Marcel Schulz

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

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

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.

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...

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...

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...

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.

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

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

#regsys session is overflowing at #ismbeccb2025 consider to go to rooms 6 and 7 for video broadcast if full

Laura Rumpf talks about the MetaFR pipeline to learn gene regulation models from unpaired and paired scATAC and scRNA data #ismbeccb2025 #regsys #schulzlab @dzhk.de @sfb1531.bsky.social

Refreshed after lunch we start with Oluwatosin Oluwadare to introduce a new approach for single cell HiC analysis #ismbeccb2025 #regsys

Last speaker before lunch is Christophe Vroland to talk about confounders in Rna-Dna interaction data analysis #regsys #ismbeccb2025

Laura Hinojosa talks about TFs that regulate replication timing
#RegSys #ismbeccb2025 @ferhatay.bsky.social

Many BPNet models will be made available also correct id is @damlaob.bsky.social

Next is
@damlaob to talk about putting new Deep learning models of TFs into #Jaspardb #RegSys #ismbeccb2025 @amathelier.bsky.social

First flash talk session starts with @aryankamal.bsky.social who represents his analysis about understanding transcriptional regulation in blood generation #regsys #ismbeccb2025

Second proceedings talk by an Panagiotis Alexiou about benchmarking methods for miRNA-target prediction #regsys #ismbeccb2025

First proceedings talk in #RegSys by Yijie Wang about GRN inference from single cell data

#RegSys is starting with the keynote from @verapancaldi.bsky.social who talks about the changes of chromatin structure and the epigenome in cancer patients #ismbeccb2025

Today marks the start of the #RegSys @iscb-regsys.bsky.social track at ##ISMBECCB2025! Very much looking forward to listening to the exciting science that will be presented.

Join us in room 11BC today and tomorrow.