PhD @Sydney_Uni ➡️ Postdoc @Yale | Applied statistics | Bioinformatics | Biomedical data science | Single cell 🧬
New Haven, CT
Joined June 2018
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Very excited that our latest version of scMerge2 to integrate multi-sample multi-condition single-cell datasets is out @NatureComms. We managed to integrate ~5 million cells from 20 COVID-19 studies. The new scMerge2 is available at github.com/SydneyBioX/scMerg….
@LinYingxin @jeanyang21 @sydneybioinfo present scMerge2 for atlas-scale single-cell multi-sample multi-condition data integration @NatureComms #singlecell #dataintegration #BioTechNatureComms nature.com/articles/s41467-0…
Yingxin Lin retweeted
Very proud of our new #SingleCell work on #PTSD and #MDD out in @Nature today.
Paper: nature.com/articles/s41586-0…
News and views: nature.com/articles/d41586-0…
Press: medicine.yale.edu/news-artic…
Data: doi.org/10.5281/zenodo.15186…
Code: github.com/mjgirgenti/PTSDsn…
Yingxin Lin retweeted
Authors @leihouyeung @LinYingxin @xin4gao @HongyuZhao2 present SANTO, a coarse-to-fine method for spatial omics data integration across platforms and modalities. #BiotechNatureComms @NatureComms
nature.com/articles/s41467-0…
Yingxin Lin retweeted
@sydneybioinfo @LinYingxin @jeanyang21 present BIDCell, a biologically informed, deep learning-based cell segmentation framework for subcellular in situ spatial transcriptomics. @NatureComms #spatialtranscriptomics #BiotechNatureComms
nature.com/articles/s41467-0…
Our new method BIDCell for segmentation of subcellular spatial transcriptomics data is finally out at @NatureComms ! BIDCell incorporates cell type and morphology info in segmentation and can be applied to Xenium, CosMx, Stereoseq and MERSCOPE. nature.com/articles/s41467-0…
BIDCell is available at github.com/SydneyBioX/BIDCel…. We also developed a Cell Segmentation Performance Assessment (CellSPA) framework available at github.com/SydneyBioX/CellSP…
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This work would not have been possible without all the members @sydneybioinfo involved! It was a wonderful experience collaborating with Helen! A special thanks to my supervisor @jeanyang21 for her great support!
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Yingxin Lin retweeted
.@LinYingxin @jeanyang21 @sydneybioinfo present scMerge2, a computational method for integrating a large COVID-19 data collection with over five million cells to reveal distinct signatures of disease progression.
#BiotechNatureComms
nature.com/articles/s41467-0…
I am very grateful to my wonderful supervisor @jeanyang21 and coauthors @YueCao16 Elijah and @TheEllisPatrick from @sydneybioinfo for their efforts and support!
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The COVID19 datasets used in scMerge2 can be downloaded from covidsc.d24h.hk, developed by @joshuawkho lab. Check out covidscope preprint for more details: doi.org/10.1101/2022.12.03.5…
Yingxin Lin retweeted
I'm excited to share our publication of Stabilized mosaic single-cell data integration using unshared features 🎉
This was one of my final projects during my postdoc @CRUK_CI @emblebi and I'm immensely grateful to @MarioniLab & Carolina Guibentif for their efforts and support!
Next Monday, Helen and I will share our latest work in cell segmentation of subcellular spatial data. Join us in person (CPC) or via zoom to know more about our new method and new evaluation framework 😬
Next Monday, two of our postdocs @LinYingxin and Xiaohang Fu will be presenting on BIDCell, a data-driven strategy which can significantly enhance single-cell spatial expression analyses, including cell-cell interactions. See you in person or on Zoom!
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Yingxin Lin retweeted
Next Monday, hear @AnnaSECuomo discuss the challenges in single-cell population genetics. She will present CellRegMap, a statistical framework to map regulatory variants across the continuous manifold of cellular environments estimated from scRNA-seq. Join in person or on Zoom!
Yingxin Lin retweeted
Altered gut microbiota has been linked to obesity and may influence weight loss. How do omic profiles respond to a weight loss intervention and how do they relate to weight loss responsiveness?
Join us in person or on Zoom next Monday with @MagStanislawski to hear more!
Yingxin Lin retweeted
We are extremely delighted to host Professor @MelanieBahlo from @WEHI_research to present on multi-Omics and AI approaches for the study of retinal diseases such as macular telangiectasia Type (MacTel). We look forward to seeing you in person or on Zoom!
Yingxin Lin retweeted
How can we increase the accuracy of inferred context-specific Gene Regulatory Networks (GRNs) from genomics data? Next week, join us on Zoom with @DurenZhana who will present on scPECA, a method which can provide 3 times higher accuracy compared to other methods.
Yingxin Lin retweeted
Next Monday, we are thrilled to have @martinjzhang discuss the benefits of using scDRS. It can identify subpopulations of disease-associated cells not captured by existing cell-type labels, providing insight into schizophrenia and inflammatory bowel disease. Join us on Zoom!
Yingxin Lin retweeted
Dr Wang is an expert in statistical network models. Her research is likely to give us clues about, for instance, how information spreads throughout a social network. She hopes her success and being awarded The Moran Medal will inspire more girls to pursue a career in STEM.
ALT A banner with a woman smiling reads 'Honorific Awards 2023, Moran Medal, Dr Rachel Wang, Sydney University' "When I was growing up, I kept hearing the message from other people around me that boys are better than girls in science, maths Girls are better at more artsy subjects. I just discovered I liked doing maths, so I didn't care."
Yingxin Lin retweeted
Congratulations to Rachel on being awarded The Moran Medal 🎉
Dr Wang is an expert in statistical network models. Her research is likely to give us clues about, for instance, how information spreads throughout a social network. She hopes her success and being awarded The Moran Medal will inspire more girls to pursue a career in STEM.
ALT A banner with a woman smiling reads 'Honorific Awards 2023, Moran Medal, Dr Rachel Wang, Sydney University' "When I was growing up, I kept hearing the message from other people around me that boys are better than girls in science, maths Girls are better at more artsy subjects. I just discovered I liked doing maths, so I didn't care."
Yingxin Lin retweeted
What are the challenges of single cell multi-omics data integration and evaluation? Next Monday, @XiuweiZhang will present on two methods, scDisInFact and scMultiSim, which can overcome some of these issues. Join us on Zoom!
