Senior Computational Biologist @TheBuellLab, University of Georgia https://teapawt.org/t.co/GSYEI2TIlE
Athens, GA
Joined July 2010
- Tweets201
- Following578
- Followers190
- Likes11.5K
John Hamilton retweeted
Orwellian Liberalism;
Diversity is our strength, Two-tier justice is our fairness, Obedience is our democracy.
DoubleThink: Trans rights are womens rights.
NewSpeak: Birthing person, Deadnaming, MAP
Thoughtcrime : Report your neighbours, friends, colleagues and family for crimes of racism.
Reject the evidence of your eyes and ears : Britain was built by immigrants.
Signal your purity to the regime wherever you can, they're listening.
John Hamilton retweeted
Excited to have our first publication on k-mer-based GWAS in bean out in @plantgenome. Great team effort by @TheBuellLab and Dr. Kelly @michiganstate led by @AndrewWiersma. Funded by @USDA @ga_res_alliance @universityofga
acsess.onlinelibrary.wiley.c…
John Hamilton retweeted
Our paper on Chia has been published in @plantgenome! We assembled the genome of Chia pinta, assessed population structure, and also examined terpene synthase composition between Chia pinta and Chia negra. doi.org/10.1002/tpg2.20494
John Hamilton retweeted
Please join the group! We work on all aspects on plant specialised metaboism including gene discovery, biosynthesis, evolution and even applications e.g. biocatalysis and SynBio
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John Hamilton retweeted
Cat thyme (T. marum) produces the iridoid dolichodial to repel insects and attract cats😼
Smit et al. generated a genome assembly & investigated the genetic and enzymatic basis of iridoid biosynthesis
@robin_buell
@LichmanLab
doi.org/10.1111/tpj.16698
@wileyplantsci @SEBiology
John Hamilton retweeted
There are open-source alternatives to CellRanger for single-cell RNA counting. For example:
Simpleaf (alevin-fry wrapper) is faster and more efficient than CR. It outputs unspliced counts by default. It also has fewer false negatives and dropouts:(1/3) #Bioinformatics
John Hamilton retweeted
Adding “best postdoc presentation at GRC plant single cell” to my CV. Photo credit: @Schmitz_Lab
John Hamilton retweeted
Here at TerpNet2023 with @CobusSmit21 from @LichmanLab hearing about @TheBuellLab's collaboration on the synthesis of kitty crack by cat thyme! Made possible by excellent genome assembly by @sefayten. Super cool plant!
John Hamilton retweeted
This Fall I'll be teaching "quick data visualization" as part of a 1st year grad student seminar again for PBGG at UGA. The graphical abstract has 7 sections, but an 8th section on figure assembly has been added as well.
Contents available on GitHub: github.com/cxli233/Online_R_…
John Hamilton retweeted
📢📢📢 New postdoc position in my lab to utilize TEs as molecular markers to study introgression, divergence, and speciation in plants. The position is available until filled. Please RT 📢📢📢 Apply here: osu.wd1.myworkdayjobs.com/OS…
John Hamilton retweeted
AND, last but not least a press release from UGA, College of Agricultural & Environmental Sciences.
Analysis of single plant cells provides insights into natural product biosynthesis: newswire.caes.uga.edu/story.…
@OConnor_lab @ChenxinLi2 @carlos_plants @UGAResearch
John Hamilton retweeted
Notice of Award! I will be working as postdoc/co-PI (an upgrade, I guess) on our newly funded NSF-EAGER to pilot single cell multiome and TF-DNA interaction assays in medicinal plants with @TheBuellLab . 🌳🌿🧬🧪💻📊
John Hamilton retweeted
This is a really well done python reimplementation of DESeq2 and apeglm, I’ve checked the code closely. Nice work @BorisMuzc @Kramarek et al
Meet PyDESeq2 – a Python-based software package for #RNAseq differential expression analysis based on DESeq2. Owkin is open-sourcing PyDESeq2 to support the growing community of bioinformaticians adopting Python for their data analysis workflows.
Check out PyDESeq2 on GitHub at github.com/owkin/PyDESeq2
Read more at owkin.com/en/publications-an…
#bioinformatics #python
John Hamilton retweeted
New paper is online! I described a gene co-expression workflow powered by the Tidyverse & graph based clustering. acsess.onlinelibrary.wiley.c…
This is also my 1st publication as the corresponding author. Step-by-step instructions are available at my GitHub: github.com/cxli233/SimpleTid…
John Hamilton retweeted
Excited to see @ChenxinLi2's Simple Tidy GeneCoEx gene coexpression workflow paper out in @plantgenome today. Great collaboration with Natalie Deans showing how Simple Tidy GeneCoEx compares with WGCNA.
acsess.onlinelibrary.wiley.c…
John Hamilton retweeted
Recent study created a chromosome-scale #genome assembly of Queen’s Wreath, an important plant species in traditional folk medicine, using our Hi-C platform. Congrats @jp_hamilton, @robin_buell, @TheBuellLab, and team! #plantscience hubs.la/Q01F-f0-0
John Hamilton retweeted
A little belated, but here's thesis chapter 2 > Genome Report: Genome sequence of 1S1, a transformable and highly regenerable diploid potato for use as a model for gene editing and genetic engineering doi.org/10.1093/g3journal/jk…
John Hamilton retweeted
Our genome alignment tool - AnchorWave has published online at:
pnas.org/content/119/1/e2113…
It has a big improvement for plant genome comparison.
John Hamilton retweeted
Guppy 5 is now available with Bonito CRF style models #nanoporeconf
- Fast 🚀
- Accurate 📈
- Calibrated Qscores ⁉️
community.nanoporetech.com/p…
John Hamilton retweeted
"The tepary bean genome provides insight into evolution and domestication under heat stress", now out in @NatureComms!
doi.org/10.1038/s41467-021-2…