Vanja
@halfacrocodile.bsky.social
bald but bearded bioinformatics buddy👨🦲 https://autosome.org
1/10 Did you know that molecular phenotypes of human skeletal muscles are vastly different? Meet FANTOMUS, the skeletal muscles promoterome-proteome atlas: doi.org/10.64898/202... made with @andreybuyan.bsky.social @nikitagryzunov.bsky.social @alforrest.bsky.social @sevamakeev.bsky.social
(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.
Our paper on LARGE-scale benchmarking of motif discovery tools is published! nature.com/articles/s42... It was a long, 7 years long journey, which coordinated efforts of 50+ researchers, proud to be on of them. More results from Codebook about poorly studied TFs are coming soon.
Cross-platform motif discovery and benchmarking to explore binding specificities of poorly studied human transcription factors - Communications Biology
Cross-platform benchmarking of DNA binding specificity models highlights top-performing motif discovery methods and demonstrates the potential of advanced models to capture alternative binding modes o...
nature.com
Vanja@halfacrocodile.bsky.social · 2y ago(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 ⬇️.
(1/15) Yet another sweet bioinformatics "software+database" couple from our team: Meet MIXALIME, a framework for assessing allelic imbalance, and UDACHA, a database of allele-specific chromatin accessibility, read more at www.nature.com/articles/s41...
(1/4) Thrilled to announce another major release of the HOCOMOCO motif collection, well-known for its silly name and rigorous approach to constructing and benchmarking DNA sequence motifs recognized by human and mouse transcription factors. hocomoco.autosome.org
The first preprint of 2025! Together with Matvei, @halfacrocodile.bsky.social, & our amazing team, we are excited to share PARADE: an AI framework for designing mRNA UTRs with enhanced cell-type specificity & stability. www.biorxiv.org/content/10.1...
A generative framework for enhanced cell-type specificity in rationally designed mRNAs
mRNA delivery offers new opportunities for disease treatment by directing cells to produce therapeutic proteins. However, designing highly stable mRNAs with programmable cell type-specificity remains ...
biorxiv.org
(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...
(1/7) Thrilled to reveal the results of the Codebook Project, an international effort to identify accurate DNA-binding motifs and genomic binding loci for the >300 uncharacterized human transcription factors (TFs) doi.org/10.1101/2024...
Perspectives on Codebook: sequence specificity of uncharacterized human transcription factors
We describe an effort (“Codebook”) to determine the sequence specificity of 332 putative and largely uncharacterized human transcription factors (TFs), as well as 61 control TFs. Nearly 5,000 independ...
doi.org
(1/8) 🚀 Excited to share our findings on a large-scale ChIP-seq assay for 166 previously uncharacterized human transcription factors (TFs) and their roles in both regulatory regions, and more strikingly, the “dark matter” genome. 🌌 doi.org/10.1101/2024....
Extensive binding of uncharacterized human transcription factors to genomic dark matter
Most of the human genome is thought to be non-functional, and includes large segments often referred to as “dark matter” DNA. The genome also encodes hundreds of putative and poorly characterized tran...
doi.org
(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 ⬇️.
(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.
