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
- Tweets3.3K
- Following1.7K
- Followers731
- Likes11.4K
Jason Fernandes retweeted
Continuous directed evolution using engineered human B cell lines: nature.com/articles/s41467-0…
Jason Fernandes retweeted
Fantastic to kick off AHA26 with a panel conversation at the innovation forum on the future of cardiovascular care with the fantastic @manesh_patelMD, @skathire and Lauren Cheung!
Please come say hi - come to the abstract session, late breaking science, and the Connor lecture. Look forward to engaging with all of our colleagues. @AHAScience
Jason Fernandes retweeted
Super happy to share that the first paper from my postdoc is now out on bioRxiv (biorxiv.org/content/10.64898…). We trained ProCapNet models on all ENCODE PRO-cap experiments (>200 datasets), representing all major human organs/tissues.
Jason Fernandes retweeted
owlposting.com/p/on-creating…
the first drug with a new knob of control has (strong!) human evidence!
Dreadds work in humans nejm.org/doi/full/10.1056/NE…
Jason Fernandes retweeted
1/4 One DNA sequence, many chromatin states.
Excited to share SMFNet, a diffusion model predicting single-molecule chromatin accessibility. Explainer video below!
With co-first author Till (his thread: bsky.app/profile/tschwammle.…), Yuliya, Roze, @anshulkundaje & Arnaud Krebs.
Jason Fernandes retweeted
Delighted to share our new work in @CellStemCell! Transient epigenome editing durably silences genes in human 🩸 stem cells and mature progeny, without changing 🧬. Congrats to @lrbzldz & our collaborators!
cell.com/cell-stem-cell/full…
Jason Fernandes retweeted
Online Now: P-TEFb regulates nucleosome positioning at promoters dlvr.it/TW9tzB
Jason Fernandes retweeted
Harmonizing whole genome bisulfite sequencing datasets in the public domain across individuals, tissues, and conditions for a compendium of 5mC methylation data. Altered methylation clusters from DNA sequence variation in brain, muscle, and adipose tissue linked to longevity nature.com/articles/s41588-0… @NatureGenet
Jason Fernandes retweeted
After four adventurous years, happy to share our work.
We asked: How much of RNA processing is written in the sequence, and how much depends on where it sits in the genome?
We built IntronTRIP to find out. Both matter, but not quite the way we thought.
biorxiv.org/content/10.64898…
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:
nitter.gq/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…