Cargando…

Comparison of computational methods for the identification of topologically associating domains

BACKGROUND: Chromatin folding gives rise to structural elements among which are clusters of densely interacting DNA regions termed topologically associating domains (TADs). TADs have been characterized across multiple species, tissue types, and differentiation stages, sometimes in association with r...

Descripción completa

Detalles Bibliográficos
Autores principales:	Zufferey, Marie, Tavernari, Daniele, Oricchio, Elisa, Ciriello, Giovanni
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	BioMed Central 2018
Materias:	Research
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6288901/ https://www.ncbi.nlm.nih.gov/pubmed/30526631 http://dx.doi.org/10.1186/s13059-018-1596-9

Ejemplares similares

Systematic inference and comparison of multi-scale chromatin sub-compartments connects spatial organization to cell phenotypes
por: Liu, Yuanlong, et al.
Publicado: (2021)

Systematic assessment of gene co-regulation within chromatin domains determines differentially active domains across human cancers
por: Zufferey, Marie, et al.
Publicado: (2021)

Whole-genome doubling drives oncogenic loss of chromatin segregation
por: Lambuta, Ruxandra A., et al.
Publicado: (2023)

Pan-cancer inference of intra-tumor heterogeneity reveals associations with different forms of genomic instability
por: Raynaud, Franck, et al.
Publicado: (2018)

P1290: A TISSUE-BASED EX VIVO CULTURE SYSTEM TO ANTICIPATE TEHRAPY RESPONSE IN LYMPHOMA.
por: Santamaria-Martínez, A., et al.
Publicado: (2022)

AlignNemo: A Local Network Alignment Method to Integrate Homology and Topology
por: Ciriello, Giovanni, et al.
Publicado: (2012)

Identification of alternative topological domains in chromatin
por: Filippova, Darya, et al.
Publicado: (2014)

A computational method to predict topologically associating domain boundaries combining histone Marks and sequence information
por: Gan, Wei, et al.
Publicado: (2019)

A topological algorithm for identification of structural domains of proteins
por: Emmert-Streib, Frank, et al.
Publicado: (2007)

A comparison of topologically associating domain callers over mammals at high resolution
por: Sefer, Emre
Publicado: (2022)

Topologically Associated Domains Delineate Susceptibility to Somatic Hypermutation
por: Senigl, Filip, et al.
Publicado: (2019)

Entropy gives rise to topologically associating domains
por: Vasquez, Paula A., et al.
Publicado: (2016)

Principles of genome folding into topologically associating domains
por: Szabo, Quentin, et al.
Publicado: (2019)

Topological comparison of methods for predicting transcriptional cooperativity in yeast
por: Aguilar, Daniel, et al.
Publicado: (2008)

Pattern recognition of topologically associating domains using deep learning
por: Yang, Jhen Yuan, et al.
Publicado: (2022)

Enhancer-promoter communication: unraveling enhancer strength and positioning within a given topologically associating domain (TAD)
por: Giaimo, Benedetto Daniele, et al.
Publicado: (2022)

Evolutionary stability of topologically associating domains is associated with conserved gene regulation
por: Krefting, Jan, et al.
Publicado: (2018)

272 Gender and Different Prevalence in Asthma Treatment With Anti-IGE (Omalizumab)
por: Patella, Vincenzo, et al.
Publicado: (2012)

Sestrin1, a tumor suppressor that can be rescued
por: Donaldson, Maria C., et al.
Publicado: (2017)

TopDom: an efficient and deterministic method for identifying topological domains in genomes
por: Shin, Hanjun, et al.
Publicado: (2016)

CASPIAN: A method to identify chromatin topological associated domains based on spatial density cluster()
por: Gong, Haiyan, et al.
Publicado: (2022)

Clustered CTCF binding is an evolutionary mechanism to maintain topologically associating domains
por: Kentepozidou, Elissavet, et al.
Publicado: (2020)

Topologically associating domains and their role in the evolution of genome structure and function in Drosophila
por: Liao, Yi, et al.
Publicado: (2021)

Topological domains/domain walls and broken symmetries in multiferroics
por: Cheong, Sang-Wook
Publicado: (2019)

A critical comparison of topology-based pathway analysis methods
por: Ihnatova, Ivana, et al.
Publicado: (2018)

Functional and topological characteristics of mammalian regulatory domains
por: Symmons, Orsolya, et al.
Publicado: (2014)

Topological characterisation and identification of critical domains within glucosyltransferase IV (GtrIV) of Shigella flexneri
por: Nair, Anesh, et al.
Publicado: (2011)

An algebraic topological method for multimodal brain networks comparisons
por: Simas, Tiago, et al.
Publicado: (2015)

Epigenome comparisons reveal linkage between gene expression and postnatal remodeling of chromatin domain topology
por: Howard, Bruce H., et al.
Publicado: (2018)

An Algebro-Topological Description of Protein Domain Structure
por: Penner, Robert Clark, et al.
Publicado: (2011)

Correction to ‘TopDom: an efficient and deterministic method for identifying topological domains in genomes’
Publicado: (2022)

TOAST: A novel method for identifying topologically associated domains based on graph auto-encoders and clustering()
por: Gong, Haiyan, et al.
Publicado: (2023)

Research in computational topology
por: Chambers, Erin, et al.
Publicado: (2018)

Computational topology: an introduction
por: Edelsbrunner, Herbert, et al.
Publicado: (2010)

Non-Hausdorff topology and domain theory
por: Goubault-Larrecq, Jean
Publicado: (2013)

Topologically associating domains are stable units of replication-timing regulation
por: Pope, Benjamin D., et al.
Publicado: (2014)

A critical assessment of topologically associating domain prediction tools
por: Dali, Rola, et al.
Publicado: (2017)

Topologically Associating Domains and Regulatory Landscapes in Development, Evolution and Disease
por: Tena, Juan J., et al.
Publicado: (2021)

KSHV Topologically Associating Domains in Latent and Reactivated Viral Chromatin
por: Campbell, Mel, et al.
Publicado: (2022)

Topologically associating domain boundaries are required for normal genome function
por: Rajderkar, Sudha, et al.
Publicado: (2023)

Cannot write session to /tmp/vufind_sessions/sess_luiqss4suac7c7m0eqs8vsuv05