Author Archives: Ludo

R packages for population genetics

Thought might be useful for many people:

http://nescent.github.io/popgenInfo/
https://github.com/NESCent/r-popgen-hackathon

Cheers,
Ludo

Postdoc position available on fungal adaptation

Please find below a two-years postdoc position open to any non-French citizen.

Ludo

A two-year postdoctoral position in molecular plant pathology at INRA Angers, France (non-French citizens only)

Applications are invited for a postdoctoral position to study molecular
determinants underlying adaptation of pathogenic fungi to their host plants, in the EcoFun team of the Horticulture and Seed Research Institute (IRHS). Our lab conducts research on the interaction between the scab fungus Venturia inaequalis and its host plants, including domesticated and wild apple trees, and firethorn. Host shifts between these hosts have been reported, making this pathosystem an adequate model to identify genes involved in fungal adaptation to different host plants. The research will employ interdisciplinary approaches, including molecular biology, microscopy and RNA-seq analyses. The first task of this position will be to take ownership of population genomic resequencing data to identify genes present in isolates that are pathogenic on a single host only. The second task will be to determine at which stages of the infection process genes involved in adaptation to different host plants are expressed, using confocal and MEB microscopy of incompatible interactions. This knowledge will be
used in a third task to harvest infected leaves for deep transcriptome sequencing (RNA-seq) and identify genes that are specifically expressed on a given host. The successful candidate is also expected to contribute to the writing of research publications and to help with student supervision.

Job requirements
Candidates should have or expected to obtain a PhD in Biology, Molecular Biology, Functional Genomics, or a closely related subject. Skills in Next Generation Sequencing data analysis are highly desirable. Candidates with a PhD in Bioinformatics are also highly encouraged to apply. Experience in fungi and practical knowledge in molecular biology, microscopy and bioinformatics are advantageous. Candidates must have proficiency in oral and written English. This position is available for non-French citizens only.

Job details
The position is full-time for 24 months and is available to start as early as 1st January 2016. Basic gross salary on appointment will be between €2,200 and €3,100 per month depending on experience. The applicant will have the possibility to obtain an additional mobility allowance from the AgreenSkills and AgreenSkills+ schemes, ranging from €1,300 to €1,700 per month depending on experience (www.agreenskills.eu).

Application
The position is open until filled.
Applications should include a cover letter summarizing your experience and describing your research interests, a curriculum vita, and at least two references.
Applications should be emailed to jerome.collemare@angers.inra.fr.
For further information, please contact Dr. J. Collemare
(email: jerome.collemare@angers.inra.fr; tel.: +33(0) 2 41 22 57 15)

Organization description
Institut de Recherche en Horticulture et Semences (IRHS)
UMR1345 INRA – Université d’Angers – Agro Campus Ouest
Evolutionary Ecology of Fungi (EcoFun)
42 rue Georges Morel
49071 Beaucouzé Cedex
http://www6.angers-nantes.inra.fr/irhs/Recherche/EcoFun

The candidate will be located in IRHS, Angers, which leads research on Rosaceae plants and seeds in France, including research on fungi and bacteria pathogenic on apple, pear and rose. The position will provide access to local excellent technical centres in molecular biology and microscopy (laser-scanning confocal microscope, table electron-scanning microscope). The candidate will have the opportunity to interact with other research teams within the institute; and will
interact with scientists with knowledge in functional genomics, population genetics and genomics, epidemiology and modelling within the EcoFun team.

Life in the Loire Valley
The laboratory is located near Angers, in the Loire Valley. This region is often called the garden of France because of fruits and vegetables production, and green calm landscapes. It is also famous for a gentle way of life, high quality regional food and wines. The banks of the Loire River are very touristic in summer, they offer diverse outdoor activities, including biking and visiting the numerous castles.

Who wants broad beans?

Hi all,

I’ve got spare (unused) broad beans from my aphid sampling. I don’t need them any longer and thus wonder if anybody would like to take them/some for their gardening rather that I throw them away.

They are of course aphid free (well for the moment, as long as they are not in a real garden) and are of the ‘Sutton’ dwarf variety.

Please let me know by Thursday if you want some as I’ll throw them away on Friday (l.duvaux@sheffield.ac.uk).

Cheers,
Ludo

Young Natural History scientists in Paris

For those that would be interested in having a meeting for “Young Natural History scientists” in the city of lovers (I speak of Paris, not Venice), please find a descriptive circulars below.

Ludovic

YNHM-first-circular

YNHM-2nd-circular

1st Young Natural History scientists’ Meeting

Hi all,

below is an announce for the first Young Natural History scientists’ Meeting hosted at the MNHN, Paris, France on February 12th-14th, 2014.

The Bureau des Doctorants et Étudiants du Muséum (association for students and young researchers working at the Muséum national d’Histoire naturelle, Paris) is pleased to announce the opening registration (for free) and abstract submission to the first Young Natural History scientists’ Meeting hosted at the MNHN, Paris, France on February 12th-14th, 2014.

We invite submissions for oral and poster presentations on all aspects of natural history within four broad themes:

– Biodiversity Dynamics and Conservation
– Earth and Planetary Sciences
– Mankind, Prehistory, Nature and Societies
– Systematics, Evolution and Comparative Anatomy

Abstract should include name(s) of author(s) and their address(es), a succint title and a text (no more than 300 words), sent by email (indicating if you want to present a talk or a poster) to assobdem@mnhn.fr. Abstract submission deadline is January 19th, 2014.

More information can be found in the first circular, attached to this email.

Please feel free to circulate to colleagues who may be interested in attending, and don’t hesitate to get in touch if you have any questions about the meeting (assobdem@mnhn.fr).

We look forward to meet you in Paris!

Kind regards,

Electric Cool box needed

Hi all,

I will need an electric cool box for some field work between the 9th and the 17th of June (yes, you read well: me Ludovic Duvaux will leave my computer screen to try to catch pea aphids in the real world!).

Would any people of the lab (or other) have one to lend me please?

Cheers,

Ludovic

Accomodation available in Sheffield in late November

Hi all,
please see below a message from Virpi Lummaa that looks for someone to take care of her home while away in late November (25th of November to 9th of December).

I am looking for someone to stay in the house while I am gone, the person can stay for free if they are willing to look after my fish (easy, just feed once a day and check that the heater and pump are working, and everything else is automatic). I will PAY 50 pounds if the person can stay in the house and also look after my dog. If someone wants to look after the house and fish but not the dog, there is an option that I put the dog in the kennels, but I preferred if I found someone who could look after the dog too, because she is very old and doesnt like kennels. She is low-maintenance: she needs to go out for a wee in the garden in the morning, go for 30 mins walk by 5pm in the nearby park daily, and food in the evening. Most of the other time she just sleeps, and unless there are fireworks, she just stays downstairs (in the event of fireworks, she wants to cuddle you!). The only thing is, that she is 65kg (Newfoundland) and does not get along very well with other dogs, so the person would need to be a bit used to dogs to make sure the walks go ok. Basically just keep her on the lead and not let go and say hello to others just in case. If anyone is interested, they can come and see her / come for a walk with us and decide then. She is very friendly with humans.

We are leaving on the 25th of Nov, and coming back on the 9th of Dec (2 weeks). The house is next to the Leppings lane tram stop (9 Willis Road, Hillsborough), 10-15 mins tramride door to door from Uni using the yellow line towards Middlewood, and very close to shops and Hillsborough park. It has 2 big bedrooms.

thank you!
virpi

Football every Wednesday

Hi all,

this is a call for people that want to make a bit of fun sport every weeks. Each Wednesday afternoon, we organize a football session for lab people on Goodwin centre pitches (usually at 17:00). The ambiance is really cool as fun is the main purpose. The participation fees are £3 per person and there is no obligation to come assiduously (just come when you feel so and pay as you go)!

If you are interested, please send me an email to l.duvaux@shef.ac.uk in order to be added to the mailing list (I’ll send an email every weeks to ask who is in a football mood).
Feel free to spread this information to any new member of the lab or friends of yours that might be interested.

Cheers,

Ludovic

generate log-uniform distribution with R

Hi All,

does anyone know how to generate a log-uniform distribution with R?

Cheers,

Ludovic

FASTQ/A short-reads pre-processing tools

Hi all,

just a quick note to tell around about convenient tools aiming at pre-process fastq/a files before DNA mapping on a reference genome:
http://hannonlab.cshl.edu/fastx_toolkit/
https://github.com/najoshi/sickle
https://github.com/vsbuffalo/scythe

http://www.usadellab.org/cms/index.php?page=trimmomatic

Cheers,
Ludovic