If you don't like a paper, it is obviously totally fine to point out the issues. But please do NOT make egregious and unpleasant comments about the first author's qualifications. A first author who is usually a trainee. Beyond inappropriate and unprofessional.

Free ebook: Fundamentals of Data Visualization clauswilke.com/dataviz/

An encyclopedia of enhancer-gene regulatory interactions — online today! nature.com/articles/s4158… Now with an improved model, expanded maps across 1400+ biosamples, larger validation CRISPR datasets, and guidance on applying the model 1/

Andreas Gschwind@argschwind.bsky.social · last mo.

Thrilled to share that our ENCODE enhancer–gene mapping paper is now out in Nature! An encyclopedia of human enhancer–gene regulatory interactions: www.nature.com/articles/s41... Thread 👇 1/

You will be surprised about the extent and impact of our acquired DNA mutations for health & disease. Including 3 new publications this past week. This is a Ground Truths not to miss. erictopol.substack.com/p/we-are-all...

We Are All Genetic Mosaics

Roxanne Khamsi's phenomenal book BEYOND INHERITANCE on the critical impact of our acquired, somatic mutations for health and disease

erictopol.substack.com

Human-supervised Agentic AI for Hypothesis Generation and Experimental Assistance in Drug Repurposing https://www.biorxiv.org/content/10.64898/2026.04.20.719538v1

The main project of my PhD 🧬🔬 is out: we developed single-cell lentiMPRA, a lentivirus-based method to measure enhancer activity and transcriptomes at single-cell resolution. We then applied sc-lentiMPRA to fully synthetic enhancers 🧩... 🔗 doi.org/10.64898/202...

We wrote a perspective "How to build the regulatory genome: a constructionist guide to the cis-regulatory code", out in Development yesterday. Title says it all. Find it here: journals.biologists.com/dev/article/...

www.sciencedirect.com/science/arti...

Comprehensive RNA-binding protein analyses and deep learning uncover genetic constraints and disease associations in protein-RNA interfaces

RNA-binding proteins (RBPs) orchestrate post-transcriptional processes, including splicing, cleavage and polyadenylation, and translation. Our updated…

sciencedirect.com

it is worrying to see how easy it is to make your way into a LLM. In these papers, there are obvious clues that the results are fake. What about fake papers where there are fewer obvious clues? How can these be detected.

Chris Stokel-Walker@stokel.bsky.social · 5mo ago

🚨 For nearly two years - and even now, depending on the day and model - AI models could tell you all about bixonimania, a totally made-up disease in a paper funded by “the Professor Sideshow Bob Foundation". My @nature.com story on AI's fallibility in medicine www.nature.com/articles/d41...

Beyond the mean: genetic control of gene expression fidelity and dispersion www.biorxiv.org/content/10.6...

Epstein-Barr Virus #EBV was linked to #MultipleSclerosis - now a plausible cause has been found, misidentification by longterm memory T-cells that pick on the wrong protein, ANO2, instead of the EBV-antigen. Massive inflection towards the elimination of MS!!! 🧪🧠Cell www.cell.com/cell/fulltex...

Anoctamin-2-specific T cells link Epstein-Barr virus to multiple sclerosis

Researchers identified anoctamin-2 (ANO2) as a frequent autoimmune target in multiple sclerosis, with T cell responses against ANO2 occurring in over half of patients. These ANO2-specific T cells shar...

cell.com

There's a really good essay by Ronald Purser in Current Affairs making the rounds: AI is Destroying the University and Learning Itself www.currentaffairs.org/news/ai-is-d...

AI is Destroying the University and Learning Itself

Students use AI to write papers, professors use AI to grade them, degrees become meaningless, and tech companies make fortunes. Welcome to the death of higher education.

currentaffairs.org

In a new work with Joseph Rich and Conrad Oakes we tackle the problem of how to best organize alluvial plots. We formalize two optimization problems and develop a solution for them based on the neighbornet algorithm, implemented in the program wompwomp: github.com/pachterlab/w...

🚀 Two exciting days of Computational Biology at the Cardio-Pulmonary Institute in Bad Nauheim @cpi-exstra.bsky.social ! 🔬 Workshop on single-cell analysis + the CPI repository data ressource; 💡 Hackathon together with the Schulz Lab @themarcelschulz.bsky.social Collaboration, coding & discovery

🎉 To mark the fourth extension of the CPI, we celebrated our success at the @mpi-hlr.bsky.social 🥳 We are delighted about the renewed funding and would like to thank everyone who made this step possible! Read more in the latest issue of "Synapse": www.unimedizin-ffm.de/fileadmin/re...

we asked a simple question: What does it take to learn the rules of RNA base pairing? using standard deep-learning technics, got a simple answer: don't need structures, nor alignments or many parameters only a few RNA sequences and 21 parameters; doi.org/10.1101/2025...

A resource of RNA-binding protein motifs across eukaryotes reveals evolutionary dynamics and gene-regulatory function go.nature.com/4mc1SmQ

A resource of RNA-binding protein motifs across eukaryotes reveals evolutionary dynamics and gene-regulatory function - Nature Biotechnology

RNA-binding motifs in eukaryotic proteins are presented in a comprehensive resource.

go.nature.com

Multi-omics with A.I. analytics demonstrates critical role of the gut microbiome and immune response and enables accurate diagnosis of ME/CFS, may also be applicable to Long Covid. www.nature.com/articles/s41... www.ft.com/content/9cdf...

AI-driven multi-omics modeling of myalgic encephalomyelitis/chronic fatigue syndrome - Nature Medicine

Analysis of a deeply phenotyped, longitudinal cohort of 249 participants elucidates the network of concurrent molecular and macroscopic patterns related to insurgence and course of ME/CFS.

nature.com

Our collaboration with Tony Mustoe's lab us out today. MPRA libraries and possible cryptic splicing in MPRA reporters, or reporters in general. The additional novelty here is that such events are controlled or influenced by AU-rich sequences. www.nature.com/articles/s41...

U-rich elements drive pervasive cryptic splicing in 3’ UTR massively parallel reporter assays - Nature Communications

Massively parallel reporter assays (MPRAs) are powerful technologies for measuring the impact of non-coding sequences on gene expression. Here, the authors demonstrate that MPRA reporters often underg...

nature.com

Very excited that our most significant work, a collaboration w/ Dr. Can Cenik at UT Austin on translational gene regulation, was finally published in Nature Biotechnology in a dual set of studies: Paper 1 -- an AI model trained to predict translation rates from mRNA sequences: rdcu.be/exN1l

Predicting the translation efficiency of messenger RNA in mammalian cells

Nature Biotechnology - A deep convolutional neural network model predicts the influence of the full-length mRNA sequence on translation efficiency.

url.de.m.mimecastprotect.com

And BIG thanks to #RegSys track organizers @abardet.bsky.social A. Emad J. Welch R. Gordan @xiuweizhang.bsky.social R. Beekman @martamele.bsky.social @anniquec.bsky.social @shaunmahony.bsky.social @ferhatay.bsky.social and co-chairs @alemedinarivera.bsky.social and @themarcelschulz.bsky.social

What a fantastic #ISMBECCB2025 conference it has been, with an outstanding #RegSys @iscb-regsys.bsky.social COSI track! Thanks, everyone, for submitting, attending, presenting, and organizing @iscb.bsky.social @eccb-europe.bsky.social

🧬 New @emblebi.bsky.social service beta launched: Perturbation Catalogue 🔎 Browse genetic perturbation datasets 🧠 Train models 🧬 Interpret variant function 🧭 Explore gene dependencies Search, test APIs, suggest datasets, send feedback! 🔗 www.ebi.ac.uk/perturbation... Funded by @opentargets.org

Last talk at #regsys today is a keynote by Mafalda Dias about modelling sequence variation in Evolution with insights into diseases #ismbeccb2025

First talk of the last session of RegSys day 1 at #ismb2025 is from Jacob Schreiber on how we read the book of DNA Spoiler: regulation is key

Laura Gunsalus talks about design of small native regulatory elements using #ML #ismbeccb2015 #regsys

Last talk in this #regsys session is Jishnu Das who talks about regulatory programs that determine B-cell fates #ismbeccb2025

Tatevik Jalatyan will talk about a new pipeline for estimating cell cycle phase from single cell data #ismbeccb2025 #regsys

Surag Nair talks about a general framework to combine different paradigms of DL genome models #ismbeccb2025 #regsys

Vitalii Kleshchenikow about a biophysical model for learning gene regulation from single cell data #ismbeccb2025 #regsys @oliverstegle.bsky.social