Dmitry Penzar
@pensarata.bsky.social
PhD student, regulatory genomics, machine learning in biology, algorithms
(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.
November 18, 2025 at 10:55 PM
(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.
Reposted by Dmitry Penzar
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)
"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)
De-novo promoters emerge more readily from random DNA than from genomic DNA
Promoters are DNA sequences that help to initiate transcription. Point mutations can create de-novo promoters, which can consequently transcribe inactive genes or create novel transcripts. We know lit...
www.biorxiv.org
August 28, 2025 at 6:37 AM
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)
"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)
Reposted by Dmitry Penzar
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...
🧵
🧬🩸 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...
🧵
Design principles of cell-state-specific enhancers in hematopoiesis
Screen of minimalistic enhancers in blood progenitor cells demonstrates widespread
dual activator-repressor function of transcription factors (TFs) and enables the model-guided
design of cell-state-sp...
www.cell.com
May 8, 2025 at 4:07 PM
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...
🧵
🧬🩸 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...
🧵
Reposted by Dmitry Penzar
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...
Large-scale discovery of potent, compact and erythroid specific enhancers for gene therapy vectors - Nature Communications
This study presents a large-scale enhancer screening approach to optimize gene therapy vectors. A compact, potent, erythroid-specific enhancer used in a therapeutic vector, improved viral titers, tran...
www.nature.com
May 9, 2025 at 2:15 PM
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...
Reposted by Dmitry Penzar
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...
Preprint: www.biorxiv.org/content/10.1...
GitHub: github.com/jmschrei/led...
Programmatic design and editing of cis-regulatory elements
The development of modern genome editing tools has enabled researchers to make such edits with high precision but has left unsolved the problem of designing these edits. As a solution, we propose Ledi...
www.biorxiv.org
April 24, 2025 at 12:59 PM
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...
Preprint: www.biorxiv.org/content/10.1...
GitHub: github.com/jmschrei/led...
Reposted by Dmitry Penzar
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/
January 17, 2025 at 5:16 PM
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/
Reposted by Dmitry Penzar
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...
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...
Modelling and design of transcriptional enhancers - Nature Reviews Bioengineering
Enhancers are genomic elements critical for regulating gene expression. In this Review, the authors discuss how sequence-to-function models can be used to unravel the rules underlying enhancer activit...
www.nature.com
February 28, 2025 at 2:45 PM
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...
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...
Reposted by Dmitry Penzar
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.
Massively parallel characterization of transcriptional regulatory elements - Nature
Lentivirus-based reporter assays for 680,000 regulatory sequences from three cell lines coupled to machine-learning models lead to insights into the grammar of cis-regulatory elements.
www.nature.com
January 15, 2025 at 5:39 PM
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.
Reposted by Dmitry Penzar
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
www.biorxiv.org/content/10.1...
A 🧵about what it can do:
#SynBio #DeepLearning #GeneRegulation
EXTRA-seq: a genome-integrated extended massively parallel reporter assay to quantify enhancer-promoter communication
Precise control of gene expression is essential for cellular function, but the mechanisms by which enhancers communicate with promoters to coordinate this process are not fully understood. While seque...
biorxiv.org
December 16, 2024 at 2:39 PM
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
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.
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.
@dereklowe.bsky.social honing in on the same bottom line message from @wpwalters.bsky.social @prof-ajay-jain.bsky.social
it's so true and hits so hard:
it's so true and hits so hard:
December 7, 2024 at 6:11 PM
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.
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.
Reposted by Dmitry Penzar
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/
autosome.org
autosome.org
November 29, 2024 at 12:57 PM
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/
Reposted by Dmitry Penzar
(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...
November 28, 2024 at 7:59 PM
(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...
Reposted by Dmitry Penzar
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
biorxiv.org/cgi/content/...
Read more below!
1/12
Mapping enhancer-gene regulatory interactions from single-cell data
Mapping enhancers and their target genes in specific cell types is crucial for understanding gene regulation and human disease genetics. However, accurately predicting enhancer-gene regulatory interac...
biorxiv.org
November 25, 2024 at 8:26 AM
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
biorxiv.org/cgi/content/...
Read more below!
1/12
Reposted by Dmitry Penzar
Pooled CRISPR screens with joint single-nucleus chromatin accessibility and transcriptome profiling go.nature.com/4hXER5O
Pooled CRISPR screens with joint single-nucleus chromatin accessibility and transcriptome profiling - Nature Biotechnology
MultiPerturb-seq profiles gene expression and chromatin accessibility in single-cell pooled CRISPR screen.
go.nature.com
November 21, 2024 at 2:26 PM
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
Super excited to share our review on genomic deep learning models for non-coding variant effect prediction, with Ayesha Bajwa and Nilah Ioannidis. We’d like this review to be a useful resource, and welcome any feedback, comments, or questions! 1/4
arxiv.org/abs/2411.11158
arxiv.org/abs/2411.11158
Leveraging genomic deep learning models for non-coding variant effect prediction
The majority of genetic variants identified in genome-wide association studies of complex traits are non-coding, and characterizing their function remains an important challenge in human genetics. Gen...
arxiv.org
November 22, 2024 at 1:55 AM
Really nice overview and systematization of things done in the area. I found a few works in there that I've completely missed
Reposted by Dmitry Penzar
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/
Paper here: www.biorxiv.org/content/10.1...
1/
November 20, 2024 at 2:55 PM
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/
Paper here: www.biorxiv.org/content/10.1...
1/
Reposted by Dmitry Penzar
Regulatory plasticity of the human genome https://www.biorxiv.org/content/10.1101/2024.11.13.623439v1
Regulatory plasticity of the human genome https://www.biorxiv.org/content/10.1101/2024.11.13.623439v1
Evolutionary turnover in non-coding regions has driven phenotypic divergence during past speciation
www.biorxiv.org
November 15, 2024 at 7:33 AM
Regulatory plasticity of the human genome https://www.biorxiv.org/content/10.1101/2024.11.13.623439v1
Reposted by Dmitry Penzar
(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... ✨🧵 ⬇️
https://dx.doi.org/10.1101/2024.11.11.619598✨
November 14, 2024 at 1:49 PM
(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
November 14, 2024 at 6:09 PM
They say science and cats should be posted here
Reposted by Dmitry Penzar
(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.
November 14, 2024 at 12:42 PM
(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.
Reposted by Dmitry Penzar
(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 ⬇️.
November 14, 2024 at 1:04 PM
(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 ⬇️.
Reposted by Dmitry Penzar
Regulation of transcription by condensates, great review by @bsabari.bsky.social and coll.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Transcription regulation by biomolecular condensates - Nature Reviews Molecular Cell Biology
Transcriptional condensates, which are formed through dynamic multivalent interactions between proteins, RNA and chromatin, regulate transcription by compartmentalizing its machinery in the crowded nu...
www.nature.com
November 13, 2024 at 6:56 PM
Regulation of transcription by condensates, great review by @bsabari.bsky.social and coll.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Dmitry Penzar
Preprint describing the systematic identification of TF binding motifs and of TFs which preferentially bind methylated DNA. #epigenomics
Identification of methylation-sensitive human transcription factors using meSMiLE-seq https://www.biorxiv.org/content/10.1101/2024.11.11.619598v1
Identification of methylation-sensitive human transcription factors using meSMiLE-seq https://www.biorxiv.org/content/10.1101/2024.11.11.619598v1
Transcription factors (TFs) are key players in eukaryotic gene regulation, but the DNA binding speci
www.biorxiv.org
November 13, 2024 at 7:04 AM
Preprint describing the systematic identification of TF binding motifs and of TFs which preferentially bind methylated DNA. #epigenomics
Reposted by Dmitry Penzar
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.
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.
Perspective on recent developments and challenges in regulatory and systems genomics
Predicting how genetic variation affects phenotypic outcomes at the organismal, cellular, and molecular levels requires deciphering the cis-regulatory code, the sequence rules by which non-coding regi...
arxiv.org
November 8, 2024 at 6:22 PM
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.
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.