We have several positions open at various levels (Research Assistant, Research Associate, Postdoctoral Fellow) across our highly interactive teams in the Division of Translational Neuroscience 🧠🔬🧪 @lieberinstitute.bsky.social www.libd.org/careers/ Links to individual positions in the thread below.

I loved the "Hmmmmmm" in the crowd when @jcheng5.bsky.social showed this data quality problem uncovered by the #positron Databot tool. No human caught this during the Tidy Tuesday for the data. I've been skeptical of AI for data analysis, but this is an extremely compelling use case. 🫣

Shiny app to search and filter posit::conf(2025) Bluesky posts with the #positconf2025 #positconf25 or #positconf hashtags. App: apps.machlis.com/shiny/positc... GitHub repo: github.com/smach/bluesk... #RStats #RShiny

@sara-altman.bsky.social and I just shared the second release of the Posit AI Newsletter! In this edition, a landmark settlement on LLM training data and copyright, the emergence of agentic browsers, and more. Read and subscribe on the Posit Blog: posit.co/blog/2025-09...

So stoked to share about the first release of the Posit AI Newsletter! @sara-altman.bsky.social and I have been working on a pilot of this newsletter internally for a few months now—an opinionated and pragmatic snapshot of AI news released every two weeks. First edition: posit.co/blog/2025-08...

(1/10) We’re excited to share our new preprint (doi.org/10.1101/2025...), which uncovers the spatiomolecular landscape of the human nucleus accumbens (NAc), by integrating snRNA-seq with Visium spatial transcriptomics across 10 control donors. 🧠 #NAcLIBD #snRNAseq #10xVisium

This paper reviews the latest computational approaches for cell-type deconvolution in spatial transcriptomics, comparing tools and data integration. 🔗 doi.org/10.1038/s415... Thanks 🙌 @lgaspardboulinc.bsky.social, Luca Gortana, @thomas-walter.bsky.social, Emmanuel Barillot & Florence Cavalli

Hi everyone! Check my journal club talk on the latest review paper: Cell-type deconvolution methods for spatial transcriptomics 🧬 🎥 www.youtube.com/watch?v=xDjF... 🛝 speakerdeck.com/manishabarse @lieberinstitute.bsky.social #Bioinformatics #SpatialTranscriptomics #Cell-TypeDeconvolution

Ready to get the day started at @jhu.edu’s Schizophrenia Center Symposium day

We are hiring into 3 (THREE!) tenure track lines this year at Wake Forest — if you’re looking please reach out, I love chatting about our department! We are a vibrant group that love & embrace the teacher-scholar model 👩‍🏫

In this interview, I explain how university research, when funded by independent #NIH #NSF federal grants, brings oversight to biotech to fuel innovation while keeping science transparent, reliable, and in service of the public good: hub.jhu.edu/2025/07/30/j... #ResearchMatters

I visualize trends in #ICE #immigration arrests and encounters over time and across select US cities using public data from deportationdata.org/data/ice.html Here is the #RStats #ggplot code so you can visualize the #dataviz trends in your own city: gist.github.com/JEFworks/0c7... #codetutorial

Congress has decided to claw back previously approved funding for public media. This decision hurts people in communities across the country, but it has only strengthened our resolve to keep Americans informed and connected. (1/2)

In this blog post, I use #RStats to analyze ICE detention data. #Datavisualization shows record numbers of detainees without any criminal records. Further more/bigger ICE facilities are popping up far from the border. Code along and take a look for yourself: jef.works/blog/2025/07... #CodeTutorial

Phenomenal talk from @hyejungwon.bsky.social who is visiting us @lieberinstitute.bsky.social for the day. Groundbreaking work w/ important implications and roadmap for using rapidly emerging information on psychiatric genetics to prioritize variants and understand their impact on 🧠 function

1/ I am beyond thrilled to share our new paper in @CellCellPress! We explored the regulatory principles underlying pleiotropy in psychiatric disorders. www.cell.com/cell/abstrac...

Biostats assistant professor @lcolladotor.bsky.social is also an investigator @lieberinstitute.bsky.social where he leads the R/Bioconductor-powered Team Data Science group. Learn more about his work in the video below: www.youtube.com/watch?v=Rz4L...

Pseudobulk DGE #RStats journal club * #muscat doi.org/10.1038/s414... @helucro.bsky.social * pbDD doi.org/10.1101/2023... @davi1893.bsky.social * #dreamlet doi.org/10.1101/2023... ‪@panosroussos.bsky.social * #distinct doi.org/10.1214/22-A... @markrobinsonca.bsky.social youtu.be/TB9dfKPfns8

Happy 18th birthday ggplot2! #rstats

#SpotSweeper is now published! Check our journal club session summary of the pre-print version by @lahuuki.bsky.social The new features @boyiguo.bsky.social + @mictott.bsky.social added in this revised manuscript enhance the use cases for #SpotSweeper: 👀 #VisiumHD data! youtu.be/f72XcXmtkfw?...

Welcome @heenadivecha.bsky.social to Bsky! ^_^ Heena is a great scientist who worked at @lieberinstitute.bsky.social before joining @jhu.edu as a PhD student, and who is now back doing her PhD with @kr-maynard.bsky.social at LIBD 🔁

App: r-graph-gallery.com/color-palett... Special thanks to @emilhvitfeldt.bsky.social for the {paletteer} package and to the @libdrstats.bsky.social club for fostering these practical #bioinformatics tips!

🎨 Struggling to pick the perfect color palette for data visualizations? Check out walkthrough of interactive tools and the awesome {paletteer} package by @emilhvitfeldt.bsky.social ! 🔗 youtu.be/9tAeTjVD7ns Let’s make our plots both beautiful and accessible! #RStats @libdrstats.bsky.social

Hi everyone! Check my beginner-friendly #RStats talk at @lieberinstitute.bsky.social on reshaping, joining, binding, & set ops- all #tidyverse way! Shared simple demo to handle data better! 🎥 youtu.be/5L133h_1SNo 🛝 speakerdeck.com/manishabarse... @libdrstats.bsky.social #DataWrangling #DataScience

🚨 New paper published in @natmethods.nature.com! We introduce SpotSweeper, the first spatially-aware QC methods for spatial transcriptomics. 📰 Paper : nature.com/articles/s41... 💻 Code: github.com/MicTott/Spot... 📈 Website: mictott.github.io/SpotSweeper/ 🧵👇

Important methods development for spatial transcriptomics (ST) data from @mictott.bsky.social @boyiguo.bsky.social @stephaniehicks.bsky.social - congrats! Applying this method to our QC workflow has substantially improved many new ST datasets generated across diverse regions/tissues in the human 🧠

Do a lot of PCA? Interested in streamlining data wrangling? In a couple recent LIBD R Stats Club @libdrstats.bsky.social sessions I talk about PCAtools, and dplyr for beginners. youtu.be/rClA0Ms-oOw youtu.be/XIbraIgPt0M #RStats

New career milestone: served on a @jhu.edu PhD thesis committee meeting for the first time 🙌🏽 Thanks @jef.works for inviting me! And thanks @mikeschatz.bsky.social @jihk.bsky.social for your guidance! Great to share this experience with Fred Tan as well ^_^ It’s exciting to talk about […]

Want to easily use LLMs from R? ellmer 0.2.0 provides: • Batch & parallel processing • A universal parameter interface • Cost tracking • Support for Mistral, Hugging Face, & Portkey And much more! Read all about it at: www.tidyverse.org/blog/2025/05... #rstats

🔬 Diving into ATAC-seq workflows? You've likely heard about Seurat, Signac, MACS2, Cicero, and chromVAR—core components in many workflows. Here’s a quick overview I put together that showcases different approaches used across recent studies. youtu.be/R5P8mGMXuIg?... #SingleCell #Epigenomics #LIBD

Learning more about APOE differences in the cell types of the brain 🧠 I presented "APOE genotype determines cell-type-specific pathological landscape of Alzheimer’s disease" from @zhaonaa.bsky.social at our team journal club, check it out! doi.org/10.1016/j.ne... ▶️ youtu.be/L4J9jFS-Pic

Kinnary Shah is a fourth-year PhD candidate and co-president of the Biostats Student Org. Learn more about Kinnary and two of her ongoing research projects, one with the @lieberinstitute.bsky.social, and one with @stephaniehicks.bsky.social, on our website: publichealth.jhu.edu/departments/...

Last month at @libdrstats.bsky.social LIBD #rstats club I showed a #GenAI multi-modal LLM prompting technique for planning and scaffolding a R-Shiny + bslib application, using Google AI Studio, with VisualStudio Code as the IDE for R development (only free tools). youtu.be/7PA45mVxZ8M

"How are you using #AI to make your work easier?" That's a FAQ right now @lieberinstitute.bsky.social. Last week I searched @adobe.com Premier Pro's AI features. I found at helpx.adobe.com/premiere-pro... that it can * create a transcript + captions * detect filler words * detect pauses In ~5 min

Recently @mbarse.bsky.social presented a journal club on a proof of concept methods paper by @daylab.bsky.social et al The pre-print at doi.org/10.1101/2024... is well written and we are interested in applying this method to future @lieberinstitute.bsky.social data. bsky.app/profile/mbar...

¡Hola! 👋 Avances en nuestra investigación sobre la habenula humana, clave en motivación y estrés. Usamos single-cell, epigenomics y spatial data para estudiarla. Presentado en el 2025 Epigenomics Sciences Symposium (JHU). 🧠✨ #SingleCell #Epigenomics #LIBD

Presented at @lieberinstitute.bsky.social #RStats club on pseudobulk analysis using pseudoBulkDGE()📊 A handy wrapper for DE analysis following OSCA guidelines-shared a demo & walked through the method!✨ 🎥 youtu.be/0OkWBLyLrfg 🛝 speakerdeck.com/manishabarse... @libdrstats.bsky.social #Bioinformatics

Check out my LIBD @lieberinstitute.bsky.social R Stats Club #rstats presentation on SLURM array jobs for efficient parallel data analysis on HPC systems-- #slurm #hpc youtu.be/Sz7LpAC1gsQ

Hi! Check my journal club talk: smart ML method to deconvolute pooled snRNA-seq using sex-specific expression🧬 Thanks @daylab.bsky.social & @rphillips3.bsky.social for this approach🙌 🎥 youtu.be/zpeCFwYfV3o 🛝 speakerdeck.com/manishabarse #snRNAseq #ML #Bioinformatics @lieberinstitute.bsky.social

The latest version of the Kasumi manuscript is now published in Nature Comms www.nature.com/articles/s41... Kasumi identifies patterns in tissue patches, enabling analysis of disease progression and treatment response while providing insights into spatial coordination at cell-type or marker level

This summer, take short-term courses in biostatistics. The 43rd Summer Institute of Epidemiology & Biostatistics will take place this June. More info on schedule, courses, registration, and tuition can be found online: publichealth.jhu.edu/academics/gr...

Register today for these short, intensive courses in biostatistics and epidemiology providing practical and tangible skills. The Summer Institute offers courses ranging in length 4 hours to 2-weeks, with online, hybrid, and in-person format options. publichealth.jhu.edu/2025/summer-...

Advance your public health expertise this summer by signing up for Graduate Summer Institute classes. The 43rd Summer Institute runs June 9-28 and offers courses ranging in length from 4-hours to 2-weeks. View our full course list online: publichealth.jhu.edu/academics/gr...

This paper was an exciting culmination of a lots of exploration with #deconvolution ! Check-out my blog post on this work for the TL;DR version: lahuuki.github.io/posts/2025-0...

We also propose and evaluate a new method for selecting cell type specific #markergenes for deconvolution: #MeanRatio implemented in #DeconvoBuddies @bioconductor.bsky.social #rstats 🛠️ research.libd.org/DeconvoBuddi...

To assess method accuracy, we compared the estimated proportions to the #RNAScope proportions for correlations and rmse 📈 #BisqueRNA and #hspe were the top performers 🏆

We ran #deconvolution on the 110 bulk RNA-seq samples, with six selected methods: #DWLS, #bisqueRNA, #MuSiC, #BayesPrism, #hspe, and #CIBERSORTx. The methods returned a wide range of proportion estimates 📊

The resulting cell type proportions had a large range across the different #DLPFC samples, and were not always correlated with the paired #snRNAseq proportions ⚠️