January 2023 Update

Bridging Atoms and Bits

Last month, we reflected upon our achievements over the past year. This month we’re starting off with an explosion of new results. And to help with the building, we welcomed more people to NewLimit this month than any other month!

• Conner Kummerlowe - Data Scientist

• Lucas Seninge - Machine Learning Scientist

• Rachel Hovde - Sr. Software Engineer

• Sophie Bax - Research Associate

In the world of Bits…

• Of course, our computer-science colleagues got right to work, building tools, pipelines and models.

Stats from our code repos.

• The first of our bioinformatics pipelines are up and running, allowing us to evaluate our first epigenetic profiles of young and aged patients.

UMAP projections of mRNA-seq profiles from young (<24 year old) and aged (>70 year old) human T cells.

• And our first glimpses of how cell populations change with age. These confirm known biology and act as a reference dataset for future experiments.

• We’ll keep building up our datasets to benchmark our models that predict the effects of delivering transcription factors to cells.

• We see our first evidence that we can predict the effects of new perturbation combinations:

Prediction error vs effect for one of our baseline gene perturbation models. “Good” is somewhere below the red line. Points represent the outcome of different gene perturbation experiments.

• And LOTS of sketching out ideas…

In the world of Atoms…

• We received the results of our first arrayed partial reprogramming screen! Here, we measured the epigenetic effects of partial reprogramming in primary T cells with 20 unique transcription factors. Already we’re uncovering interesting biology.

• We performed the largest partial reprogramming screen to date. We used a model cell line to test hundreds of reprogramming interventions in parallel. We will plug these data into the models (see above 👆) and use them to debug other components of our atoms-to-bits pipeline.

• We made further improvements to our reprogramming chemistry manufacturing process — another 10X improvement in throughput!

Elsewhere…

• We also got the whole team together IRL for dinner and a few days of intense planning and fun.

• Meanwhile, our office rebuild continues…

Brian staying late in the office.