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Marcel Schulz

@themarcelschulz.bsky.social
161 followers 297 following 24 posts

Director of Institute for Computational Genomic Medicine at Goethe University Frankfurt cgm.uni-frankfurt.de

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Reposted by Marcel Schulz
Piali Sengupta @senguptalab.bsky.social · 28/07/2026
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.
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Ming Tommy Tang @tommytang.bsky.social · 29/07/2026
Free ebook: Fundamentals of Data Visualization clauswilke.com/dataviz/
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Jesse Engreitz @jengreitz.bsky.social · 15/07/2026
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/
nature.com
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Eric Topol @erictopol.bsky.social · 25/04/2026
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...
erictopol.substack.com
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
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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 22/04/2026
Human-supervised Agentic AI for Hypothesis Generation and Experimental Assistance in Drug Repurposing www.biorxiv.org/content/10.64898/20…
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Julia Rühle @juruehle.bsky.social · 04/03/2026
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...
doi.org
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Carl de Boer @carldeboer.bsky.social · 25/02/2026
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/...
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Kurianlab @kurianlab.bsky.social · 23/04/2026
www.sciencedirect.com/science/arti...
sciencedirect.com
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…
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Marcel Schulz @themarcelschulz.bsky.social · 08/04/2026
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.
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Yoav Gilad @ygilad.bsky.social · 04/04/2026
Beyond the mean: genetic control of gene expression fidelity and dispersion www.biorxiv.org/content/10.6...
biorxiv.org
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Dr. Keith R. Brunt @profbrunt.bsky.social · 15/01/2026
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...
cell.com
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...
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Stephen Turner @stephenturner.us · 08/12/2025
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...
currentaffairs.org
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.
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Lior Pachter @lpachter.bsky.social · 05/09/2025
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...
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loosolab @loosolab.bsky.social · 28/08/2025
🚀 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
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Cardio-Pulmonary Institute | CPI @cpi-exstra.bsky.social · 04/08/2025
🎉 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...
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Elena Rivas @rivaselenarivas.bsky.social · 02/08/2025
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...
doi.org
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Nature Biotechnology @natbiotech.nature.com · 25/07/2025
A resource of RNA-binding protein motifs across eukaryotes reveals evolutionary dynamics and gene-regulatory function go.nature.com/4mc1SmQ
go.nature.com
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.
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Eric Topol @erictopol.bsky.social · 25/07/2025
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...
nature.com
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.
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DjuranovicLab at Brown University RNA Center @djuranoviclab.bsky.social · 25/07/2025
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...
nature.com
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...
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Vikram Agarwal @vagar.bsky.social · 25/07/2025
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
url.de.m.mimecastprotect.com
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.
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Anthony Mathelier @amathelier.bsky.social · 24/07/2025
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
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Anthony Mathelier @amathelier.bsky.social · 24/07/2025
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
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Mallory Freeberg @malloryfreeberg.bsky.social · 23/07/2025
🧬 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
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Marcel Schulz @themarcelschulz.bsky.social · 23/07/2025
Last talk at #regsys today is a keynote by Mafalda Dias about modelling sequence variation in Evolution with insights into diseases #ismbeccb2025
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Alejandra Medina-Rivera @alemedinarivera.bsky.social · 23/07/2025
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
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Marcel Schulz @themarcelschulz.bsky.social · 23/07/2025
Laura Gunsalus talks about design of small native regulatory elements using #ML #ismbeccb2015 #regsys
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Marcel Schulz @themarcelschulz.bsky.social · 23/07/2025
Last talk in this #regsys session is Jishnu Das who talks about regulatory programs that determine B-cell fates #ismbeccb2025
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Marcel Schulz @themarcelschulz.bsky.social · 23/07/2025
Tatevik Jalatyan will talk about a new pipeline for estimating cell cycle phase from single cell data #ismbeccb2025 #regsys
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Marcel Schulz @themarcelschulz.bsky.social · 23/07/2025
Surag Nair talks about a general framework to combine different paradigms of DL genome models #ismbeccb2025 #regsys
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Marcel Schulz @themarcelschulz.bsky.social · 23/07/2025
Vitalii Kleshchenikow about a biophysical model for learning gene regulation from single cell data #ismbeccb2025 #regsys @oliverstegle.bsky.social
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Marcel Schulz @themarcelschulz.bsky.social · 23/07/2025
#regsys session is overflowing at #ismbeccb2025 consider to go to rooms 6 and 7 for video broadcast if full
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Marcel Schulz @themarcelschulz.bsky.social · 23/07/2025
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
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Marcel Schulz @themarcelschulz.bsky.social · 23/07/2025
Refreshed after lunch we start with Oluwatosin Oluwadare to introduce a new approach for single cell HiC analysis #ismbeccb2025 #regsys
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Marcel Schulz @themarcelschulz.bsky.social · 23/07/2025
Last speaker before lunch is Christophe Vroland to talk about confounders in Rna-Dna interaction data analysis #regsys #ismbeccb2025
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Marcel Schulz @themarcelschulz.bsky.social · 23/07/2025
Laura Hinojosa talks about TFs that regulate replication timing #RegSys #ismbeccb2025 @ferhatay.bsky.social
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Marcel Schulz @themarcelschulz.bsky.social · 23/07/2025
Next is @damlaob to talk about putting new Deep learning models of TFs into #Jaspardb #RegSys #ismbeccb2025 @amathelier.bsky.social
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Marcel Schulz @themarcelschulz.bsky.social · 23/07/2025
First flash talk session starts with @aryankamal.bsky.social who represents his analysis about understanding transcriptional regulation in blood generation #regsys #ismbeccb2025
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Marcel Schulz @themarcelschulz.bsky.social · 23/07/2025
Second proceedings talk by an Panagiotis Alexiou about benchmarking methods for miRNA-target prediction #regsys #ismbeccb2025
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Marcel Schulz @themarcelschulz.bsky.social · 23/07/2025
First proceedings talk in #RegSys by Yijie Wang about GRN inference from single cell data
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Marcel Schulz @themarcelschulz.bsky.social · 23/07/2025
#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
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Anthony Mathelier @amathelier.bsky.social · 23/07/2025
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.
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Marcel Schulz @themarcelschulz.bsky.social · 22/07/2025
Join 4 #Schulzlab related talks at #ismbeccb2025 : Wed #RegSys 14:20 , Laura Rumpf: Single-cell ATAC&RNA analysis, Thu #iRNACOSI 8:40, Christina Kalk – Prediction of Split-ORFs 9:40 , Tim Warwick – Pipeline for DNA-RNA analysis 12:10 , Giulia Cantini – Transformer for miRNA-mRNA prediction
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Luis Pedro Coelho @luispedrocoelho.bsky.social · 22/07/2025
For example ismb-schedule.luispedro.org?speaker=Luis...
ismb-schedule.luispedro.org
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Anthony Mathelier @amathelier.bsky.social · 21/07/2025
The #RegSys @iscb-regsys.bsky.social track is gonna be outstanding again this year with a great selection of talks and keynotes @verapancaldi.bsky.social, Mafalda Dias, Roser Vento-Tormo, and @lucapinello.bsky.social ! www.iscb.org/ismbeccb2025...
iscb.org
RegSys
ISCB - International Society for Computational Biology
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bioRxiv Genomics @biorxiv-genomic.bsky.social · 23/06/2025
Epilogos: information-theoretic navigation of multi-tissue functional genomic annotations www.biorxiv.org/content/10.1101/202…
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Manuel Friese @manuelfriese.bsky.social · 17/06/2025
Our latest work: The immunoproteasome disturbs neuronal metabolism and drives neurodegeneration in multiple sclerosis: Cell www.cell.com/cell/fulltex...
cell.com
The immunoproteasome disturbs neuronal metabolism and drives neurodegeneration in multiple sclerosis
Neuronal proteasomal dysfunction is a hallmark of neuroinflammatory and neurodegenerative diseases. This study reveals that the interferon-induced immunoproteasome drastically decreases proteasomal ac...
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Jerelle Joseph @jerelleaj.bsky.social · 07/03/2025
Second new preprint ‼️ Work led by brilliant postdoc @alinaemelianova.bsky.social (in collab with Pablo Garcia and Daniel Tan) where we leverage multiscale simulations to predict small-molecule partitioning into condensates 💦💊🙌🏽 www.biorxiv.org/content/10.1...
biorxiv.org
Prediction of small-molecule partitioning into biomolecular condensates from simulation
Predicting small-molecule partitioning into biomolecular condensates is key to developing drugs that selectively target aberrant condensates. However, the molecular mechanisms underlying small-molecul...
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Simon Fisher @profsimonfisher.bsky.social · 14/06/2025
In the new issue of @cp-trendsgenetics.bsky.social, @wiringthebrain.bsky.social & Nick Cheney seek out a better metaphor. They propose a generative model concept to capture the indirect, distributed, & non-linear relationship between info in the genome & form of the organism. Worth a read: 🧬👇🧪 11/11
cell.com
The Genomic Code: the genome instantiates a generative model of the organism
How does the genome encode the form of the organism? What is the nature of this genomic code? Inspired by recent work in machine learning and neuroscience, we propose that the genome encodes a generat...
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Stephen Turner @stephenturner.us · 10/06/2025
Current genomic deep learning models display decreased performance in cell type-specific accessible regions
genomebiology.biomedcentral.com
Current genomic deep learning models display decreased performance in cell type-specific accessible regions - Genome Biology
Background A number of deep learning models have been developed to predict epigenetic features such as chromatin accessibility from DNA sequence. Model evaluations commonly report performance…
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Guille Luxán @gluxan.bsky.social · 04/06/2025
I am super happy to join this year's nightofscience.de. I'll represent the @cpi-exstra.bsky.social speaking on "Small vessels, big impact: How your heart's microcirculation affects ageing and disease". I am looking forward to meeting y'all! @instcardregffm.bsky.social @goetheuni.bsky.social
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