Иван Кулаковский, с.н.с., к.ф.-м.н.	Юлия Медведева, с.н.с., к.б.н.	Александр Фаворов, с.н.с., к.ф.-м.н.	Артём Касьянов, н.с., к.ф.-м.н.	Марина Фридман, н.с., к.б.н.	Людмила Данилова, н.с., к.ф.-м.н.
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Леонид Урошлев н.с., к.ф.-м.н. Google Scholar

Елизавета Пермина н.с., к.б.н.

Илья Воронцов аспирант Google Scholar

Платон Быкадоров аспирант

Мария Иванова аспирант

Андрей Ландо студент

Евгений Румынский студент

Проекты:

HOCOMOCO: motif collection

HOmo sapiens transcription factor COmprehensive MOdel COllection contains transcription factor (TF) binding models obtained by careful integration of data from different sources. In the current release (v10) models for 600 human TFs are accompanied by a separate set of models for 395 mouse TFs.

EpiFactors: epigenetic factors database

EpiFactors is a database for epigenetic factors, corresponding genes and products, read more.

ChIPMunk: motif discovery

ChIPMunk is a fast heuristic DNA motif digger based a on greedy approach accompanied by bootstrapping. Now classic and dinucleotide versions come in a single updated package, read more.

SPRY-SARUS: motif finding

Straightforward yet Powerful Rapid SuperAlphabet Representation Utilized for motif Search is as practical ChIPMunk companion, read more.

MACRO-PERFECTOS-APE: motif analysis

MAtrix CompaRisOn and PrEdicting Regulatory Functional Effect by Approximate P-value Estimation toolbox allows estimating motif P-values, comparing PWMs using natural Jaccard similarity measure and motif-based analysis of regulatory SNVs for mono- and dinucleotide PWMs, read more here and there.

GenometriCorr: spatial correlation

GenometriCorr is an R package for spatial correlation of genome-wide interval datasets, read more.

 

Избранные публикации

 

2021

 

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. Biochim Biophys Acta Gene Regul Mech. 2021 Oct 30;1865(1):194768. doi: 10.1016/j.bbagrm.2021.194768.

 

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. Nat Commun. 2021 May 12;12(1):2751. doi: 10.1038/s41467-021-23007-0.

 

Assessing Ribosome Distribution Along Transcripts with Polarity Scores and Regression Slope Estimates.

Vorontsov IE, Egorov AA, Anisimova AS, Eliseeva IA, Makeev VJ, Gladyshev VN, Dmitriev SE, Kulakovskiy IV. Methods Mol Biol. 2021;2252:269-294. doi: 10.1007/978-1-0716-1150-0_13.

 

GTRD: an integrated view of transcription regulation.

Kolmykov S, Yevshin I, Kulyashov M, Sharipov R, Kondrakhin Y, Makeev VJ, Kulakovskiy IV, Kel A, Kolpakov F. Nucleic Acids Res. 2021 Jan 8;49(D1):D104-D111. doi: 10.1093/nar/gkaa1057.

 

2020

 

A holistic view of mouse enhancer architectures reveals analogous pleiotropic effects and correlation with human disease.

Sethi S, Vorontsov IE, Kulakovskiy IV, Greenaway S, Williams J, Makeev VJ, Brown SDM, Simon MM, Mallon AM. BMC Genomics. 2020 Nov 2;21(1):754. doi: 10.1186/s12864-020-07109-5.

 

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. Genome Biol. 2020 May 11;21(1):114. doi: 10.1186/s13059-020-01996-3.

 

Functional annotation of human long noncoding RNAs via molecular phenotyping.

Ramilowski JA, Yip CW, Agrawal S, Chang JC, Ciani Y, Kulakovskiy IV, Mendez M, Ooi JLC, Ouyang JF, Parkinson N, Petri A, Roos L, Severin J, Yasuzawa K, Abugessaisa I, Akalin A, Antonov IV, Arner E, Bonetti A, Bono H, Borsari B, Brombacher F, Cameron CJ, Cannistraci CV, Cardenas R, Cardon M, Chang H, Dostie J, Ducoli L, Favorov A, Fort A, Garrido D, Gil N, Gimenez J, Guler R, Handoko L, Harshbarger J, Hasegawa A, Hasegawa Y, Hashimoto K, Hayatsu N, Heutink P, Hirose T, Imada EL, Itoh M, Kaczkowski B, Kanhere A, Kawabata E, Kawaji H, Kawashima T, Kelly ST, Kojima M, Kondo N, Koseki H, Kouno T, Kratz A, Kurowska-Stolarska M, Kwon ATJ, Leek J, Lennartsson A, Lizio M, López-Redondo F, Luginbühl J, Maeda S, Makeev VJ, Marchionni L, Medvedeva YA, Minoda A, Müller F, Muñoz-Aguirre M, Murata M, Nishiyori H, Nitta KR, Noguchi S, Noro Y, Nurtdinov R, Okazaki Y, Orlando V, Paquette D, Parr CJC, Rackham OJL, Rizzu P, Sánchez Martinez DF, Sandelin A, Sanjana P, Semple CAM, Shibayama Y, Sivaraman DM, Suzuki T, Szumowski SC, Tagami M, Taylor MS, Terao C, Thodberg M, Thongjuea S, Tripathi V, Ulitsky I, Verardo R, Vorontsov IE, Yamamoto C, Young RS, Baillie JK, Forrest ARR, Guigó R, Hoffman MM, Hon CC, Kasukawa T, Kauppinen S, Kere J, Lenhard B, Schneider C, Suzuki H, Yagi K, de Hoon MJL, Shin JW, Carninci P. Genome Res. 2020 Jul;30(7):1060-1072. doi: 10.1101/gr.254219.119

 

2019

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. Front Genet. 2019 Oct 31;10:1078. doi: 10.3389/fgene.2019.01078. eCollection 2019.

 

Heteroplasmic Variants of Mitochondrial DNA in Atherosclerotic Lesions of Human Aortic Intima.

Sobenin IA, Zhelankin AV, Khasanova ZB, Sinyov VV, Medvedeva LV, Sagaidak MO, Makeev VJ, Kolmychkova KI, Smirnova AS, Sukhorukov VN, Postnov AY, Grechko AV, Orekhov AN. Biomolecules. 2019 Sep 6;9(9):455. doi: 10.3390/biom9090455. PMID: 31500189

 

Employing toxin-antitoxin genome markers for identification of Bifidobacterium and Lactobacillus strains in human metagenomes.

Klimina KM, Kasianov AS, Poluektova EU, Emelyanov KV, Voroshilova VN, Zakharevich NV, Kudryavtseva AV, Makeev VJ, Danilenko VN. PeerJ. 2019 Mar 4;7:e6554. doi: 10.7717/peerj.6554. eCollection 2019.

 

Defensin-like peptides in wheat analyzed by whole-transcriptome sequencing: a focus on structural diversity and role in induced resistance.

Odintsova TI, Slezina MP, Istomina EA, Korostyleva TV, Kasianov AS, Kovtun AS, Makeev VJ, Shcherbakova LA, Kudryavtsev AM. PeerJ. 2019 Jan 8;7:e6125. doi: 10.7717/peerj.6125. eCollection 2019.

 

2018

 

Genome-wide map of human and mouse transcription factor binding sites aggregated from ChIP-Seq data.

Vorontsov IE, Fedorova AD, Yevshin IS, Sharipov RN, Kolpakov FA, Makeev VJ, Kulakovskiy IV. BMC Res Notes. 2018 Oct 23;11(1):756. doi: 10.1186/s13104-018-3856-x.

 

HDL activates expression of genes stimulating cholesterol efflux in human monocyte-derived macrophages.

Orekhov AN, Pushkarsky T, Oishi Y, Nikiforov NG, Zhelankin AV, Dubrovsky L, Makeev VJ, Foxx K, Jin X, Kruth HS, Sobenin IA, Sukhorukov VN, Zakiev ER, Kontush A, Le Goff W, Bukrinsky M. Exp Mol Pathol. 2018 Oct;105(2):202-207. doi: 10.1016/j.yexmp.2018.08.003

 

Modified LDL Particles Activate Inflammatory Pathways in Monocyte-derived Macrophages: Transcriptome Analysis.

Orekhov AN, Oishi Y, Nikiforov NG, Zhelankin AV, Dubrovsky L, Sobenin IA, Kel A, Stelmashenko D, Makeev VJ, Foxx K, Jin X, Kruth HS, Bukrinsky M. Curr Pharm Des. 2018;24(26):3143-3151. doi: 10.2174/1381612824666180911120039.

 

The complete genome of the oil emulsifying strain Thalassolituus oleivorans K-188 from the Barents Sea.

Shtratnikova VY, Belalov I, Kasianov AS, Schelkunov MI, Logacheva Maria DA, Novikov AD, Shatalov AA, Gerasimova TV, Yanenko AS, Makeev VJ. Mar Genomics. 2018 Feb;37:18-20. doi: 10.1016/j.margen.2017.08.005.

 

HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis.

Kulakovskiy IV, Vorontsov IE, Yevshin IS, Sharipov RN, Fedorova AD, Rumynskiy EI, Medvedeva YA, Magana-Mora A, Bajic VB, Papatsenko DA, Kolpakov FA, Makeev VJ. Nucleic Acids Res. 2018 Jan 4;46(D1):D252-D259. doi: 10.1093/nar/gkx1106. PMID: 29140464 Free PMC article.

 

2017

 

An integrated expression atlas of miRNAs and their promoters in human and mouse.

de Rie D, Abugessaisa I, Alam T, Arner E, Arner P, Ashoor H, Åström G, Babina M, Bertin N, Burroughs AM, Carlisle AJ, Daub CO, Detmar M, Deviatiiarov R, Fort A, Gebhard C, Goldowitz D, Guhl S, Ha TJ, Harshbarger J, Hasegawa A, Hashimoto K, Herlyn M, Heutink P, Hitchens KJ, Hon CC, Huang E, Ishizu Y, Kai C, Kasukawa T, Klinken P, Lassmann T, Lecellier CH, Lee W, Lizio M, Makeev V, Mathelier A, Medvedeva YA, Mejhert N, Mungall CJ, Noma S, Ohshima M, Okada-Hatakeyama M, Persson H, Rizzu P, Roudnicky F, Sætrom P, Sato H, Severin J, Shin JW, Swoboda RK, Tarui H, Toyoda H, Vitting-Seerup K, Winteringham L, Yamaguchi Y, Yasuzawa K, Yoneda M, Yumoto N, Zabierowski S, Zhang PG, Wells CA, Summers KM, Kawaji H, Sandelin A, Rehli M; FANTOM Consortium, Hayashizaki Y, Carninci P, Forrest ARR, de Hoon MJL. Nat Biotechnol. 2017 Sep;35(9):872-878. doi: 10.1038/nbt.3947

 

Preservation of methylated CpG dinucleotides in human CpG islands.

Panchin AY, Makeev VJ, Medvedeva YA. Biol Direct. 2016 Mar 22;11(1):11. doi: 10.1186/s13062-016-0113-x.

 

The single nucleotide variant rs12722489 determines differential estrogen receptor binding and enhancer properties of an IL2RA intronic region.

Afanasyeva MA, Putlyaeva LV, Demin DE, Kulakovskiy IV, Vorontsov IE, Fridman MV, Makeev VJ, Kuprash DV, Schwartz AM. PLoS One. 2017 Feb 24;12(2):e0172681. doi: 10.1371/journal.pone.0172681. eCollection

 

Use of Primary Macrophages for Searching Novel Immunocorrectors.

Nikiforov NG, Elizova NV, Bukrinsky M, Dubrovsky L, Makeev VJ, Wakabayashi Y, Liu P, Foxx KK, Kruth HS, Jin X, Zakiev ER, Orekhov AN. Curr Pharm Des. 2017;23(6):915-920. doi: 10.2174/1381612823666170125110128.

 

Role of structural water for prediction of cation binding sites in apoproteins.

Uroshlev LA, Kulakovskiy IV, Esipova NG, Tumanyan VG, Rahmanov SV, Makeev VJ. J Biomol Struct Dyn. 2018 Jan;36(1):221-232. doi: 10.1080/07391102.2016.1273136

 

Multiple single nucleotide polymorphisms in the first intron of the IL2RA gene affect transcription factor binding and enhancer activity

A.M. Schwartz, D.E. Demin, I.E. Vorontsov, A.S. Kasyanov, L.V. Putlyaeva, K.A. Tatosyan, I.V. Kulakovskiy, D.V. Kuprash

Gene, 2017 602:50-56. doi: 10.1016/j.gene.2016.11.032

 

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

N. Andreeva, E. Kulakovskaya, A. Zvonarev, A. Penin, I. Eliseeva, A. Teterina, A. Lando, I.V. Kulakovskiy, T. Kulakovskaya

Metallomics, 2017, 9:175-182. doi: 10.1039/c6mt00210b

 

2016

(2016) Architectural proteins Pita, Zw5,and ZIPIC contain homodimerization domain and support specific long-range interactions in Drosophila

Nikolay Zolotarev, Anna Fedotova, Olga Kyrchanova, Artem Bonchuk, Aleksey A. Penin, Andrey S. Lando, Irina A. Eliseeva, Ivan V. Kulakovskiy, Oksana Maksimenko, Pavel Georgiev

Nucleic Acids Res (2016) 44 (15): 7228-7241. doi: 10.1093/nar/gkw371

 

(2016) Upstream Open Reading Frames Located in the Leader of Protein Kinase Mζ mRNA Regulate Its Translation

Bal NV, Susorov D, Chesnokova E, Kasianov A, Mikhailova T, Alkalaeva E, Balaban PM, Kolosov P

Front Mol Neurosci. 2016 Oct 13;9:103. eCollection 2016. doi: 10.3389/fnmol.2016.00103

 

(2016) A high resolution map of the Arabidopsis thaliana developmental transcriptome based on RNA-seq profiling

Klepikova AV, Kasianov AS, Gerasimov ES, Logacheva MD, Penin AA

Plant J. 2016 Dec;88(6):1058-1070. Epub 2016 Nov 19. doi: 10.1111/tpj.13312

 

(2016) Association of PD-1/PD-L axis expression with cytolytic activity, mutational load, and prognosis in melanoma and other solid tumors

Ludmila Danilova, Hao Wang, Joel Sunshine, Genevieve J. Kaunitz, Tricia R. Cottrell, Haiying Xu, Jessica Esandrio, Robert A. Anders, Leslie Cope, Drew M. Pardoll, Charles G. Drake, and Janis M. Taube

Proceedings of the National Academy of Sciences; vol. 113 no. 48; E7769–E7777 doi: 10.1073/pnas.1607836113

 

(2013) 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

Nucleic Acids Res. 2013 Jan; 41(Database issue):D195-202. doi: 10.1093/nar/gks1089

 

(2016) Negative selection maintains transcription factor binding motifs in human cancer

Ilya E. Vorontsov, Grigory Khimulya, Elena N. Lukianova, Daria D. Nikolaeva, Irina A. Eliseeva, Ivan V. Kulakovskiy and Vsevolod J. Makeev

BMC Genomics 2016; 17(Suppl 2):395. doi: 10.1186/s12864-016-2728-9

 

(2016) HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models

Ivan V. Kulakovskiy; Ilya E. Vorontsov; Ivan S. Yevshin; Anastasiia V. Soboleva; Artem S. Kasianov; Haitham Ashoor; Wail Ba-alawi; Vladimir B. Bajic; Yulia A. Medvedeva; Fedor A. Kolpakov; Vsevolod J. Makeev

Nucl. Acids Res. (04 January 2016) 44 (D1): D116-D125. doi: 10.1093/nar/gkv1249

 

(2014) A promoter-level mammalian expression atlas

The FANTOM Consortium and the RIKEN PMI and CLST (DGT) (в том числе сотрудники ИОГен: Иван Кулаковский, Юлия Медведева, Александр Фаворов, Артем Касьянов, Илья Воронцов и Всеволод Макеев)

Nature 507, 462–470 (27 March 2014). doi: 10.1038/nature13182