Swetha Sundar, PhD

Journeying to understand how the chromatin landscape shapes muscle homeostasis and regeneration l JD lab alumnus 🇮🇳 l Post Doc in Puri Lab 🇺🇸 l dancer 💃 l

[Swetha Sundar, PhD @athewss]

Our new study is now online:
https://t.co/dR2x0yrvgF
@ccmb_csir @DBT_inStem @NCBS_Bangalore
@KingsCollegeLon @nainita_rb @malini_sp @ajoyaloysius

[The Reyes Lab @reyes_lab]

Swetha presented her work on AT2 cell aging at the UCSD Healthy aging conference #heathyaging #ucsd #postdoclife @athewss

[Priti S Atmakuru @priti_atmakuru]

@IndianEmbassyUS @USAndIndia @USAmbIndia @USAndHyderabad @MEAIndia @DrSJaishankar
#MedicalEmergency Sister critical, on life support. Hyderabad family MUST travel TODAY. No visa appointments available.
URGENT intervention for #EmergencyVisa
Every moment counts. PLEASE HELP.

[Swetha Sundar, PhD @athewss]

@cathaypacific . I am transiting through Hong Kong on 14th March , 2026. My flight from LA to Hong Kong is delayed severely due to which my connecting flight is 18 hrs after the first. I am trying to apply for a transit visa but am unsuccessful. Could you help?

[Swetha Sundar, PhD @athewss]

@cathaypacific @cathaypacific any help in this regard will be highly appreciated. 18hours is a very long time to be left with improper rest and accommodation in a strange country

[Swetha Sundar, PhD @athewss]

@cathaypacific . I am transiting through Hong Kong on 14th March , 2026. My flight from LA to Hong Kong is delayed severely due to which my connecting flight is 18 hrs after the first. I am trying to apply for a transit visa but am unsuccessful. Could you help?

[Swetha Sundar, PhD @athewss]

@cathaypacific after reading multiple online accounts i am lead to believe that PAR for Indians is routinely denies because of our nationality. I am now left to be in the airport for 18 hours for no mistake of mine, even if the airline provides me with accommodation.

[The Reyes Lab @reyes_lab]

Our fabulous lab technician, Julianne Carnes was awarded the Biological First Mentorship Award in recognition of her exceptional dedication to undergraduate mentorship, hands-on teaching, and her unwavering belief that anyone can succeed in science.
Congratulations, Julianne🥳

[The D2 Lab @TheD2lab]

We are hiring! The lab investigates possibly novel biological principles in Muscle repair and homeostasis mediated by known and unannotated proteins in flies. Much to be discovered! If your passion and skills fit with our lab, do apply! Post code 051024A https://t.co/IdQIJncHdp

[Swetha Sundar, PhD @athewss]

@GokulanCG @TheorApplGenet @ccmb_csir @CSIR_IND Congratulations!!

[Swetha Sundar, PhD @athewss]

@sheminMM Congratulations!!

[Swetha Sundar, PhD @athewss]

@TheD2lab Congratulations to the team!

[Bo Wang @BoWang87]

🔬 Exciting News! Our manuscript, "scGPT: toward building a foundation model for single-cell multi-omics using generative AI" is now finally published in Nature Methods (@NatureMethods) 🎉 !!!

(Re-)Introducing scGPT: A transformative foundation model engineered for single-cell omics analysis. Developed through the analysis of over 33 million human cells, scGPT sets a new benchmark for application versatility, offering both fine-tuning and zero-shot capabilities.

Since its preprint in May 2023, scGPT has significantly impacted the field, evidenced by 13K+ installations, 600+ GitHub stars 🌟, and 40+ citations before its official publication!

scGPT has been validated by numerous benchmark studies as a leading foundation model in single-cell analysis. Its pre-trained embeddings extend its utility beyond single-cell studies, enhancing a variety of downstream tasks including protein enrichment and genetic perturbation predictions.

Some key updates lately:
---Expanded zero-shot applications for efficient reference mapping and integration, now with CellXGene census integration.
---Advanced perturbation analysis capabilities, including genome-scale perturb-seq data analysis and bulk sequencing data generalization.
---Upgraded scGPT package, offering versatile model loading compatible with PyTorch and flash-attn, for both GPU and CPU.
---Cloud-based scGPT applications for reference mapping, cell annotation, and gene regulatory network inference are available on https://t.co/IaaPv7EaTB.
---Integration with Hugging Face for easier model training.

Limitations:
scGPT is an early foray into foundation models for single-cell omics, facing challenges like limited zero-shot learning in some tasks, pretraining constraints, data quality issues, and evaluation limitations. See our Supplementary Notes for details.

🚀 Future Work?

Short-Term Goals:
1. Releasing a Mouse Model for broader analysis.
2. Developing a comprehensive evaluation suite for foundation models in single-cell analysis.
3. Creating a foundation model for single-cell spatial omics.
4. Enhancing zero-shot capacity by integrating scGPT with RAG (e.g., knowledge graphs).

Long-Term Goals:
1. Expanding scGPT for comprehensive single-cell multi-omics analysis.
2. Developing an in-silico perturbation model for predicting genetic perturbation effects.
3. Merging scGPT with multi-modal genomic sequence models for a deeper understanding of cell biology.

📚 Access the paper on Nature Methods: https://t.co/4YCTQymxiA
🔬Preprint in Bioarixv: https://t.co/qyxVGkypaC
💻 All our codes/data/weights are open source: https://t.co/13n0bJvgT2

Wholehearted congratulations to all the authors, especially the two co-first authors, Haotian (@HAOTIANCUI1 ) and Chloe (@chloexwang1), who are really the emerging superstars in AI and biology!

@VectorInst @pmcc_ai @UofTCompSci @UofT_LMP @UHN @UofT

#scGPT #GenerativeAI #AI4Science #Combio #opensource

[Swetha Sundar, PhD @athewss]

@SamMathew_RCB @unescorcb @FEBSJournal @aatifa_zehra @DBTIndia @India_Alliance Congratulations to the team!

[National Centre for Biological Sciences @NCBS_Bangalore]

The 11th Annual Science Journalism Workshop conducted by @anilananth is a great place to start your journey in science writing.

Workshop dates: 17 March- 30 March 2024

Last date to apply: 19 Feb 2024

For more details check https://t.co/DnLVc2mfsc

[Swetha Sundar, PhD @athewss]

@Pradeepkumar_2 @sankarfr1 Congratulations 🎉🎉

[Swetha Sundar, PhD @athewss]

@SamMathew_RCB @unescorcb @oncogenejournal @bhargab76 @AnushreeBharad5 @MeghaAg30198515 congratulations to the team!

[Swetha Sundar, PhD @athewss]

@ppant95 Congratulations!

[Swetha Sundar, PhD @athewss]

@Pradeepkumar_2 @eLife @ccmb_csir @CSIR_IND @AcSIR_India Congratulations to the team!

[Jake Wintermute 🧬/acc @SynBio1]

If you’re looking for a prank gift for that biologist you hate consider 96 individually wrapped pipette tips

[Swetha Sundar, PhD @athewss]

@GokulanCG @biorxiv_plants @ccmb_csir Congratulations to the team!!