Researcher, teacher, programmer, chaotic something
Moscow
Joined May 2009
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По тому как ожесточенно я рублюсь в твиттере за священное право программиста носить одни штаны всю жизнь и писать на джаве, вы наверное поняли <s>что у меня нет личной жизни</s> что я покинул твиттер и завел себе более лучший твиттер.
t.me/schroedinger_jokes
Ilya Vorontsov retweeted
(1/12) The IBIS post-challenge paper is out in @CellReports (doi.org/10.1016/j.celrep.202…). We report the results of the open community benchmark of human TF binding specificity models, with a closer look at what advanced models learn that classic PWMs do not.
Ilya Vorontsov retweeted
🧬 EPIC is open: the Eukaryotic Promoter and transcription Initiation prediction Challenge.
The goal: predict where, and how strongly, RNA Pol II starts transcribing, from nothing but DNA sequence. At single-nucleotide, strand-specific resolution.
epic.autosome.org
🧵 1/7
Ilya Vorontsov retweeted
An expanded codebook of human transcription factor DNA-binding specificity @Nature @BartDeplancke
@EPFL_en @halfacrocodile @ArttuJolma @VorontsovIE @ImYellan @UofT #Hughes 🇨🇦🇷🇺🇨🇭
nature.com/articles/s41586-0…
Ilya Vorontsov retweeted
(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/s42003-0…
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.
(1/13) 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/10.1101/2024.11.1… | mex.autosome.org⬇️
Яндекс.Маркет — дно. За целый запланированный день не смогли доставить холодильник. Курьер на второй день говорит, что снова едва ли доставит. И вообще говорит, что он один и на этаж не сможет поднять.
Техподдержка отвечает по содержательности как робот, только с задержкой в час.
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Ilya Vorontsov retweeted
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…
Ilya Vorontsov retweeted
(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.
Ilya Vorontsov retweeted
(3/4) Also do not forget that HOCOMOCO also provides motifs for orthologous mouse TFs, >800 of those are covered in v13.
Ilya Vorontsov retweeted
(2/4) HOCOMOCO 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.
Ilya Vorontsov retweeted
(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
Finally we did it!
(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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Ilya Vorontsov retweeted
«Работать за еду и молиться». Как устроены рабочие дома — репортаж The Insider
youtu.be/n1QfkpnKYkc
«Работа, жилье, еда», — так рабочие дома заманивают обездоленных по всей России. В одном только Санкт-Петербурге таких домов сотни, а по стране — тысячи. Но пока их обитатели находятся на грани выживания, владельцы ведут роскошную жизнь.
Ilya Vorontsov retweeted
(13/13) .. @IvanDKoz, @nikitagryzunov, @VorontsovIE, @halfacrocodile, @legoushque, @AntoniGralak, @ZinkevichA, @JKribelbauer, @ArttuJolma and see also ibis.autosome.org/docs/about…
Ilya Vorontsov retweeted
(12/13) Kudos to the Codebook and GRECO-BIT consortium members including @BartDeplancke, @MakeevSeva, @EPD_SIB, @OFornes, @ImYellan, ..
Ilya Vorontsov retweeted
(10/13) Want something more than simple PWMs? Reaching the next level with IBIS: join the online IBIS conference on November 27, more details soon at ibis.autosome.org.
Ilya Vorontsov retweeted
(11/13) This project is only one of the multiple facets of the larger Codebook initiative, see dx.doi.org/10.1101/2024.11.1…
Ilya Vorontsov retweeted
(9/13) Check the interactive Codebook/GRECO-BIT Motif Explorer (mex.autosome.org), which provides motifs, performance metrics, ranks, logos, top-performing motifs, and structured metadata.
Ilya Vorontsov retweeted
(8/13) With that many PWMs at hand, we also demonstrate that several motifs can be easily combined into a better model with ArChIPelago: regression or Random Forest on top of PWM scans.
Ilya Vorontsov retweeted
(7/13) Comparison of different tools yielded many surprises. On the one hand, underused motif discovery tools such as Dimont excel across different types of experimental data. On the other hand, no single tool or platform is enough to get the most for each TF and each data type.
