Cargando…

Correlated mutations via regularized multinomial regression

BACKGROUND: In addition to sequence conservation, protein multiple sequence alignments contain evolutionary signal in the form of correlated variation among amino acid positions. This signal indicates positions in the sequence that influence each other, and can be applied for the prediction of intra...

Descripción completa

Detalles Bibliográficos
Autores principales:	Sreekumar, Janardanan, ter Braak, Cajo JF, van Ham, Roeland CHJ, van Dijk, Aalt DJ
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	BioMed Central 2011
Materias:	Research Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3247924/ https://www.ncbi.nlm.nih.gov/pubmed/22082126 http://dx.doi.org/10.1186/1471-2105-12-444

Ejemplares similares

Conserved and variable correlated mutations in the plant MADS protein network
por: van Dijk, Aalt DJ, et al.
Publicado: (2010)

Gene Ontology consistent protein function prediction: the FALCON algorithm applied to six eukaryotic genomes
por: Kourmpetis, Yiannis AI, et al.
Publicado: (2013)

Assessing the contribution of alternative splicing to proteome diversity in Arabidopsis thaliana using proteomics data
por: Severing, Edouard I, et al.
Publicado: (2011)

Comparative analysis indicates that alternative splicing in plants has a limited role in functional expansion of the proteome
por: Severing, Edouard I, et al.
Publicado: (2009)

Bayesian Markov Random Field Analysis for Protein Function Prediction Based on Network Data
por: Kourmpetis, Yiannis A. I., et al.
Publicado: (2010)

Continuous-time modeling of cell fate determination in Arabidopsis flowers
por: van Mourik, Simon, et al.
Publicado: (2010)

Generalized linear mixed models can detect unimodal species-environment relationships
por: Jamil, Tahira, et al.
Publicado: (2013)

Identification of miRNA biomarkers for breast cancer by combining ensemble regularized multinomial logistic regression and Cox regression
por: Li, Juntao, et al.
Publicado: (2022)

Mutational Robustness of Gene Regulatory Networks
por: van Dijk, Aalt D. J., et al.
Publicado: (2012)

Dirichlet negative multinomial regression for overdispersed correlated count data
por: Farewell, Daniel M., et al.
Publicado: (2013)

A critical issue in model-based inference for studying trait-based community assembly and a solution
por: ter Braak, Cajo J.F., et al.
Publicado: (2017)

Validation and updating of risk models based on multinomial logistic regression
por: Van Calster, Ben, et al.
Publicado: (2017)

Bayesian Lasso and multinomial logistic regression on GPU
por: Češnovar, Rok, et al.
Publicado: (2017)

Parametric estimation of P(X > Y) for normal distributions in the context of probabilistic environmental risk assessment
por: Jacobs, Rianne, et al.
Publicado: (2015)

Response to “traits and stress: keys to identify community effects of low levels of toxicants in test systems” by Liess and Beketov (2011)
por: Van den Brink, Paul J., et al.
Publicado: (2011)

Prediction uncertainty assessment of a systems biology model requires a sample of the full probability distribution of its parameters
por: van Mourik, Simon, et al.
Publicado: (2014)

Integrated probabilistic risk assessment for nanoparticles: the case of nanosilica in food
por: Jacobs, Rianne, et al.
Publicado: (2015)

Minimum sample size for developing a multivariable prediction model using multinomial logistic regression
por: Pate, Alexander, et al.
Publicado: (2023)

Analysis of genomic signatures in prokaryotes using multinomial regression and hierarchical clustering
por: Bohlin, Jon, et al.
Publicado: (2009)

RAMRSGL: A Robust Adaptive Multinomial Regression Model for Multicancer Classification
por: Wang, Lei, et al.
Publicado: (2021)

Robust Minimum Divergence Estimation for the Multinomial Circular Logistic Regression Model
por: Castilla, Elena, et al.
Publicado: (2023)

A Unimodal Species Response Model Relating Traits to Environment with Application to Phytoplankton Communities
por: Jamil, Tahira, et al.
Publicado: (2014)

PRI-CAT: a web-tool for the analysis, storage and visualization of plant ChIP-seq experiments
por: Muiño, Jose M., et al.
Publicado: (2011)

In silico miRNA prediction in metazoan genomes: balancing between sensitivity and specificity
por: van der Burgt, Ate, et al.
Publicado: (2009)

A coarsened multinomial regression model for perinatal mother to child transmission of HIV
por: Gard, Charlotte C, et al.
Publicado: (2008)

Analysis of relative abundances with zeros on environmental gradients: a multinomial regression model
por: Chong, Fiona, et al.
Publicado: (2018)

Multinomial and ordinal Logistic regression analyses with multi-categorical variables using R
por: Liang, Jiaqi, et al.
Publicado: (2020)

ChIP-seq Analysis in R (CSAR): An R package for the statistical detection of protein-bound genomic regions
por: Muiño, Jose M, et al.
Publicado: (2011)

A Geometric Approach to Average Problems on Multinomial and Negative Multinomial Models
por: Li, Mingming, et al.
Publicado: (2020)

Antimicrobial resistance clusters in commensal Escherichia coli from livestock
por: Hesp, Ayla, et al.
Publicado: (2021)

An integrative Bayesian Dirichlet-multinomial regression model for the analysis of taxonomic abundances in microbiome data
por: Wadsworth, W. Duncan, et al.
Publicado: (2017)

Evaluation of multinomial logistic regression models for predicting causative pathogens of food poisoning cases
por: INOUE, Hideya, et al.
Publicado: (2018)

Gene Regulatory Networks from Multifactorial Perturbations Using Graphical Lasso: Application to the DREAM4 Challenge
por: Menéndez, Patricia, et al.
Publicado: (2010)

Floral pathway integrator gene expression mediates gradual transmission of environmental and endogenous cues to flowering time
por: van Dijk, Aalt D.J., et al.
Publicado: (2017)

High-throughput bioinformatics with the Cyrille2 pipeline system
por: Fiers, Mark WEJ, et al.
Publicado: (2008)

Multinomial logistic regression approach to haplotype association analysis in population-based case-control studies
por: Chen, Yi-Hau, et al.
Publicado: (2006)

m:Explorer: multinomial regression models reveal positive and negative regulators of longevity in yeast quiescence
por: Reimand, Jüri, et al.
Publicado: (2012)

Erratum to: An integrative Bayesian Dirichlet-multinomial regression model for the analysis of taxonomic abundances in microbiome data
por: Wadsworth, W. Duncan, et al.
Publicado: (2017)

MicroBVS: Dirichlet-tree multinomial regression models with Bayesian variable selection - an R package
por: Koslovsky, Matthew D., et al.
Publicado: (2020)

Aberrant Structure MRI in Parkinson’s Disease and Comorbidity with Depression Based on Multinomial Tensor Regression Analysis
por: Cao, Xuan, et al.
Publicado: (2022)

Cannot write session to /tmp/vufind_sessions/sess_hdmoqm81p930qnhpemovbep66d