017)

Classification methods for the development of genomic signatures from high-dimensional data
por: Moon, Hojin, et al.
Publicado: (2006)

Phage Mu-driven two-plasmid system for integration of recombinant DNA in the Methylophilus methylotrophus genome
por: Abalakina, Elena G., et al.
Publicado: (2008)

Precision genome engineering with programmable DNA-nicking enzymes
por: Kim, Eunji, et al.
Publicado: (2012)

Celloscope: a probabilistic model for marker-gene-driven cell type deconvolution in spatial transcriptomics data
por: Geras, Agnieszka, et al.
Publicado: (2023)

Predicting the three-dimensional folding of cis-regulatory regions in mammalian genomes using bioinformatic data and polymer models
por: Brackley, Chris A., et al.
Publicado: (2016)

Genomic Marks Associated with Chromatin Compartments in the CTCF, RNAPII Loop and Genomic Windows
por: Szczepińska, Teresa, et al.
Publicado: (2021)

Accessible Region Conformation Capture (ARC-C) gives high-resolution insights into genome architecture and regulation
por: Huang, Ni, et al.
Publicado: (2022)

ConsensuSV—from the whole-genome sequencing data to the complete variant list
por: Chiliński, Mateusz, et al.
Publicado: (2022)

Optimizing complex phenotypes through model-guided multiplex genome engineering
por: Kuznetsov, Gleb, et al.
Publicado: (2017)

Finished bacterial genomes from shotgun sequence data
por: Ribeiro, Filipe J., et al.
Publicado: (2012)

iRegNet3D: three-dimensional integrated regulatory network for the genomic analysis of coding and non-coding disease mutations
por: Liang, Siqi, et al.
Publicado: (2017)

HUPAN: a pan-genome analysis pipeline for human genomes
por: Duan, Zhongqu, et al.
Publicado: (2019)

Leveraging comparative genomics to uncover alien genes in bacterial genomes
por: Sengupta, Soham, et al.
Publicado: (2023)

Genomic loci susceptible to systematic sequencing bias in clinical whole genomes
por: Freeman, Timothy M., et al.
Publicado: (2020)

Application of Machine Learning Method in Genomics and Proteomics
por: Lin, Hao, et al.
Publicado: (2015)

i-GONAD: a robust method for in situ germline genome engineering using CRISPR nucleases
por: Ohtsuka, Masato, et al.
Publicado: (2018)

Social adaptation in multi-agent model of linguistic categorization is affected by network information flow
por: Zubek, Julian, et al.
Publicado: (2017)

Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome
por: Pedersen, Jakob Skou, et al.
Publicado: (2014)

Restauro-G: A Rapid Genome Re-Annotation System for Comparative Genomics
por: Tamaki, Satoshi, et al.
Publicado: (2007)

ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads
por: MacCallum, Iain, et al.
Publicado: (2009)

Infernape uncovers cell type–specific and spatially resolved alternative polyadenylation in the brain
por: Kang, Bowei, et al.
Publicado: (2023)

Identification of Human miRNA Biomarkers Targeting the SARS-CoV-2 Genome
por: Saha, Indrajit, et al.
Publicado: (2022)

A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome
por: Chapman, Jarrod A, et al.
Publicado: (2015)

Genome-wide prediction of DNA mutation effect on nucleosome positions for yeast synthetic genomics
por: Routhier, Etienne, et al.
Publicado: (2021)

Enabling genomic island prediction and comparison in multiple genomes to investigate bacterial evolution and outbreaks
por: Bertelli, Claire, et al.
Publicado: (2022)

Multi-scale phase separation by explosive percolation with single-chromatin loop resolution
por: Sengupta, Kaustav, et al.
Publicado: (2022)

Zinc-finger nuclease-driven targeted integration into mammalian genomes using donors with limited chromosomal homology
por: Orlando, Salvatore J., et al.
Publicado: (2010)

Cannot write session to /tmp/vufind_sessions/sess_lfeugptqalb0eb0d333dppcqtb