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Vanja @halfacrocodile.bsky.social · Feb 19

(15/15) MIXALIME is written in Python, getting the stable version is as easy as 'pip install mixalime', and the source code plus tutorial are freely available at github.com/autosome-ru/...

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Vanja @halfacrocodile.bsky.social · Feb 19

(14/15) We hope you will find MIXALIME and UDACHA useful in your study of regulatory sequence variants.

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Vanja @halfacrocodile.bsky.social · Feb 19

(13/15) According to stratified LD score regression, these rSNPs correspond to regulatory regions involved in cell type-specific phenotypes. Most importantly, the collection of significant rSNPs can be fully explored at udacha.autosome.org

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Vanja @halfacrocodile.bsky.social · Feb 19

(12/15) AS-chromatin variants are predominantly located in promoter and enhancer regions and significantly overlap ADASTRA ASBs and GTEx eQTLs.

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Vanja @halfacrocodile.bsky.social · Feb 19

(11/15) Finally, we used MIXALIME to analyze 5858 chromatin accessibility datasets from gtrd.biouml.org. In the end, we identified >200 thousand allele-specific chromatin accessibility variants.

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Vanja @halfacrocodile.bsky.social · Feb 19

(10/15) In most cases, MIXALIME outperforms other popular tools for AS calling, offering a good sensitivity/specificity tradeoff.

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Vanja @halfacrocodile.bsky.social · Feb 19

(9/15) Using heart CAGE-Seq data from Deviatiiarov et al., we benchmarked MIXALIME by calling AS variants in CAGE-Seq and comparing them to allele-specific transcription factor binding from ADASTRA and eQTLs from GTEx.

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Vanja @halfacrocodile.bsky.social · Feb 19

(8/15) Copy-number variation and aneuploidy are accounted for by fitting a mixture model assuming that reads originate from haplotypes with different copy numbers.

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Vanja @halfacrocodile.bsky.social · Feb 19

(7/15) MIXALIME also handles reference mapping bias and aneuploidy, see the underlying math in arxiv.org/abs/2306.08287. To counter the mapping bias, MIXALIME uses separate fits for Alt read counts with the fixed number of Ref reads and vice versa.

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Vanja @halfacrocodile.bsky.social · Feb 19

(6/15) MIXALIME provides a variety of statistical models to fulfill particular use cases, from a standard binomial model to the beta negative binomial (BetaNB) model that accounts for extra overdispersion.

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Vanja @halfacrocodile.bsky.social · Feb 19

(5/15) MIXALIME is a novel toolbox that uses MIXture models for ALlelic IMbalance Estimation. In the paper, we describe a general workflow from FASTQ files to allelic read counts and SNV-level allele-specific statistics.

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Vanja @halfacrocodile.bsky.social · Feb 19

(4/15) Technically, the allele specificity is revealed by counting the number of reads supporting each of the alleles and estimating the statistical significance of the observed allelic imbalance.

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Vanja @halfacrocodile.bsky.social · Feb 19

(3/15) High-throughput sequencing allows tracking chromatin state, gene expression, protein-DNA interactions, and more. Eventually, all methods yield short reads that can be used to call single-nucleotide variants and assess the allele specificity.

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Vanja @halfacrocodile.bsky.social · Feb 19

(2/15) Check the original Tweetorial describing the respective preprint x.com/halfacrocodi... or follow the thread below.

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Vanja @halfacrocodile.bsky.social · Feb 19

(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...

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Vanja @halfacrocodile.bsky.social · Feb 17

Last but not least: this update became possible thanks to the experimental data & motif analysis performed within the Codebook/GRECO-BIT collaboration, ibis.autosome.org/docs/about_us

IBIS Challenge

ibis.autosome.org

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Vanja @halfacrocodile.bsky.social · Feb 17

(4/4) Don't hesitate to grab a fresh release from hocomoco.autosome.org and remember that we also provide a fancy online motif scanner, MoLoTool, in all its interactive JS-powered beauty.

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Vanja @halfacrocodile.bsky.social · Feb 17

(3/4) Also do not forget that HOCOMOCO also provides motifs for orthologous mouse TFs, >800 of those are covered in v13.

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Vanja @halfacrocodile.bsky.social · Feb 17

(2/4) v13 covers >1100 of ~1600 human TFs with >1600 primary motifs and subtypes. Since v12 we also provide a reduced non-redundant set of motifs, which are often shared between TFs with similar DBDs.

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Vanja @halfacrocodile.bsky.social · Feb 17

(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

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Reposted by Vanja

Hani Goodarzi @genophoria.bsky.social · Jan 2

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 ...

www.biorxiv.org

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Vanja @halfacrocodile.bsky.social · Nov 28

(6/6) 👏 Once again, congratulations to the winners and their mentors including @callitmagic.bsky.social y.social @yaronorenstein.bsky.social @salimovdr.bsky.social @german-roev.bsky.social

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Vanja @halfacrocodile.bsky.social · Nov 28

(5/6) 🏁 This is the finishing line of the challenge but more remains to be done to analyze the solutions in detail and perform extra tests against other models for the post-challenge manuscript.

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Vanja @halfacrocodile.bsky.social · Nov 28

(4/6) 🗣️ Check the IBIS website (ibis.autosome.org/challenge_te...) to see the detailed rankings and read the short interviews with the winners!

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Vanja @halfacrocodile.bsky.social · Nov 28

(3/6) 🏆 We congratulate the runner-up teams: Medici, Salimov & Frolov lab (Russia), callitmagic (Armenia); and, most importantly, the winners: teams Bench Pressers (US), mj (Russia), and Biology Impostor (Israel).

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