Helena Reyes Gopar
@hamarillo.bsky.social
Researching human endogenous retroviruses using sc sequencing data
🏊🏼♀️ 👩🏻💻 🇲🇽
LCG UNAM alumna 🧬
🏊🏼♀️ 👩🏻💻 🇲🇽
LCG UNAM alumna 🧬
Reposted by Helena Reyes Gopar
There's been endless talk about an AI bubble, but less about exactly how, why, and how much it's a bubble. So I turned to the framework put forward by scholars Brent Goldfarb and David A. Kirsch, authors of "Bubbles and Crashes," for assessing tech bubbles.
Spoiler: On a scale of 1 to 8, AI is an 8
Spoiler: On a scale of 1 to 8, AI is an 8
AI Is the Bubble to Burst Them All
I talked to the scholars who literally wrote the book on tech bubbles—and applied their test.
www.wired.com
October 27, 2025 at 8:58 PM
There's been endless talk about an AI bubble, but less about exactly how, why, and how much it's a bubble. So I turned to the framework put forward by scholars Brent Goldfarb and David A. Kirsch, authors of "Bubbles and Crashes," for assessing tech bubbles.
Spoiler: On a scale of 1 to 8, AI is an 8
Spoiler: On a scale of 1 to 8, AI is an 8
Why aren’t language models acting/interacting like a graph? (Or are they? Idk). It seems so obvious that while human conversations are iterative, they’re nonlinear and that’s how you get to the point/good stuff
October 20, 2025 at 1:30 PM
Why aren’t language models acting/interacting like a graph? (Or are they? Idk). It seems so obvious that while human conversations are iterative, they’re nonlinear and that’s how you get to the point/good stuff
Reposted by Helena Reyes Gopar
The strongest argument I keep hearing for AI is that it makes many admin tasks and paperwork easy. This basically rephrases what many have been saying for decades - there is a vast and unnecessary administrative bloat mandated by “business best practice” that needs to vanish.
August 17, 2025 at 2:56 PM
The strongest argument I keep hearing for AI is that it makes many admin tasks and paperwork easy. This basically rephrases what many have been saying for decades - there is a vast and unnecessary administrative bloat mandated by “business best practice” that needs to vanish.
Reposted by Helena Reyes Gopar
Yesterday I attended Harin’s excellent defense where he talked about this study, which is a great reason to give it another shoutout.
Does population size affect the diversity of the music that people listen to? Really nice example how to make use of a DAG in practice!
Does population size affect the diversity of the music that people listen to? Really nice example how to make use of a DAG in practice!
August 8, 2025 at 3:41 AM
Yesterday I attended Harin’s excellent defense where he talked about this study, which is a great reason to give it another shoutout.
Does population size affect the diversity of the music that people listen to? Really nice example how to make use of a DAG in practice!
Does population size affect the diversity of the music that people listen to? Really nice example how to make use of a DAG in practice!
Are housekeeping genes now the ones we see expressed in every single single-cell cell?
August 6, 2025 at 5:49 PM
Are housekeeping genes now the ones we see expressed in every single single-cell cell?
Reposted by Helena Reyes Gopar
We just launched Foursquare Spatial Desktop – a geospatial analysis tool powered by embedded DuckDB and built on sqlrooms.org. Everything runs locally: your data stays on your machine, no cloud needed. A modern reimagining of Kepler.gl. Mac only for now. More coming.
foursquare.com/products/spa...
foursquare.com/products/spa...
July 31, 2025 at 10:39 AM
We just launched Foursquare Spatial Desktop – a geospatial analysis tool powered by embedded DuckDB and built on sqlrooms.org. Everything runs locally: your data stays on your machine, no cloud needed. A modern reimagining of Kepler.gl. Mac only for now. More coming.
foursquare.com/products/spa...
foursquare.com/products/spa...
Reposted by Helena Reyes Gopar
A single-cell transposable element atlas of human cell identity
A single-cell transposable element atlas of human cell identity
Reyes-Gopar et al. introduce Stellarscope, a computational approach for quantifying locus-specific transposable element expression in single-cell RNA sequencing data. The authors profile human PBMCs and reveal transposable elements marking specific cell subtypes. Stellarscope is available as an open-source package and promises to enable continued study of “genomic dark matter.”
dlvr.it
June 20, 2025 at 6:50 PM
A single-cell transposable element atlas of human cell identity
Thrilled to share this work! I am honored to learn from @mlbendall.bsky.social and so grateful for his guidance and mentorship.
Stellarscope is just the beginning!
There is so much to learn about TEs and now we can all explore the uncharted territory of single cell retro-genomics 🧬🔭
Stellarscope is just the beginning!
There is so much to learn about TEs and now we can all explore the uncharted territory of single cell retro-genomics 🧬🔭
🧵1/ Introducing Stellarscope: an EM-based tool for quantifying locus-specific transposable element expression in single cells.
A single-cell transposable element atlas of human cell identity: Cell Reports Methods www.cell.com/cell-reports...
@hamarillo.bsky.social #TEHub #singlecell #genomics
A single-cell transposable element atlas of human cell identity: Cell Reports Methods www.cell.com/cell-reports...
@hamarillo.bsky.social #TEHub #singlecell #genomics
A single-cell transposable element atlas of human cell identity
Reyes-Gopar et al. introduce Stellarscope, a computational approach for quantifying
locus-specific transposable element expression in single-cell RNA sequencing data.
The authors profile human PBMCs a...
www.cell.com
July 22, 2025 at 3:52 PM
Thrilled to share this work! I am honored to learn from @mlbendall.bsky.social and so grateful for his guidance and mentorship.
Stellarscope is just the beginning!
There is so much to learn about TEs and now we can all explore the uncharted territory of single cell retro-genomics 🧬🔭
Stellarscope is just the beginning!
There is so much to learn about TEs and now we can all explore the uncharted territory of single cell retro-genomics 🧬🔭
Reposted by Helena Reyes Gopar
do you ever stare at the ceiling and think about how the worldwide scientific establishment did the impossible and created a COVID vaccine in under a year and the response of the general public has been to go on an unstoppable rampage to destroy science and scientists
July 20, 2025 at 6:46 PM
do you ever stare at the ceiling and think about how the worldwide scientific establishment did the impossible and created a COVID vaccine in under a year and the response of the general public has been to go on an unstoppable rampage to destroy science and scientists
Reposted by Helena Reyes Gopar
I’m really happy to present #SCALPEL, a new #Nextflow tool to quantify transcript isoforms at the single-cell level using conventional 3’ scRNA-seq data #scRNA-seq #single-cell #tools #isoforms
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Quantification of transcript isoforms at the single-cell level using SCALPEL - Nature Communications
Single-cell RNA-seq facilitates the study of transcriptome diversity in individual cells. Here, authors introduce a tool for isoform quantification at the single-cell level using 3’ scRNA-seq data, co...
www.nature.com
July 14, 2025 at 10:31 AM
I’m really happy to present #SCALPEL, a new #Nextflow tool to quantify transcript isoforms at the single-cell level using conventional 3’ scRNA-seq data #scRNA-seq #single-cell #tools #isoforms
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Helena Reyes Gopar
Sad news:
The dataset behind this famous chart on the decline in costs of genome sequencing has had its NIH funding cut.
I loved this chart because it was the first that made me appreciate the impact of dataviz. But it also tracked progress towards an ambitious goal ($1000 genome) that succeeded.
The dataset behind this famous chart on the decline in costs of genome sequencing has had its NIH funding cut.
I loved this chart because it was the first that made me appreciate the impact of dataviz. But it also tracked progress towards an ambitious goal ($1000 genome) that succeeded.
![The "$1,000 genome" catchphrase was first publicly recorded in December 2001 at a scientific retreat to discuss the future of biomedical research following publication of the first draft of the Human Genome Project (HGP), convened by the National Human Genome Research Institute at Airlie House in Virginia.[5] The phrase neatly highlighted the chasm between the actual cost of the Human Genome Project, estimated at $2.7 billion over a decade, and the benchmark for routine, affordable personal genome sequencing.
On 2 October 2002, Craig Venter introduced the opening session of GSAC (The Genome Sequencing and Analysis Conference) at the Hynes Convention Center in Boston: "The Future of Sequencing: Advancing Towards the $1,000 Genome." Speakers included George M. Church and executives from 454 Life Sciences, Solexa, U.S. Genomics, VisiGen and Amersham plc.[6][7] In 2003, Venter announced that his foundation would earmark $500,000 for a breakthrough leading to the $1,000 genome.[8] That sum was subsequently rolled into the Archon X Prize.
In October 2004, NHGRI introduced the first in a series of '$1,000 Genome' grants designed to advance "the development of breakthrough technologies that will enable a human-sized genome to be sequenced for $1,000 or less."[9]](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:73aicoale2mqwrap63rdzwep/bafkreigcypk33xduk2wsfjyvwbnfzzb76p5m6jl3owhbb3ft32clwov37i@jpeg)
July 19, 2025 at 8:18 AM
Sad news:
The dataset behind this famous chart on the decline in costs of genome sequencing has had its NIH funding cut.
I loved this chart because it was the first that made me appreciate the impact of dataviz. But it also tracked progress towards an ambitious goal ($1000 genome) that succeeded.
The dataset behind this famous chart on the decline in costs of genome sequencing has had its NIH funding cut.
I loved this chart because it was the first that made me appreciate the impact of dataviz. But it also tracked progress towards an ambitious goal ($1000 genome) that succeeded.
Reposted by Helena Reyes Gopar
Thanks @lecteroide.bsky.social for the opportunity to share the efforts developed in MexOmics
www.the-scientist.com/mexomics-map...
www.the-scientist.com/mexomics-map...
MexOMICs Maps the Genetic and Social Landscape of Disease in Mexico
By focusing on twins and patients with lupus and Parkinson’s disease, a Mexican consortium is generating critical data to understand health and disease in the country.
www.the-scientist.com
July 2, 2025 at 6:51 PM
Thanks @lecteroide.bsky.social for the opportunity to share the efforts developed in MexOmics
www.the-scientist.com/mexomics-map...
www.the-scientist.com/mexomics-map...
One old fish needed to sense its environment and now I have to floss every night
(Isn’t evolution the coolest thing ever?! 👹🌀🧬🤗)
(Isn’t evolution the coolest thing ever?! 👹🌀🧬🤗)
New paper from the lab: Our teeth arose as sensory organs on the outside of the body of ancient jawless fish.!! Congrats to Yara Haridy and the team!
Background and video: phys.org/news/2025-05...
Open Access Paper: www.nature.com/articles/s41...
News and Views: www.nature.com/articles/d41...
Background and video: phys.org/news/2025-05...
Open Access Paper: www.nature.com/articles/s41...
News and Views: www.nature.com/articles/d41...
Teeth first evolved as sensory tissue in the armored exoskeletons of ancient fish, fossil scans find
Anyone who has ever squirmed through a dental cleaning can tell you how sensitive teeth can be. This sensitivity gives important feedback about temperature, pressure—and yes, pain—as we bite and chew ...
phys.org
June 28, 2025 at 12:36 AM
One old fish needed to sense its environment and now I have to floss every night
(Isn’t evolution the coolest thing ever?! 👹🌀🧬🤗)
(Isn’t evolution the coolest thing ever?! 👹🌀🧬🤗)
I wonder if easy-to-remember memories that are accompanied by ‘negative’ strong emotion (i.e. the opposite of insight?) follow the same or a different pathway in the brain activity
Neuroscientists have revealed which regions of the brain are active and how they interact when discovery strikes
https://go.nature.com/4k7wpkd
https://go.nature.com/4k7wpkd
Eureka! The brain science behind lightbulb moments
Nature - Experiences of insight come with a burst of brain activity — and a memory boost.
go.nature.com
June 27, 2025 at 5:23 PM
I wonder if easy-to-remember memories that are accompanied by ‘negative’ strong emotion (i.e. the opposite of insight?) follow the same or a different pathway in the brain activity
Reposted by Helena Reyes Gopar
Been horrifying teammates by referring to undocumented information that's held only in people's heads as "locked in meat storage".
Please use this with your teams/projects and report back on how they like it?
Please use this with your teams/projects and report back on how they like it?
June 25, 2025 at 9:50 AM
Been horrifying teammates by referring to undocumented information that's held only in people's heads as "locked in meat storage".
Please use this with your teams/projects and report back on how they like it?
Please use this with your teams/projects and report back on how they like it?
Reposted by Helena Reyes Gopar
June 17, 2025 at 4:19 PM
Reposted by Helena Reyes Gopar
🚨 Excited to share our latest work: 🚨
@bhavyasighs.bsky.social et al. show that locus-specific #HERV expression can reveal the origins and heterogeneity of B-cell lymphomas!
Locus-specific human endogenous retroviruses reveal lymphoma subtypes www.cell.com/iscience/ful...
#TEsky #TEworldwide
1/
@bhavyasighs.bsky.social et al. show that locus-specific #HERV expression can reveal the origins and heterogeneity of B-cell lymphomas!
Locus-specific human endogenous retroviruses reveal lymphoma subtypes www.cell.com/iscience/ful...
#TEsky #TEworldwide
1/
Locus-specific human endogenous retroviruses reveal lymphoma subtypes
Genomics; Virology
www.cell.com
May 20, 2025 at 8:44 PM
🚨 Excited to share our latest work: 🚨
@bhavyasighs.bsky.social et al. show that locus-specific #HERV expression can reveal the origins and heterogeneity of B-cell lymphomas!
Locus-specific human endogenous retroviruses reveal lymphoma subtypes www.cell.com/iscience/ful...
#TEsky #TEworldwide
1/
@bhavyasighs.bsky.social et al. show that locus-specific #HERV expression can reveal the origins and heterogeneity of B-cell lymphomas!
Locus-specific human endogenous retroviruses reveal lymphoma subtypes www.cell.com/iscience/ful...
#TEsky #TEworldwide
1/