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Integration of multiple epigenomic marks improves prediction of variant impact in saturation mutagenesis reporter assay.
Shigaki D, Adato O, Adhikari AN, Dong S, Hawkins-Hooker A, Inoue F, Juven-Gershon T, Kenlay H, Martin B, Patra A, Penzar DD, Schubach M, Xiong C, Yan Z, Boyle AP, Kreimer A, Kulakovskiy IV, Reid J, Unger R, Yosef N, Shendure J, Ahituv N, Kircher M, Beer MA. Shigaki D, et al. Among authors: kulakovskiy iv. Hum Mutat. 2019 Sep;40(9):1280-1291. doi: 10.1002/humu.23797. Epub 2019 Jun 23. Hum Mutat. 2019. PMID: 31106481 Free PMC article.
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.
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.
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.
84 results