Madison Darmofal

computational cancer biologist @MSKCancerCenter
PhD w/ @MFBerger1 & @quaidmorris, @cbmstudent alumni | @MIT alumni
she/her/hers

[Madison Darmofal @mmdarmofal]

✨New paper alert @CD_AACR✨
- GDD-ENS distinguishes 38 cancer types (>96% of patients) w/ high accuracy using routinely collected DNA sequencing data #MSKIMPACT and generalizes well to other gene panels w/o retraining
- CNAs (arm/gene level) are key features for classification

[Elizabeth McKenna @ElizSMcKenna]

Now online in @CD_AACR: #DeepLearning Model for Tumor Type Prediction using Targeted Clinical Genomic Sequencing Data @mmdarmofal @MFBerger1 @quaidmorris https://t.co/dVGKB0bIfp @MSKCancerCenter

[Kevin Boehm @kevinmboehm]

K99/R00 funded by @theNCI at 1st %ile. Multimodal AI fusing tumor histopathology with genomics to guide cancer treatment selection. Launching my lab in '27.

[Erman Akkus @Erman_Akkus]

🧬cfDNA in biliart tract cancers
@JCOPO_ASCO

📌OncoKB level 1/2 alterations in 25% of patients
📌High tissue concordance
📌May be prognostic

✅Another data reinforcing utility of ctDNA in BTCs

👉https://t.co/aWLb9w5n0F

@ASCO @curecc @PrecisionBTCnet #cancer #oncology #MedX #biliary @OncoAlert @realbowtiedoc

[Adam Weiner @adamcweiner]

Happy to announce that PERT is now published in @NatureComms ! With PERT, we explore replication timing variability (Fig 3-4), chrXi reactivation (Fig 5), and how S-phase fractions struggle to approximate clone fitness (Fig 6). https://t.co/V0WqwX5G6e 1/n

[MSK ScienceEducation @MSKEducation]

Meet #MSKPostdoc Cassandra Burdziak (@CassBurdziak) from the @dana_peer Lab, who uses single-cell technologies and algorithms to investigate how cancer cells, regardless of where they come from, can change to mimic the biology of vastly different tissues.
#NPAW2024

[Quaid Morris @quaidmorris]

Metient reconstructs the migration histories of metastatic cancers by scoring a Pareto front of parsimonious histories. It can be auto-calibrated to different cohorts.

Superstar PhD student @divyakoyy will present at #ISMB2024 in MLCSB

Check it out:

https://t.co/jMwyEEm7Cz

[Cancer Discovery @CD_AACR]

New from the June issue—
#DeepLearning Model for Tumor Type Prediction using Targeted Clinical Genomic Sequencing Data, by @mmdarmofal, @MFBerger1, @quaidmorris et al.
https://t.co/KPMQ5EW160
@MSKCancerCenter

[Doron Haviv @DoronTheViking]

Super excited to announce that our work “Wasserstein Wormhole: Scalable Optimal Transport with Transformer” has been accepted to #ICML2024! Wormhole is method to find OT-preserving embeddings for massive cohorts of points clouds.
https://t.co/wWRwFH3NUT

[Cornell in DC @CornellinDC]

Graduate education is critical for the future. @Cornell @CornellGrad @cornell_tech @WeillCornellGS @WeillCornell grad students told their stories on Capitol Hill to demonstrate the value of research. Thank you @RepMolinaroNY19 for your support.

[Doron Haviv @DoronTheViking]

Woohoo ENVI/COVET is out in @NatureBiotech!! Couldn’t have done it without my brilliant mentor @dana_peer and the rest of the Peer lab!

[Only In Boston @OnlyInBOS]

A statue has been unveiled on Mile 2 of the Boston Marathon in honor of Spencer, the official dog of the Boston Marathon, who cheered on thousands of runners for years, rain or shine.

Spencer passed away last year after a battle with cancer at 13 years old.

💛💙

[Cancer Discovery @CD_AACR]

#OnlineFirst: Deep Learning Model for Tumor Type Prediction using Targeted Clinical Genomic Sequencing Data, by @mmdarmofal, @MFBerger1, @quaidmorris et al.
https://t.co/NmDtVFtFbt
@MSKCancerCenter

[Madison Darmofal @mmdarmofal]

Thanks to an incredible team for making this work possible! @MFBerger1 @quaidmorris @JieFuChen2 @evakiani @AnnaVarghese4 @nikolausschultz @cbmstudent + x-less Shalabh, Gurnit, Michael, Jason, Anoop, Aijaz, & the GDD-RF authors (https://t.co/LzayUoRlBL)

[Madison Darmofal @mmdarmofal]

We would also like to especially acknowledge Alex Penson, Niedzica Camacho, @zheng_youyun and @BarryTaylorLab whose initial GDD-RF model was the foundation for this work, without which our updated model would not be possible.
https://t.co/FejkUvBwtY

[Madison Darmofal @mmdarmofal]

✨New paper alert @CD_AACR✨
- GDD-ENS distinguishes 38 cancer types (>96% of patients) w/ high accuracy using routinely collected DNA sequencing data #MSKIMPACT and generalizes well to other gene panels w/o retraining
- CNAs (arm/gene level) are key features for classification

[Elizabeth McKenna @ElizSMcKenna]

Now online in @CD_AACR: #DeepLearning Model for Tumor Type Prediction using Targeted Clinical Genomic Sequencing Data @mmdarmofal @MFBerger1 @quaidmorris https://t.co/dVGKB0bIfp @MSKCancerCenter

[Madison Darmofal @mmdarmofal]

Here’s a link to the summary of the pre-print (https://t.co/RFvE6c2Skj) but please check out our manuscript, because there have been a lot of improvements due to an extremely useful and smooth review process. Thanks @ElizSMcKenna and our reviewers!

[Madison Darmofal @mmdarmofal]

Treatment options are limited for the 3-5% of patients who have cancers of unknown primary. So, we are excited to present 💥GDD-ENS💥: a highly accurate, comprehensive tumor type classifier based on data from a routinely applied FDA-authorized test 🧵
https://t.co/uYOyZ1LuqD

[Mildred Unti @MildredUnti]

So excited to announce that my most recent work has been published. If you’re interested in genetically encoding circular mRNA, or packaging circular mRNA into virus-like particles for cell-type specific delivery, this paper is for you!

[The Nobel Prize @NobelPrize]

“Ten years ago I was kicked out and forced to retire.”

Our new medicine laureate Katalin Karikó (@kkariko) told us how much it means to be awarded the Nobel Prize after a scientific career that has been full of challenges.

Ten years ago, Karikó was still doing all her experiments by hand but today she has been awarded the medicine prize for her research on mRNA, which led to the development of COVID-19 vaccines.

Listen now:

[Madison Darmofal @mmdarmofal]

@UshmaNeill Thanks, Ushma!! 🤩

[Madison Darmofal @mmdarmofal]

Treatment options are limited for the 3-5% of patients who have cancers of unknown primary. So, we are excited to present 💥GDD-ENS💥: a highly accurate, comprehensive tumor type classifier based on data from a routinely applied FDA-authorized test 🧵
https://t.co/uYOyZ1LuqD

[Madison Darmofal @mmdarmofal]

We would also like to especially acknowledge Alex Penson, Niedzica Camacho, @zheng_youyun and @BarryTaylorLab whose initial GDD-RF model was the foundation for this work, without which our updated model would not be possible.
https://t.co/FejkUvBwtY

[Madison Darmofal @mmdarmofal]

Thank you to @quaidmorris, @MFBerger1, Shalabh Suman, Gurnit Atwal, Jason Chang, @JieFuChen2 , Mike Toomey, @evakiani, @AnnaVarghese4, Anoop Balakrishnan Rema, Aijazuddin Syed and @nikolausschultz for making this possible! @cbm_student @MSKCancerCenter #MSKIMPACT