Jovana Maksimovic

Some background to this, and an example I think of Phil's attitudes towards fostering students and encouraging others. I never got a chance to meet Phil in person, but will share his act of generosity that helped myself and @hdashnow.bsky.social and I think had in indelible mark on our careers. 1/8

Remembering Phil Bourne Personal reflections on a legendary scientist, leader, builder, and mentor

'Phil was also the founding Editor-in-Chief of PLOS Computational Biology, where he created the beloved Ten Simple Rules series. He was so prolific in the series that the meta-article “Ten Simple Rules for Writing a PLOS Ten Simple Rules Article” literally includes, as Rule 4: “Be Philip E. Bourne.”

QCatch: A framework for quality control assessment and analysis of single-cell sequencing data Motivation: Single-cell sequencing data analysis requires robust quality control (QC) to mitigate technical artifacts and ensure reliable downstream results. While tools like alevin-fry and simpleaf (...

While we've been somewhat successful in spurring adoption of alevin-fry/simpleaf for scRNAseq processing, an impediment Dongze brought to our attention (now working directly w/ many experimentalists) was the need for a nice QC report for it's output; hence QCatch www.biorxiv.org/content/10.1... 1/x

Help shape the future of AI in life sciences research and training — Australian BioCommons We are inviting community input to help shape the future of AI in life sciences. By participating in our survey and focus groups, you’ll help guide infrastructure priorities and shape our training…

Help shape the future of AI in Aussie life sciences! 🤖🧬

Whether you’re an expert or a complete beginner, we need your input to guide our priorities in this space.

Find out how to take the survey or join a focus group today: buff.ly/PbOWzE6
#Bioinformatics #NCRISImpact

Check out our new preprint describing the extensions to SpatialLeiden clustering:
- it's atlas scale (supporting intergration, and fast)
- it's 3D ready (it accepts connections over serial sections)
- it's multiomic ready (it accepts multiple omics layers)

www.biorxiv.org/content/10.6...

Improving SCVI for low-count cells through self-supervised augmentation To improve utility of cells with low UMI counts, I wanted to optimize KL weighting in SCVI models.

Improving SCVI for low-count cells through self-supervised augmentation - www.nxn.se/p/improving-...

Charting single-cell lineages with synthetic and natural barcodes - Nature Reviews Genetics In this Review, Rodriguez-Fraticelli and Parreno discuss advances in single-cell lineage-tracing methods and how their application to diverse biological processes, such as development, ageing and canc...

Review | Charting single-cell lineages with synthetic and natural barcodes www.nature.com/articles/s41...

We are delighted to announce that #ABACBS2026 will be held at RMIT, Melbourne CBD campus from 16th to 20th November 2026. Big thanks to A/Prof. Sonika Tyagi and team for leading this years organising! More details and official conference launch to follow! #bioinformatics @combine1.bsky.social

Introducing kuva: A scientific plotting library in rust, along with cli binary with the option to plot directly into the terminal.

Feel free to drop me some feedback as an issue on the repo

github.com/Psy-Fer/kuva

crates.io/crates/kuva/...

The first fully Rust version of piscem! scRNA, scATAC, and bulk-RNA -> RAD files, accurately, in low memory, and FAST. And all in Rust :) anaconda.org/channels/bio...

GitHub - COMBINE-lab/cf1-rs: An subset of Cuttlefish 1, rewritten in Rust, to provide maximal unitigs and tiling information for piscem indexing. An subset of Cuttlefish 1, rewritten in Rust, to provide maximal unitigs and tiling information for piscem indexing. - COMBINE-lab/cf1-rs

Another one down. A minimal set of the Cuttlefish 1 functionality necessary to move this final component of piscem indexing completely over to Rust - ported from C++ with the help of Claude in < 2 days - github.com/COMBINE-lab/.... The next piscem release will be completely free of C++ dependencies!

[Slams the Inception button]

Home – Cell Symposia: Decoding Cellular Complexity: Single Cell Biology in the Era of AI Cell Symposia: Decoding Cellular Complexity: Single Cell Biology in the Era of AI

Join us at Cell Symposia: Single-Cell Biology in the Era of AI (Dec 2–4, 2026, Munich) 🇩🇪

From multi-omics to AI-driven models of cellular dynamics — an exciting lineup across experimental & computational biology.

Hope to see you there!
🔗 www.cell-symposia.com/single-cell-...

Australia has incredible talent, but without sustained investment and long‑term certainty, we risk losing both people and progress. Supporting medical research isn’t optional — it’s essential for better health outcomes and future prosperity.
www.theaustralian.com.au/health/medic...

I have an opening for a staff scientist or bioinformatician in my group at the Sanger Institute (closing date 24 March). Our current projects focus on disentangling rare and common variant contributions to rare neurodevelopmental conditions and to neurodevelopmental and perinatal traits. 1/2

We’re proud to celebrate Dr Aparna Rao, Dr Deborah Meyran and Associate Professor Safeera Hussainy, who have been awarded the 2026 Lea Medals.

Read more: www.petermac.org/about-us/new...

For those willing to help members of the #zebrafish community, we have a few unanswered questions/queries from the last month that we've compiled in this thread. Any insight, feedback or recommendations are thoroughly appreciated! Please reach out 🙏 #YouRock #AskZebrafish 1/8

Bioconductor Developer Forum promotional banner with the Bioconductor logo at the top left and the title “Developers’ Forum” on the right. The banner includes a QR code labelled “Meeting details.” Event information lists February 26, 2026 at 4 pm GMT, the talk title “Native GPU compute access in R and heterogeneous compute hardware frameworks,” and the speaker name Nicholas Cooley.

The Bioconductor Developer Forum is coming up on:

🗓 Thursday, February 26, 2026
🕓 4pm GMT / 11am EST / 8am PST

This session will feature Native GPU compute access in R with Nicholas Cooley

🔗 Scan the QR code below or follow this link for Zoom details: community-bioc.zulipchat.com#narrow/chann...

‎Gemini - direct access to Google AI Created with Gemini

I used it to create a microbial bioinformatics G-Funk 90's rap snippet 😆

gemini.google.com/share/1df0e1...

Phil Ewels – Reproducible Bioinformatics at Scale: nf-core + Nextflow YouTube video by The Bioinformatics CRO

Missed The Bioinformatics CRO webinar?💻 @ewels.bsky.social shared how the reproducibility crisis in bioinformatics sparked the creation of @nextflow.io and
@nf-co.re, and why it matters for your scientific workflows.

Watch now ⬇️
www.youtube.com/watch?v=7TtI...

registration – EuroBioC2026 Secure your place by registering here.

🚀 Registration for EuroBioC2026 is open!

Join the Bioconductor community to explore the latest in software packages and technologies in computational biology.

📅 June 3-5, 2026
📍 BioCity, Turku, Finland

Register by May 3 to secure your spot:
eurobioc2026.bioconductor.org/pages/regist...

A first-in-human clinical trial to assess an experimental CAR T-cell therapy, fully developed by Peter Mac and manufactured onsite by Cell Therapies has reached the milestone of treating its first patient.

Read more: www.petermac.org/about-us/new...

Postdoc alert in spatial biology!

Building upon our previous work with MSI cancers (e.g. de Vries et al, Nature, 2023), the Voest Group at the NKI is hiring a (fully funded) postdoctoral fellow with strong expertise in spatial cancer biology.

Learn more / apply here: www.nki.nl/careers-stud...

We are holding our annual Rising Stars in Genetics and Genomics Postdoc Symposium on September 24-25, 2026! Please nominate postdocs who are conducting cutting edge, creative work, and are likely to be a leader in their field. Please nominate by April 30, 2026: forms.gle/85NZaxFezUk8...
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Bioconductor-centric hackathon on spatial omics and image-derived data analysis methods We’re planning a 4-day Bioconductor-centric hackathon on spatial omics and image-derived data analysis methods, 19-23 April 2026 in San Servolo, Italy (an island in front of Venice's San Marco…

🚀 Join the Bioconductor Hackathon on Spatial Omics & Image-Derived Data in San Servolo, Italy (Venice) from 19–23 April 2026. Developers in this field are invited to participate.

💡 Limited travel support is available for junior developers

📝 Apply by 20 February:
forms.gle/Gv8EdpxV7XK7...

I am seeking a postdoc to join my group at UCLA -- ideally the candidate would have some experience in either population genetics or microbes/microbiome (computational background needed). We have a range of projects and are happy to tailer to your interests. Please dm/email me if interested.

Poster announcing Aura Raulo as a keynote speaker for EuroBioC 2026. The graphic features the Bioconductor logo and a headshot of Aura Raulo inside a teal circular frame. She is identified as Browne Junior Research Fellow in Biology at the University of Oxford. The description highlights her research on probabilistic and statistical models of complex spreading processes in social contact networks, focusing on microbiome transmission and microbial diversity in animal networks. Event details: June 3–5, 2026, BioCity Turku, Finland, with the website eurobioc2026.bioconductor.org. Logos for The Finnish Society for Bioinformatics, University of Turku, and CompuLifeSci appear at the bottom.

🎉 Speaker Reveal – EuroBioC 2026

We’re excited to announce Dr Aura Raulo as a keynote speaker at EuroBioC2026!

🚨Have work to share? Abstract submission is open!
Submit here: openreview.net/group?id=bio...

Learn more about EuroBioC2026 here: eurobioc2026.bioconductor.org

#EuroBioC2026

Research led by Peter Mac has found a new way to strengthen cancer-fighting T-cells.

Led by Profs Phil Darcy & @paulbeavis4.bsky.social (Peter Mac) and A/Prof Jason Waithman (UWA), the study shows boosting the protein Flt3L improves T-cell durability.

Read more: www.petermac.org/about-us/new...

So i've been doing this, and spamming another thread with updates. I will move that over here now.

I have built most of it. Currently testing on real data and squashing bugs and fixing performance issues.

Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny - Nature Methods This Resource paper presents a global SARS-CoV-2 phylogenetic tree of 4,471,579 high-quality genomes consistently constructed by Viridian, an efficient amplicon-aware assembler.

A long time ago in a galaxy far away, there was a SARS-CoV-2 pandemic. Our paper, led by @martibartfast.bsky.social
a) correcting errors in 4.5 million genomes & their phylogeny
b) improving representation of the Global South in public data
www.nature.com/articles/s41...
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