Basheer Becerra

Checked off an item from my PhD bucket list last weekend - finished my first full-distance Ironman!

@Throrf It’s a while till we get to that point (for lab automation that is). Research is complex and composed of experiments that are context-dependent - most labs would rather just do things in-house rather than outsourcing standardized assays to some overpriced service.

I have been thinking a lot about AI and automation in biological research recently. A bit of brain vomit to get my own thoughts in order. I think I'm pretty firmly in the camp of AI and automation INCREASING opportunities (and jobs) in biological research, not replacing them. The reason for that is that we are just so damn far from "solving" biology. We're so early we spend most of our time producing the raw materials for research. We do PCRs, run gels, column-purify nucleic acids and proteins, spend months generating new strains. Those things are all just means to an end. The more these are automated the we can focus on things that actually matter. Maybe it's just cope and everyone thinks that THEIR job won't be replaced. But if I look at what happened when DNA synthesis became cheap and accessible, or when PCR was invented it just confirms my bias. The amount of labour required to produce a piece of DNA became a fraction of what it was, but suddenly so many things became feasible that there is more to do, not less.

@CathyTie @OriginGenomics Excited to see @OriginGenomics tackle this challenging area, wishing success

Germline gene correction will happen. The focus now is doing it with precision, rigor, and clear ethical guardrails. That’s what we’re building at @OriginGenomics.

@dwarkesh_sp @michael_nielsen AlphaFold is a drop in the bucket compared to decades of work on protein structure, PDB, analytical work from Baker et al., etc. The future of AIxBio is robust experimental methods and large scale data generation (for questions that actually matter for therapies).

.@michael_nielsen on AlphaFold - the AI bit is a small part of the total investment. "A massive fraction of the success there is the Protein Data Bank. It's X-ray diffraction, NMR, cryo-EM, and the several billion dollars that was spent obtaining 180,000 protein structures."

Now published in @NatureComms! See my thread from the preprint for the full breakdown. Stay tuned for more work in this direction! 📄 nature.com/articles/s4146…

@kimmonismus Advances in functional genomics assays (ie CRISPR, MPRA, DMS, etc) to test unknown variants (in relevant contexts) has been substantially more important at understanding non-coding regions than alpha genome, imo.

Demis Hassabis: CRISPR technology can target DNA, but identifying the exact genetic cause of diseases is tough, especially in non-coding regions. AI tools like AlphaGenome are decoding this 98%, predicting mutation impacts and paving the way for CRISPR to fix genetic diseases.

Excited to share @PageLabXY and my perspective on the role of the so-called “inactive” X chromosome in autism, out today in @NatureGenet! A quick 🧵… (1/n)

Fortunate to have presented some of my PhD work “Multi-modal functional mapping of non-coding sequences regulating fetal hemoglobin” at #ASHG2025!

Come to our booth to learn more about the Harvard BIG PhD program! #SACNAS2024 #NDiSTEM

This is phenomenal. The initial collaboration between @danielevanbauer and yours truly used the kernel of this approach to discover the GATA-1 site in the BCL11A enhancer - nature.com/articles/nmeth… - to see this scaled up by many logs is nothing short of thrilling.

Excited to share our work "CRISPR-CLEAR", an end-to-end workflow for dissecting enhancers at nucleotide resolution! Check out our pre-print and @DSeruggia's tweetorial below! Lead with @SWittibschlager and @zafateniac and labs @lucapinello @DSeruggia and @danielevanbauer.

First pre-print from the lab! Together with @lucapinello and @danielevanbauer we developed CRISPR-CLEAR, an experimental and computational pipeline to dissect enhancers at nucleotide resolution. biorxiv.org/content/10.110…

Understanding genomic variation is no easy task! I’m thrilled to be part of a fantastic team in the @genome_gov-funded IGVF Consortium, working together to tackle this mission. Check also out our paper where we outline our goals and challenges: #IGVF nature.com/articles/s4158…

The BMI program retreat was in Provincetown this weekend. Among other activities, students were treated to our guest speaker Robert Gentleman, Director of the Center for Computational Biomedicine at HMS.

@ShabbosK @BillAckman @KassyDillon @yaelbt @benshapiro @LHSummers @EYakoby @ShaiDavidai @sapinker @AlanDersh @AvivaKlompas Can you provide evidence for daily antisemitism, harassment, or calling for violent destruction? I’ve been to Harvard’s encampment and found quite the opposite, Jews/Muslims/etc. together. Also agreeing to meet is not encampment’s demand, so your first statement is false rhetoric

The Harvard encampment has just ended. Do you want to see Harvard’s antisemitism in real time? Harvard has agreed with almost all of their demands. I’ve never been this disillusioned than this morning. 🧵1/5

@lucapinello @MLGenX @iclr_conf Congrats!

@MLGenX thank you for organizing a fantastic workshop at @iclr_conf and for selecting our paper on DNA-Diffusion for the Outstanding Paper Award! Congratulations to the entire team that made this possible! #ICLR2024 🎉

This week we held our Third Annual GRO Retreat @broadinstitute and it was a blast! Thank you to our keynote speaker Benjamin Ebert, our visiting speaker @sara_mostafavi & all of our contributing discussion leaders, breakout participants, poster presenters. An incredible group!

@AI4Pathology @richardjchen @HarvardDBMI @VanAllenLab @marinkazitnik @njdurr @alexander_baras Congrats @richardjchen!!

Congratulations 🎉 to Dr. @richardjchen for completing his PhD @HarvardDBMI, and special thanks to everyone on the committee @VanAllenLab @marinkazitnik @njdurr @alexander_baras Some key work from Richard's PhD includes Pathomic Fusion (IEEE TMI, 2020), MCAT (ICCV, 2021), HIPT (CVPR, 2022), Porpoise (Cancer Cell, 2022), UNI.

@UrnovFyodor @CRISPRTX @VertexPharma @danielevanbauer Wow congrats!

Bravo, @CRISPRTX @VertexPharma! Stu Orkin, @danielevanbauer and all on Team High HbF - take a bow! Genome editors of the world - we have 4,999 genetic diseases to go! statnews.com/2023/12/08/fda…

@GLettre Congrats!!

A wonderful news! FDA Approves First Gene Therapies to Treat Patients with Sickle Cell Disease fda.gov/news-events/pr…

A wonderful read about Stu Orkin and @danielevanbauer and the road to Casgevy, a landmark for medicine and gene editing. Collaborating with Dan and Stu was a highlight of my professional life and I personally will forever be in their debt for choosing to work with my team.