Kulakovskiy IV - Search Results

1

The gene regulation knowledge commons: the action area of GREEKC.

Kuiper M, Bonello J, Fernández-Breis JT, Bucher P, Futschik ME, Gaudet P, Kulakovskiy IV, Licata L, Logie C, Lovering RC, Makeev VJ, Orchard S, Panni S, Perfetto L, Sant D, Schulz S, Vercruysse S, Zerbino DR, Lægreid A; GRECO Consortium. Kuiper M, et al. Among authors: kulakovskiy iv. Biochim Biophys Acta Gene Regul Mech. 2022 Jan;1865(1):194768. doi: 10.1016/j.bbagrm.2021.194768. Epub 2021 Oct 30. Biochim Biophys Acta Gene Regul Mech. 2022. PMID: 34757206 Free 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

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

4

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

5

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.

6

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

7

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.

8

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.

9

Application of experimentally verified transcription factor binding sites models for computational analysis of ChIP-Seq data.

Levitsky VG, Kulakovskiy IV, Ershov NI, Oshchepkov DY, Makeev VJ, Hodgman TC, Merkulova TI. Levitsky VG, et al. Among authors: kulakovskiy iv. BMC Genomics. 2014 Jan 29;15(1):80. doi: 10.1186/1471-2164-15-80. BMC Genomics. 2014. PMID: 24472686 Free PMC article.

10

Single-Cell Analyses of ESCs Reveal Alternative Pluripotent Cell States and Molecular Mechanisms that Control Self-Renewal.

Papatsenko D, Darr H, Kulakovskiy IV, Waghray A, Makeev VJ, MacArthur BD, Lemischka IR. Papatsenko D, et al. Among authors: kulakovskiy iv. Stem Cell Reports. 2015 Aug 11;5(2):207-20. doi: 10.1016/j.stemcr.2015.07.004. Stem Cell Reports. 2015. PMID: 26267829 Free PMC article.

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