§ Projects

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 is a database for epigenetic factors, corresponding genes and products, read more.
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.
Straightforward yet Powerful Rapid SuperAlphabet Representation Utilized for motif Search is as practical ChIPMunk companion, read more.
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 is an R package for spatial correlation of genome-wide interval datasets, read more.

§ Featured publications

§ (2017) The single nucleotide variant rs12722489 determines differential estrogen receptor binding and enhancer properties of an IL2RA intronic region
M.A. Afanasyeva, L.V. Putlyaeva, D.E. Demin, I.V. Kulakovskiy, I.E. Vorontsov, M.V. Fridman, V.J. Makeev, D.V. Kuprash, A.M. Schwartz
PloS one, 12(2): e0172681 doi: 10.1371/journal.pone.0172681
§ (2017) 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, 602:50-56. doi: 10.1016/j.gene.2016.11.032
§ (2017) 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, 9:175-182. doi: 10.1039/c6mt00210b
§ (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
 

§ Staff

§ Vsevolod Makeev
Laboratory head, doctor of science, corresponding member of RAS
§ Ivan Kulakovskiy
senior research fellow, PhD
[+] See also

Kulakovskiy Ivan Vladimirovich (Curriculum Vitae)

Master degree in applied math (MSFU, 2006), PhD in Bioinformatics (2009, IITP RAS).

Research is focused on bioinformatics for next-generation sequencing and sequence analysis for transcriptomics and regulatory genomics. The recent successful projects include: HOCOMOCO collection of binding motifs for human and mouse transcription factors [Kulakovskiy et. al, 2016], analysis of regulatory effects from genomic variants [Vorontsov et al., 2016; Schwartz et al., 2017; Afanasyeva et al., 2017], yeast transcriptomics [Andreeva et al., 2017].

§ Yulia Medvedeva
senior research fellow, PhD
§ Alexander Favorov
senior research fellow, PhD
[+] See also
I was graduated from The Second School, then MIPT (nonlinear optics). PhD since 2005.
§ Artem Kasianov
research fellow, PhD
[+] See also
Artem received his master's degree from Computational mathematics and cybernetics department of Moscow State University(2007), followed by PhD im molecular biology from Engelhardt Institute of Molecular Biology(2012).
Sphere of his scientific interest lies in de novo genome assembly, plant genomics and transcriptomics, genome graph based algorithms areas.
§ Marina Fridman
research fellow, PhD
§ Leonid Uroshlev
research fellow, PhD
[+] See also
Урошлев Леонид Андреевич По образованию - инженер-математик(МГУЛ, 2006), закончил аспирантуру ИМБ РАН по специальности молекулярная биология (2015). Занимается применением методов машинного обучения к задачам молекулярной биологии.
§ Elizaveta Permina
research fellow, PhD
§ Ilya Vorontsov
PhD student
[+] See also

Doing PhD research: "Effect of polymorphisms in regulatory regions of DNA on transcription factor binding affinity"

§ Platon Bykadorov
PhD student
§ Maria Ivanova
PhD student
§ Evgeniy Rumynskiy
student
 
 

§ Alumni

§ Valentina Boeva
PhD, now group leader, INSERM, Institut Cochin
§ Dmitry Malko
research fellow, PhD
§ Anastasia Soboleva
student
[+] See also
Author of the SPRY-SARUS motif finding tool.