Sameed Siddiqui
@Sameed
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Californian lost in the Northeast. PhD Student @ MIT Computational Biology. @sabeti_lab member. @UCLA Bruin
California
Joined March 2008
Thrilled to share my work with my mentee @KrithikTweets, which shows how principled AI design can democratize biological sequence modeling. Excited to see how this can advance biology and bring machine learning to scientists everywhere. Also thanks to @_albertgu , @PardisSabeti.
🧬 Meet Lyra, a new paradigm for accessible, powerful modeling of biological sequences. Lyra is a lightweight SSM achieving SOTA performance across DNA, RNA, and protein tasks—yet up to 120,000x smaller than foundation models (ESM, Evo). Bonus: you can train it on your Mac. read
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8/ Finally, we thank those who helped fund our work, including @DARPA , @CDCgov, @HHMINEWS, @TheFluLab, @TheAudaciousPrj, @ELMAPhilanthro, @mackenziescott, @SkollFoundation, and @open_phil.
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7/ Our findings shed light on potential new modalities in CRISPR-dx. Eager for community insights and what lies ahead! Thanks to fellow leads @NicoleLWelch & Tien Nguyen, folks at the Broad imaging platform, @SenftRebecca, @BoSoxBioBeth, & @BlaineyLab, @PardisSabeti, @cambearon.
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6/ Key Insights 🌟: bbLuc's notable improved sensitivity over fluorescence, removing the need for fluorescence excitation lasers in CRISPR-dx;.🦠bbCARMEN's equipment-free, scalable, highly sensitive multiplexed CRISPR capabilities.#CRISPRdiagnostics.
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5/ 🦠Delving into bbCARMEN's Respiratory Virus Panel (RVP): Multiplexing with unique crRNAs attached to color-coded beads, we are able to detect 9 distinct targets, including SCoV2 with >95% sensitivity & 100% specificity vs. RT-qPCR across 135 clinical samples. 📸
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4/ Introducing bbCARMEN: A multiplexed bead-based platform tailored for point-of-care Cas13 diagnostics. Equipment-free droplet generation in <2 mins! 📸
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3/ Integration w/ SHINE: We next integrate bbLuc into the more general context of SHINE, a one-pot isothermal CRISPR-dx system which includes amplification via RPA. bbLuc shows enhanced sensitivity compared to fluorescence reporter, including in clinical specimens
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2/ 💡Introducing a bead-based split-luciferase reporter system (bbLuc): By utilizing split-luciferase reporter technology, we observed 20x improved sensitivity compared to standard fluorescence designs in amplification-free settings (Fig 1 for schematics)
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1/ 🧬 Exciting update for #CRISPR diagnostics! In our pre-print, we develop innovative bead-based techniques targeting both sensitivity and multiplexability of CRISPR-based diagnostics. Dive into our pre-print: @cambearon @sabeti_lab @BlaineyLab.
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Extremely sad to see this. To me, MIT's open access policies epitomized its commitment to the community and to a belief in open access to knowledge. I'll be signing this petition, as this shouldn't happen without more community input
Sounds like MIT campus is planning on remaining permanently closed to the public for the most part. One of my favorite parts of MIT was how open it was to the public. Really sad to see this go.
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RT @NicoleLWelch: The mCARMEN Accelerated Article Preview is live on Nature Medicine!! (with data tracking the Omicron wave!) Check it out….
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