ENJOY READING: A Human Tonsil Atlas Immunity Proud to present our Human Cell Atlas work generating an "Atlas of Cells in the Human Tonsil" at #singlecell resolution and 5 modalities. Thanks European Research Council (ERC) and superstar-teams CNAG and IDIBAPS. cell.com/immunity/fullt…

Tired of long computations and exploding memory with your single-cell data? Interested in the idea of metacells, but unsure how to use them correctly? Check our review/tutorial "Building and analyzing metacells in single-cell genomics data" biorxiv.org/content/10.110…

If you were looking for evidence that isoforms are cool, all-pervasive in the 🧠, and everybody should study them at the single cell level, our work on mouse development and brain-region variability from the Hagen Tilgner / @[email protected] lab is now live Nature Neuroscience! 1/ nature.com/articles/s4159…

Amazing talk by Vivek Swarup diving into spatial transcriptomics in the brains of people with Down syndrome and Alzheimers disease...swaruplab UCI MIND #t21rs

We are excited to publish our second-ever Registered Report! The #LRGASP Consortium evaluated various methods for transcript identification and quantification using long-read sequencing technologies. AnaConesa The Sheynkman Lab Brooks Lab Ali Mortazavi nature.com/articles/s4159…

At long last the #LRGASP project has been published (nature.com/articles/s4159…)! I'm thankful for the amazing group of people I've gotten to work with and learn from during this project, and hope y'all are proud of this great work.

Solidarity with our colleagues at Nature journals in London who are demanding fair pay. Editors are scientists like us, working hard and facing massive underpayment. Signed the open letter: docs.google.com/document/d/1Th… #Springernaturestrike

Wow, @nature has retracted the 2020 Poore et al. cancer microbiome paper that we showed (journals.asm.org/doi/10.1128/mb…) was deeply flawed. The retraction date is tomorrow so I can't yet read the official notice, but I'll update when I can Retraction Watch Professor Booty PhD

In a new work led by Rebekah Loving, joint with Ali Mortazavi and his lab, we introduce a method based on kallisto for accurate quantification of Oxford Nanopore or PacBio long-read RNA-seq, and demonstrate its accuracy with numerous comparisons and benchmarks 1/🧵 biorxiv.org/content/10.110…

We hope this helps with clinical trial design for people with Down syndrome. Very much enjoyed this productive collaboration!

Yea, compbio folks beware: Anaconda is now trying to get academic users to pay licensing fees. See this Reddit thread too: reddit.com/r/bioinformati…

Cellular communities reveal trajectories of brain ageing and Alzheimer’s disease👏👏👏 nature.com/articles/s4158…

One of the last stories from my postdoc work with Howard Chang and William J. Greenleaf is out today Science Magazine led by Laksshman Sundaram. scATAC-seq of 8 different tumor types from TCGA. science.org/doi/10.1126/sc…

Excited to share our paper on multiomic changes in PiD & AD! We uncover cell-type & disease-specific CREs and predict TF occupancy. Explore our interactive database: swaruplab.bio.uci.edu/scROAD Huge thanks to co-first authors Sam Morabito & Sudeshna! biorxiv.org/content/10.110…

Happy to see our comparative study using scATAC + scRNA to study Pick's and Alzheimer's disease out in the world 😍 Was great to work with ZeChuan Shi, Sudeshna Das, and the Swarup Lab swaruplab on this one. biorxiv.org/content/10.110…

Cross-disorder and disease-specific pathways in dementia revealed by single-cell genomics Exciting work Rexach Lab & Geschwind Lab @ UCLA, comparing #Alzheimers & other tauopathies Suggests shared & disease-specific mechanisms of selective vulnerability & glia authors.elsevier.com/a/1jlOCL7PXqRkF

STAMP is OUT! Sequencing-free #singlecell RNA and Protein profiling. Game-changing approach for scalable and cost-efficient analysis of single cells. The future starts today! Amazing ⁦Luciano Martelotto 🛠🧬💻🇦🇺⁩ ⁦Dr. Jasmine Plummer 👩🏻‍🔬🧬🇨🇦🇺🇸⁩ biorxiv.org/content/10.110…

BigSur: Statistically principled feature selection for single cell transcriptomics biorxiv.org/content/10.110…

Next week at ASHG, please join my talk on a novel computational framework, CO-expression Module Perturbation Analysis for Cellular Transcriptomes (COMPACT), which can perform in-silico gene expression perturbations in single-cell data. Huge thanks to my co-developer Sam Morabito

Congratulations to my graduate student, Ze, for presenting their exciting research to a packed audience of over 500 at #ASHG24. So proud of your dedication and the impact of your work on advancing our understanding of genomics. Keep shining! #ProudAdvisor #ASHG2024