Cargando…

The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo

We present a method (the Inferelator) for deriving genome-wide transcriptional regulatory interactions, and apply the method to predict a large portion of the regulatory network of the archaeon Halobacterium NRC-1. The Inferelator uses regression and variable selection to identify transcriptional in...

Descripción completa

Detalles Bibliográficos
Autores principales:	Bonneau, Richard, Reiss, David J, Shannon, Paul, Facciotti, Marc, Hood, Leroy, Baliga, Nitin S, Thorsson, Vesteinn
Formato:	Texto
Lenguaje:	English
Publicado:	BioMed Central 2006
Materias:	Method
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1779511/ https://www.ncbi.nlm.nih.gov/pubmed/16686963 http://dx.doi.org/10.1186/gb-2006-7-5-r36

Ejemplares similares

Comprehensive de novo structure prediction in a systems-biology context for the archaea Halobacterium sp. NRC-1
por: Bonneau, Richard, et al.
Publicado: (2004)

Regulostat Inferelator: a novel network biology platform to uncover molecular devices that predetermine cellular response phenotypes
por: Ung, Choong Yong, et al.
Publicado: (2019)

DREAM3: Network Inference Using Dynamic Context Likelihood of Relatedness and the Inferelator
por: Madar, Aviv, et al.
Publicado: (2010)

High-performance single-cell gene regulatory network inference at scale: the Inferelator 3.0
por: Skok Gibbs, Claudia, et al.
Publicado: (2022)

Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks
por: Reiss, David J, et al.
Publicado: (2006)

Predicting domain-domain interactions using a parsimony approach
por: Guimarães, Katia S, et al.
Publicado: (2006)

Derivation of genetic interaction networks from quantitative phenotype data
por: Drees, Becky L, et al.
Publicado: (2005)

The Gaggle: An open-source software system for integrating bioinformatics software and data sources
por: Shannon, Paul T, et al.
Publicado: (2006)

Most parsimonious reconciliation in the presence of gene duplication, loss, and deep coalescence using labeled coalescent trees
por: Wu, Yi-Chieh, et al.
Publicado: (2014)

Identification of cis-regulatory mutations generating de novo edges in personalized cancer gene regulatory networks
por: Kalender Atak, Zeynep, et al.
Publicado: (2017)

cMonkey(2): Automated, systematic, integrated detection of co-regulated gene modules for any organism
por: Reiss, David J., et al.
Publicado: (2015)

CIRI: an efficient and unbiased algorithm for de novo circular RNA identification
por: Gao, Yuan, et al.
Publicado: (2015)

Evaluating the effectiveness of population-based breast cancer service screening: an analysis of parsimonious patient survival information with the time-varying Cox model
por: Chang, Rene Wei-Jung, et al.
Publicado: (2022)

Parsimonious Scenario for the Emergence of Viroid-Like Replicons De Novo
por: Catalán, Pablo, et al.
Publicado: (2019)

ParsVNN: parsimony visible neural networks for uncovering cancer-specific and drug-sensitive genes and pathways
por: Huang, Xiaoqing, et al.
Publicado: (2021)

An adaptive geometric search algorithm for macromolecular scaffold selection
por: Jiang, Tian, et al.
Publicado: (2018)

New algorithms for accurate and efficient de novo genome assembly from long DNA sequencing reads
por: Gonzalez-Garcia, Laura, et al.
Publicado: (2023)

Treewidth-based algorithms for the small parsimony problem on networks
por: Scornavacca, Celine, et al.
Publicado: (2022)

Evolution of context dependent regulation by expansion of feast/famine regulatory proteins
por: Plaisier, Christopher L, et al.
Publicado: (2014)

Inference of Bacterial Small RNA Regulatory Networks and Integration with Transcription Factor-Driven Regulatory Networks
por: Arrieta-Ortiz, Mario L., et al.
Publicado: (2020)

Parsimony of Publishers
Publicado: (1852)

The Vice of Parsimony
Publicado: (1875)

On parsimony and clustering
por: Oggier, Frédérique, et al.
Publicado: (2023)

Tools enabling the elucidation of molecular pathways active in human disease: Application to Hepatitis C virus infection
por: Reiss, David J, et al.
Publicado: (2005)

Genome-wide de novo prediction of cis-regulatory binding sites in prokaryotes
por: Zhang, Shaoqiang, et al.
Publicado: (2009)

Multi-species integrative biclustering
por: Waltman, Peter, et al.
Publicado: (2010)

Leveraging chromatin accessibility for transcriptional regulatory network inference in T Helper 17 Cells
por: Miraldi, Emily R., et al.
Publicado: (2019)

Prediction of MicroRNA Precursors Using Parsimonious Feature Sets
por: Stepanowsky, Petra, et al.
Publicado: (2014)

A Partial Least Squares based algorithm for parsimonious variable selection
por: Mehmood, Tahir, et al.
Publicado: (2011)

A Desire for Parsimony
por: Cookson, Lawrence J.
Publicado: (2013)

The law of therapeutic parsimony
por: Kalra, Sanjay, et al.
Publicado: (2016)

A novel k-mer set memory (KSM) motif representation improves regulatory variant prediction
por: Guo, Yuchun, et al.
Publicado: (2018)

De novo ChIP-seq analysis
por: He, Xin, et al.
Publicado: (2015)

A benchmark and an algorithm for detecting germline transposon insertions and measuring de novo transposon insertion frequencies
por: Yu, Tianxiong, et al.
Publicado: (2021)

Streamlined analysis of duplex sequencing data with Du Novo
por: Stoler, Nicholas, et al.
Publicado: (2016)

Ray Meta: scalable de novo metagenome assembly and profiling
por: Boisvert, Sébastien, et al.
Publicado: (2012)

De novo assembly of viral quasispecies using overlap graphs
por: Baaijens, Jasmijn A., et al.
Publicado: (2017)

Accurate long-read de novo assembly evaluation with Inspector
por: Chen, Yu, et al.
Publicado: (2021)

Haploflow: strain-resolved de novo assembly of viral genomes
por: Fritz, Adrian, et al.
Publicado: (2021)

Maximum Parsimony on Phylogenetic networks
por: Kannan, Lavanya, et al.
Publicado: (2012)

Cannot write session to /tmp/vufind_sessions/sess_17s06fknprd91b5vse6f65v43h