Kulakovskiy IV - Search Results

1

Evaluation and optimization of sequence-based gene regulatory deep learning models.

Rafi AM, Nogina D, Penzar D, Lee D, Lee D, Kim N, Kim S, Kim D, Shin Y, Kwak IY, Meshcheryakov G, Lando A, Zinkevich A, Kim BC, Lee J, Kang T, Vaishnav ED, Yadollahpour P; Random Promoter DREAM Challenge Consortium; Kim S, Albrecht J, Regev A, Gong W, Kulakovskiy IV, Meyer P, de Boer C. Rafi AM, et al. Among authors: kulakovskiy iv. bioRxiv [Preprint]. 2024 Feb 17:2023.04.26.538471. doi: 10.1101/2023.04.26.538471. bioRxiv. 2024. Update in: Nat Biotechnol. 2024 Oct 11. doi: 10.1038/s41587-024-02414-w PMID: 38405704 Free PMC article. Updated. Preprint.

2

Architectural proteins Pita, Zw5,and ZIPIC contain homodimerization domain and support specific long-range interactions in Drosophila.

Zolotarev N, Fedotova A, Kyrchanova O, Bonchuk A, Penin AA, Lando AS, Eliseeva IA, Kulakovskiy IV, Maksimenko O, Georgiev P. Zolotarev N, et al. Among authors: kulakovskiy iv. Nucleic Acids Res. 2016 Sep 6;44(15):7228-41. doi: 10.1093/nar/gkw371. Epub 2016 May 2. Nucleic Acids Res. 2016. PMID: 27137890 Free PMC article.

3

What Do Neighbors Tell About You: The Local Context of Cis-Regulatory Modules Complicates Prediction of Regulatory Variants.

Penzar DD, Zinkevich AO, Vorontsov IE, Sitnik VV, Favorov AV, Makeev VJ, Kulakovskiy IV. Penzar DD, et al. Among authors: kulakovskiy iv. Front Genet. 2019 Oct 31;10:1078. doi: 10.3389/fgene.2019.01078. eCollection 2019. Front Genet. 2019. PMID: 31737053 Free PMC article.

4

Insights gained from a comprehensive all-against-all transcription factor binding motif benchmarking study.

Ambrosini G, Vorontsov I, Penzar D, Groux R, Fornes O, Nikolaeva DD, Ballester B, Grau J, Grosse I, Makeev V, Kulakovskiy I, Bucher P. Ambrosini G, et al. Genome Biol. 2020 May 11;21(1):114. doi: 10.1186/s13059-020-01996-3. Genome Biol. 2020. PMID: 32393327 Free PMC article.

5

Landscape of allele-specific transcription factor binding in the human genome.

Abramov S, Boytsov A, Bykova D, Penzar DD, Yevshin I, Kolmykov SK, Fridman MV, Favorov AV, Vorontsov IE, Baulin E, Kolpakov F, Makeev VJ, Kulakovskiy IV. Abramov S, et al. Among authors: kulakovskiy iv. Nat Commun. 2021 May 12;12(1):2751. doi: 10.1038/s41467-021-23007-0. Nat Commun. 2021. PMID: 33980847 Free PMC article.

6

Ribosomal leaky scanning through a translated uORF requires eIF4G2.

Smirnova VV, Shestakova ED, Nogina DS, Mishchenko PA, Prikazchikova TA, Zatsepin TS, Kulakovskiy IV, Shatsky IN, Terenin IM. Smirnova VV, et al. Among authors: kulakovskiy iv. Nucleic Acids Res. 2022 Jan 25;50(2):1111-1127. doi: 10.1093/nar/gkab1286. Nucleic Acids Res. 2022. PMID: 35018467 Free PMC article.

7

LegNet: a best-in-class deep learning model for short DNA regulatory regions.

Penzar D, Nogina D, Noskova E, Zinkevich A, Meshcheryakov G, Lando A, Rafi AM, de Boer C, Kulakovskiy IV. Penzar D, et al. Among authors: kulakovskiy iv. Bioinformatics. 2023 Aug 1;39(8):btad457. doi: 10.1093/bioinformatics/btad457. Bioinformatics. 2023. PMID: 37490428 Free PMC article.

8

An atlas of transcribed human cardiac promoters and enhancers reveals an important role of regulatory elements in heart failure.

Deviatiiarov RM, Gams A, Kulakovskiy IV, Buyan A, Meshcheryakov G, Syunyaev R, Singh R, Shah P, Tatarinova TV, Gusev O, Efimov IR. Deviatiiarov RM, et al. Among authors: kulakovskiy iv. Nat Cardiovasc Res. 2023 Jan;2(1):58-75. doi: 10.1038/s44161-022-00182-x. Epub 2023 Jan 16. Nat Cardiovasc Res. 2023. PMID: 39196209

9

Transcriptome profile of yeast reveals the essential role of PMA2 and uncharacterized gene YBR056W-A (MNC1) in adaptation to toxic manganese concentration.

Andreeva N, Kulakovskaya E, Zvonarev A, Penin A, Eliseeva I, Teterina A, Lando A, Kulakovskiy IV, Kulakovskaya T. Andreeva N, et al. Among authors: kulakovskiy iv. Metallomics. 2017 Feb 22;9(2):175-182. doi: 10.1039/c6mt00210b. Metallomics. 2017. PMID: 28128390 Free article.

10

Translatome and transcriptome analysis of TMA20 (MCT-1) and TMA64 (eIF2D) knockout yeast strains.

Makeeva DS, Lando AS, Anisimova A, Egorov AA, Logacheva MD, Penin AA, Andreev DE, Sinitcyn PG, Terenin IM, Shatsky IN, Kulakovskiy IV, Dmitriev SE. Makeeva DS, et al. Among authors: kulakovskiy iv. Data Brief. 2019 Feb 2;23:103701. doi: 10.1016/j.dib.2019.103701. eCollection 2019 Apr. Data Brief. 2019. PMID: 30815525 Free PMC article.

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