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KODAMA specifications

Information


Unique identifier OMICS_14339
Name KODAMA
Alternative name Knowledge Discovery by Accuracy Maximization
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++, R
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.3
Stability Stable
Requirements
Stats
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Stefano Cacciatore

Publication for Knowledge Discovery by Accuracy Maximization

KODAMA citations

 (6)
library_books

A Prospective Metagenomic and Metabolomic Analysis of the Impact of Exercise and/or Whey Protein Supplementation on the Gut Microbiome of Sedentary Adults

2018
mSystems
PMCID: 5915698
PMID: 29719871
DOI: 10.1128/mSystems.00044-18

[…] kage of the same name (V.1.1-3) (). Detection of underlying features of metabolic pathways was performed with unsupervised cross-validated partial-least-squares–discriminant analysis (PLS-DA) and the KODAMA algorithm from the R package of the same name (V.1.4) (). Measurements of alpha diversity and calculations of relative abundances were also performed with the vegan package. Relative-abundance […]

library_books

Fitness Impact of Obligate Intranuclear Bacterial Symbionts Depends on Host Growth Phase

2016
Front Microbiol
PMCID: 5177645
PMID: 28066397
DOI: 10.3389/fmicb.2016.02084

[…] p) expression caused by the symbiont (Hori and Fujishima, ). Enhanced hsp mRNA levels have also been observed for Paramecium bursaria living in symbiosis with the photosynthetic microalgae Chlorella (Kodama et al., ). If H. caryophila likewise effects the hsp expression of its host has not yet been studied. How such an elevated Hsp70 level could result in an increased host growth rate or which oth […]

library_books

Contribution of soil esterase to biodegradation of aliphatic polyester agricultural mulch film in cultivated soils

2015
PMCID: 4384995
PMID: 25852987
DOI: 10.1186/s13568-014-0088-x

[…] es. For example, a cutinase of Fusarium solani prefers pNP-butyrate to pNP-acetate as substrate, and cutinase-like enzyme of Cryptococcus sp. S-2 prefers pNP-caproate to pNP-butyrate and pNP-acetate (Kodama et al. ). The enzymes substrate spectrum, optimum temperature, pH and other conditions are expected to be varied as well. The abundance ratio of PBSA-degrading esterases in each soil is still u […]

library_books

Molecular pathway alterations in CD4 T cells of nonobese diabetic (NOD) mice in the preinsulitis phase of autoimmune diabetes

2014
PMCID: 4050318
PMID: 24918037
DOI: 10.1016/j.rinim.2014.05.001

[…] egulatory loci.The majority of the CD4 T-cell NOD altered genes were repressed, similar to the results of the spleen leukocyte study [] and supported by many other studies in both mice and humans []. Kodama et al. [] reported global repression of genes in various tissues of NOD mice (including spleen cells) in comparison to NOD.B10 controls, a strain in which the NOD MHC haplotype is replaced with […]

library_books

Molecular diversity and predictability of Vibrio parahaemolyticus along the Georgian coastal zone of the Black Sea

2014
Front Microbiol
PMCID: 3918589
PMID: 24575085
DOI: 10.3389/fmicb.2014.00045

[…] hermolabile hemolysin (TLH). It has also been reported that two type three secretion systems (TTSS1 and TTSS2) are involved in V. parahaemolyticus pathogenicity (Bhattacharjee et al., ; Ono et al., ; Kodama et al., ; Matlawska-Wasowska et al., ). The TTSS1 found in all V. parahaemolyticus strains examined to date has been shown to translocate an effector protein (VP1686) into the cytosol of macrop […]

library_books

A Computational Screen for Type I Polyketide Synthases in Metagenomics Shotgun Data

2008
PLoS One
PMCID: 2568958
PMID: 18953415
DOI: 10.1371/journal.pone.0003515

[…] marked as hypothetical, putative, probable or predicted PKS or PKS I.The classification and functionality of PKS proteins in animals is still unclear. Based on the analysis of AT and KS domains Jenke-Kodama et al. placed the animal FAS into the type I PKS family which makes them a subfamily of PKS. Castoe et al. showed that sea urchins (Strongylocentrotus purpuratus and Lytechinus variegatus), b […]

Citations

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KODAMA institution(s)
Institute of Reproductive and Developmental Biology, Imperial College London, London, UK; Department of Clinical and Experimental Medicine, University of Florence, Florence, Italy; Centro Risonanze Magnetiche, University of Florence, Florence, Italy
KODAMA funding source(s)
This project was supported by the SPARKS Children’s Medical Research Charity (P48061) and the Imperial NIHR Biomedical Research Centre. It was also funded by a Career Development Award from the Medical Research Council (MR/L009226/1) and by the EC funded project PhenoMeNal (contract 654241).

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