onuralp
@amfoes.bsky.social
vesicle trafficking, drug discovery
Any chance there is a recording of this talk?
October 24, 2025 at 2:29 AM
Any chance there is a recording of this talk?
You will have the opportunity to work with population biobanks (e.g, UK Biobank, All of Us, MVP), observational cohort studies, **and** previous clinical trials. I think this is a rare opportunity in the industry.
September 15, 2025 at 3:48 AM
You will have the opportunity to work with population biobanks (e.g, UK Biobank, All of Us, MVP), observational cohort studies, **and** previous clinical trials. I think this is a rare opportunity in the industry.
Great fit for folks who like working with multi-modal datasets and want to see their work connect directly to therapeutic development.
September 15, 2025 at 3:48 AM
Great fit for folks who like working with multi-modal datasets and want to see their work connect directly to therapeutic development.
Great work! Any speculation on the geographic clustering of TL in All of Us? Sequencing center? It's on my todo list to take a closer look.
Clustering by Townsend index might be interesting in UKBB.
h/t Joe Pickrell; cc: @pnatarajanmd.bsky.social
Clustering by Townsend index might be interesting in UKBB.
h/t Joe Pickrell; cc: @pnatarajanmd.bsky.social
June 4, 2025 at 8:07 AM
Great work! Any speculation on the geographic clustering of TL in All of Us? Sequencing center? It's on my todo list to take a closer look.
Clustering by Townsend index might be interesting in UKBB.
h/t Joe Pickrell; cc: @pnatarajanmd.bsky.social
Clustering by Townsend index might be interesting in UKBB.
h/t Joe Pickrell; cc: @pnatarajanmd.bsky.social
UDN has a Roifman patient with a causative mutation in RNU4ATAC. Not sure what's the current state of collaboration and data exchange between US/EU but good to keep this resource in mind for potential clinical development efforts.
undiagnosed.hms.harvard.edu/genes/rnu4at...
undiagnosed.hms.harvard.edu/genes/rnu4at...
RNU4ATAC Gene- Undiagnosed Diseases Network (UDN)
Changes in the RNU4ATAC gene were identified in a UDN participant with Roifman syndrome.
undiagnosed.hms.harvard.edu
May 26, 2025 at 9:53 AM
UDN has a Roifman patient with a causative mutation in RNU4ATAC. Not sure what's the current state of collaboration and data exchange between US/EU but good to keep this resource in mind for potential clinical development efforts.
undiagnosed.hms.harvard.edu/genes/rnu4at...
undiagnosed.hms.harvard.edu/genes/rnu4at...
Uff, tough one. They use couples phenotype correlation (couples PGS correlation) as the benchmark against estimated correlation. Is it fair to say that the former would correspond to 'expected increase' in your formulation?
Comparison for drinking behavior will be interesting (UKB v ESTB v MoBa).
Comparison for drinking behavior will be interesting (UKB v ESTB v MoBa).
May 26, 2025 at 9:14 AM
Uff, tough one. They use couples phenotype correlation (couples PGS correlation) as the benchmark against estimated correlation. Is it fair to say that the former would correspond to 'expected increase' in your formulation?
Comparison for drinking behavior will be interesting (UKB v ESTB v MoBa).
Comparison for drinking behavior will be interesting (UKB v ESTB v MoBa).
JF walks through the math behind PIGEAN (at high-level) here: youtu.be/b1fmzhgE3lI?...
Knowledge Portal Webinar - June 13th, 2024
YouTube video by HuGeAMP Knowledge Portals
youtu.be
May 26, 2025 at 8:59 AM
JF walks through the math behind PIGEAN (at high-level) here: youtu.be/b1fmzhgE3lI?...
Just the strength. Sensitivity to phasing errors, number of relatives available, heritability will likely be discussed in the paper - they did a bunch of simulations.
May 25, 2025 at 6:33 AM
Just the strength. Sensitivity to phasing errors, number of relatives available, heritability will likely be discussed in the paper - they did a bunch of simulations.
Pitch: handy method to study impact of imprint of time-dependent assortative mating in the context of growing social stratification (with no couples & phenotypes required).
cc: @zkutalik.bsky.social @eshg.bsky.social
cc: @zkutalik.bsky.social @eshg.bsky.social
May 25, 2025 at 6:18 AM
Pitch: handy method to study impact of imprint of time-dependent assortative mating in the context of growing social stratification (with no couples & phenotypes required).
cc: @zkutalik.bsky.social @eshg.bsky.social
cc: @zkutalik.bsky.social @eshg.bsky.social
Once assortative mating becomes measurable in every individual this way, you can get creative and ask interesting questions: whether correlations hold across biobanks (mostly yes), population-specific traits under assortment (prelim results), ++/-- assortment over time when stratified by DOB
May 25, 2025 at 6:10 AM
Once assortative mating becomes measurable in every individual this way, you can get creative and ask interesting questions: whether correlations hold across biobanks (mostly yes), population-specific traits under assortment (prelim results), ++/-- assortment over time when stratified by DOB
Use interchromosomal phasing via IBD with relatives to phase each UKB genome into maternal vs paternal sets, sum PRS for ~50 traits on each, then correlate the two halves. Couples & phenotypes not needed (convenient because, unlike ESTB, most biobanks do not have this information readily available)
May 25, 2025 at 6:06 AM
Use interchromosomal phasing via IBD with relatives to phase each UKB genome into maternal vs paternal sets, sum PRS for ~50 traits on each, then correlate the two halves. Couples & phenotypes not needed (convenient because, unlike ESTB, most biobanks do not have this information readily available)
Thanks for the write up! Some skunkworx videos are still available online. TIL Illumina had a sizable investment in ONT (2009-2013).
May 20, 2025 at 7:56 PM
Thanks for the write up! Some skunkworx videos are still available online. TIL Illumina had a sizable investment in ONT (2009-2013).
KM provides the regulatory timeline on the 'streamlined' package here: www.biotechtv.com/post/kiran-m...
ASGCT 2025: Physicians and scientists raced to make a bespoke gene editing therapy for an infant who urgently needed one in months - a first hand account, and what this means for drug development
As published in NEJM today, UPenn's Kiran Musunuru describes how the team used base editing in a matter of months to treat an infant with CPS1 deficiently, and his thoughts on what the learnings of th...
www.biotechtv.com
May 16, 2025 at 12:09 AM
KM provides the regulatory timeline on the 'streamlined' package here: www.biotechtv.com/post/kiran-m...
My recollection is hazy but maybe PopGroup45... I remember a few local popgen folks stopped by. I can't find the program though. Angus must have it somewhere.
May 7, 2025 at 7:05 AM
My recollection is hazy but maybe PopGroup45... I remember a few local popgen folks stopped by. I can't find the program though. Angus must have it somewhere.
First "GWAS" probably dates all the way back to this Mark Daly paper from 2001 (with a shout-out to HGP :)): pmc.ncbi.nlm.nih.gov/articles/PMC... @bloodgenes.bsky.social
A Genomewide Linkage-Disequilibrium Scan Localizes the Saguenay–Lac-Saint-Jean Cytochrome Oxidase Deficiency to 2p16
Leigh syndrome (LS) affects 1/40,000 newborn infants in the worldwide population and is characterized by the presence of developmental delay and lactic acidosis and by a mean life expectancy variously...
pmc.ncbi.nlm.nih.gov
April 16, 2025 at 1:11 AM
First "GWAS" probably dates all the way back to this Mark Daly paper from 2001 (with a shout-out to HGP :)): pmc.ncbi.nlm.nih.gov/articles/PMC... @bloodgenes.bsky.social
Two relevant material here: (1) FDA roadmap describing the spirit of considering alternatives: www.fda.gov/media/186092... (2) EMA perspective piece on highlighting specific areas of opportunity: www.nature.com/articles/d41...
Insights into new approach methodology innovation: an EMA perspective
Discover the world’s best science and medicine | Nature.com
www.nature.com
April 15, 2025 at 1:51 AM
Two relevant material here: (1) FDA roadmap describing the spirit of considering alternatives: www.fda.gov/media/186092... (2) EMA perspective piece on highlighting specific areas of opportunity: www.nature.com/articles/d41...
FinnGen might be a good fit for this question (e.g., r12.finngen.fi/variant/14-6...)
April 8, 2025 at 8:47 AM
FinnGen might be a good fit for this question (e.g., r12.finngen.fi/variant/14-6...)
SIX6OS1 (SIX6 opposite strand 1) looks like natural antisense transcript associated with SIX6. Given the former's association with ocular phenotypes, this reminds me of ATXN7/SCAANT1 story. It may be interesting to note the NAT link.
April 8, 2025 at 6:55 AM
SIX6OS1 (SIX6 opposite strand 1) looks like natural antisense transcript associated with SIX6. Given the former's association with ocular phenotypes, this reminds me of ATXN7/SCAANT1 story. It may be interesting to note the NAT link.
It does not let me see the pinned emails. Staring at low priority emails provides (much needed) perspective in my life. 🙃
March 19, 2025 at 1:58 AM
It does not let me see the pinned emails. Staring at low priority emails provides (much needed) perspective in my life. 🙃
I wonder if they will consider backpedaling on daylighting law and start enforcing it.
March 19, 2025 at 1:54 AM
I wonder if they will consider backpedaling on daylighting law and start enforcing it.