Modeling regulatory networks with weight matrices.

PubWeight™: 2.52‹?› | Rank: Top 2%

🔗 View Article (PMID 10380190)

Published in Pac Symp Biocomput on January 01, 1999

Authors

D C Weaver1, C T Workman, G D Stormo

Author Affiliations

1: Genomica Corporation, Boulder, CO 80303, USA. weaver@genomica.com

Articles citing this

Reverse engineering gene networks using singular value decomposition and robust regression. Proc Natl Acad Sci U S A (2002) 5.29

The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo. Genome Biol (2006) 5.22

Dynamic modeling of gene expression data. Proc Natl Acad Sci U S A (2001) 3.24

Determination of causal connectivities of species in reaction networks. Proc Natl Acad Sci U S A (2002) 2.07

Harnessing naturally randomized transcription to infer regulatory relationships among genes. Genome Biol (2007) 1.94

Big data analysis using modern statistical and machine learning methods in medicine. Int Neurourol J (2014) 1.54

Seeded Bayesian Networks: constructing genetic networks from microarray data. BMC Syst Biol (2008) 1.40

Estimating coarse gene network structure from large-scale gene perturbation data. Genome Res (2002) 1.38

Light- and carbon-signaling pathways. Modeling circuits of interactions. Plant Physiol (2003) 1.29

Boolean networks using the chi-square test for inferring large-scale gene regulatory networks. BMC Bioinformatics (2007) 1.19

Discovery of Time-Delayed Gene Regulatory Networks based on temporal gene expression profiling. BMC Bioinformatics (2006) 1.18

Comparison of probabilistic Boolean network and dynamic Bayesian network approaches for inferring gene regulatory networks. BMC Bioinformatics (2007) 1.15

Reconstructing nonlinear dynamic models of gene regulation using stochastic sampling. BMC Bioinformatics (2009) 1.07

Reverse engineering gene regulatory network from microarray data using linear time-variant model. BMC Bioinformatics (2010) 1.06

High Dimensional ODEs Coupled with Mixed-Effects Modeling Techniques for Dynamic Gene Regulatory Network Identification. J Am Stat Assoc (2012) 1.01

Systems interface biology. J R Soc Interface (2006) 1.01

Inference of dynamical gene-regulatory networks based on time-resolved multi-stimuli multi-experiment data applying NetGenerator V2.0. BMC Syst Biol (2013) 1.01

Network topologies and dynamics leading to endotoxin tolerance and priming in innate immune cells. PLoS Comput Biol (2012) 1.00

Perturbation biology: inferring signaling networks in cellular systems. PLoS Comput Biol (2013) 1.00

Network motif-based identification of transcription factor-target gene relationships by integrating multi-source biological data. BMC Bioinformatics (2008) 0.99

Deterministic and stochastic models of genetic regulatory networks. Methods Enzymol (2009) 0.98

Disentangling information flow in the Ras-cAMP signaling network. Genome Res (2006) 0.97

Evolving cell models for systems and synthetic biology. Syst Synth Biol (2010) 0.93

A framework for integrating the songbird brain. J Comp Physiol A Neuroethol Sens Neural Behav Physiol (2002) 0.92

Modelling evolutionary cell behaviour using neural networks: application to tumour growth. Biosystems (2008) 0.90

Connectivity in the yeast cell cycle transcription network: inferences from neural networks. PLoS Comput Biol (2006) 0.87

Discovery of gene-regulation pathways using local causal search. Proc AMIA Symp (2002) 0.87

Sparse Additive Ordinary Differential Equations for Dynamic Gene Regulatory Network Modeling. J Am Stat Assoc (2014) 0.86

Mean square exponential and robust stability of stochastic discrete-time genetic regulatory networks with uncertainties. Cogn Neurodyn (2010) 0.85

Unconditional global exponential stability in Lagrange sense of genetic regulatory networks with SUM regulatory logic. Cogn Neurodyn (2010) 0.84

Modeling brain dynamics using computational neurogenetic approach. Cogn Neurodyn (2008) 0.83

Multiscale modeling of mucosal immune responses. BMC Bioinformatics (2015) 0.82

Reconstruct gene regulatory network using slice pattern model. BMC Genomics (2009) 0.81

Reverse-engineering the genetic circuitry of a cancer cell with predicted intervention in chronic lymphocytic leukemia. Proc Natl Acad Sci U S A (2012) 0.80

Bridging scales in cancer progression: mapping genotype to phenotype using neural networks. Semin Cancer Biol (2014) 0.79

Constructing biological pathways by a two-step counting approach. PLoS One (2011) 0.78

Reverse engineering Boolean networks: from Bernoulli mixture models to rule based systems. PLoS One (2012) 0.77

SBMLsqueezer 2: context-sensitive creation of kinetic equations in biochemical networks. BMC Syst Biol (2015) 0.77

On the Inference of Functional Circadian Networks Using Granger Causality. PLoS One (2015) 0.76

From gene regulation to gene function: regulatory networks in bacillus subtilis. Comp Funct Genomics (2002) 0.76

Bayesian Orthogonal Least Squares (BOLS) algorithm for reverse engineering of gene regulatory networks. BMC Bioinformatics (2007) 0.76

Comprehensive analysis of gene-environmental interactions with temporal gene expression profiles in Pseudomonas aeruginosa. PLoS One (2012) 0.76

Systematic reverse engineering of network topologies: a case study of resettable bistable cellular responses. PLoS One (2014) 0.75

Sufficient and necessary conditions for Lyapunov stability of genetic networks with SUM regulatory logic. Cogn Neurodyn (2015) 0.75

An approach to inferring transcriptional regulation among genes from large-scale expression data. Comp Funct Genomics (2003) 0.75

A linear programming approach for estimating the structure of a sparse linear genetic network from transcript profiling data. Algorithms Mol Biol (2009) 0.75

Construction of Gene Regulatory Networks Using Recurrent Neural Networks and Swarm Intelligence. Scientifica (Cairo) (2016) 0.75

CMIP: a software package capable of reconstructing genome-wide regulatory networks using gene expression data. BMC Bioinformatics (2016) 0.75

Information theory, evolutionary innovations and evolvability. Philos Trans R Soc Lond B Biol Sci (2017) 0.75

Articles by these authors

Information content of binding sites on nucleotide sequences. J Mol Biol (1986) 30.48

Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics (1999) 14.36

Characterization of translational initiation sites in E. coli. Nucleic Acids Res (1982) 11.91

Use of the 'Perceptron' algorithm to distinguish translational initiation sites in E. coli. Nucleic Acids Res (1982) 9.99

A design for computer nucleic-acid-sequence storage, retrieval, and manipulation. Nucleic Acids Res (1982) 7.79

Identifying constraints on the higher-order structure of RNA: continued development and application of comparative sequence analysis methods. Nucleic Acids Res (1992) 7.51

Identification of consensus patterns in unaligned DNA sequences known to be functionally related. Comput Appl Biosci (1990) 6.16

Displaying the information contents of structural RNA alignments: the structure logos. Comput Appl Biosci (1997) 5.51

Excess information at bacteriophage T7 genomic promoters detected by a random cloning technique. Nucleic Acids Res (1989) 5.22

Selection of optimal DNA oligos for gene expression arrays. Bioinformatics (2001) 5.19

Splicing signals in Drosophila: intron size, information content, and consensus sequences. Nucleic Acids Res (1992) 4.93

Consensus patterns in DNA. Methods Enzymol (1990) 4.89

Delila system tools. Nucleic Acids Res (1984) 4.84

Finding the most significant common sequence and structure motifs in a set of RNA sequences. Nucleic Acids Res (1997) 4.04

Information content and free energy in DNA--protein interactions. J Theor Biol (1998) 3.91

ANN-Spec: a method for discovering transcription factor binding sites with improved specificity. Pac Symp Biocomput (2000) 3.66

Sequence requirements of the hammerhead RNA self-cleavage reaction. Biochemistry (1990) 3.64

Non-independence of Mnt repressor-operator interaction determined by a new quantitative multiple fluorescence relative affinity (QuMFRA) assay. Nucleic Acids Res (2001) 3.63

Identification of coding regions in genomic DNA sequences: an application of dynamic programming and neural networks. Nucleic Acids Res (1993) 3.15

Translation initiation in Escherichia coli: sequences within the ribosome-binding site. Mol Microbiol (1992) 3.10

Quantitative analysis of the relationship between nucleotide sequence and functional activity. Nucleic Acids Res (1986) 3.02

MATRIX SEARCH 1.0: a computer program that scans DNA sequences for transcriptional elements using a database of weight matrices. Comput Appl Biosci (1995) 2.83

lacZ translation initiation mutations. J Mol Biol (1984) 2.51

A comparative genomics approach to prediction of new members of regulons. Genome Res (2001) 2.37

Autogenous regulatory site on the bacteriophage T4 gene 32 messenger RNA. J Mol Biol (1988) 2.32

Identifying target sites for cooperatively binding factors. Bioinformatics (2001) 2.31

Expectation maximization algorithm for identifying protein-binding sites with variable lengths from unaligned DNA fragments. J Mol Biol (1992) 2.29

Discovering common stem-loop motifs in unaligned RNA sequences. Nucleic Acids Res (2001) 2.12

Quantitative specificity of the Mnt repressor. J Mol Biol (1997) 1.91

A consensus sequence for binding of Lrp to DNA. J Bacteriol (1995) 1.88

Identification of protein coding regions in genomic DNA. J Mol Biol (1995) 1.77

An RNA folding method capable of identifying pseudoknots and base triples. Bioinformatics (1998) 1.66

Quantitative analysis of ribosome binding sites in E.coli. Nucleic Acids Res (1994) 1.63

Escherichia coli promoter sequences: analysis and prediction. Methods Enzymol (1996) 1.61

Autoregulation of gene expression. Quantitative evaluation of the expression and function of the bacteriophage T4 gene 32 (single-stranded DNA binding) protein system. J Mol Biol (1982) 1.57

SAMIE: statistical algorithm for modeling interaction energies. Pac Symp Biocomput (2001) 1.17

Phylogenetically enhanced statistical tools for RNA structure prediction. Bioinformatics (2000) 1.14

Sequence landscapes. Nucleic Acids Res (1986) 1.10

Automated kinetic assay of beta-galactosidase activity. Biotechniques (1991) 1.10

High-level translation initiation. Methods Enzymol (1990) 1.04

Analysis of five presumptive protein-coding sequences clustered between the primosome genes, 41 and 61, of bacteriophages T4, T2, and T6. J Virol (1993) 0.96

Identifying muscle regulatory elements and genes in the nematode Caenorhabditis elegans. Pac Symp Biocomput (2002) 0.91

Detection of deletions in the mitochondrial genome of Caenorhabditis elegans. Nucleic Acids Res (1994) 0.91

PromFD 1.0: a computer program that predicts eukaryotic pol II promoters using strings and IMD matrices. Comput Appl Biosci (1997) 0.91

A phylogenetic approach to RNA structure prediction. Proc Int Conf Intell Syst Mol Biol (1999) 0.87

Injury in the era of genomics. Shock (2001) 0.87

Neural networks for determining protein specificity and multiple alignment of binding sites. Proc Int Conf Intell Syst Mol Biol (1994) 0.87

Automated alignment of RNA sequences to pseudoknotted structures. Proc Int Conf Intell Syst Mol Biol (1997) 0.85

Probing information content of DNA-binding sites. Methods Enzymol (1991) 0.85

Graph-theoretic approach to RNA modeling using comparative data. Proc Int Conf Intell Syst Mol Biol (1995) 0.83

Quantitative DNA sequencing to determine the relative protein-DNA binding constants to multiple DNA sequences. Anal Biochem (1994) 0.82

Finding common sequence and structure motifs in a set of RNA sequences. Proc Int Conf Intell Syst Mol Biol (1997) 0.82

Xlandscape: the graphical display of word frequencies in sequences. Bioinformatics (1998) 0.82

Improved statistical methods reveal direct interactions between 16S and 23S rRNA. Nucleic Acids Res (2000) 0.80

Multi-alphabet consensus algorithm for identification of low specificity protein-DNA interactions. Nucleic Acids Res (1995) 0.80

A mini-greedy algorithm for faster structural RNA stem-loop search. Genome Inform (2001) 0.77

Post-synthetically ligated ribozymes: an alternative approach to iterative solid-phase synthesis. Bioconjug Chem (1997) 0.75