🎓 PhD scholarship We are recruiting a PhD student to develop new methods for analysing spatial omics data at the University of Sydney, cosupervised by @shazanfar.bsky.social and me. Ideal for students with backgrounds in statistics, data science, computer science or bioinformatics Apply by 18 Jan

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

10 years ago I took a flight to Sydney to attend my first COMBINE. The support of @shazanfar.bsky.social @hdashnow.bsky.social and @lonsbio.bsky.social meant the world and I made so many friends that year I still get to hang out with.Thanks to everyone for a successful conference! #ABACBS2025

10 incredible years of bioinformatics and computational biology community building by @abacbs.bsky.social - enjoying catching up with old friends at #abacbs2025 🥂 @aliciao.bsky.social @nadia-davidson.bsky.social @shazanfar.bsky.social @ellispatrick.bsky.social Jean Yang Belinda Phipson Milica Ng

Huge congratulations to Associate Professor Pengyi Yang and @shazanfar.bsky.social on their new publication in Nature Methods! 🎉 Their work introduces a powerful new tool to simplify method selection for single-cell multimodal omics data. 🔗 Read the paper: go.nature.com/3JetoCh

Want to host a #bioinformatics workshop at #ABACBS2025? We’re building a program of 90-minute workshops and tutorials. Details below. EOIs to host close August 1st. www.abacbs.org/abacbs-2025-...

Finally joined Bluesky! Follow along to stay connected with ABACBS. Keep an eye out in the coming days, we’ll be releasing more details for 2025 conference, including opening abstract submissions and announcing invited speakers! www.abacbs.org/abacbs2025

🎉 A huge thank you to all the incredible speakers who shared their research in our Semester 1 Statistical Bioinformatics Seminar Series! 🧬📊 The series will be back on August 4. We look forward to seeing you soon!

📢 PostDoc opportunity in our Bioinformatics & Cellular Genomics lab at SVI! 🧬 You’d join a welcoming, supportive, and brilliant team. Why not spend a few years in Melbourne and be part of something exciting? Apply here: www.seek.com.au/job/84737876 #ScienceCareers #PostDoc #Bioinformatics

✨Next Monday, join us for our final seminar this semester with Andy Tran from our centre! 🔬From benchtop to bedside: advancing multi-omics statistical methods for precision medicine ⏱️2 June, 1pm (AEST) 🔗http://bit.ly/4hZLxiR

Introducing our new micro-credential: Data Analysis for Precision Health! This hands-on course equips health professionals and researchers with essential statistical skills for analysing real-world health and medical data. 📅 23-24 April (1.5 days) 🎓20% alumni discount 🔗Sign up: bit.ly/4iiCjyv

WEHI Spatial Technology Symposium is back! 🚨 Don’t miss out on the latest in spatial tech—rego below!!!

🎉 We're thrilled to launch our 2025 seminar series next Monday with @lucapinello.bsky.social from Harvard Medical School!✨ He will present: Computational Approaches in Functional Genomics: Understanding Gene Regulation and Development 🧬 ⏱️February 24, 1pm (AEST) 🔗bit.ly/4hZLxiR

🔬 Our Statistical Bioinformatics Seminar series returns next week! 🌟 Join us for another incredible semester with a stellar lineup of speakers. ✨ Here's a sneak peek at some of them 👀 We look forward to seeing you! 🤩 #Bioinformatics #Seminar 🔗bit.ly/4hZLxiR

#SpatialTranscriptomics There are 11 methods (CNN- or Transformer-based) enabling predicting spatial gene expression from H&E histology😆 Which behaves? DeepPT EGNv1 EGNv2 Hist2ST THItoGene DeepSpaCE TCGN ST-Net iStar HisToGene GeneCodeR @naturecomms.bsky.social 2025 www.nature.com/articles/s41...

Did you “Save the date”? If so you may have noticed these are not the right dates!!! Please save 21-23 May

Excited to see Moscot (moscot-tools.org) published in @Nature! We scaled Optimal Transport (OT) in single-cell genomics & added multimodality together with spatiotemporal trajectory inference, finding exciting new biology in the pancreas! 🚀 Read at www.nature.com/articles/s41...

I've stopped posting on Twitter and Threads. I'll stop interacting there and lock those accounts at the end of the week. If you have colleagues who used to follow me on those platforms, feel free to let them know, and that they can follow me here or Mastodon instead. 🙏

Only 7 days left to apply for the Data Science Hub Statistician positions 📈 at the Charles Perkins Centre. 🚀Join our team and contribute to cutting-edge research in biomedical, metabolomics health, public health and beyond! 🔗 bit.ly/4ghCxoS

“The PhD stipend is $33,511 … well below minimum wage of $47,627” “Universities can raise the stipend to a maximum of $52,352, but a ACGR survey found none have done so. The highest stipend is just over $40,000 … with the average at $34,244.” #RaiseTheStipend

Wishing everyone a happy and productive 2025! I'm happy to share that I have been promoted to Senior Lecturer, thank you to my wonderful colleagues and team for your encouragement and support!

Jobortunities: Shortly advertising for 2 positions, both working on the Breast Cancer Atlas, in Sydney. - Wet lab research assistant: mol bio +/- pathology desirable - Comp. Research Assistant: scRNA-Seq, spatial transcriptomics and ML Details to follow, DM or email if you are a great fit.

There's no better way to end an incredible year than with a special Statistical Bioinformatics seminar featuring Dr Jacqueline Siu (Oxford) ✨ She will present Incorporating experimental medicine into single-cell multi-omics 🧬 🔗 More details: bit.ly/4fgDJYe

I want to thank all the coauthors including @boyiguo.bsky.social, Caleb Hallinan, and most importantly, my partner in crime who co-led this work with me @shazanfar.bsky.social 😀 Finally, we want to thank @cziscience.bsky.social for the generous funding and support!

The preprint is available on @biorxivpreprint.bsky.social and we would welcome feedback 📖 doi.org/10.1101/2024...

Using simulated data, we show how spatialMNN can identify spatial domains across N=64 tissue sections with less than 5Gb memory (RAM) in under 10 mins! 🔥

Using mouse Alzheimer's Disease tissue sections profiling genes and proteins on STARmap PLUS, we found spatialMNN is able to find disease-related niches (unsupervised clusters using gene expression) where the Abeta protein accumulates (dark blue dots)

It's designed for barcode- or imaged-based spatial technologies and we compare the performance (accuracy, memory, and speed) of spatialMNN to other existing spatial clustering algorithms and find it's fast, memory-efficient, and accurate! 💃

So pleased to be a part of this brilliant effort! Thank you to all involved especially @haowen-zhou.bsky.social and @stephaniehicks.bsky.social !! This project was borne out of the need for consistent and scalable clustering across many (atlas-scale!) spatial transcriptomics samples 💻📈🧬

Interested in spatial statistics for spatial omics data? Check out our new resource: pasta. We show how different technologies lead to different data modalities give and overview of point-pattern and lattice-based spatial analysis. Feedback welcome! arxiv.org/abs/2412.01561

Biology is *spatiotemporal* Processes such as cancer, wound healing, & embryonic development occur in both time AND space. @shazanfar.bsky.social 5/

When you get to be your own caricature!! Grateful to be in #oz sharing science with #friends. For those missing out #multiomics2024 is where #singlecell #spatial #omics #immunology #oncology and #precisionmedicine is where it’s at🥳

We're delighted to announce a special seminar with a visiting professor. Co-hosted with the School of Maths & Stats, Prof Bin Yu (UC Berkeley) will present Veridical data science and alignment in medical AI. Further details on the event page at: spds.sydney.edu.au/event/veridi...

We are looking for a Data Scientist at the MBExC Excellence Cluster in Göttngen: shorturl.at/Jln3V . Please RT! Read on for more details.

What a perfect Sydney location for a mini symposium on gene regulation in health and disease! Thank you @em6wong.bsky.social & Mat Francois for the invitation to present!

Kicking off our Bluesky life by announcing our Statistical Bioinformatics Seminar Judith & David Coffey Invited Speaker. Mon 25/11 Professor Stephen Leslie, Indigenous Australian genomes show deep population structure and abundant novel variation. Online and @ USyd spds.sydney.edu.au/event/specia...

Something that's been bugging me for a while in bioinformatics data analysis is this overreliance on packages, workflows and what's been called "cargo cult science". Can we have more conceptual thinking, more theory? Asking for what we really want to achieve and what we need to do gets us there.

So many nice starter packs.. I couldn't find one related to spatial biology yet, so I started one 🧬🔬! Here's who I’ve included so far—let me know if you'd like to be added or suggest other must-follow accounts! #SpatialBiology go.bsky.app/SU34ELC

En route to Singapore for the 2nd Spatial Biology Congress: Asia. Looking forward to two full days of exciting science! Thank you to the scientific organisers for the invitation!

Really enjoyed writing this piece for @natureportfolio.bsky.social Nature Reviews Genetics 'Journal Club' section and reflecting on the path that modern in situ-based single-cell expression profiling methods have taken over the last few decades! go.nature.com/4eCCxPs

Greatly appreciative of the opportunity to catch up with old friends and meet new friends this afternoon before the start of the CZI #SingleCell #Biology conference! 🧪 🧬 💻