Laura Luebbert

🎉 Congrats to Dr. Laura Luebbert ( @lauraluebbert.com ) for receiving the 2025 FutureHouse Fellowship! She’ll develop AI tools to detect viral sequences in genomic data & analyze virome data from 4,000+ people. Creator of gget & champion of open science—go Laura! 🧬🙌

Very excited to finally see this out! 🦠🧬

Huge thanks to all of my amazing co-authors! @lpachter.bsky.social @delaneyksull.bsky.social

Original paper thread: x.com/neuroluebber...

Free access link to the paper: rdcu.be/eiIWC

Detection of viral sequences at single-cell resolution identifies novel viruses associated with host gene expression changes - Nature Biotechnology A workflow using conserved amino acid domains identifies viruses in sequence data at single-cell resolution.

Detection of viral sequences at single-cell resolution identifies novel viruses associated with host gene expression changes - @lauraluebbert.com @lpachter.bsky.social go.nature.com/4lGrSY3

Delphy: scalable, near-real-time Bayesian phylogenetics for outbreaks Pathogen genomic analysis is central to tracking, understanding, and containing outbreaks, but complexity and high costs of state-of-the-art (SOTA) phylogenetic tools limit global access and impact. W...

We’re excited to share the completed preprint of Delphy — our new tool for scalable, near-real-time #Bayesianphylogenetics for outbreaks! 🚀
Check it out here: www.biorxiv.org/content/10.1...
Explore Delphy: delphy.fathom.info
Led by #PatrickVarilly @sabetilab.bsky.social @fathom.info 🧵1/17

Does it come with an API? We could use this under the hood of gget blast as well

pachterlab.github.io/gget/

gget hit >1,000 stars on GitHub!!! 🤯

Very grateful to all gget users and contributors for continuously helping us make bioinformatics databases and tools more accessible! ✨

github.com/pachterlab/g...

JUNIPER: Reconstructing Transmission Events from Next-Generation Sequencing Data at Scale Transmission reconstruction--the inference of who infects whom in disease outbreaks--offers critical insights into how pathogens spread and provides opportunities for targeted control measures. We dev...

We present JUNIPER, our outbreak reconstruction tool that incorporates within-host variants, models missing data, and scales to large, sparsely sampled datasets to achieve state-of-the-art performance. Led by @ivan_specht et al. @sabeti_lab. www.medrxiv.org/content/10.1... 1/12 🧵

BFVD—a large repository of predicted viral protein structures Abstract. The AlphaFold Protein Structure Database (AFDB) is the largest repository of accurately predicted structures with taxonomic labels. Despite provi

Our Big Fantastic Virus Database (BFVD) contains protein structure predictions of major viral clades, enhanced by petabase-scale homology search and it's explorable on the web. Led by @eunbelivable.bsky.social
🌐 bfvd.foldseek.com
📄 academic.oup.com/nar/article/...

Fantastic slides describing gget!

Thank you for sharing #HoffmanLabTechTalk @michaelhoffman.bsky.social and Luomeng Tan.

github.com/pachterlab/g...

The Nature briefing features my work on nests. We see one picture of the Rokin nest with a lot of plastic sticking out - prior to collecting it. And the stratigraphy of plastic with all the datable pieces of the nest laid out as a timeline.

Feels kind of illegal to be featured by "Nature" with a bird's nest this artificial. But here we are. 😅🪹🪶

@nature.com 🌿🧪

Still one of the coolest things we've ever done. Two degreeless heathens in a home lab published a microbial genome so clean and complete it became THE reference for that organism.

www.ncbi.nlm.nih.gov/datasets/tax...

Thank you!

I have no problem accessing NCBI from my laptop at home in Cambridge, but the server errors out as soon as I connect to any sort of VPN (including Boston VPNs) or try to access it from GitHub Actions. Anyone know what’s going on?

JXTX + CSHL 2025 Biology of Genomes Scholarship JXTX + CSHL 2025 Biology of Genomes Scholarship

Tomorrow is the deadline for applications for JXTX Scholarships for the CSHL Biology of Genomes! The application is lightweight - just a couple brief statements about your work! @cshlmeetings.bsky.social @jxtxfoundation.bsky.social jxtxfoundation.org/news/2025-2-...

It’s been a tough few weeks. My 10yo daughter was diagnosed with a very rare, aggressive cancer called interdigitating dendritic cell sarcoma (IDCS). I’m reaching out to identify clinicians/patients who have encountered pediatric IDCS or other (non-LCH) dendritic or histiocytic sarcomas cases.

Wondering which diseases or drugs are associate with your gene of interest (including ongoing clinical trials)?

You can now answer this question directly from your command-line or Python/R environment:

pachterlab.github.io/gget/en/open...

Huge shoutout to Joseph Rich and Sam Wagenaar!

Case study: gget’s new Open Target module The new gget opentargets module allows users to communicate directly with the Open Targets database from a Python or command line environment. Amongst other tasks, gget opentargets can quickly find di...

With the gget opentargets module, you can now interact directly with the Open Targets database from a Python or command line environment

Developed by @lauraluebbert.com, gget is a free, open-source tool enabling efficient querying of large genomic databases 🖥️🧬

blog.opentargets.org/case-study-g...

Figure 1 from the pytximport manuscript. Overview of the pytximport package and its associated RNA sequencingworkflow. a) pytximport package. pytximport is available for use as a Python library orfrom the command line. It can be configured to either output AnnData objects forintegration with other scverse ecosystem software or xarray datasets. Common applicationsfor pytximport include gene count estimation from transcript quantification files, isoform-usage bias correction, filtering of transcript-level data and creation of transcript-to-genemappings. b) Pythonic RNA sequencing analysis workflow. We propose a reproducibleRNA-seq analysis workflow based on command-line software available through Bioconda(yellow line: Snakemake, fastp, Salmon) and scverse ecosystem Python packages (greenline: pytximport, PyDESeq2, decoupleR). c) Comparison with tximport. Counts frompytximport match counts from tximport exactly across different quantification modes andinput files from different transcript quantification tools. RSEM-g: RSEM gene-level input.RSEM-t: RSEM transcript-level input.

Coding in Python and looking to perform bulk RNA sequencing analysis? With pytximport recently published in Bioinformatics and version 0.11.0 out today with many improvements, it’s time for my first Bluetorial!

A thread 🧵 (1/12)

Code for RNAseq analysis: # get example data from the European Nucleotide Archive wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR105/088/SRR10574388/SRR10574388_1.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR105/088/SRR10574388/SRR10574388_2.fastq.gz # get the human genome reference files from Ensembl with gget gget ref -d -w cdna,gtf homo_sapiens # create a transcript-to-gene mapping with pytximport pytximport create-map -i ./Homo_sapiens.GRCh38.113.gtf.gz -o tx2gene.csv --target-field gene_name # preprocess your FASTQ files with fastp fastp -i SRR10574388_1.fastq.gz -I SRR10574388_2.fastq.gz -o SRR10574388_1.fastq.gz -O SRR10574388_1.fastq.gz # quantify the reads with kallisto kallisto index -i index.idx Homo_sapiens.GRCh38.cdna.all.fa.gz kallisto quant -i index.idx -o ./SRR10574388 --paired-end SRR10574388_1.fastq.gz SRR10574388_1.fastq.gz # correct for isoform-usage bias, summarize at the gene-level and save as AnnData (or .csv) pytximport -i ./SRR10574388/ -t kallisto -m tx2gene.csv -o ./counts.h5ad # run your downstream analysis python differential_gene_expression.py

With pytximport and tools like fastp by Shifu Chen, kallisto by the @lpachter.bsky.social lab and gget by @lauraluebbert.com et al, running a bulk RNA-sequencing analysis is now a 10 line bash script. (7/12)

What better way to kick off our Bluesky journey than with our annual holiday card? 🌟 Celebrate unity, humanity, and the milestones shaping a brighter future with us. Happy Holidays! 🎄✨ bit.ly/3Dsr6wk

This week was my last retreat as a postdoc at the @broadinstitute.org 🥹 I was incredibly honored to receive the Eric S. Lander award and to talk about the dark proteome of viruses. Excited to begin my next chapter at @harvardmed.bsky.social next month! (thx @lauraluebbert.com for the lovely 📸)

Casually presenting gget at the @broadinstitute.org #broadretreat - Huge thanks to all aspiring and existing users/contributors who stopped by!!

Missed the fun? Catch me at poster 44 tomorrow at noon!

Special shoutout to @michaelgatzen.bsky.social for the hype!

gget.bio

Here is a thread showcasing my GitHub repositories: 1) Friends Don't Let Friends Make Bad Graphs. An opinionated essay on good and bad graphs.

My popular one by a long shot with 6.4k stars and 248 forks. github.com/cxli233/Frie...

Here's a new starter pack for researchers at the Broad Institute of MIT and Harvard!

Could you please add me? :)

I've posted the notes/slides for my computational biology class at github.com/pachterlab/B... Topics were chosen based on appearing in >=3 bio areas, although for focus examples are all drawn from #scRNAseq. Homeworks include both theory and exploration of data (via GoogleColab).

The Journal of Scientific Integrity by Laura Luebbert and Lior Pachter Background (by LL) Four years ago, during the first year of my PhD at Caltech, I participated in a journal club organized by the lab I was rotating in. I was assi…

A friend mentioned honey bee waggle dance to me recently and I had to tell them the bad news about that literature: numerous key papers appear to be fraud. So here is me sharing the bad news with you too. Extensive blog post by the hero sleuth, Laura Luebbert, and @lpachter.bsky.social:

Great idea @lpachter.bsky.social! In the meantime, I built a Chrome extension that puts a share to Bluesky button next to the X button on any @biorxivpreprint.bsky.social preprint. Installation instructions in the repo github.com/stephenturne.... I'll get this on the Chrome web store soon. 🧬🖥️🧪

I'm delighted to share that I will be joining the Department of Microbiology at Harvard Medical School in January 2025. The Laboratory of Systems Virology will study the dark proteome of viral genomes to understand how viruses work their magic🪄 Thrilled to be back in beautiful Boston 🌟