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Plant genetics and statistics
research, news and opinions on plant genetics and statistics with emphasis on forage crop breeding and molecular plant ecology
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The Top 10 Retractions of 2015 | The Scientist Magazine®

The Top 10 Retractions of 2015 | The Scientist Magazine® | Plant genetics and statistics | Scoop.it
A look at this year’s most memorable retractions
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Breeding higher yielding crops by increasing sugar import into seeds

Breeding higher yielding crops by increasing sugar import into seeds | Plant genetics and statistics | Scoop.it

Once a mother plant releases its embryos to the outside world, they have to survive on their own without family protection.

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What have plants ever done for us?

What have plants ever done for us? | Plant genetics and statistics | Scoop.it

They provide the food we eat, the medicines we take, the fuel we use – and, of course, the oxygen we breathe. Plants have been indispensable to human beings for millennia, having a profound and often unexpected impact on our everyday lives.

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Red Clover Genome Sequenced | Genetics | Sci-News.com

Red Clover Genome Sequenced | Genetics | Sci-News.com | Plant genetics and statistics | Scoop.it

A team of researchers led by Dr Jose de Vega of Aberystwyth University has successfully sequenced the genome of a red clover variety called the Milvus B.

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What’s the probability that a significant p-value indicates a true effect?

What’s the probability that a significant p-value indicates a true effect? | Plant genetics and statistics | Scoop.it
(This article was first published on Nicebread » R, and kindly contributed to R-bloggers)
If the p-value is < .05, then the probability of falsely rejecting the null hypothesis is  <5%, right?
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Front. Plant Sci./Front. Microbiol.: Genomics and Effectomics of the crop killer Xanthomonas

Front. Plant Sci./Front. Microbiol.: Genomics and Effectomics of the crop killer Xanthomonas | Plant genetics and statistics | Scoop.it

Published articles:

 

11. Research article by Aritua et al.: Genome sequencing reveals a new lineage associated with lablab bean and genetic exchange between Xanthomonas axonopodis pv. phaseoli and Xanthomonas fuscans subsp. fuscans. Front. Microbiol. (2015)

 

10. Mini-review by Zhang et al.: TAL effectors and the executor R genes. Front. Plant Sci. (2015)

 

9. Research article by ÜStun et al.: The Xanthomonas effector XopJ triggers a conditional hypersensitive response upon treatment of N. benthamiana leaves with salicylic acid. Front. Plant Sci. (2015)

 

8. Methods by Pérez-Quintero et al.:  QueTAL: a suite of tools to classify and compare TAL effectors functionally and phylogenetically. Front. Plant Sci. (2015)

 

7. Hypothesis and theory by Wilkins et al.: TAL effectors and activation of predicted host targets distinguish Asian from African strains of the rice pathogen Xanthomonas oryzae pv. oryzicola while strict conservation suggests universal importance of five TAL effectors. Front. Plant Sci. (2015)

 

6. Review by Hutin et al.: MorTAL Kombat: the story of defense against TAL effectors through loss-of-susceptibility. Front. Plant Sci. (2015)

 

5. Research article by Jacobs et al.: Comparative genomics of a cannabis pathogen reveals insight into the evolution of pathogenicity in Xanthomonas. Front. Plant Sci. (2015)

 

4. Research article by Schwartz et al.: Phylogenomics of Xanthomonas field strains infecting pepper and tomato reveals diversity in effector repertoires and identifies determinants of host specificity. Front. Microbiol. (2015)

 

3. Perspective by Dossa et al.: Decision tools for bacterial blight resistance gene deployment in rice-based agricultural ecosystems. Front. Plant Sci. (2015)

 

2. Mini-review by Pieretti et al.: What makes Xanthomonas albilineans unique amongst xanthomonads? Front. Plant Sci. (2015)

 

1. Mini-review by S. Üstün and F. Börnke: Interactions of Xanthomonas type-III effector proteins with the plant ubiquitin and ubiquitin-like pathways. Front. Plant Sci. (2014)


Via Nicolas Denancé
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Suayib Üstün's curator insight, July 29, 2014 2:57 PM

Great topic-excited!

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CRISPR tweak may help gene-edited crops bypass biosafety regulation - Nature.com

CRISPR tweak may help gene-edited crops bypass biosafety regulation - Nature.com | Plant genetics and statistics | Scoop.it
Technique deletes plant genes without adding foreign DNA.
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First year books

First year books | Plant genetics and statistics | Scoop.it
(This article was first published on Maxwell B. Joseph, and kindly contributed to R-bloggers)
I had to read a lot of books in graduate school.
Some were life-changing, and others were forgettable.
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A quick primer on split-apply-combine problems

A quick primer on split-apply-combine problems | Plant genetics and statistics | Scoop.it
I’ve just answered my hundred billionth question on Stack Overflow that goes something like I want to calculate some statistic for lots of different groups. Although these questions provide a steady stream of easy points, its such a common and basic data analysis concept that I thought it would be useful to have a document [...]
Roland Kölliker's insight:

check out Hadley Wickham's paper!

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Mathematical annotations on R plots

Mathematical annotations on R plots | Plant genetics and statistics | Scoop.it
(This article was first published on Hyndsight » R, and kindly contributed to R-bloggers)
I’ve always struggled with using plotmath via the expression function in R for adding mathematical notation to axes or legends.
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Tutorials freely available of course I taught: including ggplot2, dplyr and shiny

Tutorials freely available of course I taught: including ggplot2, dplyr and shiny | Plant genetics and statistics | Scoop.it
(This article was first published on NumberTheory » R stuff, and kindly contributed to R-bloggers)
I was asked to write a R course for a group of innovative companies in the North of the Netherlands.
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Crop Modification Techniques Infographic | Biology Fortified, Inc. - Biofortified Blog

Crop Modification Techniques Infographic | Biology Fortified, Inc. - Biofortified Blog | Plant genetics and statistics | Scoop.it
“To help educate people about the many methods that are used to generate new traits in plants, Biology Fortified has created an infographic on six different crop modification techniques, with exampl...”
Roland Kölliker's insight:
nice graph for communicating breeding tools
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Error Control in Exploratory ANOVA’s: The How and the Why

Error Control in Exploratory ANOVA’s: The How and the Why | Plant genetics and statistics | Scoop.it

In a 2X2X2 design, there are three main effects, three two-way interactions, and one three-way interaction to test. That’s 7 statistical tests.The probability

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New Study: Research Says Plants Do Not Want to be Eaten

New Study: Research Says Plants Do Not Want to be Eaten | Plant genetics and statistics | Scoop.it

We found that feeding vibrations signal changes in the plant cells' metabolism, creating more defensive chemicals that can repel attacks from caterpillars.- Heidi Appel

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My note on multiple testing

It's not a shame to put a note on something (probably) everyone knows and you thought you know but actually you are not 100% sure.

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Gene Editing Plants Without DNA - Asian Scientist Magazine

Gene Editing Plants Without DNA - Asian Scientist Magazine | Plant genetics and statistics | Scoop.it
Researchers have developed a method to edit the genome of plants without the introduction of foreign DNA, possibly circumventing objections to genetically modified organisms.
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BMC Biology | Article collections | What is Wrong With This Picture?

BMC Biology | Article collections | What is Wrong With This Picture? | Plant genetics and statistics | Scoop.it
Roland Kölliker's insight:

Nice examples on how not to present / interpret your data

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A step forward in rice research - The Daily Star

A step forward in rice research - The Daily Star | Plant genetics and statistics | Scoop.it
Genomes of 186 Bangladeshi rice varieties have been sequenced in Beijing Genomics Institute, China as part of a global collaborative project, opening up new opportunities for varietal developments.
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Think Bayes: Bayesian Statistics Made Simple

Think Bayes: Bayesian Statistics Made Simple | Plant genetics and statistics | Scoop.it
(This article was first published on Xi'an's Og » R, and kindly contributed to R-bloggers)
By some piece of luck, I came upon the book Think Bayes: Bayesian Statistics Made Simple, written by Allen B.
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Scientists Have Drafted a Complete Tree of Life - Gizmodo

Scientists Have Drafted a Complete Tree of Life - Gizmodo | Plant genetics and statistics | Scoop.it
Humans, bacteria, daffodils: We’re a diverse bunch on the surface, but trace each and every Earthling back far enough, and you’ll arrive at a common ancestor.
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comic phylogenetic tree with ggtree and comicR

comic phylogenetic tree with ggtree and comicR | Plant genetics and statistics | Scoop.it
(This article was first published on YGC » R, and kindly contributed to R-bloggers)
ggtree applies the concepts of grammar of graphic in phylogenetic tree presentation and make it easy to add multiple layers of text and even figures above a .
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Genome Editing Writ Large - The Biological SCENE

Genome Editing Writ Large - The Biological SCENE | Plant genetics and statistics | Scoop.it
The Biological SCENE
Genome Editing Writ Large
The Biological SCENE
Information pouring in from accurate, low-cost gene-sequencing machines is allowing scientists to pose more and better genomic questions.
Roland Kölliker's insight:

excellent overview

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Minimalist Maps

(This article was first published on Freakonometrics » R-english, and kindly contributed to R-bloggers) This week, I mentioned a series of maps, on Twitter, some minimalist maps http://t.co/YCNPf3AR9n (poke @visionscarto)...
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Seeing Data as the Product of Underlying Structural Forms

Seeing Data as the Product of Underlying Structural Forms | Plant genetics and statistics | Scoop.it
“(This article was first published on Engaging Market Research, and kindly contributed to R-bloggers) Matrix factorization follows from the realization that nothing forces us to accept the data as given.”
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