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Ivan V. Kulakovskiy
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2020 – today
- 2023
- [j16]Dmitry Penzar
, Daria Nogina
LegNet: a best-in-class deep learning model for short DNA regulatory regions. Bioinform. 39(8) (2023) - [j15]Daria Marakulina
EpiFactors 2022: expansion and enhancement of a curated database of human epigenetic factors and complexes. Nucleic Acids Res. 51(D1): 564-570 (2023) - 2022
- [j14]Alexandr Boytsov
ANANASTRA: annotation and enrichment analysis of allele-specific transcription factor binding at SNPs. Nucleic Acids Res. 50(W1): 51-56 (2022) - 2021
- [j13]Semyon Kolmykov
GTRD: an integrated view of transcription regulation. Nucleic Acids Res. 49(Database-Issue): D104-D111 (2021)
2010 – 2019
- 2019
- [j12]Artyom A. Egorov
svist4get: a simple visualization tool for genomic tracks from sequencing experiments. BMC Bioinform. 20(1): 113:1-113:6 (2019) - 2018
- [j11]Ivan V. Kulakovskiy
HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis. Nucleic Acids Res. 46(Database-Issue): D252-D259 (2018) - 2016
- [j10]Ivan V. Kulakovskiy
HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models. Nucleic Acids Res. 44(Database-Issue): 116-125 (2016) - 2015
- [j9]Yulia A. Medvedeva
EpiFactors: a comprehensive database of human epigenetic factors and complexes. Database J. Biol. Databases Curation 2015 (2015) - [c2]Ilya E. Vorontsov, Ivan V. Kulakovskiy, Grigory Khimulya, Daria D. Nikolaeva, Vsevolod J. Makeev:
PERFECTOS-APE - Predicting Regulatory Functional Effect of SNPs by Approximate P-value Estimation. BIOINFORMATICS 2015: 102-108 - 2014
- [j8]The Fantom Consortium, RIKEN PMII, RIKEN CLST (DGT), Alistair R. R. Forrest, Hideya Kawaji, Michael Rehli, J. Kenneth Baillie, Michiel J. L. de Hoon, Vanja Haberle, Timo Lassmann, Ivan V. Kulakovskiy, Marina Lizio, Masayoshi Itoh, Robin Andersson, Christopher J. Mungall, Terrence F. Meehan, Sebastian Schmeier, Nicolas Bertin, Mette Jørgensen, Emmanuel Dimont, Erik Arner, Christian Schmidl, Ulf Schaefer, Yulia A. Medvedeva
A promoter-level mammalian expression atlas. Nat. 507(7493): 462-470 (2014) - 2013
- [j7]Ilya E. Vorontsov
Jaccard index based similarity measure to compare transcription factor binding site models. Algorithms Mol. Biol. 8: 23 (2013) - [j6]Ivan V. Kulakovskiy
From binding motifs in Chip-seq Data to Improved Models of transcription factor binding Sites. J. Bioinform. Comput. Biol. 11(1) (2013) - [j5]Ivan V. Kulakovskiy
HOCOMOCO: a comprehensive collection of human transcription factor binding sites models. Nucleic Acids Res. 41(Database-Issue): 195-202 (2013) - [c1]Ivan V. Kulakovskiy, Victor G. Levitsky, Dmitry G. Oschepkov, Ilya E. Vorontsov, Vsevolod J. Makeev:
Learning Advanced TFBS Models from Chip-Seq Data - diChIPMunk: Effective Construction of Dinucleotide Positional Weight Matrices. BIOINFORMATICS 2013: 146-150 - 2011
- [j4]Ivan V. Kulakovskiy
A deeper look into transcription regulatory code by preferred pair distance templates for transcription factor binding sites. Bioinform. 27(19): 2621-2624 (2011) - 2010
- [j3]Ivan V. Kulakovskiy
Deep and wide digging for binding motifs in ChIP-Seq data. Bioinform. 26(20): 2622-2623 (2010) - [j2]Sergei Rahmanov, Ivan V. Kulakovskiy
Empirical Potentials for ion Binding in proteins. J. Bioinform. Comput. Biol. 8(3): 427-435 (2010)
2000 – 2009
- 2009
- [j1]Ivan V. Kulakovskiy
Motif discovery and motif finding from genome-mapped DNase footprint data. Bioinform. 25(18): 2318-2325 (2009)
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