Jovana Maksimovic
@jovmaksimovic.bsky.social
Senior Research Associate in Bioinformatics & Computational Biology in the Oshlack Lab @petermaccc.bsky.social Australia. Mum. Sci-fi nerd. Cat person. Really loves cheese. And dancing.
Reposted by Jovana Maksimovic
💾 Prokka 1.15.6 is released!
This is the last major release of Prokka. But don't be sad, because @oschwengers.bsky.social already has an excellent replacement called Bakta you can migrate to.
#bioinformatics #microbiology #genomics
github.com/tseemann/pro...
This is the last major release of Prokka. But don't be sad, because @oschwengers.bsky.social already has an excellent replacement called Bakta you can migrate to.
#bioinformatics #microbiology #genomics
github.com/tseemann/pro...
Release Heading into the sunset · tseemann/prokka
The future
This is probably the last release of Prokka. I won't be making any code changes except bug fixes. I will update the databases occasionally. I strongly recommend you use Bakta by @oschwen...
github.com
December 15, 2025 at 9:09 PM
💾 Prokka 1.15.6 is released!
This is the last major release of Prokka. But don't be sad, because @oschwengers.bsky.social already has an excellent replacement called Bakta you can migrate to.
#bioinformatics #microbiology #genomics
github.com/tseemann/pro...
This is the last major release of Prokka. But don't be sad, because @oschwengers.bsky.social already has an excellent replacement called Bakta you can migrate to.
#bioinformatics #microbiology #genomics
github.com/tseemann/pro...
Reposted by Jovana Maksimovic
HEY! YOU! ggdibbler 0.6.1 is finally up on CRAN!
harriet-mason.github.io/ggdibbler/in...
You can now pass random variables to any aesthetic in any ggplot geom/stat. If you can express it as a distribution, ggdibbler can plot it. It also works with ggplot extensions, like gganimate. #rstats
harriet-mason.github.io/ggdibbler/in...
You can now pass random variables to any aesthetic in any ggplot geom/stat. If you can express it as a distribution, ggdibbler can plot it. It also works with ggplot extensions, like gganimate. #rstats
December 6, 2025 at 3:16 PM
HEY! YOU! ggdibbler 0.6.1 is finally up on CRAN!
harriet-mason.github.io/ggdibbler/in...
You can now pass random variables to any aesthetic in any ggplot geom/stat. If you can express it as a distribution, ggdibbler can plot it. It also works with ggplot extensions, like gganimate. #rstats
harriet-mason.github.io/ggdibbler/in...
You can now pass random variables to any aesthetic in any ggplot geom/stat. If you can express it as a distribution, ggdibbler can plot it. It also works with ggplot extensions, like gganimate. #rstats
Reposted by Jovana Maksimovic
Glowing millipedes in hand ✨🪱
New Motyxia in the lab #FluorescenceFriday
New Motyxia in the lab #FluorescenceFriday
December 5, 2025 at 8:27 PM
Glowing millipedes in hand ✨🪱
New Motyxia in the lab #FluorescenceFriday
New Motyxia in the lab #FluorescenceFriday
Reposted by Jovana Maksimovic
I made a small wrapper library for reading slow5/blow5 files in #julialang based on the C slow5lib. If anyone working with #Nanopore sequencing is interested, you can find it here: https://codeberg.org/mzdravkov/Slow5.jl
Slow5.jl
A Julia wrapper for slow5lib
codeberg.org
December 5, 2025 at 9:38 AM
I made a small wrapper library for reading slow5/blow5 files in #julialang based on the C slow5lib. If anyone working with #Nanopore sequencing is interested, you can find it here: https://codeberg.org/mzdravkov/Slow5.jl
Reposted by Jovana Maksimovic
Thanks @natbiotech.nature.com for the shoutout and supporting our work at attempting QC in this emerging field of #spatial #transcriptomics @lgmartelotto.bsky.social @christophermason.bsky.social
Spatial Touchstone brings quality control to spatial transcriptomics #NBTintheNews via @stjuderesearch.bsky.social www.stjude.org/media-resour...
Spatial Touchstone brings quality control to spatial transcriptomics
Explore Spatial Touchstone’s open-source tools and data for standardized spatial transcriptomics, enabling reliable, cross-institutional gene expression analysis.
www.stjude.org
December 5, 2025 at 10:55 PM
Thanks @natbiotech.nature.com for the shoutout and supporting our work at attempting QC in this emerging field of #spatial #transcriptomics @lgmartelotto.bsky.social @christophermason.bsky.social
Reposted by Jovana Maksimovic
This poster design was the hard work of @wytamma.bsky.social who is implementing Snippy-NG. You should follow him now - an amazing ECR who produces a lot of very cool stuff.
It's not just because @torstenseemann.bsky.social is a bioinformatics legend but this may be my favourite #abacbs2025 poster because I'm a #trek tragic 🖖
December 4, 2025 at 1:42 AM
This poster design was the hard work of @wytamma.bsky.social who is implementing Snippy-NG. You should follow him now - an amazing ECR who produces a lot of very cool stuff.
Reposted by Jovana Maksimovic
📢 We are taking applications for our Postdoctoral Fellows Program at Harvard/DFCI!
🔹Join a research group in our department
🔹Co-mentoring opportunities with 2+ faculty
🔹Collaborate with investigators beyond our department
🔹Salary starts at $75K
Apply here: t.co/B7SLZzQFKu
🔹Join a research group in our department
🔹Co-mentoring opportunities with 2+ faculty
🔹Collaborate with investigators beyond our department
🔹Salary starts at $75K
Apply here: t.co/B7SLZzQFKu
https://ds.dfci.harvard.edu/postdocs/
t.co
December 1, 2025 at 6:59 PM
📢 We are taking applications for our Postdoctoral Fellows Program at Harvard/DFCI!
🔹Join a research group in our department
🔹Co-mentoring opportunities with 2+ faculty
🔹Collaborate with investigators beyond our department
🔹Salary starts at $75K
Apply here: t.co/B7SLZzQFKu
🔹Join a research group in our department
🔹Co-mentoring opportunities with 2+ faculty
🔹Collaborate with investigators beyond our department
🔹Salary starts at $75K
Apply here: t.co/B7SLZzQFKu
This is probably of interest to all the @abacbs.bsky.social binfies 🙂
We are thrilled to announce the first official release (v0.1.8) of #𝗯𝗲𝗱𝗱𝗲𝗿, the successor to one of our flagship tool, #𝗯𝗲𝗱𝘁𝗼𝗼𝗹𝘀! Based on ideas we conceived of long ago (!), this was achieved thanks to the dedication of Brent Pedersen.
1/n
1/n
Intro to Bedder – The Quinlan Lab
quinlanlab.org
December 2, 2025 at 4:32 AM
This is probably of interest to all the @abacbs.bsky.social binfies 🙂
Reposted by Jovana Maksimovic
Client-side bioinformatics workshop done ✅ massive thanks to legends @lonsbio.bsky.social @lfeatherstone.bsky.social @torstenseemann.bsky.social #ABACBS2025
November 27, 2025 at 7:23 AM
Client-side bioinformatics workshop done ✅ massive thanks to legends @lonsbio.bsky.social @lfeatherstone.bsky.social @torstenseemann.bsky.social #ABACBS2025
Reposted by Jovana Maksimovic
To add context, part of why there were so many more applicants is because they moved DECRA back six months, effectively skipping funding the scheme for a year. They had to extend eligibility as a result, so this was essentially two years in one. But with no adjustment to number of grants awarded.
November 28, 2025 at 4:51 AM
To add context, part of why there were so many more applicants is because they moved DECRA back six months, effectively skipping funding the scheme for a year. They had to extend eligibility as a result, so this was essentially two years in one. But with no adjustment to number of grants awarded.
Reposted by Jovana Maksimovic
Wonderful week at ABACBS and BioCAsia conferences in Adelaide, Australia.
Thanks everyone who joined the workshop on Orchestrating Microbiome Analysis with Bioconductor, you made it awesome!
@abacbs.bsky.social
@bioconductor.bsky.social
#ABACBS2025
#BioCAsia2025
Thanks everyone who joined the workshop on Orchestrating Microbiome Analysis with Bioconductor, you made it awesome!
@abacbs.bsky.social
@bioconductor.bsky.social
#ABACBS2025
#BioCAsia2025
November 28, 2025 at 6:20 AM
Wonderful week at ABACBS and BioCAsia conferences in Adelaide, Australia.
Thanks everyone who joined the workshop on Orchestrating Microbiome Analysis with Bioconductor, you made it awesome!
@abacbs.bsky.social
@bioconductor.bsky.social
#ABACBS2025
#BioCAsia2025
Thanks everyone who joined the workshop on Orchestrating Microbiome Analysis with Bioconductor, you made it awesome!
@abacbs.bsky.social
@bioconductor.bsky.social
#ABACBS2025
#BioCAsia2025
Reposted by Jovana Maksimovic
That’s a wrap! Huge thank you to everyone who joined us for #ABACBS2025 & a big shout-out to the Adelaide bioinfo community who worked their butts off. Couldn’t have asked for a better crew or a better venue than Adelaide Oval. @wessidepraxis.bsky.social @linsalrob.bsky.social
November 28, 2025 at 5:58 AM
That’s a wrap! Huge thank you to everyone who joined us for #ABACBS2025 & a big shout-out to the Adelaide bioinfo community who worked their butts off. Couldn’t have asked for a better crew or a better venue than Adelaide Oval. @wessidepraxis.bsky.social @linsalrob.bsky.social
Reposted by Jovana Maksimovic
Long read Metagenomics, #phage and #prophage in the gut by Ami Bhatt's group. Beautiful data showing changes in phages over two years
#phagesky
www.nature.com/articles/s41...
#phagesky
www.nature.com/articles/s41...
Long-read metagenomics reveals phage dynamics in the human gut microbiome - Nature
Complex prophage integration dynamics, including low-level induction, cross-family host range and transposase-mediated mobilization, challenge existing paradigms and deepen our understanding of phage–...
www.nature.com
November 26, 2025 at 9:55 PM
Long read Metagenomics, #phage and #prophage in the gut by Ami Bhatt's group. Beautiful data showing changes in phages over two years
#phagesky
www.nature.com/articles/s41...
#phagesky
www.nature.com/articles/s41...
Reposted by Jovana Maksimovic
Woot! The mim preprint is live now. www.biorxiv.org/content/10.1...
Happy Thanksgiving!
Cc @curiouscoding.nl
Happy Thanksgiving!
Cc @curiouscoding.nl
mim: A lightweight auxiliary index to enable fast, parallel, gzipped FASTQ parsing
The FASTQ file format is the lingua franca of primary data distribution and processing across most of bioinformatics. Over time, the compression, storage, transmission, and decompression of gzip compr...
www.biorxiv.org
November 27, 2025 at 5:22 PM
Woot! The mim preprint is live now. www.biorxiv.org/content/10.1...
Happy Thanksgiving!
Cc @curiouscoding.nl
Happy Thanksgiving!
Cc @curiouscoding.nl
Reposted by Jovana Maksimovic
The {colorize} 📦 now on CRAN
github.com/friendly/col...
github.com/friendly/col...
November 28, 2025 at 2:09 AM
The {colorize} 📦 now on CRAN
github.com/friendly/col...
github.com/friendly/col...
This is wonderful ❤️
I was lucky enough to inherit a bunch of racks where a graduate student had labelled all of them with Rack jokes 😂, perfect. I am dead at Racksputin.
November 27, 2025 at 4:44 AM
This is wonderful ❤️
Reposted by Jovana Maksimovic
The first conference for our Lab! Amazing environment at #ABACBS2025! 🙏
Congrats, Mengyuan, Chen and Galen, for the great posters, and Haroon for being a finalist with his talk on the democratisation of foundational models. 🚀
Congrats, Mengyuan, Chen and Galen, for the great posters, and Haroon for being a finalist with his talk on the democratisation of foundational models. 🚀
November 27, 2025 at 3:43 AM
The first conference for our Lab! Amazing environment at #ABACBS2025! 🙏
Congrats, Mengyuan, Chen and Galen, for the great posters, and Haroon for being a finalist with his talk on the democratisation of foundational models. 🚀
Congrats, Mengyuan, Chen and Galen, for the great posters, and Haroon for being a finalist with his talk on the democratisation of foundational models. 🚀
It's time... theconversation.com/how-the-war-...
How the war was won: the campaign to stop medical research cuts
One day in April, Walter and Eliza Hall Institute of Medical Research director Douglas Hilton called his communications manager, Penny Fannin, into his office. “He said he’d heard significant cuts wer...
theconversation.com
November 26, 2025 at 10:07 PM
Reposted by Jovana Maksimovic
And also a fantastic keynote at #ABACBS2025 on this story!
Long read Metagenomics, #phage and #prophage in the gut by Ami Bhatt's group. Beautiful data showing changes in phages over two years
#phagesky
www.nature.com/articles/s41...
#phagesky
www.nature.com/articles/s41...
Long-read metagenomics reveals phage dynamics in the human gut microbiome - Nature
Complex prophage integration dynamics, including low-level induction, cross-family host range and transposase-mediated mobilization, challenge existing paradigms and deepen our understanding of phage–...
www.nature.com
November 26, 2025 at 9:56 PM
And also a fantastic keynote at #ABACBS2025 on this story!
Reposted by Jovana Maksimovic
The success rate for NHMRC Ideas Grants announced yesterday was just over 8%. That means 11 of every 12 people who applied got rejected. This is a culture changing level of rejection and frankly a point of national shame. This is a crisis for research.
I will not rest until we see this resolved.
I will not rest until we see this resolved.
November 26, 2025 at 8:34 PM
The success rate for NHMRC Ideas Grants announced yesterday was just over 8%. That means 11 of every 12 people who applied got rejected. This is a culture changing level of rejection and frankly a point of national shame. This is a crisis for research.
I will not rest until we see this resolved.
I will not rest until we see this resolved.
Reposted by Jovana Maksimovic
Ok — here's the current version of the mim preprint: bit.ly/4pygyyc! Hopefully it will make it to @biorxivpreprint.bsky.social soon, but who knows with the holiday week. Anyway, by the time it hits, we'll probably already have interesting updates to share. Happy to answer questions :).
November 26, 2025 at 9:34 PM
Ok — here's the current version of the mim preprint: bit.ly/4pygyyc! Hopefully it will make it to @biorxivpreprint.bsky.social soon, but who knows with the holiday week. Anyway, by the time it hits, we'll probably already have interesting updates to share. Happy to answer questions :).
Thanks to the Adelaide Bioinformatics SUPERHEROES for making #abacbs2025 a massive success!
November 26, 2025 at 10:45 AM
Thanks to the Adelaide Bioinformatics SUPERHEROES for making #abacbs2025 a massive success!
Reposted by Jovana Maksimovic
A purpose built solution to Australia’s biomedical funding crisis….. release the #MRFF = invest in our future scientists & their discoveries. #DiscoveriesNeedDollars www.smh.com.au/politics/fed...
September 29, 2025 at 1:52 AM
A purpose built solution to Australia’s biomedical funding crisis….. release the #MRFF = invest in our future scientists & their discoveries. #DiscoveriesNeedDollars www.smh.com.au/politics/fed...
Reposted by Jovana Maksimovic
You know if the scientists are protesting en masse something is broken. We did this in Aus for #discoveriesNeedDollars #Rally4Research in like 2011? When it leaked the research budget was gonna be cut. It was not cut. Honestly probably need to think about a repeat situation is so poor here now
November 7, 2024 at 10:02 PM
You know if the scientists are protesting en masse something is broken. We did this in Aus for #discoveriesNeedDollars #Rally4Research in like 2011? When it leaked the research budget was gonna be cut. It was not cut. Honestly probably need to think about a repeat situation is so poor here now
Reposted by Jovana Maksimovic
this is unsustainable, the $600M underspend of the #MRFF could be funnelled, or at least partially funnelled, to supporting excellent #NHMRC applications that fall below the funding cut off because there is too little money in the pot #DiscoveriesNeedDollars #SaveOzScience
An abismal 8% success rate for this year’s #NHMRC #IdeasGrant scheme. Must be an all time low. Congratulations to those successful, you really earned it! Commiserations to the NINETY TWO percent of applicants who didn’t get it… #australianresearch #discoveriesneeddollars 🥼🧪🔬🧫 🇦🇺
November 26, 2025 at 10:28 AM
this is unsustainable, the $600M underspend of the #MRFF could be funnelled, or at least partially funnelled, to supporting excellent #NHMRC applications that fall below the funding cut off because there is too little money in the pot #DiscoveriesNeedDollars #SaveOzScience