Mike O'Leary

USDA-ARS postdoctoral researcher. Opinions are my own.

[Mike Tisza @MikeTisza]

Our paper is out today! Bacterial genomics has exploded in recent years, but, with a few exceptions, researchers have ignored bacterial epigenomes. We analyzed hundreds of Bacteroides (and friends) isolates and found astonishing epigenomic diversity.
https://t.co/SUpvmBbcLD

[Burstein lab @BursteinLab]

Imagine you’re a plasmid conjugating into a recipient cell. How would you overcome CRISPR-Cas and other bacterial defense systems? Encoding anti-defense mechanisms is one obvious way.

But where? And how? @BruriaSamuel set out to explore! 🧵 1/6

https://t.co/dsf3U0bsjs

[Dr. Melanie Blokesch @MBlokesch]

Extremely happy to announce the preprint of our Acinetobacter baumannii competence paper spearheaded by Nina @vesel_nina who also did almost all wet-lab experiments....🧵below .... 1/n

[Gang Fang @gangfang_1]

Interested in DNA/RNA modification? Glad to share our paper @NatureRevGenet “Navigating pitfalls of mapping DNA & RNA modification”. VERY promising field, BUT we highlight *common yet not widely recognized pitfalls*. Congrats @kong_yimeng! High-level🧵1/11 https://t.co/6f2ddrDLz9

[Mike O'Leary @mloleary2]

Finally out! Thanks @AlanTourancheau and @iamfanggang for building a tool that let me do some easy hypothesis testing around bacterial R-M systems. Getting modification target data was much more interesting than just IDing genotypes.

https://t.co/lAhATTnEyd

[bioRxiv Microbiology @biorxiv_micrbio]

Restriction-modification systems have shaped the evolution and distribution of plasmids across bacteria https://t.co/MApAllcV5a #biorxiv_micrbio

[Mike O'Leary @mloleary2]

@iamfanggang @nanopore @_Alan_T Coincidental timing - I just had a manuscript accepted that used NanoDisco to ID methylation motifs in a bunch of strains, which was one of the more interesting parts. Really grateful to you and @AlanTourancheau for developing this tool!

[Gitta Coaker @GittaCoaker]

Let’s see how UC responds to the largest postdoc and student strike in US history. These people represent future intellectual and STEM leaders. They deserve protection and a living wage.

[Gang Fang @gangfang_1]

Have you ever wished to sequence SPECIFIC bacteria but NOT the vast background in #microbiome? Today, we introduce *mEnrich-seq*: #methylation-guided enrichment sequencing of bacterial taxa of interest from microbiome. 4yr project led by @clannabel7! https://t.co/7sraPxwRdk🧵1/10

[Mike O'Leary @mloleary2]

@surt_lab The read length is probably more important than depth for long reads for this purpose. Is the N50 larger than some of your plasmids / prophages?

@rrwick has some assembly troubleshooting suggestions on Unicycler’s GitHub page, may be useful to start with https://t.co/l4WHHZdrEG

[Heng Li @lh3lh3]

Miniprot, a new mapper for aligning proteins to genomes with splicing and frameshift. Can be used for annotating new genomes. ~20k mouse proteins to the human genome in 5 mins over 16 threads. Still WIP. Feedback welcomed. https://t.co/ILAvmF3VBO

[Mike O'Leary @mloleary2]

Really happy to finally start sharing this work that started from a strange dotplot. Type I R-M systems are absolutely fascinating/bizarre! They've popped up in a few Xylella fastidiosa studies over the years, but have never been comprehensively examined in Xylella.

[APSbacteriology 🧫🌿🌾 @APSbacteriology]

Natural recombination among Type I restriction-modification systems creates diverse genomic methylation patterns among Xylella fastidiosa strains https://t.co/wSUgi7FHVy
@mloleary2 @LindseyBurbank

[APSbacteriology 🧫🌿🌾 @APSbacteriology]

Natural recombination among Type I restriction-modification systems creates diverse genomic methylation patterns among Xylella fastidiosa strains https://t.co/wSUgi7FHVy
@mloleary2 @LindseyBurbank

[Jonathan Jacobs 🧬🦠🕹️🏕️ @bioinformer]

Oh boy... check your packages for #python #malware 🙁

10 malicious PyPI packages found stealing developer's credentials https://t.co/A601nRTGBS #ITsecurity #devops @pypi

[Ensembl @ensembl]

1/ You’ve sequenced your samples and identified variants. Great! 🙌

Now, here's how you can use @ensembl to find out the effect of your variants on #protein structures and interactions. A thread...🧵

#genomics #bioinformatics #tweetorial #Ensembltraining 🧬

[Mike O'Leary @mloleary2]

@CunrathOlivier That looks like a hmgA knockout mutant. Found them in naturally occurring isolates and made them in the lab!

[Ex Center for Algorithmic Biotechnology @bioinf_spbu]

Dear Bandage users and friends! As you might know, original Bandage by @rrwick entered maintenance stage. Together with our student @wafemand from @spbifmo_en we are presenting a pre-release of improved Bandage 0.9.5 (https://t.co/0BhTp0vX73) which features:
1/3

[Mike O'Leary @mloleary2]

@Jhonmart3 Yep! It’s a good tool for sure.

[Dr. Amanda Warr 🧬 @Amandatron89]

I'm having fun playing with this.

I mean working... definitely not playing.

Really nice tool for visualising methylation data, plays well with output from different callers, pretty pictures.

https://t.co/RUj48nqMuI

[Aaron Streets @airstreets]

DiMeLo-Seq: a new method for mapping protein-DNA interactions with long-read sequencing. This work was the result of an incredible collaboration with @astraight, @khmiga and @czbiohub. @NAltemose @AnnieMaslan @SmithOwenK @KousikSun were the dream team!
https://t.co/TUvVZqA370