Sumit Mukherjee

Postdoctoral Fellow at Cancer Data Science Laboratory, NCI/NIH, USA
Research Interests: Bioinformatics, Transcriptomics, Immuno-Oncology, Cancer Evolution

[Sumit Mukherjee @SumitMu16795854]

Excited to share our new preprint, led by me as first author!
We present TIME_ACT, a pan-cancer, interpretable predictor of ICB response from transcriptomics and H&E slides.
#CancerImmunotherapy #DigitalPathology

[Eytan Ruppin, MD, PhD @EytanRuppin]

Proud to introduce TIME_ACT: an unsupervised, #pancancer signature, which accurately identifies hot tumors and predicts response to #ICB across #Cancer from tumor transcriptomics and histopathology. 🧵 (1/6)
📄 https://t.co/Vrn3NimCSy

[Eytan Ruppin, MD, PhD @EytanRuppin]

🔥 TIME_ACT delivers a fast and low-cost predictor of ICB response. With its pan-cancer accuracy and slide-based deployment, it sets the stage for next-generation #PrecisionOncology immunotherapy in the clinic for every patient. 🔬✨ 🧵(6/6)

[Eytan Ruppin, MD, PhD @EytanRuppin]

We inferred TIME_ACT scores directly from H&E slides using our deep learning model, Path2Omics. In 8 new unpublished ICB cohorts, slide-inferred scores predicted response with a mean AUC of 0.72 and mean OR of 5.02. 🧵(5/6)

#DigitalPathology #CancerImmunotherapy

[Eytan Ruppin, MD, PhD @EytanRuppin]

In 15 anti-PD1-treated #RNAseq cohorts, TIME_ACT outperformed 15 immune signatures and 7 transcriptomic-based predictors.
It achieved higher accuracy in identifying responders across cancers (mean AUC = 0.76, OR = 6.11). 🧵(4/6)

[Eytan Ruppin, MD, PhD @EytanRuppin]

🧭 TIME_ACT is strongly associated with immune-active tumor states and inversely linked to exhausted or inactive immune profiles. TIME_ACT also highlights spatially immune-active regions that co-localize with dense lymphocyte infiltrates near tumor cells. 🧵 (3/6) #SpatialOmics

[Eytan Ruppin, MD, PhD @EytanRuppin]

Derived from TCGA #melanoma using immune infiltration score, inflammation score, and TIL patterns, TIME_ACT accurately identifies hot tumors across multiple cancers, demonstrating strong pan-cancer generalizability. 🧵(2/6)

#CancerImmunotherapy #HotTumors

[Eytan Ruppin, MD, PhD @EytanRuppin]

Proud to introduce TIME_ACT: an unsupervised, #pancancer signature, which accurately identifies hot tumors and predicts response to #ICB across #Cancer from tumor transcriptomics and histopathology. 🧵 (1/6)
📄 https://t.co/Vrn3NimCSy

[Arashdeep Singh @arash_stardust]

Preprint alert 🚨
We develop a computational pipeline, CSI-TME, to infer interactions in the TME of IDH-Mut glioma by using bulk RNA-seq data and typically requires scRNA-seq data.
@NCIDataSci @NCIKenAldape @NCIEytanRuppin @hannenhalli

[Sumit Mukherjee @SumitMu16795854]

Thrilled to announce the publication of my latest paper in Trends in Biotechnology (Cell Press): "Designing RNA switches for synthetic biology using inverse-RNA-folding." 🧬📑Exciting insights into the future of synthetic biology! Check it out.

https://t.co/bdc6xPSDqu

[Sanju Sinha @Sanjusinha7]

I am hiring multiple Computational Biologists for my new lab @sbpdiscovery , San Diego.

An alternative to a postdoc, it will pay higher (70-90K$; Be the change you want to see in the world) & is tailored to develop skills to industry transition. https://t.co/tU4Z1HqSXN

My lab focuses on developing machine learning techniques at the intersection of aging and cancer to discover preventative therapies against cancer.

If you find this problem motivating and have pre-existing ML skills, I think you could make an enormous contribution. I want to especially encourage folks from underrepresented backgrounds to apply. Can also email directly to: [email protected]

Pls share this opportunity with relevant folks.

#AcademicTwitter #AcademicChatter #PostdoctoralFellow #ScienceJobs #Job #MachineLearning #Bioinformatics

[Sanju Sinha @Sanjusinha7]

With a mixed bag of emotions - nervousness, excitement, fear & determination, I am announcing the start of my lab at @sbpdiscovery, San Diego.

Our focus will be to develop new preventative therapies for cancer using machine learning.

[M i l a n a M o r g e n s t e r n @Milana_FM]

Our new paper of 2023 has been published in the WIREs RNA journal of Wiley.
The "Functional and regulatory impact of chimeric RNAs in
human normal and cancer cells" paper reveals a fascinating area of fusions in cancers as well as the potential functiona…https://t.co/aKBGka8H7r

[Sumit Mukherjee @SumitMu16795854]

We have published a comprehensive and most updated review paper on chimeric RNAs in WIREs RNA...
@Milana_FM

#ChimericRNA #Fusiongene #Cancers #Precisionmedicine

https://t.co/kVbjEd9fv7

[Sanju Sinha @Sanjusinha7]

Spatial Transcriptomics in cancer.

We will start by answering how are ST expected to drive the next generation of research and diagnostic and therapeutic strategies for cancer?

https://t.co/mbJotyAJAK

[Vivek Subbiah, MD @VivekSubbiah]

🚨🥁Hot off the Press @NatureMedicine 👉 Delighted to share
✅Accelerated approvals hit the target in precision oncology🧬🏹🎯
@FDAOncology Drs. Lori Wirth @Dr_R_Kurzrock @realrickpazdur @DrJuliaBeaver @harpreet_md @GautamMehtaMD @tmprowell https://t.co/2Sirx5hjIN

[Eytan Ruppin, MD, PhD @EytanRuppin]

Excited to see our review out in @NatureRevCancer on applications of big data in basic and translational cancer research!
@PengJiang20 @NCIKenAldape @hannenhalli @cenksahinalp @Sanjusinha7

[Sumit Mukherjee @SumitMu16795854]

Our paper on an adverse event of the BNT162b2 COVID-19 vaccine is online now. We characterized the clinical and molecular features of a rare case of BNT162b2 mRNA vaccine-associated myositis in which the patient was severely affected. @Milana_FM

https://t.co/V8diHaZjiY

[Eytan Ruppin, MD, PhD @EytanRuppin]

Can we provide precision oncology to cancer patients without high-cost sequencing just by using their tumor H&E images🔬?
We are excited to present the first framework for sequencing-less transcriptome-based precision oncology.⚡️ https://t.co/6Ny0NGUfxs

[ANI @ANI]

#WATCH | Singer KK died hours after a concert in Kolkata on May 31st. The auditorium shares visuals of the event held some hours ago. KK was known for songs like 'Pal' and 'Yaaron'. He was brought dead to the CMRI, the hospital told.

Video source: Najrul Manch FB page

[Nature Communications @NatureComms]

Predictive value of tumor microbial abundances for cancer prognosis and drug response.
https://t.co/sOtd3OYVop
@NCIEytanRuppin #CancerResearch @natrescancer