Kulakovskiy IV - Search Results

1

HOCOMOCO in 2024: a rebuild of the curated collection of binding models for human and mouse transcription factors.

Vorontsov IE, Eliseeva IA, Zinkevich A, Nikonov M, Abramov S, Boytsov A, Kamenets V, Kasianova A, Kolmykov S, Yevshin IS, Favorov A, Medvedeva YA, Jolma A, Kolpakov F, Makeev VJ, Kulakovskiy IV. Vorontsov IE, et al. Among authors: kulakovskiy iv. Nucleic Acids Res. 2024 Jan 5;52(D1):D154-D163. doi: 10.1093/nar/gkad1077. Nucleic Acids Res. 2024. PMID: 37971293 Free PMC article.

2

Motif discovery and motif finding from genome-mapped DNase footprint data.

Kulakovskiy IV, Favorov AV, Makeev VJ. Kulakovskiy IV, et al. Bioinformatics. 2009 Sep 15;25(18):2318-25. doi: 10.1093/bioinformatics/btp434. Epub 2009 Jul 15. Bioinformatics. 2009. PMID: 19605419

3

Intergenic, gene terminal, and intragenic CpG islands in the human genome.

Medvedeva YA, Fridman MV, Oparina NJ, Malko DB, Ermakova EO, Kulakovskiy IV, Heinzel A, Makeev VJ. Medvedeva YA, et al. Among authors: kulakovskiy iv. BMC Genomics. 2010 Jan 19;11:48. doi: 10.1186/1471-2164-11-48. BMC Genomics. 2010. PMID: 20085634 Free PMC article.

4

Empirical potentials for ion binding in proteins.

Rahmanov S, Kulakovskiy I, Uroshlev L, Makeev V. Rahmanov S, et al. J Bioinform Comput Biol. 2010 Jun;8(3):427-35. doi: 10.1142/s0219720010004641. J Bioinform Comput Biol. 2010. PMID: 20556854

5

Deep and wide digging for binding motifs in ChIP-Seq data.

Kulakovskiy IV, Boeva VA, Favorov AV, Makeev VJ. Kulakovskiy IV, et al. Bioinformatics. 2010 Oct 15;26(20):2622-3. doi: 10.1093/bioinformatics/btq488. Epub 2010 Aug 24. Bioinformatics. 2010. PMID: 20736340

6

A deeper look into transcription regulatory code by preferred pair distance templates for transcription factor binding sites.

Kulakovskiy IV, Belostotsky AA, Kasianov AS, Esipova NG, Medvedeva YA, Eliseeva IA, Makeev VJ. Kulakovskiy IV, et al. Bioinformatics. 2011 Oct 1;27(19):2621-4. doi: 10.1093/bioinformatics/btr453. Epub 2011 Aug 18. Bioinformatics. 2011. PMID: 21852305

7

HOCOMOCO: a comprehensive collection of human transcription factor binding sites models.

Kulakovskiy IV, Medvedeva YA, Schaefer U, Kasianov AS, Vorontsov IE, Bajic VB, Makeev VJ. Kulakovskiy IV, et al. Nucleic Acids Res. 2013 Jan;41(Database issue):D195-202. doi: 10.1093/nar/gks1089. Epub 2012 Nov 21. Nucleic Acids Res. 2013. PMID: 23175603 Free PMC article.

8

From binding motifs in ChIP-Seq data to improved models of transcription factor binding sites.

Kulakovskiy I, Levitsky V, Oshchepkov D, Bryzgalov L, Vorontsov I, Makeev V. Kulakovskiy I, et al. J Bioinform Comput Biol. 2013 Feb;11(1):1340004. doi: 10.1142/S0219720013400040. Epub 2013 Jan 16. J Bioinform Comput Biol. 2013. PMID: 23427986

9

DNA sequence motif: a jack of all trades for ChIP-Seq data.

Kulakovskiy IV, Makeev VJ. Kulakovskiy IV, et al. Adv Protein Chem Struct Biol. 2013;91:135-71. doi: 10.1016/B978-0-12-411637-5.00005-6. Adv Protein Chem Struct Biol. 2013. PMID: 23790213 Review.

10

Jaccard index based similarity measure to compare transcription factor binding site models.

Vorontsov IE, Kulakovskiy IV, Makeev VJ. Vorontsov IE, et al. Among authors: kulakovskiy iv. Algorithms Mol Biol. 2013 Sep 30;8(1):23. doi: 10.1186/1748-7188-8-23. Algorithms Mol Biol. 2013. PMID: 24074225 Free PMC article.

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