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pensarata.bsky.social
PhD student, regulatory genomics, machine learning in biology, algorithms
7 posts 1,898 followers 588 following
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Posts 18 Comments 4

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.

submitted 41 days ago • 2 comments

submitted 45 days ago • 173 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

submitted 72 days ago • 5 comments

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.

submitted 80 days ago • 0 comments

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/

submitted 89 days ago • 0 comments

(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...

submitted 89 days ago • 1 comment

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

submitted 93 days ago • 1 comment

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

submitted 97 days ago • 0 comments

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

submitted 96 days ago • 0 comments

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/

submitted 97 days ago • 2 comments

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

submitted 103 days ago • 0 comments

(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... ✨🧵 ⬇️

submitted 104 days ago • 1 comment

They say science and cats should be posted here

submitted 103 days ago • 0 comments

(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.

submitted 104 days ago • 2 comments

(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 ⬇️.

submitted 104 days ago • 1 comment

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

submitted 104 days ago • 3 comments

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

submitted 105 days ago • 0 comments

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.

submitted 109 days ago • 1 comment