Head of Epigenetic Engineering @scribetx Views are my own. PhD: Overlapping genes w/ Alan Frankel (UCSF) Postdoc: KZNFs w/ David Haussler (UCSC/HHMI)
Joined September 2015
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Jason Fernandes retweeted
Thrilled to share my freshly "baked" Baker lab paper. We took a bottom-up approach to designing transcriptional regulators. Instead of relying on natural activation domains, we designed compact proteins that recruit specific cofactors. Activators for now, repressors to come!
Jason Fernandes retweeted
1/ Most genes and variants matter somewhere but look silent in any one cell model. Can we build conditions that reveal phenotypes? With @kanishkadey, we engineer cell states to expose hidden disease biology and trace how genetic risk reaches disease genes. biorxiv.org/content/10.64898…
ALT Visual abstract: activating TFs singly and in pairs engineers new cell states, and the Mosaic model learns how TFs combine. Findings: hidden AMD risk variants, state-dependent convergence, and chromatin priming.
Jason Fernandes retweeted
Making iPS cells usually takes four factors, including OCT4. City of Hope and UChicago scientists found an enzyme, PUS7, can replace OCT4. It marks a small RNA (7SK) that helps open up DNA, and the new cells looked more like embryonic stem cells. nature.com/articles/s41589-0…
Jason Fernandes retweeted
Here, we introduce the next generation of CRISPR technology for characterizing hundreds of regulatory elements in one experiment: Swap-seq. Using pooled twin prime editing, Swap-seq generates precise tiled deletions across a locus and replaces them with barcoded DNA cassettes.
Jason Fernandes retweeted
New Epigenome Technologies Blog! u.epigenome.us/RIPipZpR
"Promoter Reinforcement Revealed as a New Therapeutic Resistance Mechanism"
Analyzing chromatin conformation identifies promoter reinforcement as a cancer treatment resistance mechanism.
#Epigenetics #Chromatin #Cancer
Jason Fernandes retweeted
🧵 Biohub, @ENERGY, @NIH, and new funding partners today announced a major expansion of an international effort to generate and make accessible the data enabling predictive AI models of biology. Together, the organizations are investing $1.8 billion in funding, data, computation and new measurement technology - largest coordinated commitment to map the biology of the cell to power development of digital models of biology. bit.ly/3UhjoxD
Jason Fernandes retweeted
Congratulations to Ioana L. Aanei, our Director of Business Development and Alliance Management, for being honored in @biospace's 40 Under 40! Here’s what makes her one of biotech’s most exemplary leaders:
⭐ Drives Scribe’s strategic partnerships to advance engineered CRISPR-based genetic medicines for heart disease and more
⭐ Community builder dedicated to connecting cross-functional resources within the biotech ecosystem to better serve patients and the broader field
⭐ Co-founded Calamores, an organization focused on parental well-being and science-backed self-care
⭐ Sustained advocate for emerging talent and active mentor through @Biocom and the @UCBerkeley Big Ideas program
Read more here: biospace.com/biospace-40-und…
Huge thanks to BioSpace for recognizing our Scribe team two years in a row. 💪
Jason Fernandes retweeted
At FutureHouse, we focused on scientific discovery. However, if we want to actually accelerate progress in medicine, we need to work across the entire R&D stack. We are now deploying specialized Kosmos agents for Clinical Protocol Design and Regulatory Authoring to several of our partners, which can cut months off the amount of time needed to get molecules into the clinic, save companies tens of millions of dollars, and dramatically reduce the likelihood that submissions get stuck at the FDA. Super excited to be able to share this story now, thanks to our work with Population Health Partners, one of the best drug developers in the world and a fantastic development partner for us.
The AI-native pharma stack is here now, and the future of medicine is around the corner. Read more:
xitter.cf/EdisonSci/status/21053…
Writing an Investigational New Drug (IND) application is a major hurdle for drug developers. It can take a team of specialists three to four months, and mistakes can trigger protocol amendments or clinical holds.
In June, we started working with Population Health Partners (PHP) to leverage specialized Kosmos Clinical Protocol Design (“CPD”) and Kosmos Regulatory Authoring (“RA”) products to support PHP’s process of IND preparation.
Since then, specially trained Kosmos products produced a first acceptable draft of the Nonclinical Overview in 4.2 hours, against 100 hours of expert time, flagged an error that roughly fifteen human reviewers missed, and authored 70% of the text in a Pre-IND Briefing Meeting Request submitted to FDA.
PHP is now bringing Kosmos products to a second program and expects to complete IND preparation in as little as 1 month, instead of the 4 month industry standard.
PHP's experts can spend their time reviewing and deciding, not just drafting. The time recovered by Kosmos products means that drugs could make their way to patients faster.
Jason Fernandes retweeted
This week, tune into two events where our VP of Research Sarah Denny will break down the science and engineering approach behind our CRISPR-based genetic medicines.
1️⃣ 7th Genome Editing Therapeutics Summit hosted by the Cell & Gene Therapy Event Series, AKA #crispr2.0 (September 28-30, Boston)
2️⃣ Tech Spotlight: AI and CRISPR Genome Editing Webinar hosted by @Tech_Networks (September 29, virtual)
Jason Fernandes retweeted
I’ll be presenting in Scribe technology platform in two venues this week. Thanks to everyone who tunes in!
This week, tune into two events where our VP of Research Sarah Denny will break down the science and engineering approach behind our CRISPR-based genetic medicines.
1️⃣ 7th Genome Editing Therapeutics Summit hosted by the Cell & Gene Therapy Event Series, AKA #crispr2.0 (September 28-30, Boston)
2️⃣ Tech Spotlight: AI and CRISPR Genome Editing Webinar hosted by @Tech_Networks (September 29, virtual)
Jason Fernandes retweeted
First RP patient dosed in our Phase 1B/2 w/ OCT-980 Rho corrector for retinitis pigmentosa. Really thankful to the clinicians, staff, CRO partners & Octonauts for helping get this drug to patients w/ no other approved treatments. Exciting times! octant.bio/news/octant-annou…
Jason Fernandes retweeted
Zheng et al, 2026. Transcription factors read a second regulatory code in chromatin. biorxiv.org/content/10.64898…
"TFs interpret two complementary layers of genomic information: the primary DNA sequence and a second code written into the nucleosome architecture"
Jason Fernandes retweeted
Excited to share our new preprint! 🎉
Using base-editor screens, we reveal how individual residues within the intrinsically disordered region of YTHDF2 control protein interactions, condensate recruitment, and m⁶A-dependent mRNA decay.
biorxiv.org/content/10.64898…
🧵👇
Jason Fernandes retweeted
This is cool — of the ~20,000 human proteins, 610 are the targets of approved drugs:
The evolving landscape of drug targets
nature.com/articles/s41573-0…
rdcu.be/22o1FPpNJ3Ga
In the past 25 years, advances in areas such as genomics and the diversification of therapeutic modalities have expanded the drug target landscape, which now includes ~700 targets mapped here
Great thoughts from @owl_posting on organoids as models for Alzehimers.
Raises the more important general point that "all models are wrong but some are useful" and more importantly some are useful in particular ways even as they are wrong in other ways. Often in drug discovery it's unclear if a model is useful. Ideally it would discriminate between successful and unsuccseful drug but you don't know that until years later, if ever. And then even in cases where we are pretty sure a model system is useful (maybe it's predicting downstream advancement well), you often aren't sure why.
With so many ways to be wrong, you can always take the negative view and point out what's almost certainly wrong, or you can try to find better things and see how they work out.
Are organoids useful for Alzheimer’s research?
(3.8k words, 17 minutes reading time)
owlposting.com/p/are-organoi…
the final organoid essay; a case study into how useful organoids have been for one of the hardest-to-address diseases that exist today
also: i moved to san francisco!
Jason Fernandes retweeted
ʙɪɴᴅᴄʀᴀꜰᴛ2 is out, and we're not waiting for the paper. The full code drops today, free for academic and industry use.
We're releasing it early so you can start designing right now, and bring its full power to the current Adaptyv competition.
github.com/PacesaLab/BindCra…
Jason Fernandes retweeted
Oriented binding of transcription factors to nucleosomes remodels chromatin at human promoters dlvr.it/TVXnmw
Jason Fernandes retweeted
Exciting research from the labs of MCB’s David Savage (@SavageCatsOnly) and Christina Listgarten, featuring MCB postdoc Maria Lukarska (@MariaLukarska)! 🧬🔬
.@UCBerkeley researchers developed ProteinGuide, an AI strategy that steers protein generative models toward specific properties using experimental data—without retraining the underlying models.
Read more about this research in QB3-Berkeley faculty labs: bit.ly/4AlhcFC
ALT Graphic illustrating how ProteinGuide was tested on adenine base editors: In the first round, generative models produced a library of variants that were experimentally tested for editing activity; ProteinGuide then used those results to guide a second round of designs toward higher activity.
ALT Side-by-side headshots of Maria Lukarska (left, a postdoctoral scholar in Professor Dave Savage's lab) and Junhao Xiong (right, a recently graduated PhD student in Professor Jennifer Listgarten’s lab).
Jason Fernandes retweeted
Cryo-EM structure, enzymatic activity and genome targeting of canonical PRC1 nature.com/articles/s41594-0…
Jason Fernandes retweeted
Eukaryotic AUG initiation contexts consist of a broad range of nucleotide patterns associated with distinct biological functions dlvr.it/TVV3Gz
