NestedMICA statistics

info info

Citations per year

Number of citations per year for the bioinformatics software tool NestedMICA

Tool usage distribution map

This map represents all the scientific publications referring to NestedMICA per scientific context
info info

Associated diseases

This word cloud represents NestedMICA usage per disease context

Popular tool citations

chevron_left Motif discovery chevron_right
Want to access the full stats & trends on this tool?


NestedMICA specifications


Unique identifier OMICS_06280
Name NestedMICA
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages C, Java
Computer skills Advanced
Stability Stable
Maintained Yes


No version available

Publication for NestedMICA

NestedMICA citations


MOST+: A de novo motif finding approach combining genomic sequence and heterogeneous genome wide signatures

BMC Genomics
PMCID: 4474412
PMID: 26099518
DOI: 10.1186/1471-2164-16-S7-S13

[…] s orthologous sequence alignments extracted from multiple genomes, and the other uses genome regions enriched with particular motifs in a single genome []. The first type of methods, such as MEME [], NestedMICA [], and Gibbs sampler [] utilize Bayesian model, EM algorithm, or Gibbs sampling techniques to obtain a Maximum A Posteriori (MAP) for motifs with a given length. Based on these methods, th […]


Motif discovery and transcription factor binding sites before and after the next generation sequencing era

Brief Bioinform
PMCID: 3603212
PMID: 22517426
DOI: 10.1093/bib/bbs016

[…] : the expected frequency of an oligo is estimated by analyzing the oligos that appear at approximately the same distance from the genes transcription start site with a Bayesian segmentation algorithm.NestedMICA [] introduced mosaic background modeling. The idea is to use four different higher order background models according to the overall nucleotide composition of the input sequences, and in par […]


Genomic Targets of Brachyury (T) in Differentiating Mouse Embryonic Stem Cells

PLoS One
PMCID: 3316570
PMID: 22479388
DOI: 10.1371/journal.pone.0033346
call_split See protocol

[…] n was applied to assess the significance of enrichment ratios. Target probes and surrounding promoter sequences were scanned for the published consensus in vitro T-box binding motif TCACACCT , using NestedMICA . We also used Regulatory Sequence Analysis Tools (RSAT) , to scan each target gene over a region −5 […]


Waves of Retrotransposon Expansion Remodel Genome Organization and CTCF Binding in Multiple Mammalian Lineages

PMCID: 3368268
PMID: 22244452
DOI: 10.1016/j.cell.2011.11.058

[…] after exclusion of CTCF and NRSF/REST: length versus GERP Spearman's rho = 0.34, p value = 0.42; IC versus GERP rho = 0, p value = 1. Motif Discovery and Analysis Motif discovery was conducted with NestedMica using the parameters “-minLength 5 -maxLength 30 -numMotifs 6” and a fourth order background model trained on mammalian regulatory regions data. Discovered motifs were confirmed using MEME, […]


Computational biology for ageing

PMCID: 3001313
PMID: 21115530
DOI: 10.1098/rstb.2010.0286

[…] find shared motifs across co-expressed genes, which could indicate a direct co-regulation by the same transcription factor. There are two general ways to address this: ab initio motif discovery (e.g. NestedMICA []) and library-based motif discovery (e.g. Clover []). The big advantage of ab initio methods is that they can discover novel motifs. However, motifs have to be strongly defined and/or ove […]


Metamotifs a generative model for building families of nucleotide position weight matrices

BMC Bioinformatics
PMCID: 2906491
PMID: 20579334
DOI: 10.1186/1471-2105-11-348

[…] LE) Dirichlet distribution estimated from all the motif columns in the input data. It is computed with the optimisation procedure described in [].Our metamotif inference algorithm is a variant of the NestedMICA nested sampling algorithm described in detail in []. Nested sampling, originally introduced by [], is a generic Bayesian MCMC sampling strategy that allows drawing samples from a posterior […]

Want to access the full list of citations?
NestedMICA institution(s)
Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK

NestedMICA reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review NestedMICA