Cargando…

Quantifying how post-transcriptional noise and gene copy number variation bias transcriptional parameter inference from mRNA distributions

Transcriptional rates are often estimated by fitting the distribution of mature mRNA numbers measured using smFISH (single molecule fluorescence in situ hybridization) with the distribution predicted by the telegraph model of gene expression, which defines two promoter states of activity and inactiv...

Descripción completa

Detalles Bibliográficos
Autores principales:	Fu, Xiaoming, Patel, Heta P, Coppola, Stefano, Xu, Libin, Cao, Zhixing, Lenstra, Tineke L, Grima, Ramon
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	eLife Sciences Publications, Ltd 2022
Materias:	Computational and Systems Biology
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9648968/ https://www.ncbi.nlm.nih.gov/pubmed/36250630 http://dx.doi.org/10.7554/eLife.82493

Ejemplares similares

DNA supercoiling restricts the transcriptional bursting of neighboring eukaryotic genes
por: Patel, Heta P., et al.
Publicado: (2023)

Following the tracks: How transcription factor binding dynamics control transcription
por: de Jonge, Wim J., et al.
Publicado: (2022)

The Hda1 histone deacetylase limits divergent non‐coding transcription and restricts transcription initiation frequency
por: Gowthaman, Uthra, et al.
Publicado: (2021)

Lack of evidence for increased transcriptional noise in aged tissues
por: Ibañez-Solé, Olga, et al.
Publicado: (2022)

Transcription factor clusters enable target search but do not contribute to target gene activation
por: Meeussen, Joseph V W, et al.
Publicado: (2023)

Accuracy of parameter estimation for auto-regulatory transcriptional feedback loops from noisy data
por: Cao, Zhixing, et al.
Publicado: (2019)

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

Brownian Ratchet Mechanism for Faithful Segregation of Low-Copy-Number Plasmids
por: Hu, Longhua, et al.
Publicado: (2017)

Optimized protocol for single-molecule RNA FISH to visualize gene expression in S. cerevisiae
por: Patel, Heta P., et al.
Publicado: (2021)

Post-decision biases reveal a self-consistency principle in perceptual inference
por: Luu, Long, et al.
Publicado: (2018)

Reverse Engineering Cancer: Inferring Transcriptional Gene Signatures from Copy Number Aberrations with ICAro
por: Angeli, Davide, et al.
Publicado: (2019)

Noise regulation by quorum sensing in low mRNA copy number systems
por: Weber, Marc, et al.
Publicado: (2011)

Conference on Fundamental Issues of Nonlinear Laser Dynamics
por: Krauskopf, Bernd, et al.
Publicado: (2000)

Dynamic epistasis analysis reveals how chromatin remodeling regulates transcriptional bursting
por: Brouwer, Ineke, et al.
Publicado: (2023)

Global Associations between Copy Number and Transcript mRNA Microarray Data: An Empirical Study
por: Gu, Wenjuan, et al.
Publicado: (2008)

Mitochondrial DNA copy number variation across human cancers
por: Reznik, Ed, et al.
Publicado: (2016)

Neural network aided approximation and parameter inference of non-Markovian models of gene expression
por: Jiang, Qingchao, et al.
Publicado: (2021)

Molecular Filters for Noise Reduction
por: Laurenti, Luca, et al.
Publicado: (2018)

Dosage compensation can buffer copy-number variation in wild yeast
por: Hose, James, et al.
Publicado: (2015)

An Experimental Framework for Quantifying Bacterial Tolerance
por: Brauner, Asher, et al.
Publicado: (2017)

SplintQuant: a method for accurately quantifying circular RNA transcript abundance without reverse transcription bias
por: Conn, Vanessa, et al.
Publicado: (2019)

Correction: Dosage compensation can buffer copy-number variation in wild yeast
por: Hose, James, et al.
Publicado: (2016)

Quantitative dissection of transcription in development yields evidence for transcription-factor-driven chromatin accessibility
por: Eck, Elizabeth, et al.
Publicado: (2020)

Langevin equation with the deterministic algebraically correlated noise
por: Ploszajczak, M, et al.
Publicado: (1995)

Solving the generalized Langevin equation with the algebraically correlated noise
por: Srokowski, T, et al.
Publicado: (1997)

Transcription-replication coordination revealed in single live cells
por: Tsirkas, Ioannis, et al.
Publicado: (2022)

A continuum model of transcriptional bursting
por: Corrigan, Adam M, et al.
Publicado: (2016)

CNApp, a tool for the quantification of copy number alterations and integrative analysis revealing clinical implications
por: Franch-Expósito, Sebastià, et al.
Publicado: (2020)

CNValidator: validating somatic copy-number inference
por: Smith, Lucian P, et al.
Publicado: (2019)

Network modeling of the transcriptional effects of copy number aberrations in glioblastoma
por: Jörnsten, Rebecka, et al.
Publicado: (2011)

Salmon: fast and bias-aware quantification of transcript expression using dual-phase inference
por: Patro, Rob, et al.
Publicado: (2017)

Further support for aneuploidy tolerance in wild yeast and effects of dosage compensation on gene copy-number evolution
por: Gasch, Audrey P, et al.
Publicado: (2016)

Single-Molecule Fluorescence Imaging in Living Saccharomyces cerevisiae Cells
por: Brouwer, Ineke, et al.
Publicado: (2020)

ProteInfer, deep neural networks for protein functional inference
por: Sanderson, Theo, et al.
Publicado: (2023)

On the Choice and Number of Microarrays for Transcriptional Regulatory Network Inference
por: Cosgrove, Elissa J, et al.
Publicado: (2010)

Experimental noise cutoff boosts inferability of transcriptional networks in large-scale gene-deletion studies
por: Blum, C. F., et al.
Publicado: (2018)

Turbulence, chaos and thermal noise in globally coupled Josephson junction arrays
por: Domínguez, D, et al.
Publicado: (1995)

Spatio-temporal chaos and thermal noise in Josephson junction series arrays
por: Domínguez, D, et al.
Publicado: (1995)

Trust as Extended Control: Human-Machine Interactions as Active Inference
por: Schoeller, Felix, et al.
Publicado: (2021)

Inferring transcript phylogenies
por: Christinat, Yann, et al.
Publicado: (2012)

Cannot write session to /tmp/vufind_sessions/sess_bmu0kt3uq1rlnsbo2n4ffjopnj