Лаборатория системной биологии и вычислительной генетики

 

Всеволод Макеев

Заведующий лабораторией, д.ф.-м.н., член-корреспондент РАН

 

Внешний сайт лаборатории   lab.autosome.ru

 

Сотрудники лаборатории

 

 


 

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.

Google Scholar

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Леонид Урошлев

н.с., к.ф.-м.н.

Google Scholar

Елизавета Пермина

н.с., к.б.н.

 

Илья Воронцов

аспирант

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Платон Быкадоров

аспирант

 

Мария Иванова

аспирант

 

Андрей Ландо

студент

 

Евгений Румынский

студент

 

 

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

 

(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