We are hiring fellows for a pilot initiative at @mskcancercenter.bsky.social – The Theory Group. The Group is centered around tumor-immune interactions and, post-AI, theoretical approaches that can unlock fundamental questions with translational impact. msk.wd108.myworkdayjobs.com/MSKCC_Career...

Matching T cells to their cognate peptides presented on MHC molecules from sequence data is a key unsolved problem in computational immunology. A transformative collaboration with @quaidmorris.bsky.social. Led by Olga Lyudovyk, @levinejon.bsky.social & Melissa Pathil! 👇 @mskcancercenter.bsky.social

Quaid Morris@quaidmorris.bsky.social · 2w ago

Can we predict which T cells recognize which peptides? A lot of the signal is hiding in AlphaFold3's (AF3's) hallucinations. enFoldX: instead of one predicted structure, we use the whole noisy ensemble to predict TCR:pMHC binding. www.biorxiv.org/content/10.6... 💻 🧬 github.com/jonlevi/enFoldX

The first is from former PhD student Zhiru Liu @zzzhiru.bsky.social (now in @bengrbm.bsky.social's group @ MSK) examining the long-term patterns of selective constraint – measured by the classical ratio of nonsynonymous to synonymous mutations (dN/dS) – within recombining populations of bacteria.

Dynamics of dN/dS within recombining bacterial populations

The ratio of nonsynonymous to synonymous substitutions (dN/dS) encodes important information about the selection pressures acting on protein-coding genes. In bacterial populations, dN/dS often decline...

biorxiv.org

Thank you @mskcancercenter.bsky.social for highlighting our work on #viralmimicry in our genome, its evolution, the selective forces on it, and its potential role in cancer. A great years long collaborative effort with @petrsulc.bsky.social, @daniel-decarvalho.bsky.social, & many great colleagues!

Memorial Sloan Kettering Cancer Center@mskcancercenter.bsky.social · 10mo ago

Dr. @bengrbm.bsky.social has tried to shed light on the innate immune system and how it affects cancer cells as they evolve. Now Dr. Greenbaum’s lab has been taking a deep dive into modeling viral mimicry, trying to understand how this could shape cancer cells’ development process. bit.ly/3VWadA8

Sharing a paper below in Cell Genomics @cellpress.bsky.social that took us literally 10 years+ (!) to write on the topics of:

Excited to have this paper out today! Repeats mimic pathogen-associated patterns across a vast evolutionary landscape." It was a fun and productive collaboration with Benjamin Greenbaum John LaCava, Simona Cocco, Petr Šulc and many others! www.cell.com/cell-genomic...

Repeats mimic pathogen-associated patterns across a vast evolutionary landscape

An emerging hallmark of disease is transcription of pathogen-associated molecular patterns from within the genome–known as viral mimicry. We propose a statistical physics framework to measure “selecti...

cell.com

Nice to see this story out! The idea that viral mimicry is an intrinsic feedback mechanism for sensing cellular dysregulation is fascinating and this paper explores this idea really well. It was inspiring to be part of this collaborative work. Thanks to @bengrbm.bsky.social and the rest!

Repeats mimic pathogen-associated patterns across a vast evolutionary landscape

An emerging hallmark of disease is transcription of pathogen-associated molecular patterns from within the genome–known as viral mimicry. We propose a statistical physics framework to measure “selecti...

cell.com

Early registration rates end this coming Monday for #mDNASRC. Join your colleagues in beautiful Porto alongside organizers like @bengrbm.bsky.social. Save your space: buff.ly/P6hZjQz

MSK is pleased to announce @time.com has named two MSK physician-scientists, Dr. Andrea Cercek and Dr. Vinod Balachandran, to the 2025 TIME100 Health, a list of the most influential individuals in health and medicine who have made significant contributions to industry. Learn more: bit.ly/3GGblTR

Call for abstracts! #mDNASRC is in beautiful Porto this year! Organizers @bengrbm.bsky.social, John LaCava, Zhao Zhang, and Vera Gorbunova may select you for a poster session or short talk. You can even register now and submit your abstract later. Save your space: buff.ly/PAKp55o

Come out tomorrow at 10 am to learn about transposable elements in cancer - it will be a great session with @chiappinellilab.bsky.social & Ting Wang #AACR25! @theaacr.bsky.social

Kate Chiappinelli@chiappinellilab.bsky.social · last yr.

Looking forward to #AACR25! If you want to learn more about transposable elements in cancer, our educational session is at 10 am on Saturday 4/26! @bengrbm.bsky.social @theaacr.bsky.social

Great article in @science.org highlighting our efforts to target the #darkproteome! Nice to see our colleagues David Ting, Daniel De Carvalho, and Marty Taylor highlighted along with the amazing work of @rometx.bsky.social👇👇👇 www.science.org/content/arti...

Could blocking ‘jumping genes’ help fight disease and aging?

The first clinical trials are testing inhibitors of transposons, DNA sequences that hop around the genome on their own

science.org

#mDNASRC is back and stronger than ever after 30 years! Discover how transposable elements shape our genomes and impact health, featuring keynote speaker @bengrbm.bsky.social, and more! Save your space: buff.ly/QiSc4E6

Thank you @mskcancercenter.bsky.social for highlighting our work and our great collaborators!

Memorial Sloan Kettering Cancer Center@mskcancercenter.bsky.social · last yr.

(1/2) MSK researchers are trying to understand how the immune system senses cancer in order to make better #immunotherapies.

Our latest work on the #darkgenome is out now in @naturecomms.bsky.social. LINE-1 is the only known autonomous retrotransposon still active in our genome. Co-led by our Alexander Solovyov @MSKCancerCenter - our work was also great collaboration with @rome_tx 👇👇👇 nature.com/articles/s4146

We’re excited to announce a new publication in Nature Communications: the first large-scale, pan-cancer analysis of LINE-1 expression levels and retrotransposition (RT) activity. These data demonstrate the potential for precision LINE-1 RT-targeted therapeutic approaches. rometx.com/press-releas...

An new publication in @Nature by SU2C Convergence Team leaders @thevinodlab.bsky.social @bengrbm.bsky.social @mskcancercenter.bsky.social showed an individualized neoantigen mRNA vaccine for #pancreaticcancer led to prolonged survival and effector T cell responses www.nature.com/articles/s41...

RNA neoantigen vaccines prime long-lived CD8+ T cells in pancreatic cancer - Nature

In a phase 1 trial, patients with pancreatic ductal adenocarcinoma who were treated with surgery and bespoke neoantigen mRNA vaccines combined with anti-PD-L1 and chemotherapy exhibited marked lo...

nature.com

(1/2) Results from a phase 1 clinical trial of the #mRNA-based therapeutic cancer vaccine autogene cevumeran for treating #pancreaticcancer is published in @nature.com. bit.ly/4b9ofEZ

A new study in @cellpress.bsky.social Immunity from the lab of Dr. Benjamin Greenbaum provides insights into how #PancreaticCancer cells accommodate active retrotransposons without triggering the innate immune response. #oncsky #medsky

Cancer cells restrict immunogenicity of retrotransposon expression via distinct mechanisms

Overexpression of transposable elements is a common feature of cancer. Sun, You, et al. show that, in pancreatic ductal adenocarcinoma, tumor cells adapt through different mechanisms to mitigate a spe...

cell.com