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Our paper is online🦃! no better timing to thank my mentors collaborators and colleagues Feng Zhang Arlotta Lab Aviv R Joshua Levin Sean Simmons Ashwin Shetty Simona Lodato Elise Robinson grateful to learn from you & proud of the work we accomplished together science.sciencemag.org/content/370/65…

Congratulations to Aakash Basu whose postdoctoral work on measuring DNA mechanics on the genome scale has just been published in Nature! nature.com/articles/s4158…

Our latest review on lncRNA and its roles in gene regulation is out! A fantastic collaboration with Ling-ling Chen, and wonderful work of Luisa Statello and Chun-Jie Guo. Check it out in Nature Reviews Molecular Cell Biology Nature Reviews Molecular Cell Biology nature.com/articles/s4158…

We developed a scalable, quantitative and ultra-high sensitivity workflow for true single cell proteome analysis - one by one. Single cells have a stable proteome but not transcriptome. Great collaboration with @Bruker Evosep Fabian Theis. Preprint: rb.gy/l4q32n

Our study, funded by an ERC grant, is now out in Cell! Read how protein structures can be barcoded in situ. The resulting 3D proteome snapshots pinpoint protein functional alterations at high resolution Cell @ERC_research D-BIOL @ ETH Zurich cell.com/cell/fulltext/…

A paper published in Nature demonstrates the MuZero algorithm from DeepMind, which uses model-based reinforcement learning to achieve superhuman performance in games without knowing anything about their rules. go.nature.com/37KeMFd

I love when you find out your paper is out from Twitter:)) This Nature Reviews Methods Primers has everything you ever wanted to know about open chromatin and more! Very nice collab with Keji Zhao Liesbeth Minnoye William J. Greenleaf Bob Schmitz Christoph Bock Lab @ CeMM & MedUni Vienna @steinaerts and their top students & post-docs

Check out these fun, hands-on Peter Doherty projects for young scientists, artists & makers ages 0-16+. kiwico.com/?utm_source=tw…

We develop MCML (multi-class multi-label) dimensionality reduction for this purpose. We're far from the first to argue for semi-supervised learning for single-cell genomics applications, we're just jumping on the (right) train. See, e.g. bianca dumitrascu et al. nature.com/articles/s4146…

Are you curious about using organic dyes in your microscopy experiments but not sure where to start? This Perspective from @rhodamine110 and Jon Grimm @dyerfulchymist.bsky.social introduces readers to the world of dyes and their pros and cons for biological applications. nature.com/articles/s4159…

Analysis of #scRNAseq requires constant, tedious, interaction with genomics databases. To facilitate querying from Ensembl et al., Laura Luebbert, PhD developed gget: biorxiv.org/content/10.110… (code @ github.com/pachterlab/gget). gget has many uses; a 🧵on the its amazing versatility: 1/

You may know the GREAT tool (great.stanford.edu) which performs functional enrichment directly on genomic regions. Here the rGREAT package implements the GREAT algorithm. Theoretically it can work with any organism and any type of gene sets. Check jokergoo.github.io/rGREAT/article…

Congratulations to Sangita Choudhury, August Yue Huang, Eunjung Alice Lee, ChrisAWalsh, and DrMingHuiChen for this beautiful paper on somatic mutations in aging cardiomyocytes! Highly creative work navigating many complexities to study mutations in the heart. nature.com/articles/s4358…

An atlas of late prenatal human neurodevelopment resolved by single-nucleus transcriptomics | Nature Communications nature.com/articles/s4146…

SSGG's Spring 2023 #shortcourse organized by George Tseng and Katerina Kechris, with other instructors. Topic: Introduction to Multi-Omics Analysis Date/Time: April 11, 13, 18 and 20th 3:00-4:30 ET Registration: Forthcoming #Bioinformatics #MultiOmics #Genomics

A mind-blowing paper has come out today in nature In 2016, JC Venter Institute scientists trimmed a bacterial genome to its barest minimum required for life to synthesize what they called a "minimal genome" (science.org/doi/10.1126/sc…). Today, a group of scientists from

Is having even more gene-disease associations still useful for picking drug targets? For which types of programs does it matter? Has pharma shifted focus towards genetically validated targets? New paper by me, Matt Nelson, Coco (Chengliang) Dong, & Jeffery Painter doi.org/10.1101/2023.0…👇

Alzheimer's GWAS gets a diversity boost with new samples from Hispanics, African Americans and East Asians leading to novel ancestry-specific signals (e.g. PTPRK, GRB14). A new preprint from Alzheimer's disease genetics consortium (ADGC) medrxiv.org/content/10.110…

This is a beautiful paper that introduces the "right" generalization of probabilistic canonical correlation analysis. CCA is the under-appreciated cousin of PCA (and in a formal way closely related), that has many applications in genomics (in this paper genetics is explored).

Ever analyze a scRNAseq dataset and wonder if a specific cell state has been seen before? And if so, where in the human body? Under what conditions? Well, now you can use our lightning fast SCimilarity search and foundational model for that! ⚡️🔎🧬 biorxiv.org/content/10.110… (1/11)