Yusuf Roohani @yusufroohani

Yusuf Roohani

@yusufroohani.bsky.social

Machine Learning & Systems Biology. ML Group Leader @arcinstitute. PhD @StanfordAILab http://www.yusufroohani.com

177 Followers | 124 Following | 8 Posts | Joined: 26.11.2024 | 1.8534

Latest posts by yusufroohani.bsky.social on Bluesky

We're hiring! Come join the team and scale new heights with us! 🏔️

arcinstitute.org/jobs

25.02.2025 14:35 — 👍 1 🔁 0 💬 0 📌 0

Arc Virtual Cell Atlas launches, combining data from over 300 million cells | Arc Institute Arc Institute today launched the Arc Virtual Cell Atlas, a growing resource for computation-ready single-cell measurements, starting with data from over 300 million cells. The initial release of the A...

scBaseCamp is released as part of the Arc Virtual Cell Atlas!

Great work by Nick Youngblut, Chris Carpenter, Alex Dobin, Dave Burke, @genophoria.bsky.social and team

📢Announcement: arcinstitute.org/news/news/ar...

🔗Data access: github.com/ArcInstitute...

📄Report: arcinstitute.org/manuscripts/...

25.02.2025 14:35 — 👍 1 🔁 2 💬 1 📌 0

Uniform processing lowers technical variation between scBaseCamp datasets.

Technical factors such as library chemistry and suspension type (single-cell vs single-nucleus) exhibited comparable or lower silhouette scores than biologically meaningful categories like tissue type

25.02.2025 14:35 — 👍 0 🔁 0 💬 1 📌 0

scBaseCamp is the first large biological data repository curated by an AI agent

We built a hierarchical agentic workflow (SRAgent) to automate discovery, metadata extraction & data processing

It is consistent, easily scalable and automatically updates when new data is available

25.02.2025 14:35 — 👍 0 🔁 0 💬 1 📌 0

scBaseCamp was built by directly mining all publicly accessible 10X Genomics scRNAseq data from the Sequence Read Archive (SRA)

With over 230M cells drawn from 21 species and 72 tissues, scBaseCamp is significantly larger and more diverse than existing single-cell data repositories

25.02.2025 14:35 — 👍 0 🔁 0 💬 1 📌 0

At the @arcinstitute.org we are building AI models of cell state from the ground up, rethinking every step, from data generation to biologically relevant evaluation

Today we launch scBaseCamp, the largest public repository of single cell RNAseq data, uniformly processed from raw sequencing reads.

25.02.2025 14:35 — 👍 16 🔁 5 💬 1 📌 0

Why do you want to switch

04.12.2024 21:01 — 👍 0 🔁 0 💬 1 📌 0

very easy to do this in Pycharm

04.12.2024 20:43 — 👍 1 🔁 0 💬 1 📌 0

@yusufroohani is following 20 prominent accounts

Muneeb Sultan
@mmsltn

GenAI for proteins @abscibio. Prev. founding team @insitro, @Stanford PhD, and @Yale alumni. 🇵🇰🇺🇸

Yanay Rosen
@yanayrosen

CS PhD Student at Stanford. Machine Learning + CompBio Website: http://yanay.ai

Christopher Manning
@chrmanning

Stanford Linguistics and Computer Science. Director, Stanford AI Lab. Founder of @stanfordnlp.bsky.social . #NLP https://nlp.stanford.edu/~manning/

Hani Goodarzi
@genophoria

Core Investigator @ Arc Institute | Associate Professor @ UCSF | {Computational, Systems, Cancer, RNA} biologist | Co-founder @exaibio @vevo_ai

Ahmed Alaa
@amalaa

Assistant Professor at UC Berkeley and UCSF. Machine Learning and AI for Healthcare. https://alaalab.berkeley.edu/

Aidan Winters
@aidanwinters

Working in functional genomics, machine learning, and single-cell with a focus on multi-perturbation modeling. PhD Candidate in labs of Hani Goodarzi and Luke Gilbert @ UCSF and Arc Institute Comp Bio and ML at Tahoe Therapeutics (formerly Vevo)

Aaron Wenteler
@aaronwtr

PhD AI for Drug Discovery @QMUL, @EPFL, @MSDintheUK. ex-{@TUDelft, @CureVacRNA}. Researching the intersection of AI and biology to improve human health. 🧬🤖

Di Jiang
@dijiang319

Senior editor @science.org. Molecular biology, #DNA, #RNA, #gene regulation, #epigenetics, nuclear biology, #chromatin biology, 3D #genome, #synbio, #CRISPR and gene editing, other bacterial immune systems, and #AI in all these

Kasia Kedzierska
@kasia.codes

AI Research Scientist @alleninstitute.org | PhD from @ox.ac.uk | prev: intern @msftresearch.bsky.social New England & Novo Nordisk | she/her | kasia.codes

Will Fondrie
@willfondrie.com

Head of Data Science & Engineering at Talus Bio. I post about data science, BioML, AI drug discovery, Python, mass spec, proteomics, and silly things my kids do. I also blog sometimes: https://willfondrie.com/post

Surag Nair
@suragnair

Machine learning and genetics @Genentech. Previously CS PhD @Stanford. suragnair.github.io

David Fischer
@davidsebfischer

I develop mechanistic machine learning tools for single-cell and spatial omics data to understand the regulatory patterns underlying human disease dynamics. ai4biomedicine.org

Samuel Stanton
@activelearner

Principal Machine Learning Scientist @PrescientDesign @Genentech @Roche | @NYUDataScience PhD | developing AI agents for scientific discovery in biotech

Mohsen Sadeghi
@mohsensadeghi

comp. (bio)physics + AI for science + pretending to do bio/neuro stuff Staff Scientist at @fmp-berlin.de Opinions expressed are solely my own. https://mohsensadeghi.github.io https://linkedin.com/in/drmohsensadeghi

Hammad Farooq
@hammad-farooq

Bioinformatics PhD Candidate at University of Illinois Chicago | 3D genome folding | Human genetics

Zeming Lin
@ebetica

Bio/ML. Co-founder at EvoScale, worked on Pytorch and StarCraft back at meta. Most likely not skynet.

Amy Lu
@amyxlu

CS PhD Student at UC Berkeley & AI for drug discovery at Prescient Design 🇨🇦

Mae Woods
@maewoods

Passionate about compbio | high performance computing | mathematics | digitalization | cell & gene therapy. Opinions are my own. GitHub: https://github.com/MaeWoods

Julia Zeitlinger
@juliazeitlinger

Genomics, AI, sequence-to-function models, mechanisms of the cis-regulatory code. Investigator at the Stowers Institute.

Jacob Schreiber
@jmschreiber91

Studying genomics, machine learning, and fruit. My code is like our genomes -- most of it is junk. Guest Scientist IMP Vienna, Board of Directors NumFOCUS Incoming Prof UMass Chan Medical Previously Stanford Genetics, UW CSE.