1/ I'm excited to share that we're launching NECB 2026, the inaugural New England Computational Biology Symposium. Oct 1-2 at Microsoft Research New England, Cambridge. Two days of keynotes,talks, and posters to bring our community together across institutions.Space is limited. newenglandcompbio.org

1/ Thrilled to share our DNA-Diffusion paper, co-led by Lucas Ferreira and @ssenan.bsky.social is now out in @NatureGenet! New experimental results: STARR-Seq validation across 3 cell types (episomal) and EXTRA-Seq for endogenous activation of AXIN2, a leukemia protective gene! x.com/lucapinello/...

We are thrilled to announce the first official release (v0.1.8) of #𝗯𝗲𝗱𝗱𝗲𝗿, the successor to one of our flagship tool, #𝗯𝗲𝗱𝘁𝗼𝗼𝗹𝘀! Based on ideas we conceived of long ago (!), this was achieved thanks to the dedication of Brent Pedersen. 1/n

Very proud of our new paper! Great job @mweilert.bsky.social, our experimentalists and modeling collaborator Rosa Martinez-Corral. It was fun to see the story grow and get feedback from various experts. Thank you all!

Zeitlinger Lab@zeitlingerlab.bsky.social · 9mo ago

We are pleased to announce a new preprint by @mlweilert.bsky.social: “Widespread low-affinity motifs enhance chromatin accessibility and regulatory potential in mESCs” (www.biorxiv.org/content/10.1...). See summary and longer recap below: (TLDR; low-affinity motifs matter as pioneers!)

🚨 Exciting opportunity! The Eric and Wendy Schmidt Center at the Broad Institute of MIT and Harvard is recruiting exceptional postdocs for 2026 at the intersection of ML/math and biomedicine. Shape the future of computational biology 🧵👇

I'm happy to share that our gReLU package is now published in Nature Methods! www.nature.com/articles/s41...

gReLU: a comprehensive framework for DNA sequence modeling and design - Nature Methods

gReLU advances deep-learning-based modeling and analysis of DNA sequences with comprehensive toolsets and versatile applications.

nature.com

🧬Excited to be at #ASHG2025! My lab is presenting 5 studies this week. Join us for talks and posters on #SingleCell #CRISPR, #DeepLearning & more! Thread below with all presentation details 👇

15 years in the making, we confirmed that mitochondria - the powerhouse of the cell - have an unusual localization in patients who experience psychosis (including schizophrenia and bipolar disorders). You’ll never guess what kind of patient cells we used to make this discovery… 🧵

I wrote about gene-gene interactions (epistasis) and the implications for heritability, trait definitions, natural selection, and therapeutic interventions. Biology is clearly full of causal interactions, so why don't we see them in the data? A 🧵:

Beneath the surface of the sum

When genetic interactions matter and when they don't

open.substack.com

🎉 The revised version of CORNETO, our unified Python framework for knowledge-driven network inference from omics data, is published in peer reviewed form 🔗 Paper: www.nature.com/articles/s42... 📖 News & Views: www.nature.com/articles/s42... 💻 Code: corneto.org 🧵 Thread 👇

Interested in using functional data to understand clinical variants? Been hunting for a good review of the topic? We just wrote one! rdcu.be/exaEU

Multiplexed assays of variant effect for clinical variant interpretation

Nature Reviews Genetics - Multiplexed assays of variant effect (MAVEs) are highly scalable experimental approaches used to generate functional data for genetic variants. In this Review, McEwen et...

nature.com

Excited to be at #ISMBECCB2025! I'll be presenting at RegSys on "Learning the Regulatory Genome by Destruction and Creation" (Thursday 3:15PM in Room 11BC). I'm looking forward to connecting with both new and old friends throughout the conference! 🧬 #CRISPR #Genomics #Diffusion

🧵 It's raining outside, perfect for some vibe coding... ☔ So I built something cool with @anthropic.com's Claude Desktop! Introducing Claude Text Editor - edit ANY text, ANYWHERE on macOS with Claude's help. No more copy-paste gymnastics! 🚀

Great to see it finally out —such a fantastic collaboration with @bkleinstiver.bsky.social , @rachelsilverstein9.bsky.social and team!

Ben Kleinstiver@bkleinstiver.bsky.social · last yr.

In @nature.com we describe the use of scalable #proteinengineering & #machinelearning to predict millions of bespoke CRISPR enzymes, offering safer & more efficient genome editing tools 🧬🖥️ @rachelsilverstein9.bsky.social @mgbresearch.bsky.social @harvardmed.bsky.social www.nature.com/articles/s41...

Excited to share James Jusuf's preprint: By integrating Micro-C with SuperRes Live-Imaging we can calibrate genomics&imaging to perform absolute quantification of looping (e.g. this loop is present 3%) We quantify mESC 36k loops: <loops> are generally rare (2.3%) www.biorxiv.org/content/10.1...

Out today in @naturegenet.bsky.social -- PERFF-seq! With @tsionabay.bsky.social , @ronanchaligne.bsky.social, Bob Stickels, Meril Takizawa, + Ansu Satpathy, we describe this new assay to study rare populations with programmable nucleic acid cytometry. 1/n www.nature.com/articles/s41...

Transcript-specific enrichment enables profiling of rare cell states via single-cell RNA sequencing - Nature Genetics

Programmable Enrichment via RNA FlowFISH by sequencing (PERFF-seq) isolates rare cells based on RNA marker transcripts for single-cell RNA sequencing profiling of complex tissues, with applicability t...

nature.com

1/ 🎄 What’s the best gift under the tree for a computational biologist? 🎁 A new experimental assay that refines our view of gene regulation: ACCESS-ATAC! This creative idea from Richard Sherwood was developed collaboratively between his lab and mine. #Genomics www.biorxiv.org/content/10.1...

Excited to be visiting Duke University to share insights on computational methods for single-cell genomics and CRISPR genome editing! Thank you for hosting me @yi-zhang-compbio.bsky.social 🙏

The Gregory Lab @ DukeU@gregorylab.bskyverified.social · 2y ago

Happening this week with special guest @lucapinello.bsky.social! Check out dmpi.duke.edu/duke-single-... for more information. We hope to see you all there 🧬

Amazing new assay that allows testing of multiple DNA sequences, similar to MPRA, but in an endogenous setting. Incredible potential! Congrats @jk-swietek.bsky.social , @bartdeplancke.bsky.social and the entire team – grateful and lucky to be an early adopter. Check it out!

Judith Kribelbauer@jk-swietek.bsky.social · 2y ago

Finally out! We present EXTRA-seq, a new EXTended Reporter Assay to quantify endogenous enhancer-promoter communication at kb scale! www.biorxiv.org/content/10.1... A 🧵about what it can do: #SynBio #DeepLearning #GeneRegulation

Attending #NeurIPS2024 this week and excited to connect with anyone exploring the intersection of #GenerativeAI, #DeepLearning, and #Genomics! I’m presenting our DNA-diffusion work at the LatinX in AI workshop today at 2:30—drop by if you’re around. Looking forward to meeting and learning from you!

Excited to visit the @humantechnopole.bsky.social 🇮🇹today to share our work on computational approaches in functional genomics! Looking forward to discussions with amazing scientists about #singlecell, #CRISPR, and #syntheticbiology. 🧬Special thanks to @nicolesoranzo for the invitation 🙏

Hello World! Very glad to be here and see the scientific community growing 🌱. It’s so refreshing to scroll through a feed full of exciting science! Looking forward to reconnecting with old friends and collaborators and meeting new ones. Let’s keep the science flowing! 🌟

Interested in #singlecell and #spatial #metabolomics? Then book your calendar for December 10th! – Our online, free event will summarize major achievements of the field in 2024. #metabolism #omics #MALDI #EPFL With Giovanni D'Angelo and our #PhD students we prepared for you a fantastic lineup. 🧵 1/5

There are ~40k postdocs in the US, according to the NIH. While PhD students generally have good support (their committees, external advisors, and classmates), the postdocs do not. To help with this, we're starting the 'Postdoc Night Science' club in Boston this Thursday! (1/3)