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Lemon-Tree specifications


Unique identifier OMICS_19213
Name Lemon-Tree
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes
Wikipedia https://github.com/eb00/lemon-tree/wiki




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  • person_outline Eric Bonnet
  • person_outline Tom Michoel

Publication for Lemon-Tree

Lemon-Tree citations


Inferring the Minimal Genome of Mesoplasma florum by Comparative Genomics and Transposon Mutagenesis

PMCID: 5893858
PMID: 29657968
DOI: 10.1128/mSystems.00198-17

[…] n M. mycoides JCVI-syn3.0, highlighting the difficulty of identifying and understanding the roles of essential genes, even in the simplest cells.Mesoplasma florum is a bacterium first isolated from a lemon tree flower in 1984 (). Unlike many other members of the class Mollicutes, M. florum shows a short doubling time of <40 min, requires no sterol for growth, and has no known pathogenic potential. […]


Gene co expression networks in liver and muscle transcriptome reveal sex specific gene expression in lambs fed with a mix of essential oils

BMC Genomics
PMCID: 5885410
PMID: 29618337
DOI: 10.1186/s12864-018-4632-y

[…] The ConsM_K module, identified in liver, was further analysed with the Lemon-Tree algorithm to investigate potential regulator genes. In the males we found two regulatory genes involved in immune and inflammation pathways: catenin alpha like 1 (CTNNAL1) and nuclear trans […]


Sodium Hypochlorite Irrigation and Its Effect on Bond Strength to Dentin

Biomed Res Int
PMCID: 5585644
PMID: 28904947
DOI: 10.1155/2017/1930360

[…] Proanthocyanidin has been found in high concentration in grape seed extract, pin bark extract, cocoa beans, lemon tree bark, and hazel nut tree leaves []. It has been observed that the antioxidant ability of proanthocyanidin is 20 times higher than that reported for sodium ascorbate; its absorbtion can be q […]


Draft Genome Sequence of Cronobacter sakazakii GP1999, Sequence Type 145, an Epiphytic Isolate Obtained from the Tomato’s Rhizoplane/Rhizosphere Continuum

Genome Announc
PMCID: 5543640
PMID: 28774978
DOI: 10.1128/genomeA.00723-17

[…] environmental sources like soil, household dust, and powdered infant formula production lines, as well as from fruits, vegetables, herbs, cereals, and grains (), and they have also been isolated from lemon tree, wheat, rice, and soybean plant rhizoplane/rhizosphere continuums ().Several lines of evidence suggest environmental origins for Cronobacter spp., with plants as the ancestral econiche prom […]


Distribution and community composition of lichens on mature mangroves (Avicennia marina subsp. australasica (Walp.) J.Everett) in New Zealand

PLoS One
PMCID: 5493409
PMID: 28666019
DOI: 10.1371/journal.pone.0180525

[…] s habitat []. Some terrestrial invertebrates have been recorded from mangroves in New Zealand. This includes several moth species, including Planotortrix avicenniae, a mite (Acalitus avicenniae), the lemon tree borer (Oemona hirta) and several ant species []. Despite several international studies describing epiphytic plant and/or lichen diversity on mangroves [, –], there is very little published […]


More Is Better: Recent Progress in Multi Omics Data Integration Methods

Front Genet
PMCID: 5472696
PMID: 28670325
DOI: 10.3389/fgene.2017.00084

[…] It is another unsupervised method focused on reconstructing module networks (Bonnet et al., ). After finding co-expressed clusters from the expression data matrix, Lemon-Tree helps to identify consensus modules and upstream regulatory programs through ensemble methods. First, a gene expression matrix is employed to infer co-expressed gene clusters through a mode […]

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Lemon-Tree institution(s)
Institut Curie, Paris, France; INSERM U900, Paris, France; Mines ParisTech, Fontainebleau, France; Division of Genetics & Genomics, The Roslin Institute, The University of Edinburgh, Midlothian, UK
Lemon-Tree funding source(s)
Supported by Roslin Institute Strategic Grant funding from the BBSRC andthe European Community’s; Seventh Framework Programme (FP7/2007–2013) under grant agreement number FP7-HEALTH-2010-259348 (ASSET project).

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