Aditi Qamra
@aditiq.bsky.social
Computational biologist working on #digitalpathology and #doseoptimization in #clinicaltrials at Roche Canada 🧬
Opinions my own
Opinions my own
Reposted by Aditi Qamra
It’s been a tough few weeks. My 10yo daughter was diagnosed with a very rare, aggressive cancer called interdigitating dendritic cell sarcoma (IDCS). I’m reaching out to identify clinicians/patients who have encountered pediatric IDCS or other (non-LCH) dendritic or histiocytic sarcomas cases.
February 8, 2025 at 9:21 PM
It’s been a tough few weeks. My 10yo daughter was diagnosed with a very rare, aggressive cancer called interdigitating dendritic cell sarcoma (IDCS). I’m reaching out to identify clinicians/patients who have encountered pediatric IDCS or other (non-LCH) dendritic or histiocytic sarcomas cases.
Reposted by Aditi Qamra
Why Recursion Pharmaceuticals abandoned cell painting for brightfield imaging
www.owlposting.com/p/why-recurs...
After over a decade,Recursion Pharmaceuticals changed its primary assay. Why is that? I answer that question over 5.6k words (26 minutes to read)
first journalism-y piece!
www.owlposting.com/p/why-recurs...
After over a decade,Recursion Pharmaceuticals changed its primary assay. Why is that? I answer that question over 5.6k words (26 minutes to read)
first journalism-y piece!
Why Recursion Pharmaceuticals abandoned cell painting for brightfield imaging
5.7k words, 26 minutes reading time
www.owlposting.com
November 8, 2024 at 3:59 PM
Why Recursion Pharmaceuticals abandoned cell painting for brightfield imaging
www.owlposting.com/p/why-recurs...
After over a decade,Recursion Pharmaceuticals changed its primary assay. Why is that? I answer that question over 5.6k words (26 minutes to read)
first journalism-y piece!
www.owlposting.com/p/why-recurs...
After over a decade,Recursion Pharmaceuticals changed its primary assay. Why is that? I answer that question over 5.6k words (26 minutes to read)
first journalism-y piece!
*Thread*
The life science community frequently publishes new, often fundamental, insights in molecular and cellular biology.
However, there does not exist a way to access this information in a summarized manner. We only access the information we need for our specific questions/use case.
1/yy
The life science community frequently publishes new, often fundamental, insights in molecular and cellular biology.
However, there does not exist a way to access this information in a summarized manner. We only access the information we need for our specific questions/use case.
1/yy
January 4, 2025 at 2:30 AM
*Thread*
The life science community frequently publishes new, often fundamental, insights in molecular and cellular biology.
However, there does not exist a way to access this information in a summarized manner. We only access the information we need for our specific questions/use case.
1/yy
The life science community frequently publishes new, often fundamental, insights in molecular and cellular biology.
However, there does not exist a way to access this information in a summarized manner. We only access the information we need for our specific questions/use case.
1/yy
Reposted by Aditi Qamra
Finally out! We present EXTRA-seq, a new EXTended Reporter Assay to quantify endogenous enhancer-promoter communication at kb scale!
www.biorxiv.org/content/10.1...
A 🧵about what it can do:
#SynBio #DeepLearning #GeneRegulation
www.biorxiv.org/content/10.1...
A 🧵about what it can do:
#SynBio #DeepLearning #GeneRegulation
EXTRA-seq: a genome-integrated extended massively parallel reporter assay to quantify enhancer-promoter communication
Precise control of gene expression is essential for cellular function, but the mechanisms by which enhancers communicate with promoters to coordinate this process are not fully understood. While seque...
biorxiv.org
December 16, 2024 at 2:39 PM
Finally out! We present EXTRA-seq, a new EXTended Reporter Assay to quantify endogenous enhancer-promoter communication at kb scale!
www.biorxiv.org/content/10.1...
A 🧵about what it can do:
#SynBio #DeepLearning #GeneRegulation
www.biorxiv.org/content/10.1...
A 🧵about what it can do:
#SynBio #DeepLearning #GeneRegulation
Super cool - esp the breadth of markers being covered. I especially love fig 6 showing gene density enrichment in different groups of histone mods co-occurring with k4me3. I think this is going to be adopted real fast by discovery teams!
Gene regulation involves thousands of proteins that bind DNA, yet comprehensively mapping these is challenging. Our paper in Nature Genetics describes ChIP-DIP, a method for genome-wide mapping of hundreds of DNA-protein interactions in a single experiment.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
ChIP-DIP maps binding of hundreds of proteins to DNA simultaneously and identifies diverse gene regulatory elements - Nature Genetics
ChIP-DIP (ChIP done in parallel) is a highly multiplex assay for protein–DNA binding, scalable to hundreds of proteins including modified histones, chromatin regulators and transcription factors, offe...
www.nature.com
November 27, 2024 at 8:46 PM
Super cool - esp the breadth of markers being covered. I especially love fig 6 showing gene density enrichment in different groups of histone mods co-occurring with k4me3. I think this is going to be adopted real fast by discovery teams!
Well articulated post on what if Bluesky goes awry one day.
I like the idea of building real relationships that may originate here, outside of it. But, connections existing only here are no less real or meaningful.The rate at which the scientific community reconnected here is good evidence of that.
I like the idea of building real relationships that may originate here, outside of it. But, connections existing only here are no less real or meaningful.The rate at which the scientific community reconnected here is good evidence of that.
I'm going to try using BlueSky more reliably for a while. Here are a few thoughts that are guiding my engagement here, and hopefully learning from our collective experience over at Twitter.
chrisholdgraf.com/blog/2024/bl...
chrisholdgraf.com/blog/2024/bl...
Thoughts on moving from Twitter/X to BlueSky - Welcome
Some quick thoughts on moving from Twitter/X to BlueSky and how I'll try to use social media after being burned once by Twitter.
chrisholdgraf.com
November 26, 2024 at 1:05 AM
Well articulated post on what if Bluesky goes awry one day.
I like the idea of building real relationships that may originate here, outside of it. But, connections existing only here are no less real or meaningful.The rate at which the scientific community reconnected here is good evidence of that.
I like the idea of building real relationships that may originate here, outside of it. But, connections existing only here are no less real or meaningful.The rate at which the scientific community reconnected here is good evidence of that.
Join in to meet people who like to focus on science and answer interesting questions in biology with computational tools
TechBio Transformers (founded by @dr-alphalyrae.bsky.social) is a growing global community of folks who want to (+)ly impact the field of technology & biology, while also intentionally building healthy dialogue and community
Follow along, & even consider joining the group!
bsky.app/starter-pack...
Follow along, & even consider joining the group!
bsky.app/starter-pack...
November 25, 2024 at 10:02 PM
Join in to meet people who like to focus on science and answer interesting questions in biology with computational tools
changes in chromatin accessibility and loss of cell identity with age
Our recent study in Cell Metabolism provides compelling evidence that chromatin accessibility and transcription factor network remodeling in aging reflect the predictable degrading effects of a mechanism initially driving organismal maturation.
Link: doi.org/10.1016/j.cmet.2024.06.006
Thread 🧵👇1/9
Link: doi.org/10.1016/j.cmet.2024.06.006
Thread 🧵👇1/9
November 24, 2024 at 1:07 AM
changes in chromatin accessibility and loss of cell identity with age
One of my dream for this year is to host a Jeffersonian dinner. I hope to reconnect with old connections and meet cool new ones to make this dream a reality.
November 23, 2024 at 2:46 AM
One of my dream for this year is to host a Jeffersonian dinner. I hope to reconnect with old connections and meet cool new ones to make this dream a reality.
Reposted by Aditi Qamra
Like ‘old Twitter’: The scientific community finds a new home on Bluesky https://www.science.org/content/article/old-twitter-scientific-community-finds-new-home-bluesky 🧬🖥️🧪
www.science.org
November 22, 2024 at 9:00 PM
Like ‘old Twitter’: The scientific community finds a new home on Bluesky https://www.science.org/content/article/old-twitter-scientific-community-finds-new-home-bluesky 🧬🖥️🧪
Bluesky (so far) is a blast from the past when Twitter buzzed with good scientific conversations and scientists !
November 22, 2024 at 8:22 PM
Bluesky (so far) is a blast from the past when Twitter buzzed with good scientific conversations and scientists !
Reposted by Aditi Qamra
Genomics, Evolution, and More @jlsteenwyk.bsky.social bsky.app/starter-pack...
November 15, 2024 at 9:57 AM
Genomics, Evolution, and More @jlsteenwyk.bsky.social bsky.app/starter-pack...
Reposted by Aditi Qamra
Prepping for class this spring, this playlist of videos on diffusion models for proteins are great! Series is led by @maom.bsky.social and Nick Randolph of UNC.
www.youtube.com/playlist?lis...
www.youtube.com/playlist?lis...
Molecular ML Reading Group
The Molecular ML Reading Group aims to explore foundational and recent applications of machine learning models to modeling molecular system.
www.youtube.com
December 18, 2023 at 7:56 PM
Prepping for class this spring, this playlist of videos on diffusion models for proteins are great! Series is led by @maom.bsky.social and Nick Randolph of UNC.
www.youtube.com/playlist?lis...
www.youtube.com/playlist?lis...
Reposted by Aditi Qamra
New on BioRxiv: We report a new, endogenous molecular clock in unmodified human cells and tissues. It is ticking away right now in almost every cell in your body.
Paper here: www.biorxiv.org/content/10.1...
1/
Paper here: www.biorxiv.org/content/10.1...
1/
November 20, 2024 at 2:55 PM
New on BioRxiv: We report a new, endogenous molecular clock in unmodified human cells and tissues. It is ticking away right now in almost every cell in your body.
Paper here: www.biorxiv.org/content/10.1...
1/
Paper here: www.biorxiv.org/content/10.1...
1/