Ivan Specht

We present JUNIPER, our outbreak reconstruction tool that incorporates within-host variants, models missing data, and scales to large, sparsely sampled datasets to achieve state-of-the-art performance. Led by @ivan_specht et al. @sabeti_lab. medrxiv.org/content/10.110… 1/12 🧵

(1/4) Excited to introduce ProCyon: a multimodal foundation model to model, generate, and predict protein phenotypes, led by stellar @oq_35 @YepHuang Robert Calef @valegiunca 👉 biorxiv.org/content/10.110… ProCyon is an 11B parameter multimodal model that integrates protein sequences, structures, and natural language ProCyon models, predicts, and generates phenotypes with zero-shot task transfer, breaking past the limits of fixed vocabularies or ontologies 🔬 The Challenge: Predicting protein structure is advanced, but predicting protein phenotypes—observable traits linking molecular function to biology—is still an open problem. 40% of human proteins lack context-specific insights, while 20% remain almost entirely uncharacterized

Talent shines in the Sabeti Lab! ✨ Ivan Specht's senior thesis, 'Reconstructing Viral Epidemics: A Random Tree Approach,' is now featured on the Harvard Math website. Dive into Ivan's groundbreaking work and join us in celebrating his achievement! 🎉 rb.gy/zvfscu

Meet @ivan_specht! Ivan's work in the @sabeti_lab involves epidemiological modeling of infectious diseases as a means to inform public health policy. Read more about his work here: buff.ly/3sTACmW #OperationOutbreak #STEM #education

Thrilled to be here at #NCTMDC23 sharing Operation Outbreak (@OutbreakEdu) with math teachers from all around the country! Operation Outbreak is an outbreak simulation technology that spreads a ‘virtual pathogen’ between smartphones via Bluetooth to teach epidemiology.

@fathominfo Thank you Fathom!!

Ivan spent some time with us this summer working on visualizing these outbreak transmission networks. Awesome to see the progress on this work! 👏

@dmaccannell @PardisSabeti @sabeti_lab @PetrosBrittany @GageKMoreno Thank you @dmaccannell I’m honored! Would love to present

@PardisSabeti @ivan_specht @sabeti_lab @PetrosBrittany @GageKMoreno Or with a little extra seasoning: Intra-host Variant Analysis for transmission Networks, Reconstruction, Observation, Characterization and Knowledge Synthesis.

Pleased to share @ivan_specht @sabeti_lab‘s method for reconstructing outbreak transmission networks by modeling within-host viral evolution. We look forward to others using it. Let us know what you think & appreciate any name suggestions 🙏

…@glipsnort, @DannyJPark, @bronwynmacinnis, Al Ozonoff, @ben_fry, Michael Mitzenmacher, Patrick Varilly, and @PardisSabeti.

Thanks to our authors, full list: @ivan_specht, @PetrosBrittany, @GageKMoreno, @tbrockfi, @lakrasil, @mschifferli, Katherine Yang, Paul Cronan, @orglennon, …

We developed a new model for within-host viral evolution, which we used to reconstruct outbreak transmission networks. A thread on our genomic epidemiology paper with @PetrosBrittany, @GageKMoreno et al. @sabeti_lab medrxiv.org/content/10.110…

The @sabeti_lab has developed a smartphone app that helps users model viral outbreaks, using Bluetooth to “spread” a virtual human virus to nearby participating phones. Read about findings from deployments on two college campuses in a Q&A with the team: broad.io/OperationOutbr…

@lakrasil Thank you Lydia!

Go read @ivan_specht's excellent tweet thread here: twitter.com/ivan_specht/st…

I've gotten to watch this work come together from a distance— Really proud especially of the new trainees on this paper! ! Give it some love! 👏✨🥳