Emma Dann
@emmamarydann.bsky.social
Postdoc fellow @ Stanford & Gladstone Institutes
Core team @scverse-team.bsky.social
Bringing the single-cell genomics in human complex trait genetics
https://emdann.github.io/
Core team @scverse-team.bsky.social
Bringing the single-cell genomics in human complex trait genetics
https://emdann.github.io/
Reposted by Emma Dann
🧬 2026 Internship: Marioni Group @genentech.bsky.social Seeking PhD intern for Deep Learning on large-scale genetic screens (Perturb-seq/Optical).
Focus: ML for single-cell + imaging to decode phenotypes.
📍 SSF (On-site) | 12-wk paid
⚠️ Apply via portal only: 🔗 bit.ly/45P7TQB
#CompBio #AI #Genetics
Focus: ML for single-cell + imaging to decode phenotypes.
📍 SSF (On-site) | 12-wk paid
⚠️ Apply via portal only: 🔗 bit.ly/45P7TQB
#CompBio #AI #Genetics
2026 Summer Intern (Computational Sciences - Cluster of Excellence)
2026 Summer Intern (Computational Sciences - Cluster of Excellence) The Marioni group in the Computational Sciences (CS) department studies the molecular mechanisms of cell fate decisions in early dev...
roche.wd3.myworkdayjobs.com
February 4, 2026 at 12:42 AM
🧬 2026 Internship: Marioni Group @genentech.bsky.social Seeking PhD intern for Deep Learning on large-scale genetic screens (Perturb-seq/Optical).
Focus: ML for single-cell + imaging to decode phenotypes.
📍 SSF (On-site) | 12-wk paid
⚠️ Apply via portal only: 🔗 bit.ly/45P7TQB
#CompBio #AI #Genetics
Focus: ML for single-cell + imaging to decode phenotypes.
📍 SSF (On-site) | 12-wk paid
⚠️ Apply via portal only: 🔗 bit.ly/45P7TQB
#CompBio #AI #Genetics
Reposted by Emma Dann
How well does TWAS estimate a gene’s direction of effect on a trait? We think of this as an important stress-test for the accuracy of TWAS.
In a new pre-print, we find that TWAS gets the sign wrong around 20-30% of the time!
doi.org/10.64898/202...
1/n
In a new pre-print, we find that TWAS gets the sign wrong around 20-30% of the time!
doi.org/10.64898/202...
1/n
High false sign rates in transcriptome-wide association studies
Transcriptome-wide association studies (TWAS) are widely used to identify genes involved in complex traits and to infer the direction of gene effects on traits. However, despite their popularity, it r...
doi.org
January 6, 2026 at 2:30 AM
How well does TWAS estimate a gene’s direction of effect on a trait? We think of this as an important stress-test for the accuracy of TWAS.
In a new pre-print, we find that TWAS gets the sign wrong around 20-30% of the time!
doi.org/10.64898/202...
1/n
In a new pre-print, we find that TWAS gets the sign wrong around 20-30% of the time!
doi.org/10.64898/202...
1/n
Together with @ronghuizhu.bsky.social, we are thrilled to present our new perturb-seq study of 22M primary CD4+ T cells, across donors and timepoints – the result of a decade-long collaboration between the Marson @marsonlab.bsky.social and Pritchard @jkpritch.bsky.social labs 🧵 tinyurl.com/gwt2025
Genome-scale perturb-seq in primary human CD4+ T cells maps context-specific regulators of T cell programs and human immune traits
Gene regulatory networks encode the fundamental logic of cellular functions, but systematic network mapping remains challenging, especially in cell states relevant to human biology and disease. Here, ...
tinyurl.com
January 5, 2026 at 6:42 PM
Together with @ronghuizhu.bsky.social, we are thrilled to present our new perturb-seq study of 22M primary CD4+ T cells, across donors and timepoints – the result of a decade-long collaboration between the Marson @marsonlab.bsky.social and Pritchard @jkpritch.bsky.social labs 🧵 tinyurl.com/gwt2025
Reposted by Emma Dann
GWAS has been an incredible discovery tool for human genetics: it regularly identifies *causal* links from 1000s of SNPs to any given trait. But mechanistic interpretation is usually difficult.
Our latest work on causal models for this is out yesterday:
www.nature.com/articles/s41...
A short🧵:
Our latest work on causal models for this is out yesterday:
www.nature.com/articles/s41...
A short🧵:
Causal modelling of gene effects from regulators to programs to traits - Nature
Approaches combining genetic association and Perturb-seq data that link genetic variants to functional programs to traits are described.
www.nature.com
December 11, 2025 at 5:54 PM
GWAS has been an incredible discovery tool for human genetics: it regularly identifies *causal* links from 1000s of SNPs to any given trait. But mechanistic interpretation is usually difficult.
Our latest work on causal models for this is out yesterday:
www.nature.com/articles/s41...
A short🧵:
Our latest work on causal models for this is out yesterday:
www.nature.com/articles/s41...
A short🧵:
Reposted by Emma Dann
Thank you Alex! Excited to see our paper published in @nature.com ! Huge thanks to @jeffspence.github.io , @tkyzeng.bsky.social , @emmamarydann.bsky.social, @nikhilmilind.dev, @marsonlab.bsky.social, @jkpritch.bsky.social, and all the members of the Pritchard and Marson labs for your enormous help!
December 11, 2025 at 3:04 AM
Thank you Alex! Excited to see our paper published in @nature.com ! Huge thanks to @jeffspence.github.io , @tkyzeng.bsky.social , @emmamarydann.bsky.social, @nikhilmilind.dev, @marsonlab.bsky.social, @jkpritch.bsky.social, and all the members of the Pritchard and Marson labs for your enormous help!
Reposted by Emma Dann
@hakha.bsky.social and I wrote a Research Briefing (with a lay summary + "behind the scenes") of our paper on how genes are prioritized by GWAS and rare variant burden tests. 🧬🧪
www.nature.com/articles/d41...
www.nature.com/articles/d41...
How do genetic association studies rank genes?
Genome-wide association studies and rare-variant burden tests reveal complementary aspects of trait biology.
www.nature.com
November 19, 2025 at 6:43 PM
@hakha.bsky.social and I wrote a Research Briefing (with a lay summary + "behind the scenes") of our paper on how genes are prioritized by GWAS and rare variant burden tests. 🧬🧪
www.nature.com/articles/d41...
www.nature.com/articles/d41...
Reposted by Emma Dann
Excited to see a home for MCP servers in bioinformatics emerge! The community needs a central hub for developing MCP servers for key bioinfo tools. At @scverse.bsky.social we're contributing to this effort - can't wait to share what we're building
BioContextAI is a community hub for agentic biomedical systems - @puellesv.bsky.social @biocontext.ai go.nature.com/3JmqKux
BioContextAI is a community hub for agentic biomedical systems - Nature Biotechnology
Nature Biotechnology - BioContextAI is a community hub for agentic biomedical systems
go.nature.com
November 6, 2025 at 7:28 PM
Excited to see a home for MCP servers in bioinformatics emerge! The community needs a central hub for developing MCP servers for key bioinfo tools. At @scverse.bsky.social we're contributing to this effort - can't wait to share what we're building
Reposted by Emma Dann
I'm recruiting a postdoc for my group (based in beautiful Eugene, OR). Please get in touch if you're interested, esp if you'd like to chat at #ASHG25!
We'll primarily work at the intersection of statistical and population genetics, and we also have active projects related to the ethical and social implications of human genetics (ELSI). Please get in touch if that's a combination that sounds interesting to you!
October 15, 2025 at 12:52 PM
I'm recruiting a postdoc for my group (based in beautiful Eugene, OR). Please get in touch if you're interested, esp if you'd like to chat at #ASHG25!
En route to Boston for #ASHG25 #ASHG2025!
👉 I'll be presenting a poster on our new work on genome-wide perturb-seq screens in primary human T cells (5049W, Wed 2.30pm)
👉 you can hear me talk about it at the Industry Education session presented by Ultima Genomics (Thu 3pm) [1/2]
👉 I'll be presenting a poster on our new work on genome-wide perturb-seq screens in primary human T cells (5049W, Wed 2.30pm)
👉 you can hear me talk about it at the Industry Education session presented by Ultima Genomics (Thu 3pm) [1/2]
October 13, 2025 at 11:19 PM
Reposted by Emma Dann
Last call, scverse community!
🐦 Early-bird closes October 17 for the scverse Conference 2025.
Single-cell, open science, and the people behind it — all in one place.
📝 Register here: www.eventbrite.com/e/scverse-co...
2 days of talks + 1 day of workshops
ℹ️ Info: scverse.org/conference2025
🐦 Early-bird closes October 17 for the scverse Conference 2025.
Single-cell, open science, and the people behind it — all in one place.
📝 Register here: www.eventbrite.com/e/scverse-co...
2 days of talks + 1 day of workshops
ℹ️ Info: scverse.org/conference2025
October 10, 2025 at 2:48 AM
Last call, scverse community!
🐦 Early-bird closes October 17 for the scverse Conference 2025.
Single-cell, open science, and the people behind it — all in one place.
📝 Register here: www.eventbrite.com/e/scverse-co...
2 days of talks + 1 day of workshops
ℹ️ Info: scverse.org/conference2025
🐦 Early-bird closes October 17 for the scverse Conference 2025.
Single-cell, open science, and the people behind it — all in one place.
📝 Register here: www.eventbrite.com/e/scverse-co...
2 days of talks + 1 day of workshops
ℹ️ Info: scverse.org/conference2025
Reposted by Emma Dann
🚀 NEW PANEL ANNOUNCEMENT: Agentic Workflows in Bioinformatics at scverse 2025! 🚀
We're thrilled to introduce an exciting panel discussion at the upcoming scverse Conference 2025!
More information in 🧵
#scverse2025 #Bioinformatics #AgenticAI #Conference
We're thrilled to introduce an exciting panel discussion at the upcoming scverse Conference 2025!
More information in 🧵
#scverse2025 #Bioinformatics #AgenticAI #Conference
October 3, 2025 at 3:43 PM
🚀 NEW PANEL ANNOUNCEMENT: Agentic Workflows in Bioinformatics at scverse 2025! 🚀
We're thrilled to introduce an exciting panel discussion at the upcoming scverse Conference 2025!
More information in 🧵
#scverse2025 #Bioinformatics #AgenticAI #Conference
We're thrilled to introduce an exciting panel discussion at the upcoming scverse Conference 2025!
More information in 🧵
#scverse2025 #Bioinformatics #AgenticAI #Conference
Reposted by Emma Dann
🧬 Tahoe Workshop at scverse conference 2025 🧬
Disease Biology and Therapeutics in the Age of Frontier Datasets
🧵
@tahoetherapeutics.bsky.social
#scverse2025 #ComputationalBiology #DrugDiscovery #TahoeTherapeutics #SingleCell #PerturbationBiology
Disease Biology and Therapeutics in the Age of Frontier Datasets
🧵
@tahoetherapeutics.bsky.social
#scverse2025 #ComputationalBiology #DrugDiscovery #TahoeTherapeutics #SingleCell #PerturbationBiology
September 2, 2025 at 4:03 PM
🧬 Tahoe Workshop at scverse conference 2025 🧬
Disease Biology and Therapeutics in the Age of Frontier Datasets
🧵
@tahoetherapeutics.bsky.social
#scverse2025 #ComputationalBiology #DrugDiscovery #TahoeTherapeutics #SingleCell #PerturbationBiology
Disease Biology and Therapeutics in the Age of Frontier Datasets
🧵
@tahoetherapeutics.bsky.social
#scverse2025 #ComputationalBiology #DrugDiscovery #TahoeTherapeutics #SingleCell #PerturbationBiology
Reposted by Emma Dann
🎉scverse conference 2025 Call for Abstracts DEADLINE EXTENDED! 🎉
We're excited to announce that the deadline to submit abstracts for the scverse Conference 2025 has been extended to September 15, 2025!
🧵
#scverse #scverse2025 #SingleCell #Conference
We're excited to announce that the deadline to submit abstracts for the scverse Conference 2025 has been extended to September 15, 2025!
🧵
#scverse #scverse2025 #SingleCell #Conference
September 1, 2025 at 4:18 PM
🎉scverse conference 2025 Call for Abstracts DEADLINE EXTENDED! 🎉
We're excited to announce that the deadline to submit abstracts for the scverse Conference 2025 has been extended to September 15, 2025!
🧵
#scverse #scverse2025 #SingleCell #Conference
We're excited to announce that the deadline to submit abstracts for the scverse Conference 2025 has been extended to September 15, 2025!
🧵
#scverse #scverse2025 #SingleCell #Conference
Reposted by Emma Dann
Meet the keynote speakers for the 2025 scverse conference!
Elham Azizi, Associate Professor of Cancer Data Research and Biomedical Engineering at Columbia University
🧵
@elhamazizi.bsky.social
@columbiauniversity.bsky.social
#scverse #scverse2025 #machinelearning #genomics #cancerimmunology
Elham Azizi, Associate Professor of Cancer Data Research and Biomedical Engineering at Columbia University
🧵
@elhamazizi.bsky.social
@columbiauniversity.bsky.social
#scverse #scverse2025 #machinelearning #genomics #cancerimmunology
August 28, 2025 at 3:04 PM
Meet the keynote speakers for the 2025 scverse conference!
Elham Azizi, Associate Professor of Cancer Data Research and Biomedical Engineering at Columbia University
🧵
@elhamazizi.bsky.social
@columbiauniversity.bsky.social
#scverse #scverse2025 #machinelearning #genomics #cancerimmunology
Elham Azizi, Associate Professor of Cancer Data Research and Biomedical Engineering at Columbia University
🧵
@elhamazizi.bsky.social
@columbiauniversity.bsky.social
#scverse #scverse2025 #machinelearning #genomics #cancerimmunology
Reposted by Emma Dann
🧫 Meet the keynote speakers for the 2025 scverse conference!
Erika Alden DeBenedictis, Co-founder of The Align Foundation & CEO of Pioneer Labs
@erika-alden.bsky.social
@alignbio.bsky.social
@pioneerlabs.bsky.social
#scverse #scverse2025 #StructuralBiology #Biotech #Stanford
Erika Alden DeBenedictis, Co-founder of The Align Foundation & CEO of Pioneer Labs
@erika-alden.bsky.social
@alignbio.bsky.social
@pioneerlabs.bsky.social
#scverse #scverse2025 #StructuralBiology #Biotech #Stanford
August 26, 2025 at 2:36 PM
🧫 Meet the keynote speakers for the 2025 scverse conference!
Erika Alden DeBenedictis, Co-founder of The Align Foundation & CEO of Pioneer Labs
@erika-alden.bsky.social
@alignbio.bsky.social
@pioneerlabs.bsky.social
#scverse #scverse2025 #StructuralBiology #Biotech #Stanford
Erika Alden DeBenedictis, Co-founder of The Align Foundation & CEO of Pioneer Labs
@erika-alden.bsky.social
@alignbio.bsky.social
@pioneerlabs.bsky.social
#scverse #scverse2025 #StructuralBiology #Biotech #Stanford
We're committed to support as many attendees as possible join us at #scverse2025 - feel free to reach out if you have questions!
💰 Travel Grants Available for scverse conference 2025! 💰
Did you know we are offering grants to help anyone in financial need attend our annual conference? 🌍
🧵
#scverse #scverse2025 #SingleCell #Conference #StanfordUniversity #TravelGrant
Did you know we are offering grants to help anyone in financial need attend our annual conference? 🌍
🧵
#scverse #scverse2025 #SingleCell #Conference #StanfordUniversity #TravelGrant
August 25, 2025 at 5:17 PM
We're committed to support as many attendees as possible join us at #scverse2025 - feel free to reach out if you have questions!
Reposted by Emma Dann
🧠 Meet the keynote speakers for the 2025 scverse conference!
Panos Roussos, Professor at Icahn School of Medicine at Mount Sinai
🧵
@panosroussos.bsky.social
#scverse #scverse2025 #SingleCell #SpatialTranscriptomics #Conference #Keynote
Panos Roussos, Professor at Icahn School of Medicine at Mount Sinai
🧵
@panosroussos.bsky.social
#scverse #scverse2025 #SingleCell #SpatialTranscriptomics #Conference #Keynote
August 19, 2025 at 3:37 PM
🧠 Meet the keynote speakers for the 2025 scverse conference!
Panos Roussos, Professor at Icahn School of Medicine at Mount Sinai
🧵
@panosroussos.bsky.social
#scverse #scverse2025 #SingleCell #SpatialTranscriptomics #Conference #Keynote
Panos Roussos, Professor at Icahn School of Medicine at Mount Sinai
🧵
@panosroussos.bsky.social
#scverse #scverse2025 #SingleCell #SpatialTranscriptomics #Conference #Keynote
Reposted by Emma Dann
I have an opportunity to hire a staff scientist for my lab. Looking for someone with outstanding skillset in ML/statistics, genomics applications; interest in mentoring, strong publication record, PD experience required.
Email CV to me+cc my assistant (see 'contact' on my website). Ad to follow.
Email CV to me+cc my assistant (see 'contact' on my website). Ad to follow.
June 1, 2025 at 3:33 PM
I have an opportunity to hire a staff scientist for my lab. Looking for someone with outstanding skillset in ML/statistics, genomics applications; interest in mentoring, strong publication record, PD experience required.
Email CV to me+cc my assistant (see 'contact' on my website). Ad to follow.
Email CV to me+cc my assistant (see 'contact' on my website). Ad to follow.
It's happening! 🙌
📣 Mark your calendars! The 2025 edition of the scverse conference will take place on 17-19 November at Stanford University (US) scverse.org/conference20...
Call for abstracts and registrations coming soon!
Call for abstracts and registrations coming soon!
scverse conference 2025
Follow us on our channels to learn more details in the coming weeks
scverse.org
May 12, 2025 at 11:24 PM
It's happening! 🙌
Reposted by Emma Dann
🎉 Scanpy 1.11.0 is out! 🎉 just after reaching 2000 stars on GitHub!
- sc.pp.sample replaces subsample with many new features
- Sparse Dask support pca
- session-info2 package for more reproducible notebooks
See the release notes:
- sc.pp.sample replaces subsample with many new features
- Sparse Dask support pca
- session-info2 package for more reproducible notebooks
See the release notes:
Release notes
Version 1.11: 1.11.0 2025-02-14: Release candidates: rc2 2025-01-24, rc1 2024-12-20. Features: rc1 sample() supports both upsampling and downsampling of observations and variables. subsample() is n...
buff.ly
February 14, 2025 at 12:08 PM
🎉 Scanpy 1.11.0 is out! 🎉 just after reaching 2000 stars on GitHub!
- sc.pp.sample replaces subsample with many new features
- Sparse Dask support pca
- session-info2 package for more reproducible notebooks
See the release notes:
- sc.pp.sample replaces subsample with many new features
- Sparse Dask support pca
- session-info2 package for more reproducible notebooks
See the release notes:
Reposted by Emma Dann
I’m racing a Half Ironman triathlon this June. 2km swim, 90km cycle, 20km run and raising money for the Meningitis Research Foundation.
Meningitis has ~2.5 million cases and 250,000 deaths annually predominantly among children. Any donation would be great!
gofund.me/a958252f
Meningitis has ~2.5 million cases and 250,000 deaths annually predominantly among children. Any donation would be great!
gofund.me/a958252f
Donate to Half Iron(wo)man for Meningitis Research, organized by Sophie Belman
I will be racing my first Half Ironman triathlon in Zurich this June. It includ… Sophie Belman needs your support for Half Iron(wo)man for Meningitis Research
gofund.me
February 9, 2025 at 7:29 PM
I’m racing a Half Ironman triathlon this June. 2km swim, 90km cycle, 20km run and raising money for the Meningitis Research Foundation.
Meningitis has ~2.5 million cases and 250,000 deaths annually predominantly among children. Any donation would be great!
gofund.me/a958252f
Meningitis has ~2.5 million cases and 250,000 deaths annually predominantly among children. Any donation would be great!
gofund.me/a958252f
Reposted by Emma Dann
Don't forget to apply to the upcoming @scverse.bsky.social x @owkin.bsky.social hackathon - applications due this Friday, February 7th!
📆March 17-19, 2025
📍Owkin Office, Paris
docs.google.com/forms/d/e/1F...
📆March 17-19, 2025
📍Owkin Office, Paris
docs.google.com/forms/d/e/1F...
Scverse x Owkin Hackathon in Paris
We're pleased to announce the next Scverse Hackathon will take place in the Owkin offices in Paris from 17/03/2025 9am to 19/03/2025 1:30pm.
This hackathon is a joint initiative between the scverse c...
docs.google.com
February 5, 2025 at 9:39 AM
Don't forget to apply to the upcoming @scverse.bsky.social x @owkin.bsky.social hackathon - applications due this Friday, February 7th!
📆March 17-19, 2025
📍Owkin Office, Paris
docs.google.com/forms/d/e/1F...
📆March 17-19, 2025
📍Owkin Office, Paris
docs.google.com/forms/d/e/1F...
Reposted by Emma Dann
Come work at the European Molecular Biology Laboratory in the beautiful science & university city Heidelberg as a Research Software Engineer on R/Bioconductor tools for biological data science and AI !
embl.wd103.myworkdayjobs.com/EMBL/job/Hei...
embl.wd103.myworkdayjobs.com/EMBL/job/Hei...
January 31, 2025 at 4:03 PM
Come work at the European Molecular Biology Laboratory in the beautiful science & university city Heidelberg as a Research Software Engineer on R/Bioconductor tools for biological data science and AI !
embl.wd103.myworkdayjobs.com/EMBL/job/Hei...
embl.wd103.myworkdayjobs.com/EMBL/job/Hei...
Reposted by Emma Dann
🚨🚨 MEGA JOB ALERT 🚨🚨
Independent Group Leader Positions in Computational Biology @humantechnopole.bsky.social!
Are you ready to start your own lab? Do you know someone who is? Repost this + share with everyone who might want to know about it. Thanks!!! 🙏
More details below... check it out! 🧵 1/3
Independent Group Leader Positions in Computational Biology @humantechnopole.bsky.social!
Are you ready to start your own lab? Do you know someone who is? Repost this + share with everyone who might want to know about it. Thanks!!! 🙏
More details below... check it out! 🧵 1/3
January 29, 2025 at 10:40 AM
🚨🚨 MEGA JOB ALERT 🚨🚨
Independent Group Leader Positions in Computational Biology @humantechnopole.bsky.social!
Are you ready to start your own lab? Do you know someone who is? Repost this + share with everyone who might want to know about it. Thanks!!! 🙏
More details below... check it out! 🧵 1/3
Independent Group Leader Positions in Computational Biology @humantechnopole.bsky.social!
Are you ready to start your own lab? Do you know someone who is? Repost this + share with everyone who might want to know about it. Thanks!!! 🙏
More details below... check it out! 🧵 1/3