Shila Ghazanfar
@shazanfar.bsky.social
Reposted by Shila Ghazanfar
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
Their work introduces a powerful new tool to simplify method selection for single-cell multimodal omics data.
🔗 Read the paper: go.nature.com/3JetoCh
October 15, 2025 at 12:15 AM
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
Their work introduces a powerful new tool to simplify method selection for single-cell multimodal omics data.
🔗 Read the paper: go.nature.com/3JetoCh
Reposted by Shila Ghazanfar
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-...
We’re building a program of 90-minute workshops and tutorials.
Details below. EOIs to host close August 1st.
www.abacbs.org/abacbs-2025-...
July 10, 2025 at 5:39 AM
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-...
We’re building a program of 90-minute workshops and tutorials.
Details below. EOIs to host close August 1st.
www.abacbs.org/abacbs-2025-...
Reposted by Shila Ghazanfar
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
www.abacbs.org/abacbs2025
ABACBS 2025 Conference
Adelaide, South Australia. Nov. 24-
www.abacbs.org
July 2, 2025 at 6:40 AM
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
www.abacbs.org/abacbs2025
Reposted by Shila Ghazanfar
🎉 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!
The series will be back on August 4. We look forward to seeing you soon!
June 20, 2025 at 3:36 AM
🎉 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!
The series will be back on August 4. We look forward to seeing you soon!
Reposted by Shila Ghazanfar
📢 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
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
Research Officer - Bioinformatics Job in Fitzroy, Melbourne VIC - SEEK
Seeking a Postdoc to develop computational toolkits to enable large-scale studies of single-cell and spatial 'omics and statistical genetics
www.seek.com.au
June 16, 2025 at 7:07 AM
📢 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
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
Reposted by Shila Ghazanfar
✨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
🔬From benchtop to bedside: advancing multi-omics statistical methods for precision medicine
⏱️2 June, 1pm (AEST)
🔗http://bit.ly/4hZLxiR
May 28, 2025 at 12:21 AM
✨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
🔬From benchtop to bedside: advancing multi-omics statistical methods for precision medicine
⏱️2 June, 1pm (AEST)
🔗http://bit.ly/4hZLxiR
Reposted by Shila Ghazanfar
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
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
March 3, 2025 at 2:57 AM
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
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
Reposted by Shila Ghazanfar
WEHI Spatial Technology Symposium is back! 🚨
Don’t miss out on the latest in spatial tech—rego below!!!
Don’t miss out on the latest in spatial tech—rego below!!!
February 27, 2025 at 5:40 AM
WEHI Spatial Technology Symposium is back! 🚨
Don’t miss out on the latest in spatial tech—rego below!!!
Don’t miss out on the latest in spatial tech—rego below!!!
Reposted by Shila Ghazanfar
🎉 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
He will present: Computational Approaches in Functional Genomics: Understanding Gene Regulation and Development 🧬
⏱️February 24, 1pm (AEST)
🔗bit.ly/4hZLxiR
February 19, 2025 at 3:52 AM
🎉 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
He will present: Computational Approaches in Functional Genomics: Understanding Gene Regulation and Development 🧬
⏱️February 24, 1pm (AEST)
🔗bit.ly/4hZLxiR
Reposted by Shila Ghazanfar
🔬 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
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
February 17, 2025 at 11:38 PM
🔬 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
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
Reposted by Shila Ghazanfar
#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...
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...
February 16, 2025 at 12:33 PM
#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...
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...
Reposted by Shila Ghazanfar
Did you “Save the date”? If so you may have noticed these are not the right dates!!!
Please save 21-23 May
Please save 21-23 May
January 7, 2025 at 11:54 PM
Did you “Save the date”? If so you may have noticed these are not the right dates!!!
Please save 21-23 May
Please save 21-23 May
Reposted by Shila Ghazanfar
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...
Mapping cells through time and space with moscot - Nature
Moscot is an optimal transport approach that overcomes current limitations of similar methods to enable multimodal, scalable and consistent single-cell analyses of datasets across spatial and temporal...
www.nature.com
January 22, 2025 at 10:46 PM
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...
Reposted by Shila Ghazanfar
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.
🙏
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.
🙏
January 22, 2025 at 3:58 AM
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.
🙏
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.
🙏
Reposted by Shila Ghazanfar
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
🚀Join our team and contribute to cutting-edge research in biomedical, metabolomics health, public health and beyond!
🔗 bit.ly/4ghCxoS
📢 Job Alert!
We are recruiting 5 x Data Science Hub Statisticians 📈at the Charles Perkins Centre.
🚀Join us to drive impactful research in biomedical and metabolomics 🧬health, public health 🩺 and beyond!
📆 Applications close 27 Jan
🔗 bit.ly/4ghCxoS
We are recruiting 5 x Data Science Hub Statisticians 📈at the Charles Perkins Centre.
🚀Join us to drive impactful research in biomedical and metabolomics 🧬health, public health 🩺 and beyond!
📆 Applications close 27 Jan
🔗 bit.ly/4ghCxoS
January 20, 2025 at 2:52 AM
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
🚀Join our team and contribute to cutting-edge research in biomedical, metabolomics health, public health and beyond!
🔗 bit.ly/4ghCxoS
Reposted by Shila Ghazanfar
“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
“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
PhD student Jesse Gardner-Russell earns $20 an hour. Experts say low pay is turning Australia’s best and brightest away
The University of Melbourne student whose work could contribute to curing blindness says ‘people are shocked to find out how unlivable it is’
www.theguardian.com
January 16, 2025 at 11:37 PM
“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
“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!
January 13, 2025 at 2:17 AM
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!
Reposted by Shila Ghazanfar
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.
- 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.
December 12, 2024 at 3:13 AM
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.
- 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.
Reposted by Shila Ghazanfar
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
She will present Incorporating experimental medicine into single-cell multi-omics 🧬
🔗 More details: bit.ly/4fgDJYe
December 12, 2024 at 12:19 AM
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
She will present Incorporating experimental medicine into single-cell multi-omics 🧬
🔗 More details: bit.ly/4fgDJYe
Reposted by Shila Ghazanfar
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!
Finally, we want to thank @cziscience.bsky.social for the generous funding and support!
December 5, 2024 at 4:31 PM
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!
Finally, we want to thank @cziscience.bsky.social for the generous funding and support!
Reposted by Shila Ghazanfar
The preprint is available on @biorxivpreprint.bsky.social and we would welcome feedback
📖 doi.org/10.1101/2024...
📖 doi.org/10.1101/2024...
doi.org
December 5, 2024 at 4:31 PM
The preprint is available on @biorxivpreprint.bsky.social and we would welcome feedback
📖 doi.org/10.1101/2024...
📖 doi.org/10.1101/2024...
Reposted by Shila Ghazanfar
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! 🔥
December 5, 2024 at 4:31 PM
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! 🔥
Reposted by Shila Ghazanfar
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)
December 5, 2024 at 4:31 PM
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)
Reposted by Shila Ghazanfar
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! 💃
December 5, 2024 at 4:31 PM
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 💻📈🧬
This project was borne out of the need for consistent and scalable clustering across many (atlas-scale!) spatial transcriptomics samples 💻📈🧬
Excited to share a new algorithm that we have been working on over the last year.
💡 idea is to extend mutual nearest neighbors for
#spatial data. We call it spatial mutual nearest neighbors (spatialMNN) 😄
Thank you @haowen-zhou.bsky.social @pratibha-panwar.bsky.social who led this work! 👏 🧬🖥️🧪
💡 idea is to extend mutual nearest neighbors for
#spatial data. We call it spatial mutual nearest neighbors (spatialMNN) 😄
Thank you @haowen-zhou.bsky.social @pratibha-panwar.bsky.social who led this work! 👏 🧬🖥️🧪
December 5, 2024 at 10:26 PM
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 💻📈🧬
This project was borne out of the need for consistent and scalable clustering across many (atlas-scale!) spatial transcriptomics samples 💻📈🧬