
A Forest Tree Genome and Phenome Database | Georeferenced Data Integration | Featuring 2,130 Tree Species & Counting | Submit Your Data! #FAIRdata
Storrs, Connecticut
Joined December 2011
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TreeGenes retweeted
Excited to have my latest genome featured in #G3journal!
📢 NEW GENOME ALERT: Researchers at @sbbotanicgarden generated a reference genome of the endangered Gaviota tarplant, Deinandra increscens subsp. villosa, an annual herb endemic to the California coast, to understand potential environmental adaptation. bit.ly/4c4w79U
TreeGenes retweeted
Recently finished your undergraduate degree? Looking for a job to prepare you with skills & knowledge for a career in plant research & conservation? Apply to one year traineeship (40K salary) at botanic gardens including @MortonArboretum! Please RT atlantabg.org/conservation-r…
TreeGenes retweeted
For anyone learning or teaching bioinformatics, or if you’re interested in getting started, you may like to check out some of many (>230!) integrated tutorials for the Galaxy bioinformatics platform at training.galaxyproject.org/t… .
The Galaxy platform is a free, easy-to-join, easy-to-use bioinformatics workflow management system that enables scientists to share, analyse and visualise their own data, without needing powerful computers and programming expertise.
Galaxy was first started in 2005, and it’s grown year-on-year into an amazingly useful resource for scientists worldwide, with a global community of developers and end-users. You can read about it here:
The Galaxy Community. (2022). The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update. Nucleic acids research, 50(W1).
academic.oup.com/nar/article…
To get started, you could first go through a few tutorials to find out how the platform works…
training.galaxyproject.org/t…
And then take a look at some very cool tutorials with Oxford @nanopore MinION data, for example:
⭐Analysing data to detect microbial pathogens such as Salmonella in food
training.galaxyproject.org/t…
⭐Characterise the microbiome of beer
training.galaxyproject.org/t…
⭐Or dive into the bacterial biodiversity of soil
training.galaxyproject.org/t…
Galaxy also has a well-developed community, which you can find out more about here:
galaxyproject.org/community/
And, if you have a particular application you have in mind, you may be able to find a Galaxy pipeline that’s already been created as part of a published study (e.g. by searching in Google Scholar). For example, if you’d like to find antimicrobial resistance genes in Salmonella, this article and workflow may be for you:
Lamas et al. (2023). Whole genome sequencing in the palm of your hand: how to implement a MinION Galaxy-based workflow in a food safety laboratory for rapid Salmonella spp. serotyping, virulence, and antimicrobial resistance gene identification. Frontiers in Microbiology, 14.
ncbi.nlm.nih.gov/pmc/article…
Or if you’d like to find out how to produce a reference genome for a vertebrate as part of the Earth Genome project, this will explain how it’s done:
Larivière et al. (2024). Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy. Nature Biotechnology, 1-4.
nature.com/articles/s41587-0…
All amazing resources for people already in the bioinformatics field, but possibly even more useful for teaching the bioinformaticians of the future.
This of course only covers a few aspects of the Galaxy “ecosystem”, so if it seems like it could be useful, be sure to have a look around and see what else there is out there for you.
And, if you are using Galaxy for teaching, we’d love to hear about how you’re using it, especially if you have any tips or online/published resources to share!
Disclaimer: Bento Lab has no affiliation with Galaxy - we just love cool tools and platforms that enable science!
TreeGenes retweeted
Galaxy is ecstatic to share a new paper in Nature Biotechnology! Congratulations to all contributing authors, what an outstanding accomplishment!
Read now: nature.com/articles/s41587-0…
TreeGenes retweeted
New Article: "A designer synthetic chromosome fragment functions in moss" rdcu.be/dxdbV
... redesigned and replaced a 155 kb chromosomal region with synthetic sequence in Physcomitrium patens. The simplified sequence obtains the correct epigenetic landscape.
TreeGenes retweeted
Replying to @UConn_Bioinfo
@UConn_Bioinfo is running a 4 day online workshop on variant detection next week and there are still spaces left. Check it out here: bioinformatics.uconn.edu/cbc… and let us know if you have questions.
TreeGenes retweeted
Red Oak sampling in Gatineau-Ottawa region. Urban vs natural forest #genetic diversity @Lisa_TischNko PhD project #2BT project @NRCan @cwfc_ccfb @cflscf @CEF_CFR @IPorth @raju_aafc @PetitRmy1 @andrewlhipp
TreeGenes retweeted
Yey! Finally out. Check out our work on Douglas-fir transcriptome and genome annotation! #AlyssaFerreira, @Sumaira_Zaman_ , @ensmingerlab, @JillWegrzyn. #IsoSeq @CoAdapTree @TreeGenes academic.oup.com/g3journal/a…
TreeGenes retweeted
Great webinar today with @Irene_Cobo about #CartograPlant @TreeGenes. You can rewatch it here youtu.be/63bheER6eX4
TreeGenes retweeted
We haven’t had that conversation at PAG - Justice, Equity, Diversity, Inclusion + in plant, animal, and biodiversity genomics.
#PAG30 come visit the @EBPJEDI poster (12); grab (or see me) for a ribbon. Join the mailing list bit.ly/pag30jedi?r=qr
TreeGenes retweeted
Thanks to all the speakers and the working groups' hard efforts and volunteer jobs! We had a great workshop! @naithani_s @annaritamarran1 @marcelakarey Meg Staton Monica Poelchau Shabari Subramaniam Kapper Chougule
TreeGenes retweeted
A happy bunch of #genomic databases part of the @AgBioData Consortium. @tair_news @sorghumbase @BAR_PlantBio @TreeGenes @Micropub7n @rightIess @GrameneDatabase #PAG30
TreeGenes retweeted
In addition to the Tripal Cofest, join us for the Tripal Database Network and Initiatives session at #PAG30 on Sat, Jan 14th starting at 4pm PST! Check out the exciting list of speakers and the new features they will be covering! @DrupalCMS @AgBioData @GMODProject @UseGalaxyP
TreeGenes retweeted
Reminder - there are just 2 weeks remaining in @Hacktoberfest! Everyone, of all skill levels, is welcome to join. Visit hacktoberfest.com/ to see current project needs and to register! @TripalProject @usejbrowse @galaxyproject @biocurator @drupal_org #genomics #Fairdata
TreeGenes retweeted
If you are working on a Tripal site, interested in starting a Tripal site, or want to stay connected to our updates, we invite you to join the Tripal Project Slack channel (link at tripal.info/support)! @gmodproject @AgBioData @galaxyproject @usejbrowse #Genomics #FairData
TreeGenes retweeted
🧬You'll hear from David Neale (@WhitebarkFound director/UC Davis) on projects to sequence 1st reference genomes for whitebark & bristlecone pines to advance conservation genetic tools. #WhitebarkPine seq to be published in @TreeGenes this year. More info: whitebarkfound.org/our-work/…
TreeGenes retweeted
The global consortium for oaks carry on working. Today, Juli Pujade-Villar from Barcelona University visited JBUUAP and gave a wonderful lecture. He found a possible new gall species in the Garden. @MortonGTCP @ArbNetorg @bgci @JardinBuap this is what collaboration does! Thanks!
TreeGenes retweeted
This is an opportunity that I cannot recommend enough👇 You'll learn so much, trust me!
Plant Physiology invites applications for the Assistant Features Editor program. buff.ly/3vCYLg6. Applications are due by October 3, 2022.
TreeGenes retweeted
Fantastic postdoc opportunity, Evolution of Sexual Systems in Lausanne with John Pannell, please share!
career5.successfactors.eu/ca…





































