Lemon-Tree protocols

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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 in pipeline

PMCID: 4537561
PMID: 26276125
DOI: 10.1186/s12864-015-1816-6

[…] in the module network core (fig. ).fig. 7, regulator genes are not readily identifiable from the wgcna co-expression network modules as they are non-directed. to identify regulator genes, we used lemon-tree software [] first to generated 50 tight clusters (clusters 0–49) covering 839 of the 1301 faags through ten gibbs sampler runs [], and then to examine the 96 candidate regulators […]

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Lemon-Tree in publications

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

[…] 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 potenti […]

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

[…] nal file ., we also identified 76 consms in muscle. none of them were significant in both males and females (p-value< 0.05)., 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 […]

PMCID: 5585644
PMID: 28904947
DOI: 10.1155/2017/1930360

[…] 0 s was effective in increasing the bond durability of etch and rinse system to dentin []., 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 […]

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

[…] 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 […]

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

[…] 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 […]

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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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