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emmamarydann.bsky.social
Emma Dann
@emmamarydann.bsky.social
770 followers 480 following 5 posts
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/
Posts Replies Media Videos
Reposted by Emma Dann
lukasheumos.bsky.social
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
November 6, 2025 at 7:28 PM
Reposted by Emma Dann
roshnipatel.bsky.social
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!
roshnipatel.bsky.social Roshni Patel @roshnipatel.bsky.social · Aug 6
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
emmamarydann.bsky.social
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]
October 13, 2025 at 11:19 PM
Reposted by Emma Dann
scverse.bsky.social
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
October 10, 2025 at 2:48 AM
Reposted by Emma Dann
scverse.bsky.social
🚀 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
October 3, 2025 at 3:43 PM
Reposted by Emma Dann
scverse.bsky.social
🧬 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
September 2, 2025 at 4:03 PM
Reposted by Emma Dann
scverse.bsky.social
🎉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
September 1, 2025 at 4:18 PM
Reposted by Emma Dann
scverse.bsky.social
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
August 28, 2025 at 3:04 PM
Reposted by Emma Dann
scverse.bsky.social
🧫 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
August 26, 2025 at 2:36 PM
emmamarydann.bsky.social
We're committed to support as many attendees as possible join us at #scverse2025 - feel free to reach out if you have questions!
scverse.bsky.social scverse @scverse.bsky.social · Aug 25
💰 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
August 25, 2025 at 5:17 PM
Reposted by Emma Dann
scverse.bsky.social
🧠 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
August 19, 2025 at 3:37 PM
Reposted by Emma Dann
scverse.bsky.social
🎉 scverse conference 2025 Registration & Call for Abstracts NOW OPEN! 🎉
We're excited to announce that registration and the call for abstracts are officially open for the scverse Conference 2025!
Details in thread!
🧵 1/3
August 2, 2025 at 3:00 PM
Reposted by Emma Dann
jkpritch.bsky.social
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.
June 1, 2025 at 3:33 PM
emmamarydann.bsky.social
It's happening! 🙌
scverse.bsky.social scverse @scverse.bsky.social · May 12
📣 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!
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
Reposted by Emma Dann
scverse.bsky.social
🎉 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:
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
Reposted by Emma Dann
sophiebelman.bsky.social
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
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
Reposted by Emma Dann
scverse.bsky.social
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...
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
Reposted by Emma Dann
wkhuber.bsky.social
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...
January 31, 2025 at 4:03 PM
Reposted by Emma Dann
florianjug.bsky.social
🚨🚨 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
January 29, 2025 at 10:40 AM
Reposted by Emma Dann
jkpritch.bsky.social
I posted a couple days ago about our new paper on building causal graphs from genetic associations + Perturb-seq.

Here I want to expand on the value of using DIRECTIONAL information contained in LoF burden tests.🧵
[work led by @minetoota.bsky.social ]

bsky.app/profile/jkpr...
January 27, 2025 at 7:19 PM
emmamarydann.bsky.social
@minetoota.bsky.social set the groundwork for many ongoing projects in @jkpritch.bsky.social and Marson lab. Great to see this out!
jkpritch.bsky.social Jonathan Pritchard @jkpritch.bsky.social · Jan 26
Modern GWAS can identify 1000s of significant hits but it can be hard to turn this into biological insight. What key cellular functions link genetic variation to disease?

I'm very excited to present our new work combining associations and Perturb-seq to build interpretable causal graphs! A 🧵
January 26, 2025 at 7:29 PM
Reposted by Emma Dann
jkpritch.bsky.social
Very excited about this new work from our lab! Explainer thread coming soon
@minetoota.bsky.social
biorxiv-genetic.bsky.social bioRxiv Genetics @biorxiv-genetic.bsky.social · Jan 24
Causal modeling of gene effects from regulators to programs to traits: integration of genetic associations and Perturb-seq https://www.biorxiv.org/content/10.1101/2025.01.22.634424v1
January 24, 2025 at 4:45 PM
Reposted by Emma Dann
gbart.bsky.social
1/n Some time ago my colleague, excellent cook, and friend Ivan told me: "Cacio e pepe is the recipe that I screw up more often. Let's make a project studying systematically the physics of that sauce".

Prepare to get cheesy, I'm glad to share the Cacio e paper preprint:

arxiv.org/abs/2501.00536
January 4, 2025 at 9:34 AM
Reposted by Emma Dann
const-ae.bsky.social
After 4y in the making, I am super excited that my main PhD project is published 🎉🥳🎉🎉🥳

www.nature.com/articles/s41...

LEMUR is a tool to analyze multi-condition single-cell data and model differential expression as a continuous function of the cell-state space.

Some highlights⬇️
Overview of the LEMUR steps: (1) subspace alignment, (2) differential expression, (3) DE neighborhoods, (4) pseudobulking.
January 3, 2025 at 7:25 PM
Reposted by Emma Dann
jeffspence.github.io
What do GWAS and rare variant burden tests discover, and why?

Do these studies find the most IMPORTANT genes? If not, how DO they rank genes?

Here we present a surprising result: these studies actually test for SPECIFICITY! A 🧵on what this means... (🧪🧬)

www.biorxiv.org/content/10.1...
Specificity, length, and luck: How genes are prioritized by rare and common variant association studies
Standard genome-wide association studies (GWAS) and rare variant burden tests are essential tools for identifying trait-relevant genes. Although these methods are conceptually similar, we show by anal...
www.biorxiv.org
December 17, 2024 at 7:05 AM