Cargando…

Probabilistic Inference for Nucleosome Positioning with MNase-Based or Sonicated Short-Read Data

We describe a model-based method, PING, for predicting nucleosome positions in MNase-Seq and MNase- or sonicated-ChIP-Seq data. PING compares favorably to NPS and TemplateFilter in scalability, accuracy and robustness to low read density. To demonstrate that PING predictions from widely available so...

Descripción completa

Detalles Bibliográficos
Autores principales:	Zhang, Xuekui, Robertson, Gordon, Woo, Sangsoon, Hoffman, Brad G., Gottardo, Raphael
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Public Library of Science 2012
Materias:	Research Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3290535/ https://www.ncbi.nlm.nih.gov/pubmed/22393380 http://dx.doi.org/10.1371/journal.pone.0032095

Ejemplares similares

Quantitative MNase-seq accurately maps nucleosome occupancy levels
por: Chereji, Răzvan V., et al.
Publicado: (2019)

MNase titration reveals differences between nucleosome occupancy and chromatin accessibility
por: Mieczkowski, Jakub, et al.
Publicado: (2016)

Aberrant nucleosome organization in mouse SCNT embryos revealed by ULI-MNase-seq
por: Yang, Lingyue, et al.
Publicado: (2022)

MNase, as a probe to study the sequence-dependent site exposures in the +1 nucleosomes of yeast
por: Luo, Di, et al.
Publicado: (2018)

Subtracting the sequence bias from partially digested MNase-seq data reveals a general contribution of TFIIS to nucleosome positioning
por: Gutiérrez, Gabriel, et al.
Publicado: (2017)

MNase Profiling of Promoter Chromatin in Salmonella typhimurium-Stimulated GM12878 Cells Reveals Dynamic and Response-Specific Nucleosome Architecture
por: Cole, Lauren, et al.
Publicado: (2020)

High Sensitivity Profiling of Chromatin Structure by MNase-SSP
por: Ramani, Vijay, et al.
Publicado: (2019)

MNase Digestion Protection Patterns of the Linker DNA in Chromatosomes
por: Shen, Chang-Hui, et al.
Publicado: (2021)

CAM: A quality control pipeline for MNase-seq data
por: Hu, Sheng’en, et al.
Publicado: (2017)

Adaptable probabilistic mapping of short reads using position specific scoring matrices
por: Kerpedjiev, Peter, et al.
Publicado: (2014)

Standardized collection of MNase-seq experiments enables unbiased dataset comparisons
por: Rizzo, Jason M, et al.
Publicado: (2012)

Probabilistic inference of short-term synaptic plasticity in neocortical microcircuits
por: Costa, Rui P., et al.
Publicado: (2013)

An Integrated Pipeline for the Genome-Wide Analysis of Transcription Factor Binding Sites from ChIP-Seq
por: Mercier, Eloi, et al.
Publicado: (2011)

Probabilistic Inference for Dynamical Systems
por: Davis, Sergio, et al.
Publicado: (2018)

Inferring nucleosome positions with their histone mark annotation from ChIP data
por: Mammana, Alessandro, et al.
Publicado: (2013)

Nucleosome Positioning with Set of Key Positions and Nucleosome Affinity
por: Wang, Jia, et al.
Publicado: (2014)

Nucleosome Positioning
por: Nishida, Hiromi
Publicado: (2012)

Probabilistic Phylogenetic Inference with Insertions and Deletions
por: Rivas, Elena, et al.
Publicado: (2008)

On the Origins of Suboptimality in Human Probabilistic Inference
por: Acerbi, Luigi, et al.
Publicado: (2014)

Inferring signaling pathways with probabilistic programming
por: Merrell, David, et al.
Publicado: (2020)

Direct Inference and Probabilistic Accounts of Induction
por: Williamson, Jon
Publicado: (2022)

Probabilistic Inference with Polymerizing Biochemical Circuits
por: Katz, Yarden, et al.
Publicado: (2022)

SonicParanoid: fast, accurate and easy orthology inference
por: Cosentino, Salvatore, et al.
Publicado: (2019)

Inferring short tandem repeat variation from paired-end short reads
por: Cao, Minh Duc, et al.
Publicado: (2014)

Efficient probabilistic inference in generic neural networks trained with non-probabilistic feedback
por: Orhan, A. Emin, et al.
Publicado: (2017)

Inter-nucleosomal potentials from nucleosomal positioning data
por: Li, Kunhe, et al.
Publicado: (2022)

Accelerated probabilistic inference of RNA structure evolution
por: Holmes, Ian
Publicado: (2005)

Synaptic and nonsynaptic plasticity approximating probabilistic inference
por: Tully, Philip J., et al.
Publicado: (2014)

Probabilistic inference of lateral gene transfer events
por: Khan, Mehmood Alam, et al.
Publicado: (2016)

Probabilistic inference of synaptic dynamics in neocortical microcircuits
por: Costa, Rui P, et al.
Publicado: (2013)

The effects of probabilistic context inference on motor adaptation
por: Cuevas Rivera, Dario, et al.
Publicado: (2023)

Structural Probing with MNase Tethered to Ribosome Assembly Factors Resolves Flexible RNA Regions within the Nascent Pre-Ribosomal RNA
por: Dielforder, Tom, et al.
Publicado: (2022)

DINTD: Detection and Inference of Tandem Duplications From Short Sequencing Reads
por: Dong, Jinxin, et al.
Publicado: (2020)

A nucleosomal approach to inferring causal relationships of histone modifications
por: Le, Ngoc Tu, et al.
Publicado: (2014)

Probabilistic reasoning in intelligent systems: networks of plausible inference
por: Pearl, Judea
Publicado: (1988)

Bayesian methods for hackers: probabilistic programming and Bayesian inference
por: Davidson-Pilon, Cameron
Publicado: (2016)

Higher-order probabilistic perceptrons as bayesian inference engines
por: Clark, J W, et al.
Publicado: (1999)

Neural substrates of cognitive biases during probabilistic inference
por: Soltani, Alireza, et al.
Publicado: (2016)

Probabilistic Inference of Biological Networks via Data Integration
por: Rogers, Mark F., et al.
Publicado: (2015)

A self-consistent probabilistic formulation for inference of interactions
por: Fernandez-de-Cossio, Jorge, et al.
Publicado: (2020)

Cannot write session to /tmp/vufind_sessions/sess_6d012rsv9in7p3a1ra37dsalnp