Nathan Abell (@n_s_abell) 's Twitter Profile
Nathan Abell

@n_s_abell

computational genetics @OctantBio | previously @StanfordMed and @UTAustin | 🏳️‍🌈

ID: 936683790348333056

linkhttp://nsabell.github.io calendar_today01-12-2017 19:49:53

100 Tweet

178 Followers

200 Following

gagneurlab (@gagneurlab) 's Twitter Profile Photo

New release of the Detection of RNA Outliers Pipeline (DROP) introducing variant calling from #RNAseq. Identify variants in your #RNA samples to interpret expression and splicing outliers! github.com/gagneurlab/drop 1/3

New release of the Detection of RNA Outliers Pipeline (DROP) introducing variant calling from #RNAseq. Identify variants in your #RNA samples to interpret expression and splicing outliers! github.com/gagneurlab/drop 1/3
Connor W. Coley (@cwcoley) 's Twitter Profile Photo

1/ Learning compound-protein interactions (CPI) w/ sequence & compound alone is tantalizing, but time and time again, CPI models fail to beat simple baselines. Does this paper do so successfully? An analysis from Sam Goldman :

Connor W. Coley (@cwcoley) 's Twitter Profile Photo

4/ We must temper our claims to avoid burning ML credibility and sending false signals to early-career trainees; for Kcat prediction, the bottleneck is data quality, not deep learning

Leonid Kruglyak (@leonidkruglyak) 's Twitter Profile Photo

In a recent paper, Shen et al. reported that most synonymous mutations in yeast genes were strongly deleterious. In a new preprint, we argue that this result is largely or entirely artifactual and arose from a lack of appropriate controls. biorxiv.org/content/10.110…

Michael Haney (@michael_s_haney) 's Twitter Profile Photo

Excited to share our work on in vivo hematopoietic stem cell CRISPR screens to study hematopoiesis and the aging immune system in the Tony Wyss-Coray lab w/ Wilkinson Group at Oxford & Nakauchi lab at Stanford! biorxiv.org/content/10.110… Find our screen data at hematopoiesiscrisprscreens.com

Excited to share our work on in vivo hematopoietic stem cell CRISPR screens to study hematopoiesis and the aging immune system in the <a href="/wysscoray/">Tony Wyss-Coray</a> lab w/ <a href="/awilkinsongroup/">Wilkinson Group</a> at Oxford &amp; Nakauchi lab at Stanford! 
biorxiv.org/content/10.110…
Find our screen data at hematopoiesiscrisprscreens.com
Sri Kosuri (@srikosuri) 's Twitter Profile Photo

Hiring a scientist into our Deep Mutational Scanning team for an exciting project in partnership with Robert Plenge and BMS. If you are into reporter & cell engineering, multiplexed screens & how to use DMS for identifying and drugging targets, please apply! octant.bio/jobs?gh_jid=47…

Sri Kosuri (@srikosuri) 's Twitter Profile Photo

You'd be working with some great scientists including Diane Dickel who leads the team, and Conor Howard, Erin Thompson Nathan Abell et al. If you have any questions, please feel free to reach out to any of us.

Nalin Ratnayeke (@nalinratnayeke) 's Twitter Profile Photo

Excited to share my PhD work in the @TobiasMeyerLab, out now in Molecular Cell! “CDT1 inhibits CMG helicase in early S phase to separate origin licensing from DNA synthesis” 1/11 cell.com/molecular-cell…

Dmitry Kobak (@hippopedoid) 's Twitter Profile Photo

We held a reading group on Transformers (watched videos / read blog posts / studied papers by Lucas Beyer (bl16) Andrej Karpathy Chris Olah Aman Arora Jay Alammar Sasha Rush et al.), and now I _finally_ roughly understand what attention does. Here is my take on it. A summary thread. 1/n

We held a reading group on Transformers (watched videos / read blog posts / studied papers by <a href="/giffmana/">Lucas Beyer (bl16)</a> <a href="/karpathy/">Andrej Karpathy</a> <a href="/ch402/">Chris Olah</a> <a href="/amaarora/">Aman Arora</a> <a href="/JayAlammar/">Jay Alammar</a> <a href="/srush_nlp/">Sasha Rush</a> et al.), and now I _finally_ roughly understand what attention does.

Here is my take on it. A summary thread. 1/n
Sasha Gusev (@sashagusevposts) 's Twitter Profile Photo

Another outlier: In [Okbay et al. 2022] the relative accuracy of an Education PGI in (UK Biobank) individuals with African ancestry was ~0%, far lower than expected from genetic differences. This is the finding that makes me wonder if *any* EA GWAS hits are direct effects at all.

Another outlier: In [Okbay et al. 2022] the relative accuracy of an Education PGI in (UK Biobank) individuals with African ancestry was ~0%, far lower than expected from genetic differences. This is the finding that makes me wonder if *any* EA GWAS hits are direct effects at all.
bioRxiv (@biorxivpreprint) 's Twitter Profile Photo

A multiplex, prime editing framework for identifying drug resistance variants at scale biorxiv.org/cgi/content/sh… #bioRxiv

AJHG (@ajhgnews) 's Twitter Profile Photo

💫New AJHG from Dong et al. 📰An RNA-informed dosage sensitivity map reflects intrinsic functional nature of genes 👇 cell.com/ajhg/fulltext/…

Greg Egan (@gregegansf) 's Twitter Profile Photo

My new novel MORPHOTROPHIC will be published on 9 April. Amazon is now accepting preorders for the ebook; other venues will follow soon. There will also be print-on-demand editions from Amazon available on 9 April, but they can't be pre-ordered. amazon.com/dp/B0CZ46L396

dana_peer (@dana_peer) 's Twitter Profile Photo

Thinking that programming skills is enough to design a computational pipeline is equivalent to thinking knowing how to pipette is enough to design a complex molecular protocol. There are many pitfalls in computation and therefore many controls are needed.

Sri Kosuri (@srikosuri) 's Twitter Profile Photo

We've started IND-enabling studies on a small molecule corrector for Rho-associated autosomal dominant retinitis pigmentosa (Rho-adRP). I thought it would be fun to spend some time walking through our approach and why we are excited. Long 🧵1/

Andrew Marderstein (@amarderstein) 's Twitter Profile Photo

🧵 Thrilled to share our latest in nature! We’ve mapped fetal blood development in Down syndrome (DS) using single-cell multi-omics, studying why children with DS face a 150-fold higher leukemia risk and blood abnormalities at birth. nature.com/articles/s4158…

Sri Kosuri (@srikosuri) 's Twitter Profile Photo

Excited to open up work on improving the power of Deep Mutational Scanning and applying it to drug discovery. I’ll comment on the preprint itself, which is work from a few years ago on DMS of MC4R, as well as talk about how this has evolved Octant Bio over time. 1/🧵

Excited to open up work on improving the power of Deep Mutational Scanning and applying it to  drug discovery. I’ll comment on the preprint itself, which is work from a few years ago on DMS of MC4R, as well as talk about how this has evolved <a href="/OctantBio/">Octant Bio</a> over time. 1/🧵
Buffy Wicks (@buffywicks) 's Twitter Profile Photo

CEQA and other permitting regimes, once envisioned as protections for our environment, have morphed into obstacles for meeting our housing and climate goals. This is a perfect opportunity for us to exercise broader permitting reform in the face of our new climate reality.