Our team achieved first place in the CAGI7 lentiMPRA challenge on predicting the effects of single-nucleotide mutations in regulatory elements, surpassing the nearest competitors by a significant margin.

(1/13) Excited to share the outcome of the IBIS Challenge! The IBIS challenge united dozens of teams across the world in tackling the problem of modeling transcription factor (TF) binding specificity using a diverse collection of experimental datasets for understudied human TFs.

Excited / nervous to share the “magnum opus” of my postdoc in Andreas Wagner’s lab! "De-novo promoters emerge more readily from random DNA than from genomic DNA" This project is the accumulation of 4 years of work, and lays the foundation for my future group. In short, we… (1/4)

Out in Cell @cp-cell.bsky.social: Design principles of cell-state-specific enhancers in hematopoiesis 🧬🩸 screen of fully synthetic enhancers in blood progenitors 🤖 AI that creates new cell state specific enhancers 🔍 negative synergies between TFs lead to specificity! www.cell.com/cell/fulltex... 🧵

Finally published! We developed an epigenomics to therapeutics screening approach that identifies naturally occurring elements that can titrate expression of transgenes at various levels including single elements stronger than the B-globin LCR. www.nature.com/articles/s41...

Our preprint on designing and editing cis-regulatory elements using Ledidi is out! Ledidi turns *any* ML model (or set of models) into a designer of edits to DNA sequences that induce desired characteristics. Preprint: www.biorxiv.org/content/10.1... GitHub: github.com/jmschrei/led...

We share a lot of our ideas, code, datasets (that we spend years sanitizing) early. Often way before we release preprints. We do this so that others can use, build on, improve & even "beat" our approaches. But I want to say a few things about some simple expectations 1/

We wrote a review article on modelling and design of transcriptional enhancers using sequence-to-function models. From conventional machine learning methods to CNNs and using models as oracles/generative AI for synthetic enhancer design! @natrevbioeng.bsky.social www.nature.com/articles/s44...

Super excited to announce our latest work. On a personal note, it's not an exaggeration to say that blood, sweat, and tears got us to the finish line on this: working w/ an outstanding global team of scientists in Germany, Japan, Russia, and USA responding in >100 pages of complex reviewer comments.

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

Wonderful. Just two weeks ago I was explaining to a junior colleague the problem of exaggerated claims in science. This paragraph is exactly what should be printed in place of a user agreement when anybody submits a paper.

Join us for our next Kipoi Seminar with with Dmitry Penzar, @pensarata.bsky.social @ autosome.org! 👉LegNet: parameter-efficient modeling of gene regulatory regions using modern convolutional neural network 📅Wed Dec 4, 5:30pm CET 🧬 kipoi.org/seminar/

(1/6) 🐦‍🔥 In IBIS #ibischallenge, we challenged teams from all over the world to decipher the DNA recognition code of human transcription factors. The IBIS Final Conference took place on November 27, 2024. Recordings and slides: disk.yandex.ru/d/82FEnwPn15...

Excited to share our latest preprint on scE2G – a new model to link enhancers to target genes using single-cell data – with state-of-the-art performance across multiple perturbation benchmarks. biorxiv.org/cgi/content/... Read more below! 1/12

Pooled CRISPR screens with joint single-nucleus chromatin accessibility and transcriptome profiling go.nature.com/4hXER5O

Really nice overview and systematization of things done in the area. I found a few works in there that I've completely missed

New on BioRxiv: We report a new, endogenous molecular clock in unmodified human cells and tissues. It is ticking away right now in almost every cell in your body. Paper here: www.biorxiv.org/content/10.1... 1/

Regulatory plasticity of the human genome https://www.biorxiv.org/content/10.1101/2024.11.13.623439v1

(1/8)📢Excited to announce the bioRxiv submission of my work from the past three years! Introducing meSMiLE-seq, a microfluidic assay aimed to understand how DNA modifications impact transcription factor (TF) binding, as part of the large Codebook/GRECO-BIT collab dx.doi.org/10.1101/2024... ✨🧵 ⬇️

They say science and cats should be posted here

(1/4) In IBIS (ibis.autosome.org), we challenged teams from all over the world to decipher the DNA recognition code of human transcription factors. Today, we are excited to announce the Final IBIS Conference scheduled for November 27, 2024.

(1/12) Excited to present the results of the large-scale benchmarking of DNA motif discovery tools using the Codebook data compendium on poorly studied human transcription factors and the Codebook Motif Explorer: dx.doi.org/10.1101/2024..., mex.autosome.org ⬇️.

Regulation of transcription by condensates, great review by @bsabari.bsky.social and coll. www.nature.com/articles/s41...

Preprint describing the systematic identification of TF binding motifs and of TFs which preferentially bind methylated DNA. #epigenomics

Perspective on recent developments and challenges in regulatory and systems genomics arxiv.org/abs/2411.04363 Great perspective piece from an all-star author list on the current state of regulatory genomics and the challenges ahead.